diff --git a/.gitignore b/.gitignore
index da18743e87cee2eec8c60431c40fa70563d79927..0838ab626bce9b7fb4937f85e584d22e01270e76 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,4 +1,5 @@
examples/dev/
+examples*dev/
examples/tmp/
docs/olds/
*.simg
diff --git a/CHANGELOG b/CHANGELOG
index c6df0aa8ba771b0b903e11b332116cbe191841f7..8bde8a12e94f93dd8cf9bf15ac654980d71df09f 100644
--- a/CHANGELOG
+++ b/CHANGELOG
@@ -1,32 +1,32 @@
-1. What's new in version 2.4 ?
+What's new in version 2.4 ?
--------------------------------
- 1.1 Potential of Mean Forces for dihedral angles () and H-bonds ()
- 1.2 Clustering step during the iterative process
- 1.3 Extended scoring function including PMF, coulombic and full Lennard Jones functions
- 1.4 Restraints generation from evolutionary couplings and secondary structure prediction
+ * Potential of Mean Forces for dihedral angles () and H-bonds ()
+ * Clustering step during the iterative process
+ * Extended scoring function including PMF, coulombic and full Lennard Jones functions
+ * Restraints generation from evolutionary couplings and secondary structure prediction
-1. What's new in version 2.3?
+What's new in version 2.3?
----------------------------------
-- bug fixes
-
-- support of CCPN version 2 (instead of CCPN v1)
-
-- extension of symmetric oligomers support (C3, C5 and D2)
- (in the GUI, go to "Data > Symmetry")
-
-- introduction of the log-harmonic potential for distance restraints (Nilges et al. Structure, 2008)
- (go to "Structure Generation > CNS > Annealing Parameters > Log-Hamonic potential")
-
-- import of CCPN Models/Structure ensembles as initial structure for the minimization protocol or
- as template structures for the initial assignment/calibration step.
-
-- addition of Zinc ions coordination (through covalent bonds)
- (go to "Add > Zinc Coordination")
-
-- Automated Molprobilty (clashlist) analysis
- (go to "Analyses > Molprobity Clashlist")
-
-- addition of old aria1.x features (keep_structures, only fully assigned peaks)
+ * bug fixes
+
+ * support of CCPN version 2 (instead of CCPN v1)
+
+ * extension of symmetric oligomers support (C3, C5 and D2)
+ (in the GUI, go to "Data > Symmetry")
+
+ * introduction of the log-harmonic potential for distance restraints (Nilges et al. Structure, 2008)
+ (go to "Structure Generation > CNS > Annealing Parameters > Log-Hamonic potential")
+
+ * import of CCPN Models/Structure ensembles as initial structure for the minimization protocol or
+ as template structures for the initial assignment/calibration step.
+
+ * addition of Zinc ions coordination (through covalent bonds)
+ (go to "Add > Zinc Coordination")
+
+ * Automated Molprobilty (clashlist) analysis
+ (go to "Analyses > Molprobity Clashlist")
+
+ * addition of old aria1.x features (keep_structures, only fully assigned peaks)
diff --git a/README.rst b/README.rst
index c552de7690a66c9d0301bf0e06c7809af29ec3db..394dc0eb2455a411796a3f2c24605085acb54151 100644
--- a/README.rst
+++ b/README.rst
@@ -1,50 +1,48 @@
+=====================================================
de Novo Ambiguous Restraints for Iterative Assignment
=====================================================
**A pipeline for automated de novo contact map assignment**
-|Pipeline status| |Coverage report|
+.. image:: https://gitlab.pasteur.fr/bis-aria/ariaec/badges/master/pipeline.svg
+ :target: https://gitlab.pasteur.fr/bis-aria/ariaec/commits/master
+ :alt: Pipeline status
+
+.. image:: https://gitlab.pasteur.fr/bis-aria/ariaec/badges/master/coverage.svg
+ :target: https://gitlab.pasteur.fr/bis-aria/ariaec/commits/master
+ :alt: Coverage report
+
``ariaec`` is a Python_ library that provides *de novo* structure prediction
based on ARIA_ pipeline and evolutionary restraints inferred from co-evolution.
-The package add several command line interfaces aside the usual ARIA commands in
- order to convert data, setup an ARIA project with evolutionary restraints,
- analyze contact maps or protein structures and generate statistics from a culled
- list of PDB files. An exhaustive list of the commands is available in the
- section
-``nbsphinx`` is a Sphinx_ extension that provides a source parser for
-``*.ipynb`` files.
-Custom Sphinx directives are used to show `Jupyter `_ code cells (and of
-course their results) in both HTML and LaTeX output.
-Un-evaluated notebooks -- i.e. notebooks without stored output cells -- will be
-automatically executed during the Sphinx build process.
-Quick Start:
-------------
- #. Be sure to check if ``pip`` (>= 9.0), ``setuptools`` (>= 18.0), ``numpy``
-(>= 1.11) and ``matplotlib`` are actually instaled in your personnal python
-installation or virtual environment.
+The package add a new command line interface aside the usual ARIA commands in
+order to convert data, setup an ARIA project with evolutionary restraints,
+analyze contact maps or protein structures and generate statistics from a culled
+list of PDB files.
+
+
+Quick Start
+-----------
+ 1. Be sure to check if the following packages are correctly installed with
+ your python installation or virtual environment.
- #. Download the ``zip`` or ``tar`` version at https://gitlab.pasteur.fr/bis-aria/ariaec
+ * ``pip`` (>= 9.0)
+ * ``setuptools`` (>= 18.0)
+ * ``numpy`` (>= 1.11)
+ * ``matplotlib``
- #. Edit your ``index.rst`` and add the names of your ``*.ipynb`` files
- to the ``toctree``.
+ 2. Download the ``zip`` or ``tar`` version at Gitlab_
- #. Run Sphinx!
+ 3. Extract the files and run ``pip install .`` inside the new directory
-Online documentation (and example of use):
- http://nbsphinx.readthedocs.io/
+More explanation about the ``pip`` installation can be found in the
+:doc: `installation` section
-Source code repository (and issue tracker):
- https://github.com/spatialaudio/nbsphinx/
-License:
---------
-.. MIT -- see the file ``LICENSE`` for details.
.. Hyperlinks
+.. _Gitlab: https://gitlab.pasteur.fr/bis-aria/ariaec
.. _ARIA: http://aria.pasteur.fr
.. _Python: https://www.python.org
-.. _Sphinx: http://sphinx-doc.org/
-.. _Jupyter Notebook: http://jupyter.org/
diff --git a/aria/conbox/commands.py b/aria/conbox/commands.py
index eb19a88698e11b1f16cb83a8a568df0cd5e819cd..bcac5fe5b0c1faf855b2a577c62657bf57919056 100644
--- a/aria/conbox/commands.py
+++ b/aria/conbox/commands.py
@@ -212,8 +212,8 @@ class AriaEcCommands(object):
help="secondary structure prediction file")
group.add_argument("-p", "--ariaproject", dest="ariaproject",
action=ReadableFile,
- help="ARIA project file. This file will be used as"
- "an initialization file if")
+ help="ARIA project file used to initialize a new "
+ "project with contact map data.")
group.add_argument("-t", "--type",
nargs="*", dest="contact_types",
choices=self.contact_types, help="Infile(s) contact "
@@ -231,7 +231,7 @@ class AriaEcCommands(object):
group.add_argument("--no-filter", dest="no_filter", action="store_true",
default=False, help="Do not filter contact map.")
group.add_argument("--extract-all", dest="extractall", action="store_true",
- default=False, help="Extract data or all data and"
+ default=False, help="Extract data or all data and "
"parameters if an ARIA project"
"is defined with -p option")
return parser
diff --git a/docs/_build/doctrees/contents.doctree b/docs/_build/doctrees/contents.doctree
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diff --git a/docs/_build/doctrees/installation.doctree b/docs/_build/doctrees/installation.doctree
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diff --git a/docs/_build/doctrees/tutorial.doctree b/docs/_build/doctrees/tutorial.doctree
deleted file mode 100644
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diff --git a/docs/_build/html/_sources/contents.rst.txt b/docs/_build/html/_sources/contents.rst.txt
deleted file mode 100644
index d34d8cf2d0e26f91c4253bf5186d43280bf19aee..0000000000000000000000000000000000000000
--- a/docs/_build/html/_sources/contents.rst.txt
+++ /dev/null
@@ -1,29 +0,0 @@
-.. _contents:
-
-Sphinx documentation contents
-=============================
-
-.. toctree::
- :maxdepth: 2
-
- installation
- tutorial
- modules
-
- copyright
-
-
-Indices and tables
-==================
-
-.. only:: builder_html
-
- * :ref:`genindex`
- * :ref:`modindex`
- * :ref:`search`
- * :ref:`glossary`
-
-.. only:: not builder_html
-
- * :ref:`modindex`
- * :ref:`glossary`
\ No newline at end of file
diff --git a/docs/_build/html/_sources/copyright.rst.txt b/docs/_build/html/_sources/copyright.rst.txt
deleted file mode 100644
index 6a3311cee021bc5f238d0380c5ef9650d863bf22..0000000000000000000000000000000000000000
--- a/docs/_build/html/_sources/copyright.rst.txt
+++ /dev/null
@@ -1,9 +0,0 @@
-:tocdepth: 2
-
-.. _copyright:
-
-Sphinx authors
-==============
-
-.. include:: ../COPYRIGHT
-
diff --git a/docs/_build/html/_sources/glossary.rst.txt b/docs/_build/html/_sources/glossary.rst.txt
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/docs/_build/html/_sources/installation.rst.txt b/docs/_build/html/_sources/installation.rst.txt
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/docs/_build/html/_sources/tutorial.rst.txt b/docs/_build/html/_sources/tutorial.rst.txt
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
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-
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-
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diff --git a/docs/api/conbox.rst b/docs/api/conbox.rst
new file mode 100644
index 0000000000000000000000000000000000000000..8ba7229ed8b561046f4ce5f136a9b72e8ec13c8c
--- /dev/null
+++ b/docs/api/conbox.rst
@@ -0,0 +1,122 @@
+Conbox
+======
+
+.. automodule:: aria.conbox
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+Analysis
+--------
+
+.. automodule:: aria.conbox.analysis
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+
+
+Commands
+--------
+
+.. automodule:: aria.conbox.commands
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+Common
+------
+
+.. automodule:: aria.conbox.common
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+Converter
+---------
+
+.. automodule:: aria.conbox.converter
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+Maplot
+------
+
+.. automodule:: aria.conbox.maplot
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+NDConv
+------
+
+.. automodule:: aria.conbox.ndconv
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+PDBDist
+-------
+
+.. automodule:: aria.conbox.pdbdist
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+PDBQual
+-------
+
+.. automodule:: aria.conbox.pdbqual
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+PDBStat
+-------
+
+.. automodule:: aria.conbox.pdbqual
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+Protein
+--------
+
+.. automodule:: aria.conbox.protein
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+ProtMap
+-------
+
+.. automodule:: aria.conbox.protmap
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+Reader
+------
+
+.. automodule:: aria.conbox.reader
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+Settings
+---------
+
+.. automodule:: aria.conbox.settings
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+Setup
+------
+
+.. automodule:: aria.conbox.setup
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
diff --git a/docs/api/core.rst b/docs/api/core.rst
new file mode 100644
index 0000000000000000000000000000000000000000..14ae33fc6f8ac77ed7417cc1c212bdb995fd945b
--- /dev/null
+++ b/docs/api/core.rst
@@ -0,0 +1,7 @@
+Core
+====
+
+.. automodule:: aria.core
+ :members:
+ :undoc-members:
+ :show-inheritance:
diff --git a/docs/changelog.rst b/docs/changelog.rst
new file mode 100644
index 0000000000000000000000000000000000000000..4ccd5096370565eb279899ef8f2fc8a9671ef913
--- /dev/null
+++ b/docs/changelog.rst
@@ -0,0 +1,4 @@
+Changelog
+=========
+
+.. include:: ../CHANGELOG
diff --git a/docs/conf.py b/docs/conf.py
index 9524adead624494b5b48a5c6430a53c069a1390f..ad64ddb849fb214e216514ce527b8492ccd16280 100644
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -19,7 +19,10 @@
# import os
# import sys
# sys.path.insert(0, os.path.abspath('.'))
+import time
import sphinx_rtd_theme
+import sphinx_bootstrap_theme
+from setup import get_version
# -- General configuration ------------------------------------------------
@@ -38,7 +41,7 @@ extensions = [
'sphinx.ext.mathjax',
'sphinx.ext.viewcode',
'sphinx.ext.napoleon',
- 'sphinx.ext.nbsphinx'
+ # 'sphinx.ext.nbsphinx'
]
# Add any paths that contain templates here, relative to this directory.
@@ -51,11 +54,10 @@ templates_path = ['_templates']
source_suffix = '.rst'
# The master toctree document.
-master_doc = 'index'
+master_doc = 'introduction'
# General information about the project.
project = u'ARIAEC'
-import time
author = u'Benjamin Bardiaux, Michael Habeck, Therese Malliavin, ' \
u'Wolfgang Rieping, and Michael Nilges'
copyright = u'{}, {}'.format(
@@ -66,10 +68,9 @@ copyright = u'{}, {}'.format(
# built documents.
#
# The short X.Y version.
-import setup
-version = setup.get_version()
+version = get_version(full=False)
# The full version, including alpha/beta/rc tags.
-release = setup.get_version()
+release = get_version(full=True)
# The language for content autogenerated by Sphinx. Refer to documentation
# for a list of supported languages.
@@ -96,20 +97,35 @@ todo_include_todos = False
# a list of builtin themes.
#
html_theme = "sphinx_rtd_theme"
+# html_theme = "bootstrap"
html_theme_path = [sphinx_rtd_theme.get_html_theme_path()]
+# html_theme_path = sphinx_bootstrap_theme.get_html_theme_path()
# Theme options are theme-specific and customize the look and feel of a theme
# further. For a list of options available for each theme, see the
# documentation.
#
-# html_theme_options = {}
+html_theme_options = {
+ 'logo_only': True
+}
+
+html_logo = "_static/logo.jpg"
# Add any paths that contain custom static files (such as style sheets) here,
# relative to this directory. They are copied after the builtin static files,
# so a file named "default.css" will overwrite the builtin "default.css".
html_static_path = ['_static']
+
+html_context = {
+ 'css_files': [
+ '_static/theme_overrides.css', # override wide tables in RTD theme
+ ],
+ }
+
+html_favicon = "_static/favicon.ico"
+
# Custom sidebar templates, must be a dictionary that maps document names
# to template names.
#
diff --git a/docs/configuration.rst b/docs/configuration.rst
new file mode 100644
index 0000000000000000000000000000000000000000..960825888e02841a22906ef430b6193bc4ca2dca
--- /dev/null
+++ b/docs/configuration.rst
@@ -0,0 +1,85 @@
+Configuration
+=============
+
+The following tables list the available parameters with the corresponding
+sections. In order to change default parameters, the tool can accept a
+configuration file with the ``-c`` option in the :doc:`usage`. This
+configuration file should follow the `INI <https://en.wikipedia.org/wiki/INI_file>`_ format.
+
+**Example:**
+
+.. code-block:: guess
+
+ [section]
+ ; comment
+ parameter: value
+
+
+main
+----
+
+.. rst-class:: table-hover
+
++--------------------------+------+----------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| Name | Type | Default | Description |
++--------------------------+------+----------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| ss_dist_file | path | `ss_dist.txt`_ | Distances between stable secondary structures. Those distances are used to make supplementary distance restraints related to secondary structure predictions. |
++--------------------------+------+----------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| scsc_min_file | path | | |
++--------------------------+------+----------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| interlowerbounds_pdbstat | path | | |
++--------------------------+------+----------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| intertarget_pdbstat | path | | |
++--------------------------+------+----------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| interupperbounds_pdbstat | path | | |
++--------------------------+------+----------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| intralowerbounds_pdbstat | path | | |
++--------------------------+------+----------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| intratarget_pdbstat | path | | |
++--------------------------+------+----------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| intraupperbounds_pdbstat | path | | |
++--------------------------+------+----------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| ariaproject_template | str | `2.3.6`_ | |
++--------------------------+------+----------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| procheck_executable | path | | |
++--------------------------+------+----------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| prosa_executable | | | |
++--------------------------+------+----------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| whatif_executable | | | |
++--------------------------+------+----------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| clashlist_executable | | | |
++--------------------------+------+----------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------+
+
+
+ss_dist.txt
++++++++++++
+.. _ss_dist.txt:
+
+.. literalinclude:: ../aria/conbox/data/ss_dist.txt
+
+A
++++++++++++
+
+contactdef
+----------
+
+setup
+-----
+
+maplot
+------
+
+bbconv
+------
+
+pdbqual
+-------
+
+pdbdist
+-------
+
+pdbstat
+-------
+
+analysis
+--------
diff --git a/docs/contents.rst b/docs/contents.rst
new file mode 100644
index 0000000000000000000000000000000000000000..706adb8980527bff2a916488c0d4fb50e2d395d0
--- /dev/null
+++ b/docs/contents.rst
@@ -0,0 +1,21 @@
+.. toctree::
+ :maxdepth: 2
+ :caption: Documentation
+
+ changelog
+ installation
+ usage
+ configuration
+
+.. toctree::
+ :maxdepth: 2
+ :caption: API
+
+ api/core
+ api/conbox
+
+.. toctree::
+ :maxdepth: 2
+ :caption: Examples
+
+ examples/index
diff --git a/docs/copyright.rst b/docs/copyright.rst
deleted file mode 100644
index 6a3311cee021bc5f238d0380c5ef9650d863bf22..0000000000000000000000000000000000000000
--- a/docs/copyright.rst
+++ /dev/null
@@ -1,9 +0,0 @@
-:tocdepth: 2
-
-.. _copyright:
-
-Sphinx authors
-==============
-
-.. include:: ../COPYRIGHT
-
diff --git a/docs/examples/index.rst b/docs/examples/index.rst
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..d975cbf3387d50c7c5774e499bec8f0e3f9ebb62 100644
--- a/docs/examples/index.rst
+++ b/docs/examples/index.rst
@@ -0,0 +1,4 @@
+.. _examples:
+
+Examples
+========
diff --git a/docs/glossary.rst b/docs/glossary.rst
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/docs/installation.rst b/docs/installation.rst
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..9eb2c73e025579ce01003f9a560602e5ca62a1f4 100644
--- a/docs/installation.rst
+++ b/docs/installation.rst
@@ -0,0 +1,18 @@
+Installation
+============
+
+.. note::
+
+ Installation procedure may change in the future
+
+Dependencies
+------------
+
+
+Basic installation
+------------------
+
+
+Singularity
+-----------
+
diff --git a/docs/index.rst b/docs/introduction.rst
similarity index 68%
rename from docs/index.rst
rename to docs/introduction.rst
index 746aac6c4c6c149b75e76bc89c0e30d32cb843a7..fe448a97b8795d230c924fa7994124cedb443f54 100644
--- a/docs/index.rst
+++ b/docs/introduction.rst
@@ -6,16 +6,11 @@
.. include:: ../README.rst
-.. toctree::
- :maxdepth: 1
- :caption: Contents
+License
+-------
+.. include:: ../COPYRIGHT
- introduction
- changelog
- installation
- tutorial
- examples/index
- api
+.. include:: contents.rst
Indices and tables
@@ -23,4 +18,4 @@ Indices and tables
* :ref:`genindex`
* :ref:`modindex`
-* :ref:`search`
+* :ref:`search`
\ No newline at end of file
diff --git a/docs/tutorial.rst b/docs/tutorial.rst
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/docs/usage.rst b/docs/usage.rst
new file mode 100644
index 0000000000000000000000000000000000000000..ed54d2636daafeb15e1efb2e215547dd450a1603
--- /dev/null
+++ b/docs/usage.rst
@@ -0,0 +1,156 @@
+Command Line Interface
+======================
+
+The command line interface is accessible by calling ``ariaec`` (or ``ec2aria``
+for older versions) within the terminal at the end of the installation process.
+
+.. code-block:: bash
+
+ $ ariaec [-h] -o OUTPUT_DIRECTORY [-c CONF_FILE] [--nolog] [-d] COMMAND
+
+
+**Commands**
+
+.. rst-class:: table-hover
+
+
++-------------------------+-----------------------------------------------------+
+| Name | Short description |
++-------------------------+-----------------------------------------------------+
+| `setup <Setup_>`_ | Setup ARIA project with EC data |
++-------------------------+-----------------------------------------------------+
+| `bbconv <BBconv_>`_ | Translate BBcontacts as distance restraints |
++-------------------------+-----------------------------------------------------+
+| `maplot <Maplot_>`_ | Contact map visualisation tool |
++-------------------------+-----------------------------------------------------+
+| `pdbqual <PDBQual_>`_ | Call PDB quality tools |
++-------------------------+-----------------------------------------------------+
+| `analysis <Analysis_>`_ | Analyze results from an ARIA project |
++-------------------------+-----------------------------------------------------+
+| `tbl2xml <TBL2XML_>`_ | Convert TBL restraints in ARIA XML format |
++-------------------------+-----------------------------------------------------+
+| `pdbdist <PDBDist_>`_ | Extract distance from a culled list of PDBs |
++-------------------------+-----------------------------------------------------+
+| `pdbstat <PDBStat_>`_ | Statistical analysis of ``pdbdist`` results |
++-------------------------+-----------------------------------------------------+
+| `iniconv <Iniconv_>`_ | Convert a INI file as csv for easy readability |
++-------------------------+-----------------------------------------------------+
+
+
+**Options**
+
+
+.. rst-class:: table-hover
+
+
++--------------------------------------------------------+-----------------------------------------------------+
+| Name | Description |
++--------------------------------------------------------+-----------------------------------------------------+
+| ``-h``, ``--help`` | show help message and exit |
++--------------------------------------------------------+-----------------------------------------------------+
+| ``-o OUTPUT_DIRECTORY``, ``--output OUTPUT_DIRECTORY`` | Output directory (default: None) |
++--------------------------------------------------------+-----------------------------------------------------+
+| ``-c CONF_FILE``, ``--conf CONF_FILE`` | configuration file (default: None) |
++--------------------------------------------------------+-----------------------------------------------------+
+| ``--nolog`` | Don't generate log files (default: False) |
++--------------------------------------------------------+-----------------------------------------------------+
+| ``-d``, ``--debug`` | Increase output verbosity (default: False) |
++--------------------------------------------------------+-----------------------------------------------------+
+
+
+Setup
+--------------
+Translate contact maps as distance restraints and setup ARIA infrastructure.
+
+.. code-block:: bash
+
+ $ ariaec setup [-options] seq infile [infile ...] -t intype [intype ...]
+
+
+
+**Arguments**
+
+.. rst-class:: table-hover
+
+
++-------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| Name | Short description |
++-------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| ``seq`` | Sequence file [``FASTA``] |
++-------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| ``infile`` | Contact or pdb file(s) used to build aria distance restraints |
++-------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| ``intype`` | Contact Map file format:sup:`*` |
++-------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| :sup:`*` Accepted contact map formats combining formats supported by ConKit_ with few supplementary formats: ``gremlin``, ``pconsc1``, ``pconsc3``, ``pconsc2``, ``bbcontacts``, ``metapsicov_stg1``, ``membrain``, ``metapsicovhb``, ``comsat``, ``casprr``, ``ccmpred``, ``plm``, ``bclcontact``, ``epcmap``, ``evfold``, ``native``, ``pconsc``, ``psicov``, ``freecontact``, ``genericstructure``, ``ncont``, ``plmc``, ``plmdca``, ``metapsicov_stg2``, ``native_full``, ``metapsicov``, ``evcoupling``, ``contactlist``, ``plmev``, ``mmcif``, ``casp``, ``pdb``, ``flib`` |
++----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+
+.. _ConKit: http://www.conkit.org/en/latest/
+
+
+**Options**
+
+
+.. rst-class:: table-hover
+
+
++--------------------------------------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------+
+| Name | Description |
++--------------------------------------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------+
+| ``-d DISTFILE``, ``--distfile DISTFILE`` | Pdb or distance matrix iif distance_type set to distfile in conf file, use distances in the given file as target distance to build distance restraints |
++--------------------------------------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------+
+| ``-s SSPRED``, ``--ssfile SSPRED`` | Secondary structure prediction file |
++--------------------------------------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------+
+| ``-p ARIAPROJECT``, ``--ariaproject ARIAPROJECT`` | ARIA project file. This project will be updated with data generated during the ``ariaec setup`` call |
++--------------------------------------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------+
+| ``-r SEQRANGE``, ``--range SEQRANGE`` | Index range if we don't want tu use the whole sequence and map |
++--------------------------------------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------+
+| ``-n REF``, ``--native REF`` | Native pdb. Allow TP/FP detection |
++--------------------------------------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------+
+| ``--hb HB`` | H-bonds contact file (eg: metapsicov.hb) |
++--------------------------------------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------+
+| ``--ssidx`` | Use secondary structure index |
++--------------------------------------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------+
+| ``--no-filter`` | Do not filter contact map |
++--------------------------------------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------+
+| ``--extract-all`` | Extract data or all data and parameters if an ARIA project is defined with ``-p`` option |
++--------------------------------------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------+
+
+
+Bbconv
+--------------
+Translate BBcontacts as distance restraints which can be used during
+`setup <Setup_>`_.
+
+
+Maplot
+--------------
+Contactmap analysis and visualisation tool.
+
+
+Analysis
+--------------
+Analyze results from an ARIA project.
+
+
+PDBQual
+--------------
+Call PDB quality tools.
+
+
+TBL2XML
+--------------
+Convert TBL restraints in ARIA XML format.
+
+
+PDBDist
+--------------
+Extract distance from a culled list of PDBs.
+
+PDBStat
+--------------
+Statistical analysis of ``pdbdist`` results.
+
+IniConv
+--------------
+Convert a INI file as csv for easy readability.
diff --git a/examples-dev/olds/Makefile b/examples-dev/olds/Makefile
new file mode 100644
index 0000000000000000000000000000000000000000..5146caba7730eaa0c27c8746ef95bfe8acf7f6b6
--- /dev/null
+++ b/examples-dev/olds/Makefile
@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS =
+SPHINXBUILD = sphinx-build
+SPHINXPROJ = AriaEc
+SOURCEDIR = .
+BUILDDIR = _build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+ @$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+ @$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
\ No newline at end of file
diff --git a/examples-dev/olds/_build/doctrees/ariaec.doctree b/examples-dev/olds/_build/doctrees/ariaec.doctree
new file mode 100644
index 0000000000000000000000000000000000000000..873ef5ec80ab1638d3d206ad59d8ac749e5f2ed5
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diff --git a/examples-dev/olds/_build/doctrees/environment.pickle b/examples-dev/olds/_build/doctrees/environment.pickle
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diff --git a/docs/_build/doctrees/index.doctree b/examples-dev/olds/_build/doctrees/index.doctree
similarity index 78%
rename from docs/_build/doctrees/index.doctree
rename to examples-dev/olds/_build/doctrees/index.doctree
index 35d9479b9c171bcec89bfaa738a62daf4279a8c4..7418f750a0ccf7476bd3785a4573aa1e8c31c6e1 100644
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diff --git a/docs/_build/doctrees/modules.doctree b/examples-dev/olds/_build/doctrees/modules.doctree
similarity index 92%
rename from docs/_build/doctrees/modules.doctree
rename to examples-dev/olds/_build/doctrees/modules.doctree
index d0ad5fd7c140f844f56a5fa75dac6569a2f7b02a..ec92b93586bb0a0c21ccfea1e77eff648e441d22 100644
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diff --git a/docs/_build/html/.buildinfo b/examples-dev/olds/_build/html/.buildinfo
similarity index 82%
rename from docs/_build/html/.buildinfo
rename to examples-dev/olds/_build/html/.buildinfo
index a74d88eb5f9bfd2bd0479b43d3800aff49234441..eaba7c828628918b200b6e94bafcb3ae8dea753f 100644
--- a/docs/_build/html/.buildinfo
+++ b/examples-dev/olds/_build/html/.buildinfo
@@ -1,4 +1,4 @@
# Sphinx build info version 1
# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: 4da5904f1f9b1887d948b51687bdfaa0
+config: cbf8f1a8c4c0d68994ae9bd4f214590d
tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/examples-dev/olds/_build/html/_modules/ariaec/analysis.html b/examples-dev/olds/_build/html/_modules/ariaec/analysis.html
new file mode 100644
index 0000000000000000000000000000000000000000..23be1773aec7f242e42281db56e9c900886bfccd
--- /dev/null
+++ b/examples-dev/olds/_build/html/_modules/ariaec/analysis.html
@@ -0,0 +1,729 @@
+
+
+<!DOCTYPE html>
+<!--[if IE 8]><html class="no-js lt-ie9" lang="en" > <![endif]-->
+<!--[if gt IE 8]><!--> <html class="no-js" lang="en" > <!--<![endif]-->
+<head>
+ <meta charset="utf-8">
+
+ <meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+ <title>ariaec.analysis — AriaEc 0.2 documentation</title>
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ <link rel="stylesheet" href="../../_static/css/theme.css" type="text/css" />
+
+
+
+
+
+ <link rel="index" title="Index"
+ href="../../genindex.html"/>
+ <link rel="search" title="Search" href="../../search.html"/>
+ <link rel="top" title="AriaEc 0.2 documentation" href="../../index.html"/>
+ <link rel="up" title="Module code" href="../index.html"/>
+
+
+ <script src="../../_static/js/modernizr.min.js"></script>
+
+</head>
+
+<body class="wy-body-for-nav" role="document">
+
+
+ <div class="wy-grid-for-nav">
+
+
+ <nav data-toggle="wy-nav-shift" class="wy-nav-side">
+ <div class="wy-side-scroll">
+ <div class="wy-side-nav-search">
+
+
+
+ <a href="../../index.html" class="icon icon-home"> AriaEc
+
+
+
+ </a>
+
+
+
+
+ <div class="version">
+ 0.2
+ </div>
+
+
+
+
+<div role="search">
+ <form id="rtd-search-form" class="wy-form" action="../../search.html" method="get">
+ <input type="text" name="q" placeholder="Search docs" />
+ <input type="hidden" name="check_keywords" value="yes" />
+ <input type="hidden" name="area" value="default" />
+ </form>
+</div>
+
+
+ </div>
+
+ <div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="main navigation">
+
+
+
+
+
+
+ <!-- Local TOC -->
+ <div class="local-toc"></div>
+
+
+ </div>
+ </div>
+ </nav>
+
+ <section data-toggle="wy-nav-shift" class="wy-nav-content-wrap">
+
+
+ <nav class="wy-nav-top" role="navigation" aria-label="top navigation">
+
+ <i data-toggle="wy-nav-top" class="fa fa-bars"></i>
+ <a href="../../index.html">AriaEc</a>
+
+ </nav>
+
+
+
+ <div class="wy-nav-content">
+ <div class="rst-content">
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+<div role="navigation" aria-label="breadcrumbs navigation">
+
+ <ul class="wy-breadcrumbs">
+
+ <li><a href="../../index.html">Docs</a> »</li>
+
+ <li><a href="../index.html">Module code</a> »</li>
+
+ <li>ariaec.analysis</li>
+
+
+ <li class="wy-breadcrumbs-aside">
+
+
+
+ </li>
+
+ </ul>
+
+
+ <hr/>
+</div>
+ <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
+ <div itemprop="articleBody">
+
+ <h1>Source code for ariaec.analysis</h1><div class="highlight"><pre>
+<span></span><span class="c1"># coding=utf-8</span>
+<span class="sd">"""</span>
+<span class="sd">Created on 4/7/17</span>
+
+<span class="sd">@author: fallain</span>
+<span class="sd">"""</span>
+<span class="kn">import</span> <span class="nn">re</span>
+<span class="kn">import</span> <span class="nn">os</span>
+<span class="kn">import</span> <span class="nn">logging</span>
+<span class="kn">import</span> <span class="nn">numpy</span> <span class="k">as</span> <span class="nn">np</span>
+<span class="kn">import</span> <span class="nn">seaborn</span> <span class="k">as</span> <span class="nn">sns</span>
+<span class="kn">import</span> <span class="nn">matplotlib.pyplot</span> <span class="k">as</span> <span class="nn">plt</span>
+<span class="kn">from</span> <span class="nn">glob</span> <span class="k">import</span> <span class="n">glob</span>
+<span class="kn">from</span> <span class="nn">collections</span> <span class="k">import</span> <span class="n">OrderedDict</span>
+<span class="kn">from</span> <span class="nn">Bio.PDB</span> <span class="k">import</span> <span class="n">PDBParser</span><span class="p">,</span> <span class="n">PDBIO</span>
+<span class="kn">from</span> <span class="nn">sklearn.decomposition</span> <span class="k">import</span> <span class="n">PCA</span>
+<span class="kn">from</span> <span class="nn">aria.AriaXML</span> <span class="k">import</span> <span class="n">AriaXMLPickler</span>
+<span class="kn">from</span> <span class="nn">matplotlib.lines</span> <span class="k">import</span> <span class="n">Line2D</span>
+<span class="kn">from</span> <span class="nn">mpl_toolkits.mplot3d</span> <span class="k">import</span> <span class="n">Axes3D</span>
+<span class="kn">from</span> <span class="nn">aria.SuperImposer</span> <span class="k">import</span> <span class="n">SuperImposer</span>
+<span class="kn">from</span> <span class="nn">.converter</span> <span class="k">import</span> <span class="n">AriaEcXMLConverter</span>
+<span class="kn">from</span> <span class="nn">.common</span> <span class="k">import</span> <span class="n">NotDisordered</span><span class="p">,</span> <span class="n">Capturing</span>
+<span class="kn">from</span> <span class="nn">matplotlib.colors</span> <span class="k">import</span> <span class="n">ListedColormap</span>
+<span class="kn">from</span> <span class="nn">aria.DataContainer</span> <span class="k">import</span> <span class="n">DATA_SEQUENCE</span>
+<span class="kn">from</span> <span class="nn">aria.StructureEnsemble</span> <span class="k">import</span> <span class="n">StructureEnsemble</span><span class="p">,</span> <span class="n">StructureEnsembleSettings</span>
+
+
+<span class="n">LOG</span> <span class="o">=</span> <span class="n">logging</span><span class="o">.</span><span class="n">getLogger</span><span class="p">(</span><span class="vm">__name__</span><span class="p">)</span>
+
+
+<div class="viewcode-block" id="colscatter"><a class="viewcode-back" href="../../ariaec.html#ariaec.analysis.colscatter">[docs]</a><span class="k">def</span> <span class="nf">colscatter</span><span class="p">(</span><span class="n">X</span><span class="p">,</span> <span class="n">axe</span><span class="p">,</span> <span class="n">colors</span><span class="p">,</span> <span class="n">ndim</span><span class="o">=</span><span class="mi">2</span><span class="p">,</span> <span class="n">axtitle</span><span class="o">=</span><span class="s2">""</span><span class="p">,</span> <span class="n">xlabel</span><span class="o">=</span><span class="s2">"x"</span><span class="p">,</span>
+ <span class="n">ylabel</span><span class="o">=</span><span class="s2">"y"</span><span class="p">,</span> <span class="n">zlabel</span><span class="o">=</span><span class="s2">"z"</span><span class="p">,</span> <span class="n">legend_prefix</span><span class="o">=</span><span class="s2">""</span><span class="p">,</span> <span class="n">others</span><span class="o">=</span><span class="kc">False</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Scatter plot with palette colors</span>
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> X :</span>
+
+<span class="sd"> axe :</span>
+
+<span class="sd"> colors :</span>
+
+<span class="sd"> ndim :</span>
+<span class="sd"> (Default value = 2)</span>
+<span class="sd"> axtitle :</span>
+<span class="sd"> (Default value = "")</span>
+<span class="sd"> xlabel :</span>
+<span class="sd"> (Default value = "x")</span>
+<span class="sd"> ylabel :</span>
+<span class="sd"> (Default value = "y")</span>
+<span class="sd"> zlabel :</span>
+<span class="sd"> (Default value = "z")</span>
+<span class="sd"> legend_prefix :</span>
+<span class="sd"> (Default value = "")</span>
+<span class="sd"> others :</span>
+<span class="sd"> (Default value = False)</span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+<span class="sd"> """</span>
+ <span class="n">palette</span> <span class="o">=</span> <span class="n">sns</span><span class="o">.</span><span class="n">color_palette</span><span class="p">(</span><span class="s2">"hls"</span><span class="p">,</span> <span class="nb">len</span><span class="p">(</span><span class="nb">set</span><span class="p">(</span><span class="n">colors</span><span class="p">)))</span>
+ <span class="n">dims</span> <span class="o">=</span> <span class="p">[</span><span class="n">X</span><span class="p">[:,</span> <span class="n">i</span><span class="p">]</span> <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="n">ndim</span><span class="p">)]</span>
+ <span class="n">axe</span><span class="o">.</span><span class="n">scatter</span><span class="p">(</span><span class="o">*</span><span class="n">dims</span><span class="p">,</span> <span class="n">c</span><span class="o">=</span><span class="n">colors</span><span class="p">,</span>
+ <span class="n">cmap</span><span class="o">=</span><span class="n">ListedColormap</span><span class="p">(</span><span class="n">palette</span><span class="p">))</span>
+ <span class="n">axe</span><span class="o">.</span><span class="n">invert_xaxis</span><span class="p">()</span>
+
+ <span class="k">if</span> <span class="n">others</span><span class="p">:</span>
+ <span class="n">axe</span><span class="o">.</span><span class="n">legend</span><span class="p">([</span><span class="n">Line2D</span><span class="p">([</span><span class="mi">0</span><span class="p">],</span> <span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">linestyle</span><span class="o">=</span><span class="s2">"none"</span><span class="p">,</span> <span class="n">c</span><span class="o">=</span><span class="n">palette</span><span class="p">[</span><span class="n">colidx</span><span class="p">],</span>
+ <span class="n">marker</span><span class="o">=</span><span class="s2">"o"</span><span class="p">)</span>
+ <span class="k">for</span> <span class="n">colidx</span> <span class="ow">in</span> <span class="nb">set</span><span class="p">(</span><span class="n">colors</span><span class="p">)],</span>
+ <span class="p">[</span><span class="n">legend_prefix</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">colidx</span><span class="p">)</span> <span class="k">if</span> <span class="n">colidx</span> <span class="o">!=</span> <span class="nb">max</span><span class="p">(</span>
+ <span class="n">colors</span><span class="p">)</span> <span class="k">else</span> <span class="s2">"Others"</span> <span class="k">for</span> <span class="n">colidx</span> <span class="ow">in</span> <span class="nb">set</span><span class="p">(</span><span class="n">colors</span><span class="p">)],</span>
+ <span class="n">numpoints</span><span class="o">=</span><span class="mi">1</span><span class="p">)</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="n">axe</span><span class="o">.</span><span class="n">legend</span><span class="p">([</span><span class="n">Line2D</span><span class="p">([</span><span class="mi">0</span><span class="p">],</span> <span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">linestyle</span><span class="o">=</span><span class="s2">"none"</span><span class="p">,</span> <span class="n">c</span><span class="o">=</span><span class="n">palette</span><span class="p">[</span><span class="n">colidx</span><span class="p">],</span>
+ <span class="n">marker</span><span class="o">=</span><span class="s2">"o"</span><span class="p">)</span>
+ <span class="k">for</span> <span class="n">colidx</span> <span class="ow">in</span> <span class="nb">set</span><span class="p">(</span><span class="n">colors</span><span class="p">)],</span>
+ <span class="p">[</span><span class="n">legend_prefix</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">colidx</span><span class="p">)</span> <span class="k">for</span> <span class="n">colidx</span> <span class="ow">in</span>
+ <span class="nb">set</span><span class="p">(</span><span class="n">colors</span><span class="p">)],</span> <span class="n">numpoints</span><span class="o">=</span><span class="mi">1</span><span class="p">)</span>
+
+ <span class="n">axe</span><span class="o">.</span><span class="n">set_title</span><span class="p">(</span><span class="n">axtitle</span><span class="p">)</span>
+ <span class="n">axe</span><span class="o">.</span><span class="n">set_xlabel</span><span class="p">(</span><span class="n">xlabel</span><span class="p">)</span>
+ <span class="n">axe</span><span class="o">.</span><span class="n">set_ylabel</span><span class="p">(</span><span class="n">ylabel</span><span class="p">)</span>
+ <span class="k">if</span> <span class="n">ndim</span> <span class="o">==</span> <span class="mi">3</span><span class="p">:</span>
+ <span class="n">axe</span><span class="o">.</span><span class="n">set_zlabel</span><span class="p">(</span><span class="n">zlabel</span><span class="p">)</span></div>
+
+
+<div class="viewcode-block" id="EnsembleAnalysis"><a class="viewcode-back" href="../../ariaec.html#ariaec.analysis.EnsembleAnalysis">[docs]</a><span class="k">class</span> <span class="nc">EnsembleAnalysis</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span>
+ <span class="sd">"""ARIA extended ensemble analysis"""</span>
+
+ <span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">settings</span><span class="p">):</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">settings</span> <span class="o">=</span> <span class="n">settings</span>
+
+ <span class="nd">@staticmethod</span>
+ <span class="k">def</span> <span class="nf">_get_ensemble_paths</span><span class="p">(</span><span class="n">iteration_path</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Get list of pdb files related to aria ensemble(s)</span>
+<span class="sd"> </span>
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> iteration_path : str</span>
+<span class="sd"> ARIA iteration path where all pdb files are saved </span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+<span class="sd"> </span>
+<span class="sd"> """</span>
+ <span class="c1"># Get the list of all the generated structures in iteration path if no</span>
+ <span class="c1"># clustering. Otherwise, get the list of all generated structures</span>
+ <span class="n">list_of_pdb</span> <span class="o">=</span> <span class="p">[]</span>
+ <span class="k">if</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">iteration_path</span><span class="p">,</span> <span class="s2">"report.clustering"</span><span class="p">)):</span>
+ <span class="c1"># Get the list of pdb for each cluster</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s2">"Clusters found in this iteration, compute analysis for"</span>
+ <span class="s2">"each generated cluster ensemble"</span><span class="p">)</span>
+ <span class="k">for</span> <span class="n">clustlist</span> <span class="ow">in</span> <span class="n">glob</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">iteration_path</span><span class="p">,</span> <span class="s1">'*clust*.list'</span><span class="p">)):</span>
+ <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">clustlist</span><span class="p">)</span> <span class="k">as</span> <span class="n">cluster</span><span class="p">:</span>
+ <span class="n">list_of_pdb</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">cluster</span><span class="o">.</span><span class="n">read</span><span class="p">()</span><span class="o">.</span><span class="n">splitlines</span><span class="p">())</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="c1"># no clustering, pdb list correspond to all generated structures</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s2">"No cluster found in this iteration, compute analysis for"</span>
+ <span class="s2">" iteration ensemble"</span><span class="p">)</span>
+ <span class="n">list_of_pdb</span><span class="o">.</span><span class="n">append</span><span class="p">(</span>
+ <span class="p">[</span><span class="n">foo</span> <span class="k">for</span> <span class="n">foo</span> <span class="ow">in</span> <span class="n">glob</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">iteration_path</span><span class="p">,</span> <span class="s2">"*.pdb"</span><span class="p">))</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">basename</span><span class="p">(</span><span class="n">foo</span><span class="p">)</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s1">'fitted_'</span><span class="p">)])</span>
+
+ <span class="n">LOG</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="s2">"Lists of structures:</span><span class="se">\n</span><span class="si">%s</span><span class="s2">"</span><span class="p">,</span> <span class="s2">"</span><span class="se">\n</span><span class="s2">"</span><span class="o">.</span><span class="n">join</span><span class="p">(</span>
+ <span class="p">[</span><span class="nb">str</span><span class="p">(</span><span class="n">_</span><span class="p">)</span> <span class="k">for</span> <span class="n">_</span> <span class="ow">in</span> <span class="n">list_of_pdb</span><span class="p">]))</span>
+ <span class="k">return</span> <span class="n">list_of_pdb</span>
+
+<div class="viewcode-block" id="EnsembleAnalysis.violation_analysis"><a class="viewcode-back" href="../../ariaec.html#ariaec.analysis.EnsembleAnalysis.violation_analysis">[docs]</a> <span class="nd">@staticmethod</span>
+ <span class="k">def</span> <span class="nf">violation_analysis</span><span class="p">(</span><span class="n">project</span><span class="p">,</span> <span class="n">iteration_id</span><span class="p">,</span> <span class="n">restraints</span><span class="p">,</span> <span class="n">ensemble</span><span class="p">,</span> <span class="n">out_file</span><span class="p">,</span>
+ <span class="n">dists_ref</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">headerflag</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">clusteridx</span><span class="o">=</span><span class="mi">0</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> </span>
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> clusteridx</span>
+<span class="sd"> project : aria.Project.Project object</span>
+<span class="sd"> iteration_id : </span>
+<span class="sd"> restraints :</span>
+<span class="sd"> </span>
+<span class="sd"> ensemble :</span>
+<span class="sd"> </span>
+<span class="sd"> out_file :</span>
+<span class="sd"> </span>
+<span class="sd"> dists_ref : </span>
+<span class="sd"> Reference distances (Default value = None)</span>
+<span class="sd"> headerflag :</span>
+<span class="sd"> (Default value = True)</span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+<span class="sd"> </span>
+<span class="sd"> """</span>
+ <span class="n">protein_id</span> <span class="o">=</span> <span class="n">project</span><span class="o">.</span><span class="n">getSettings</span><span class="p">()[</span><span class="s1">'name'</span><span class="p">]</span>
+ <span class="n">nbest</span> <span class="o">=</span> <span class="n">project</span><span class="o">.</span><span class="n">getProtocol</span><span class="p">()</span><span class="o">.</span><span class="n">getIterationSettings</span><span class="p">(</span><span class="n">iteration_id</span><span class="p">)[</span>
+ <span class="s2">"number_of_best_structures"</span><span class="p">]</span>
+ <span class="n">cutoff</span> <span class="o">=</span> <span class="n">project</span><span class="o">.</span><span class="n">getProtocol</span><span class="p">()</span><span class="o">.</span><span class="n">getIterationSettings</span><span class="p">(</span><span class="n">iteration_id</span><span class="p">)[</span>
+ <span class="s2">"violation_analyser_settings"</span><span class="p">][</span><span class="s2">"violation_tolerance"</span><span class="p">]</span>
+ <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">out_file</span><span class="p">,</span> <span class="s1">'w'</span><span class="p">)</span> <span class="k">if</span> <span class="n">headerflag</span> <span class="k">else</span> <span class="nb">open</span><span class="p">(</span><span class="n">out_file</span><span class="p">,</span> <span class="s1">'a'</span><span class="p">)</span> <span class="k">as</span> <span class="n">out</span><span class="p">:</span>
+
+ <span class="k">for</span> <span class="n">restraintlist</span> <span class="ow">in</span> <span class="n">restraints</span><span class="p">:</span>
+
+ <span class="k">for</span> <span class="n">rest</span> <span class="ow">in</span> <span class="n">restraintlist</span><span class="p">:</span>
+
+ <span class="n">output</span> <span class="o">=</span> <span class="p">[]</span>
+ <span class="n">dd</span> <span class="o">=</span> <span class="p">[]</span>
+ <span class="n">ddref</span> <span class="o">=</span> <span class="p">[]</span>
+
+ <span class="k">for</span> <span class="n">contrib</span> <span class="ow">in</span> <span class="n">rest</span><span class="o">.</span><span class="n">getContributions</span><span class="p">():</span>
+
+ <span class="n">dist</span> <span class="o">=</span> <span class="kc">None</span>
+ <span class="k">try</span><span class="p">:</span>
+ <span class="n">dist</span> <span class="o">=</span> <span class="p">[</span><span class="n">ensemble</span><span class="o">.</span><span class="n">getDistances</span><span class="p">(</span><span class="o">*</span><span class="n">sp</span><span class="o">.</span><span class="n">getAtoms</span><span class="p">())</span>
+ <span class="k">for</span> <span class="n">sp</span> <span class="ow">in</span> <span class="n">contrib</span><span class="p">]</span>
+ <span class="c1"># Liste des distances pour la contribution c pour</span>
+ <span class="c1"># chaque structure de l'ensemble (une ou plusieur</span>
+ <span class="c1"># distance(s) par structure de l'ensemble si contribution</span>
+ <span class="c1"># ambigue ou non)</span>
+ <span class="n">dist</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">power</span><span class="p">(</span>
+ <span class="n">np</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">power</span><span class="p">(</span><span class="n">dist</span><span class="p">,</span> <span class="o">-</span> <span class="mf">6.</span><span class="p">),</span> <span class="n">axis</span><span class="o">=</span><span class="mi">0</span><span class="p">),</span> <span class="o">-</span><span class="mf">1.</span> <span class="o">/</span> <span class="mi">6</span><span class="p">)</span>
+ <span class="c1"># Liste des distances pour chaque structure de l'ensemble</span>
+ <span class="c1"># (liste associant une distance par structure de l'ensemble).</span>
+ <span class="c1"># Si contrib non ambig (associee a une seule paire de spins),</span>
+ <span class="c1"># cette liste devrait etre identique a la precedente</span>
+ <span class="n">dd</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">dist</span><span class="p">)</span>
+
+ <span class="k">except</span> <span class="ne">Exception</span> <span class="k">as</span> <span class="n">msg</span><span class="p">:</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">warning</span><span class="p">(</span><span class="s2">"</span><span class="si">%s</span><span class="s2">: </span><span class="si">%s</span><span class="s2">"</span> <span class="o">%</span> <span class="p">(</span><span class="ne">Exception</span><span class="p">,</span> <span class="n">msg</span><span class="p">))</span>
+ <span class="k">pass</span>
+
+ <span class="n">dref</span> <span class="o">=</span> <span class="kc">None</span>
+ <span class="k">if</span> <span class="n">dists_ref</span><span class="p">:</span>
+ <span class="k">try</span><span class="p">:</span>
+ <span class="n">dref</span> <span class="o">=</span> <span class="p">[</span><span class="n">dists_ref</span><span class="p">(</span><span class="o">*</span><span class="n">sp</span><span class="o">.</span><span class="n">getAtoms</span><span class="p">())</span> <span class="k">for</span> <span class="n">sp</span> <span class="ow">in</span> <span class="n">contrib</span><span class="p">]</span>
+ <span class="n">dref</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">power</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">power</span><span class="p">(</span><span class="n">dref</span><span class="p">,</span> <span class="o">-</span><span class="mf">6.</span><span class="p">),</span> <span class="n">axis</span><span class="o">=</span><span class="mi">0</span><span class="p">),</span>
+ <span class="o">-</span><span class="mf">1.</span> <span class="o">/</span> <span class="mi">6</span><span class="p">)</span>
+ <span class="n">ddref</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">dref</span><span class="p">)</span>
+
+ <span class="k">except</span> <span class="ne">Exception</span> <span class="k">as</span> <span class="n">msg</span><span class="p">:</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">warning</span><span class="p">(</span><span class="s2">"</span><span class="si">%s</span><span class="s2">: </span><span class="si">%s</span><span class="s2">"</span> <span class="o">%</span> <span class="p">(</span><span class="ne">Exception</span><span class="p">,</span> <span class="n">msg</span><span class="p">))</span>
+ <span class="k">pass</span>
+
+ <span class="n">tmp</span> <span class="o">=</span> <span class="n">OrderedDict</span><span class="p">()</span>
+ <span class="n">tmp</span><span class="p">[</span><span class="s1">'protein'</span><span class="p">]</span> <span class="o">=</span> <span class="n">protein_id</span>
+ <span class="n">tmp</span><span class="p">[</span><span class="s1">'data'</span><span class="p">]</span> <span class="o">=</span> <span class="n">rest</span><span class="o">.</span><span class="n">getReferencePeak</span><span class="p">()</span><span class="o">.</span><span class="n">getSpectrum</span><span class="p">()</span><span class="o">.</span><span class="n">getName</span><span class="p">()</span>
+ <span class="n">tmp</span><span class="p">[</span><span class="s1">'iteration'</span><span class="p">]</span> <span class="o">=</span> <span class="n">iteration_id</span>
+ <span class="n">tmp</span><span class="p">[</span><span class="s1">'clust'</span><span class="p">]</span> <span class="o">=</span> <span class="n">clusteridx</span>
+ <span class="n">tmp</span><span class="p">[</span><span class="s1">'ens_size'</span><span class="p">]</span> <span class="o">=</span> <span class="n">nbest</span>
+ <span class="n">tmp</span><span class="p">[</span><span class="s1">'rest_no'</span><span class="p">]</span> <span class="o">=</span> <span class="n">rest</span><span class="o">.</span><span class="n">getId</span><span class="p">()</span>
+ <span class="n">tmp</span><span class="p">[</span><span class="s1">'contrib_no'</span><span class="p">]</span> <span class="o">=</span> <span class="n">contrib</span><span class="o">.</span><span class="n">getId</span><span class="p">()</span>
+ <span class="c1"># Assuming there is only one spin per contribution</span>
+ <span class="n">tmp</span><span class="p">[</span><span class="s1">'resid_1'</span><span class="p">]</span> <span class="o">=</span> <span class="n">contrib</span><span class="p">[</span><span class="mi">0</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">getResidue</span><span class="p">()</span><span class="o">.</span><span class="n">getNumber</span><span class="p">()</span>
+ <span class="n">tmp</span><span class="p">[</span><span class="s1">'resid_2'</span><span class="p">]</span> <span class="o">=</span> <span class="n">contrib</span><span class="p">[</span><span class="mi">0</span><span class="p">][</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">getResidue</span><span class="p">()</span><span class="o">.</span><span class="n">getNumber</span><span class="p">()</span>
+ <span class="n">tmp</span><span class="p">[</span><span class="s1">'res_1'</span><span class="p">]</span> <span class="o">=</span> <span class="n">contrib</span><span class="p">[</span><span class="mi">0</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">getResidue</span><span class="p">()</span><span class="o">.</span><span class="n">getName</span><span class="p">()[:</span><span class="mi">3</span><span class="p">]</span>
+ <span class="n">tmp</span><span class="p">[</span><span class="s1">'res_2'</span><span class="p">]</span> <span class="o">=</span> <span class="n">contrib</span><span class="p">[</span><span class="mi">0</span><span class="p">][</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">getResidue</span><span class="p">()</span><span class="o">.</span><span class="n">getName</span><span class="p">()[:</span><span class="mi">3</span><span class="p">]</span>
+ <span class="n">tmp</span><span class="p">[</span><span class="s1">'atm_1'</span><span class="p">]</span> <span class="o">=</span> <span class="n">contrib</span><span class="p">[</span><span class="mi">0</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">getName</span><span class="p">()</span>
+ <span class="n">tmp</span><span class="p">[</span><span class="s1">'atm_2'</span><span class="p">]</span> <span class="o">=</span> <span class="n">contrib</span><span class="p">[</span><span class="mi">0</span><span class="p">][</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">getName</span><span class="p">()</span>
+ <span class="n">tmp</span><span class="p">[</span><span class="s1">'viol_cutoff'</span><span class="p">]</span> <span class="o">=</span> <span class="n">cutoff</span>
+ <span class="n">tmp</span><span class="p">[</span><span class="s1">'d_target'</span><span class="p">]</span> <span class="o">=</span> <span class="n">rest</span><span class="o">.</span><span class="n">getDistance</span><span class="p">()</span>
+ <span class="n">tmp</span><span class="p">[</span><span class="s1">'lower_bound'</span><span class="p">]</span> <span class="o">=</span> <span class="n">rest</span><span class="o">.</span><span class="n">getLowerBound</span><span class="p">()</span> <span class="o">-</span> <span class="n">cutoff</span>
+ <span class="n">tmp</span><span class="p">[</span><span class="s1">'upper_bound'</span><span class="p">]</span> <span class="o">=</span> <span class="n">rest</span><span class="o">.</span><span class="n">getUpperBound</span><span class="p">()</span> <span class="o">+</span> <span class="n">cutoff</span>
+ <span class="n">tmp</span><span class="p">[</span><span class="s1">'rest_weight'</span><span class="p">]</span> <span class="o">=</span> <span class="n">rest</span><span class="o">.</span><span class="n">getWeight</span><span class="p">()</span>
+ <span class="n">tmp</span><span class="p">[</span><span class="s1">'dc_min'</span><span class="p">]</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">min</span><span class="p">(</span><span class="n">dist</span><span class="p">)</span> <span class="k">if</span> <span class="n">dist</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span> <span class="k">else</span> <span class="s1">''</span>
+ <span class="n">tmp</span><span class="p">[</span><span class="s1">'dc_avg'</span><span class="p">]</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">mean</span><span class="p">(</span><span class="n">dist</span><span class="p">)</span> <span class="k">if</span> <span class="n">dist</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span> <span class="k">else</span> <span class="s1">''</span> <span class="c1"># Moyenne des distances associes a la contrib c dans l'ensemble</span>
+ <span class="n">tmp</span><span class="p">[</span><span class="s1">'dc_med'</span><span class="p">]</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">median</span><span class="p">(</span><span class="n">dist</span><span class="p">)</span> <span class="k">if</span> <span class="n">dist</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span> <span class="k">else</span> <span class="s1">''</span>
+ <span class="n">tmp</span><span class="p">[</span><span class="s1">'dc_ref'</span><span class="p">]</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">mean</span><span class="p">(</span><span class="n">dref</span><span class="p">)</span> <span class="k">if</span> <span class="n">dref</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span> <span class="k">else</span> <span class="s1">''</span>
+
+ <span class="n">output</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">tmp</span><span class="p">)</span>
+
+ <span class="c1"># Liste des distances (effective si plusieurs spin par</span>
+ <span class="c1"># contribution) associe aux contraintes</span>
+ <span class="n">dd</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="n">dd</span><span class="p">)</span>
+ <span class="n">ddref</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="n">ddref</span><span class="p">)</span> <span class="c1"># Idem pour natif</span>
+
+ <span class="n">dd_eff</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">power</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">power</span><span class="p">(</span><span class="n">dd</span><span class="p">,</span> <span class="o">-</span><span class="mi">6</span><span class="p">),</span> <span class="n">axis</span><span class="o">=</span><span class="mi">0</span><span class="p">),</span> <span class="o">-</span><span class="mf">1.</span> <span class="o">/</span> <span class="mi">6</span><span class="p">)</span>
+ <span class="n">ddref_eff</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">power</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">power</span><span class="p">(</span><span class="n">ddref</span><span class="p">,</span> <span class="o">-</span><span class="mi">6</span><span class="p">),</span> <span class="n">axis</span><span class="o">=</span><span class="mi">0</span><span class="p">),</span> <span class="o">-</span><span class="mf">1.</span> <span class="o">/</span> <span class="mi">6</span><span class="p">)</span>
+
+ <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">output</span><span class="p">)):</span>
+ <span class="c1"># Moyenne des distances effectives dans l'ensemble de</span>
+ <span class="c1"># structure. Peut etre biaisee si on a des structures qui</span>
+ <span class="c1"># ont une distance anormalement elevee. Dans ce cas, on ne</span>
+ <span class="c1"># peut evaluer si la contrainte a ete correctement supprimee</span>
+ <span class="c1"># dans l'ensemble etudie.</span>
+ <span class="n">output</span><span class="p">[</span><span class="n">x</span><span class="p">][</span><span class="s1">'Deff_min'</span><span class="p">]</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">min</span><span class="p">(</span><span class="n">dd_eff</span><span class="p">)</span>
+ <span class="n">output</span><span class="p">[</span><span class="n">x</span><span class="p">][</span><span class="s1">'Deff_avg'</span><span class="p">]</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">mean</span><span class="p">(</span><span class="n">dd_eff</span><span class="p">)</span>
+ <span class="n">output</span><span class="p">[</span><span class="n">x</span><span class="p">][</span><span class="s1">'Deff_med'</span><span class="p">]</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">median</span><span class="p">(</span><span class="n">dd_eff</span><span class="p">)</span>
+ <span class="n">output</span><span class="p">[</span><span class="n">x</span><span class="p">][</span><span class="s1">'Deff_sdev'</span><span class="p">]</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">std</span><span class="p">(</span><span class="n">dd_eff</span><span class="p">)</span>
+ <span class="n">output</span><span class="p">[</span><span class="n">x</span><span class="p">][</span><span class="s1">'Deff_ref'</span><span class="p">]</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">mean</span><span class="p">(</span><span class="n">ddref_eff</span><span class="p">)</span>
+ <span class="n">output</span><span class="p">[</span><span class="n">x</span><span class="p">][</span><span class="s1">'pc_viol'</span><span class="p">]</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span>
+ <span class="n">np</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">greater</span><span class="p">(</span><span class="n">dd_eff</span><span class="p">,</span> <span class="n">rest</span><span class="o">.</span><span class="n">getUpperBound</span><span class="p">()</span> <span class="o">+</span> <span class="n">cutoff</span><span class="p">)))</span> <span class="o">/</span> <span class="n">nbest</span>
+ <span class="c1"># Normalement d_ref ne contient qu'un seul elt puisqu'il y a</span>
+ <span class="c1"># qu'une seule structure ( a verifier )</span>
+ <span class="c1"># distance effective native</span>
+ <span class="c1"># Distance effective minimum dans l'ensemble</span>
+ <span class="n">output</span><span class="p">[</span><span class="n">x</span><span class="p">][</span><span class="s1">'viol'</span><span class="p">]</span> <span class="o">=</span> <span class="kc">True</span> <span class="k">if</span> \
+ <span class="n">output</span><span class="p">[</span><span class="n">x</span><span class="p">][</span><span class="s1">'pc_viol'</span><span class="p">]</span> <span class="o">>=</span> <span class="mf">0.5</span> <span class="k">else</span> <span class="kc">False</span>
+ <span class="c1"># Contrainte consideree comme valide si la distance effective</span>
+ <span class="c1"># dans la structure de reference est en dessous du seuil de</span>
+ <span class="c1"># violations.</span>
+ <span class="n">output</span><span class="p">[</span><span class="n">x</span><span class="p">][</span><span class="s1">'valid'</span><span class="p">]</span> <span class="o">=</span> <span class="kc">True</span> <span class="k">if</span> \
+ <span class="n">output</span><span class="p">[</span><span class="n">x</span><span class="p">][</span><span class="s1">'upper_bound'</span><span class="p">]</span> <span class="o">>=</span> <span class="n">output</span><span class="p">[</span><span class="n">x</span><span class="p">][</span><span class="s1">'dc_ref'</span><span class="p">]</span> <span class="o">>=</span> <span class="n">output</span><span class="p">[</span><span class="n">x</span><span class="p">][</span><span class="s1">'lower_bound'</span><span class="p">]</span> <span class="k">else</span> <span class="kc">False</span>
+ <span class="n">output</span><span class="p">[</span><span class="n">x</span><span class="p">][</span><span class="s1">'contact_5'</span><span class="p">]</span> <span class="o">=</span> <span class="kc">True</span> <span class="k">if</span> \
+ <span class="n">output</span><span class="p">[</span><span class="n">x</span><span class="p">][</span><span class="s1">'dc_ref'</span><span class="p">]</span> <span class="o"><=</span> <span class="mf">5.0</span> <span class="k">else</span> <span class="kc">False</span>
+ <span class="n">output</span><span class="p">[</span><span class="n">x</span><span class="p">][</span><span class="s1">'contact_8'</span><span class="p">]</span> <span class="o">=</span> <span class="kc">True</span> <span class="k">if</span> \
+ <span class="n">output</span><span class="p">[</span><span class="n">x</span><span class="p">][</span><span class="s1">'dc_ref'</span><span class="p">]</span> <span class="o"><=</span> <span class="mf">8.0</span> <span class="k">else</span> <span class="kc">False</span>
+
+ <span class="k">if</span> <span class="n">output</span><span class="p">[</span><span class="n">x</span><span class="p">][</span><span class="s1">'contact_8'</span><span class="p">]</span> <span class="ow">and</span> <span class="n">output</span><span class="p">[</span><span class="n">x</span><span class="p">][</span><span class="s1">'viol'</span><span class="p">]:</span>
+ <span class="n">output</span><span class="p">[</span><span class="n">x</span><span class="p">][</span><span class="s1">'group'</span><span class="p">]</span> <span class="o">=</span> <span class="s1">'VP viol'</span>
+ <span class="k">elif</span> <span class="n">output</span><span class="p">[</span><span class="n">x</span><span class="p">][</span><span class="s1">'contact_8'</span><span class="p">]</span> <span class="ow">and</span> <span class="ow">not</span> <span class="n">output</span><span class="p">[</span><span class="n">x</span><span class="p">][</span><span class="s1">'viol'</span><span class="p">]:</span>
+ <span class="n">output</span><span class="p">[</span><span class="n">x</span><span class="p">][</span><span class="s1">'group'</span><span class="p">]</span> <span class="o">=</span> <span class="s1">'VP'</span>
+ <span class="k">elif</span> <span class="ow">not</span> <span class="n">output</span><span class="p">[</span><span class="n">x</span><span class="p">][</span><span class="s1">'contact_8'</span><span class="p">]</span> <span class="ow">and</span> <span class="n">output</span><span class="p">[</span><span class="n">x</span><span class="p">][</span><span class="s1">'viol'</span><span class="p">]:</span>
+ <span class="n">output</span><span class="p">[</span><span class="n">x</span><span class="p">][</span><span class="s1">'group'</span><span class="p">]</span> <span class="o">=</span> <span class="s1">'FP viol'</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="n">output</span><span class="p">[</span><span class="n">x</span><span class="p">][</span><span class="s1">'group'</span><span class="p">]</span> <span class="o">=</span> <span class="s1">'FP'</span>
+
+ <span class="k">if</span> <span class="n">headerflag</span><span class="p">:</span>
+ <span class="n">out</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">","</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">output</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">keys</span><span class="p">()))</span>
+ <span class="n">headerflag</span> <span class="o">=</span> <span class="kc">False</span>
+
+ <span class="n">out</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">"</span><span class="se">\n</span><span class="s2">"</span> <span class="o">+</span> <span class="s2">","</span><span class="o">.</span><span class="n">join</span><span class="p">([</span><span class="s2">"</span><span class="si">%s</span><span class="s2">"</span> <span class="o">%</span> <span class="n">output</span><span class="p">[</span><span class="n">x</span><span class="p">][</span><span class="n">k</span><span class="p">]</span>
+ <span class="k">for</span> <span class="n">k</span> <span class="ow">in</span> <span class="n">output</span><span class="p">[</span><span class="n">x</span><span class="p">]</span><span class="o">.</span><span class="n">keys</span><span class="p">()]))</span>
+
+ <span class="n">LOG</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s2">"Writing violation analysis of clust </span><span class="si">%s</span><span class="s2"> </span><span class="si">%s</span><span class="s2"> file"</span><span class="p">,</span> <span class="n">clusteridx</span><span class="p">,</span>
+ <span class="n">out_file</span><span class="p">)</span></div>
+
+ <span class="c1"># def extract_ariaensemble_matrix(self):</span>
+ <span class="c1"># """</span>
+ <span class="c1">#</span>
+ <span class="c1"># Returns</span>
+ <span class="c1"># -------</span>
+ <span class="c1">#</span>
+ <span class="c1"># """</span>
+ <span class="c1"># pass</span>
+
+ <span class="c1"># TODO: As described in Guillaume paper, clustering on aligned CA</span>
+ <span class="c1"># coordinates highly depends on the efficiency of the alignment method</span>
+<div class="viewcode-block" id="EnsembleAnalysis.pca_projection"><a class="viewcode-back" href="../../ariaec.html#ariaec.analysis.EnsembleAnalysis.pca_projection">[docs]</a> <span class="nd">@staticmethod</span>
+ <span class="k">def</span> <span class="nf">pca_projection</span><span class="p">(</span>
+ <span class="n">ensemble</span><span class="p">,</span> <span class="n">molecule</span><span class="p">,</span> <span class="n">infos</span><span class="p">,</span> <span class="n">atmask</span><span class="o">=</span><span class="s2">"CA"</span><span class="p">,</span>
+ <span class="n">title</span><span class="o">=</span><span class="s2">"3D PCA projection on backbone coordinates"</span><span class="p">,</span> <span class="n">outfile</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> PCA projection of ensemble coordinates</span>
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> ensemble :</span>
+<span class="sd"> molecule :</span>
+<span class="sd"> infos</span>
+<span class="sd"> atmask :</span>
+<span class="sd"> (Default value = "CA")</span>
+<span class="sd"> title</span>
+<span class="sd"> outfile</span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+<span class="sd"> </span>
+<span class="sd"> """</span>
+ <span class="n">sns</span><span class="o">.</span><span class="n">set_style</span><span class="p">(</span><span class="s1">'ticks'</span><span class="p">)</span>
+ <span class="n">pca</span> <span class="o">=</span> <span class="n">PCA</span><span class="p">(</span><span class="n">n_components</span><span class="o">=</span><span class="mi">3</span><span class="p">)</span>
+ <span class="n">mask</span> <span class="o">=</span> <span class="p">[</span><span class="n">a</span><span class="o">.</span><span class="n">getId</span><span class="p">()</span> <span class="k">for</span> <span class="n">c</span> <span class="ow">in</span> <span class="n">molecule</span><span class="o">.</span><span class="n">get_chains</span><span class="p">()</span> <span class="k">for</span> <span class="n">r</span> <span class="ow">in</span> <span class="n">c</span><span class="o">.</span><span class="n">getResidues</span><span class="p">()</span>
+ <span class="k">for</span> <span class="n">a</span> <span class="ow">in</span> <span class="n">r</span><span class="o">.</span><span class="n">getAtoms</span><span class="p">()</span> <span class="k">if</span> <span class="n">a</span><span class="o">.</span><span class="n">getName</span><span class="p">()</span> <span class="o">==</span> <span class="n">atmask</span><span class="p">]</span>
+
+ <span class="c1"># Align all structures on ca backbone</span>
+ <span class="n">si</span> <span class="o">=</span> <span class="n">SuperImposer</span><span class="p">(</span><span class="n">ensemble</span><span class="p">,</span> <span class="n">molecule</span><span class="p">)</span>
+ <span class="n">si</span><span class="o">.</span><span class="n">getSettings</span><span class="p">()[</span><span class="s1">'number_of_best_structures'</span><span class="p">]</span> <span class="o">=</span> <span class="s1">'all'</span>
+ <span class="n">si</span><span class="o">.</span><span class="n">_fit</span><span class="p">(</span><span class="n">mask</span><span class="p">)</span>
+
+ <span class="c1"># Get matrix of coordinates</span>
+ <span class="n">fitcoords</span> <span class="o">=</span> <span class="n">si</span><span class="o">.</span><span class="n">getFittedCoordinates</span><span class="p">()</span>
+ <span class="n">fitcoords</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">take</span><span class="p">(</span><span class="n">fitcoords</span><span class="p">,</span> <span class="n">mask</span><span class="p">,</span> <span class="n">axis</span><span class="o">=</span><span class="mi">1</span><span class="p">)</span>
+ <span class="n">ns</span><span class="p">,</span> <span class="n">na</span><span class="p">,</span> <span class="n">xyz</span> <span class="o">=</span> <span class="n">fitcoords</span><span class="o">.</span><span class="n">shape</span>
+ <span class="c1"># Change the shape of coords matrix in order to use pca, kmeans, ...</span>
+ <span class="n">fitcoords</span><span class="o">.</span><span class="n">shape</span> <span class="o">=</span> <span class="n">ns</span><span class="p">,</span> <span class="n">na</span> <span class="o">*</span> <span class="n">xyz</span>
+
+ <span class="n">ensemble</span><span class="o">.</span><span class="n">getSettings</span><span class="p">()[</span><span class="s1">'number_of_best_structures'</span><span class="p">]</span> <span class="o">=</span> <span class="mi">15</span>
+
+ <span class="n">fitcoords_reduced</span> <span class="o">=</span> <span class="n">pca</span><span class="o">.</span><span class="n">fit_transform</span><span class="p">(</span><span class="n">fitcoords</span><span class="p">)</span>
+
+ <span class="c1">#</span>
+ <span class="n">fig</span> <span class="o">=</span> <span class="n">plt</span><span class="o">.</span><span class="n">figure</span><span class="p">()</span>
+
+ <span class="n">ax</span> <span class="o">=</span> <span class="n">Axes3D</span><span class="p">(</span><span class="n">fig</span><span class="p">)</span>
+
+ <span class="n">colscatter</span><span class="p">(</span>
+ <span class="n">fitcoords_reduced</span><span class="p">,</span> <span class="n">ax</span><span class="p">,</span> <span class="n">infos</span><span class="p">,</span> <span class="n">ndim</span><span class="o">=</span><span class="mi">3</span><span class="p">,</span> <span class="n">axtitle</span><span class="o">=</span><span class="n">title</span><span class="p">,</span>
+ <span class="n">xlabel</span><span class="o">=</span><span class="s2">"Principal component 1"</span><span class="p">,</span> <span class="n">ylabel</span><span class="o">=</span><span class="s2">"Principal component 2"</span><span class="p">,</span>
+ <span class="n">zlabel</span><span class="o">=</span><span class="s2">"Principal component 3"</span><span class="p">,</span> <span class="n">legend_prefix</span><span class="o">=</span><span class="s2">"Clust "</span><span class="p">)</span>
+ <span class="k">if</span> <span class="n">outfile</span><span class="p">:</span>
+ <span class="n">plt</span><span class="o">.</span><span class="n">savefig</span><span class="p">(</span><span class="n">outfile</span><span class="p">)</span></div>
+
+<div class="viewcode-block" id="EnsembleAnalysis.run"><a class="viewcode-back" href="../../ariaec.html#ariaec.analysis.EnsembleAnalysis.run">[docs]</a> <span class="k">def</span> <span class="nf">run</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="sd">"""Execute Ensemble analysis"""</span>
+ <span class="c1"># Args</span>
+ <span class="n">project_path</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">analysis</span><span class="o">.</span><span class="n">args</span><span class="p">[</span><span class="s2">"project"</span><span class="p">]</span>
+ <span class="c1"># restraints_path = self.settings.analysis.args["restraints"]</span>
+ <span class="n">native_path</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">analysis</span><span class="o">.</span><span class="n">args</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"ref"</span><span class="p">)</span>
+ <span class="n">out_path</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">analysis</span><span class="o">.</span><span class="n">args</span><span class="p">[</span><span class="s2">"output_directory"</span><span class="p">]</span>
+ <span class="n">list_name</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">analysis</span><span class="o">.</span><span class="n">args</span><span class="p">[</span><span class="s2">"listname"</span><span class="p">]</span>
+
+ <span class="c1"># Create Aria objects</span>
+ <span class="n">pickler</span> <span class="o">=</span> <span class="n">AriaXMLPickler</span><span class="p">()</span>
+ <span class="n">project</span> <span class="o">=</span> <span class="n">pickler</span><span class="o">.</span><span class="n">load</span><span class="p">(</span><span class="n">project_path</span><span class="p">)</span>
+ <span class="n">molecule_path</span> <span class="o">=</span> <span class="n">project</span><span class="o">.</span><span class="n">getData</span><span class="p">(</span><span class="n">DATA_SEQUENCE</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">getLocation</span><span class="p">()[</span><span class="mi">0</span><span class="p">]</span>
+ <span class="n">molecule</span> <span class="o">=</span> <span class="n">pickler</span><span class="o">.</span><span class="n">load</span><span class="p">(</span><span class="n">molecule_path</span><span class="p">)</span>
+
+ <span class="c1"># If we are at the first iteration, we select the related ensemble and</span>
+ <span class="c1"># restraints, otherwise we take the ensemble from the previous iteration</span>
+ <span class="n">iteration_path</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">analysis</span><span class="o">.</span><span class="n">args</span><span class="p">[</span><span class="s2">"iteration"</span><span class="p">]</span>
+ <span class="n">iteration_id</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">re</span><span class="o">.</span><span class="n">search</span><span class="p">(</span>
+ <span class="s1">'[0-9]+'</span><span class="p">,</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">basename</span><span class="p">(</span><span class="n">iteration_path</span><span class="p">))</span><span class="o">.</span><span class="n">group</span><span class="p">(</span><span class="mi">0</span><span class="p">))</span>
+ <span class="k">if</span> <span class="n">iteration_id</span> <span class="o">!=</span> <span class="mi">0</span><span class="p">:</span>
+ <span class="c1"># If we are not at the first iteration, we select analysis</span>
+ <span class="c1"># parameters related to user input iteration and update iteration</span>
+ <span class="c1"># path in order to get ensemble of structures from previous</span>
+ <span class="c1"># iteration</span>
+ <span class="n">iteration_path</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span>
+ <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">dirname</span><span class="p">(</span><span class="n">iteration_path</span><span class="p">),</span> <span class="s2">"it</span><span class="si">%d</span><span class="s2">"</span> <span class="o">%</span> <span class="p">(</span><span class="n">iteration_id</span> <span class="o">-</span> <span class="mi">1</span><span class="p">))</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s2">"Ensemble analysis will be done on restraints and "</span>
+ <span class="s2">"ensemble from it</span><span class="si">%d</span><span class="s2"> with violation criteria of it</span><span class="si">%d</span><span class="s2">"</span><span class="p">,</span>
+ <span class="p">(</span><span class="n">iteration_id</span> <span class="o">-</span> <span class="mi">1</span><span class="p">),</span> <span class="n">iteration_id</span><span class="p">)</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">(</span><span class="n">iteration_path</span><span class="p">):</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">error</span><span class="p">(</span><span class="s2">"Can not found previous iteration (</span><span class="si">%s</span><span class="s2">)"</span><span class="p">,</span>
+ <span class="n">iteration_path</span><span class="p">)</span>
+
+ <span class="c1"># Load restraints related to the actual iteration</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s2">"Reading distance restraints file(s)"</span><span class="p">)</span>
+ <span class="c1"># restraints = glob(os.path.join(iteration_path, '*restraints.xml')) if\</span>
+ <span class="c1"># not self.settings.analysis.args.get('restraint') else \</span>
+ <span class="c1"># [self.settings.analysis.args.get('restraint')]</span>
+ <span class="c1"># if not restraints:</span>
+ <span class="c1"># # Load tbl restraints and convert them into aria xml format</span>
+ <span class="n">restraints</span> <span class="o">=</span> <span class="n">glob</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">iteration_path</span><span class="p">,</span> <span class="s1">'*.tbl'</span><span class="p">))</span>
+ <span class="n">restraints</span> <span class="o">=</span> <span class="n">AriaEcXMLConverter</span><span class="o">.</span><span class="n">tbl2xml</span><span class="p">(</span>
+ <span class="n">iteration_path</span><span class="p">,</span> <span class="n">molecule_path</span><span class="p">,</span> <span class="n">restraints</span><span class="p">,</span> <span class="n">list_name</span><span class="p">)</span>
+ <span class="n">restraints</span> <span class="o">=</span> <span class="p">[</span><span class="n">pickler</span><span class="o">.</span><span class="n">load</span><span class="p">(</span><span class="n">restraint</span><span class="p">)</span><span class="o">.</span><span class="n">restraint</span>
+ <span class="k">for</span> <span class="n">restraint</span> <span class="ow">in</span> <span class="n">restraints</span><span class="p">]</span>
+
+ <span class="c1"># Read structure ensembles</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s2">"Reading structure ensemble(s)"</span><span class="p">)</span>
+
+ <span class="c1"># Load ensemble parameters</span>
+ <span class="n">protein_id</span> <span class="o">=</span> <span class="n">project</span><span class="o">.</span><span class="n">getSettings</span><span class="p">()[</span><span class="s1">'name'</span><span class="p">]</span>
+ <span class="n">nbest</span> <span class="o">=</span> <span class="n">project</span><span class="o">.</span><span class="n">getProtocol</span><span class="p">()</span><span class="o">.</span><span class="n">getIterationSettings</span><span class="p">(</span><span class="n">iteration_id</span><span class="p">)[</span>
+ <span class="s2">"number_of_best_structures"</span><span class="p">]</span>
+ <span class="n">sort_crit</span> <span class="o">=</span> <span class="n">project</span><span class="o">.</span><span class="n">getProtocol</span><span class="p">()</span><span class="o">.</span><span class="n">getIterationSettings</span><span class="p">(</span><span class="n">iteration_id</span><span class="p">)[</span>
+ <span class="s2">"sort_criterion"</span><span class="p">]</span>
+ <span class="n">se_settings</span> <span class="o">=</span> <span class="n">StructureEnsembleSettings</span><span class="p">()</span>
+ <span class="n">se_settings</span><span class="p">[</span><span class="s1">'sort_criterion'</span><span class="p">]</span> <span class="o">=</span> <span class="n">sort_crit</span>
+ <span class="n">se_settings</span><span class="p">[</span><span class="s1">'number_of_best_structures'</span><span class="p">]</span> <span class="o">=</span> <span class="n">nbest</span>
+
+ <span class="c1"># Get list of pdb related to structure ensemble(s)</span>
+ <span class="n">ens_paths</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_get_ensemble_paths</span><span class="p">(</span><span class="n">iteration_path</span><span class="p">)</span>
+
+ <span class="k">with</span> <span class="n">Capturing</span><span class="p">()</span> <span class="k">as</span> <span class="n">output</span><span class="p">:</span>
+ <span class="c1"># We define here as many structure ensemble object as number of</span>
+ <span class="c1"># list in ens_paths (if clustering used)</span>
+ <span class="n">clustensembles</span> <span class="o">=</span> <span class="p">[</span>
+ <span class="n">StructureEnsemble</span><span class="p">(</span><span class="n">se_settings</span><span class="p">)</span> <span class="k">for</span> <span class="n">_</span> <span class="ow">in</span> <span class="n">ens_paths</span><span class="p">]</span>
+ <span class="p">[</span><span class="n">ensemble</span><span class="o">.</span><span class="n">read</span><span class="p">(</span><span class="n">ens_paths</span><span class="p">[</span><span class="n">i</span><span class="p">],</span> <span class="n">molecule</span><span class="p">,</span> <span class="nb">format</span><span class="o">=</span><span class="s1">'cns'</span><span class="p">)</span>
+ <span class="k">for</span> <span class="n">i</span><span class="p">,</span> <span class="n">ensemble</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">clustensembles</span><span class="p">)]</span>
+ <span class="p">[</span><span class="n">ensemble</span><span class="o">.</span><span class="n">sort</span><span class="p">()</span>
+ <span class="k">for</span> <span class="n">i</span><span class="p">,</span> <span class="n">ensemble</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">clustensembles</span><span class="p">)]</span>
+ <span class="k">if</span> <span class="n">output</span><span class="p">:</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="n">output</span><span class="p">)</span>
+
+ <span class="c1"># Get the lowest energy ensemble</span>
+ <span class="c1"># LOG.info("Sorting structure ensemble(s) with %s criteria", sort_crit)</span>
+ <span class="c1"># energies = np.array([</span>
+ <span class="c1"># np.mean([d['total_energy'] for d in ens.getInfo()[:, 1]][:nbest])</span>
+ <span class="c1"># if len(ens) >= nbest else None for ens in clustensembles],</span>
+ <span class="c1"># dtype=np.float)</span>
+
+ <span class="c1"># Get native structure</span>
+ <span class="c1"># Issue with several pdb files which have the same residue_number in</span>
+ <span class="c1"># atm and hetatm sections ... We remove them with bio pdb</span>
+ <span class="n">dists_ref</span> <span class="o">=</span> <span class="kc">None</span>
+ <span class="k">if</span> <span class="n">native_path</span><span class="p">:</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s2">"Reading native structure"</span><span class="p">)</span>
+ <span class="n">logging</span><span class="o">.</span><span class="n">captureWarnings</span><span class="p">(</span><span class="kc">True</span><span class="p">)</span>
+ <span class="n">native</span> <span class="o">=</span> <span class="n">PDBParser</span><span class="p">()</span><span class="o">.</span><span class="n">get_structure</span><span class="p">(</span><span class="n">protein_id</span><span class="p">,</span> <span class="n">native_path</span><span class="p">)</span>
+ <span class="n">native_path</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">out_path</span><span class="p">,</span> <span class="n">protein_id</span> <span class="o">+</span> <span class="s2">"_ordered.native.pdb"</span><span class="p">)</span>
+ <span class="n">io</span> <span class="o">=</span> <span class="n">PDBIO</span><span class="p">()</span>
+ <span class="n">io</span><span class="o">.</span><span class="n">set_structure</span><span class="p">(</span><span class="n">native</span><span class="p">)</span>
+ <span class="n">io</span><span class="o">.</span><span class="n">save</span><span class="p">(</span><span class="n">native_path</span><span class="p">,</span> <span class="n">select</span><span class="o">=</span><span class="n">NotDisordered</span><span class="p">())</span>
+
+ <span class="n">native</span> <span class="o">=</span> <span class="n">StructureEnsemble</span><span class="p">(</span><span class="n">se_settings</span><span class="p">)</span>
+ <span class="n">native</span><span class="o">.</span><span class="n">display_warnings</span> <span class="o">=</span> <span class="mi">0</span>
+ <span class="n">native</span><span class="o">.</span><span class="n">read</span><span class="p">([</span><span class="n">native_path</span><span class="p">],</span> <span class="n">molecule</span><span class="p">,</span> <span class="nb">format</span><span class="o">=</span><span class="s1">'cns'</span><span class="p">)</span>
+
+ <span class="n">dists_ref</span> <span class="o">=</span> <span class="n">native</span><span class="o">.</span><span class="n">getDistances</span>
+
+ <span class="c1"># We get here the distance of 'number_of_best_structures' in the</span>
+ <span class="c1"># ensemble</span>
+ <span class="c1"># ens_getdists = ensemble.getDistances</span>
+
+ <span class="n">LOG</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s2">"Violation analysis"</span><span class="p">)</span>
+ <span class="k">for</span> <span class="n">clustidx</span><span class="p">,</span> <span class="n">clustensemble</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">clustensembles</span><span class="p">):</span>
+ <span class="n">out_file</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">out_path</span><span class="p">,</span> <span class="s1">'violations.csv'</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">violation_analysis</span><span class="p">(</span><span class="n">project</span><span class="p">,</span> <span class="n">iteration_id</span><span class="p">,</span> <span class="n">restraints</span><span class="p">,</span>
+ <span class="n">clustensemble</span><span class="p">,</span> <span class="n">out_file</span><span class="p">,</span>
+ <span class="n">clusteridx</span><span class="o">=</span><span class="n">clustidx</span><span class="p">,</span> <span class="n">dists_ref</span><span class="o">=</span><span class="n">dists_ref</span><span class="p">,</span>
+ <span class="n">headerflag</span><span class="o">=</span><span class="kc">True</span> <span class="k">if</span> <span class="n">clustidx</span> <span class="o">==</span> <span class="mi">0</span> <span class="k">else</span> <span class="kc">False</span><span class="p">)</span>
+
+ <span class="c1"># For the plotting part, we need a StructureEnsemble instance with all</span>
+ <span class="c1"># pdb files from the iteration</span>
+
+ <span class="n">allensemble</span> <span class="o">=</span> <span class="n">StructureEnsemble</span><span class="p">(</span><span class="n">se_settings</span><span class="p">)</span>
+ <span class="n">allensemble</span><span class="o">.</span><span class="n">read</span><span class="p">(</span>
+ <span class="n">files</span><span class="o">=</span><span class="p">[</span><span class="n">pdbfile</span> <span class="k">for</span> <span class="n">se</span> <span class="ow">in</span> <span class="n">ens_paths</span> <span class="k">for</span> <span class="n">pdbfile</span> <span class="ow">in</span> <span class="n">se</span><span class="p">],</span>
+ <span class="n">molecule</span><span class="o">=</span><span class="n">molecule</span><span class="p">,</span> <span class="nb">format</span><span class="o">=</span><span class="s1">'cns'</span><span class="p">)</span>
+
+ <span class="n">infos</span> <span class="o">=</span> <span class="p">[</span><span class="n">inf</span> <span class="k">for</span> <span class="n">inf</span> <span class="ow">in</span> <span class="n">allensemble</span><span class="o">.</span><span class="n">getInfo</span><span class="p">()]</span>
+ <span class="p">[</span><span class="n">info</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">update</span><span class="p">({</span><span class="s1">'clust'</span><span class="p">:</span> <span class="n">idx</span><span class="p">})</span> <span class="k">for</span> <span class="n">info</span> <span class="ow">in</span> <span class="n">infos</span> <span class="k">for</span> <span class="n">idx</span><span class="p">,</span> <span class="n">clustlist</span> <span class="ow">in</span>
+ <span class="nb">enumerate</span><span class="p">(</span><span class="n">ens_paths</span><span class="p">)</span> <span class="k">if</span> <span class="nb">filter</span><span class="p">(</span><span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span><span class="n">info</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span><span class="o">.</span><span class="n">match</span><span class="p">,</span> <span class="n">clustlist</span><span class="p">)]</span>
+
+ <span class="c1"># Compute pca projection of cluster labels on all the</span>
+ <span class="c1"># generated structures. Add later an option to visualize extra</span>
+ <span class="c1"># information like RMSD, quality, ... with a csv file</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">pca_projection</span><span class="p">(</span>
+ <span class="n">allensemble</span><span class="p">,</span> <span class="n">molecule</span><span class="p">,</span> <span class="p">[</span><span class="n">info</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">'clust'</span><span class="p">,</span> <span class="mi">0</span><span class="p">)</span> <span class="k">for</span> <span class="n">info</span> <span class="ow">in</span> <span class="n">infos</span><span class="p">],</span>
+ <span class="n">atmask</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">analysis</span><span class="o">.</span><span class="n">config</span><span class="p">[</span><span class="s2">"atmask"</span><span class="p">],</span>
+ <span class="n">title</span><span class="o">=</span><span class="s2">"3D PCA projection on </span><span class="si">%s</span><span class="s2"> backbone coordinates </span><span class="se">\n</span><span class="si">%s</span><span class="s2"> contacts"</span>
+ <span class="s2">" at iteration </span><span class="si">%s</span><span class="s2">"</span> <span class="o">%</span> <span class="p">(</span><span class="n">protein_id</span><span class="p">,</span> <span class="n">list_name</span><span class="p">,</span>
+ <span class="nb">str</span><span class="p">(</span><span class="n">iteration_id</span><span class="p">)),</span>
+ <span class="n">outfile</span><span class="o">=</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">out_path</span><span class="p">,</span> <span class="s2">"</span><span class="si">%s</span><span class="s2">_</span><span class="si">%s</span><span class="s2">_it</span><span class="si">%s</span><span class="s2">_clusts.3dpca.png"</span> <span class="o">%</span>
+ <span class="p">(</span><span class="n">protein_id</span><span class="p">,</span> <span class="n">list_name</span><span class="p">,</span> <span class="nb">str</span><span class="p">(</span><span class="n">iteration_id</span><span class="p">)))</span>
+ <span class="p">)</span></div></div>
+
+ <span class="c1"># with open(os.path.join(iter_dir,</span>
+ <span class="c1"># "analysis/pyfit/accuracydssp/RMSD.dat")) as rmsdfile:</span>
+ <span class="c1"># accdssp = {key: float(value) for key, value in</span>
+ <span class="c1"># [line.split() for line in rmsdfile if</span>
+ <span class="c1"># re.search("pdb", line)]}</span>
+
+ <span class="c1"># [info[1].update({'ensemble': False})</span>
+ <span class="c1"># for info in infos]</span>
+ <span class="c1"># [info[1].update({'ensemble': True})</span>
+ <span class="c1"># for info in infos</span>
+ <span class="c1"># for clustlist in [clustlist[0:15] for clustlist in clustlists] if</span>
+ <span class="c1"># filter(re.compile(info[0]).match, clustlist)]</span>
+ <span class="c1"># [info[1].update(</span>
+ <span class="c1"># {'accdssp': accdssp.get(os.path.basename(info[0]), None)})</span>
+ <span class="c1"># for info in infos]</span>
+</pre></div>
+
+ </div>
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+
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diff --git a/examples-dev/olds/_build/html/_modules/ariaec/base.html b/examples-dev/olds/_build/html/_modules/ariaec/base.html
new file mode 100644
index 0000000000000000000000000000000000000000..ab2ba1d55268cf527ef9a6e3a969117c11bdf762
--- /dev/null
+++ b/examples-dev/olds/_build/html/_modules/ariaec/base.html
@@ -0,0 +1,755 @@
+
+
+<!DOCTYPE html>
+<!--[if IE 8]><html class="no-js lt-ie9" lang="en" > <![endif]-->
+<!--[if gt IE 8]><!--> <html class="no-js" lang="en" > <!--<![endif]-->
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+
+ <h1>Source code for ariaec.base</h1><div class="highlight"><pre>
+<span></span><span class="c1"># coding=utf-8</span>
+<span class="sd">"""</span>
+<span class="sd"> Basic tools aria_ec</span>
+<span class="sd">"""</span>
+<span class="kn">from</span> <span class="nn">__future__</span> <span class="k">import</span> <span class="n">absolute_import</span><span class="p">,</span> <span class="n">division</span><span class="p">,</span> <span class="n">print_function</span>
+<span class="kn">from</span> <span class="nn">abc</span> <span class="k">import</span> <span class="n">ABCMeta</span><span class="p">,</span> <span class="n">abstractmethod</span>
+<span class="kn">from</span> <span class="nn">Bio.PDB</span> <span class="k">import</span> <span class="n">Select</span>
+
+<span class="kn">import</span> <span class="nn">six</span>
+<span class="kn">import</span> <span class="nn">logging</span>
+<span class="kn">import</span> <span class="nn">logging.config</span>
+<span class="kn">import</span> <span class="nn">os</span>
+<span class="kn">import</span> <span class="nn">json</span>
+<span class="kn">import</span> <span class="nn">re</span>
+<span class="kn">import</span> <span class="nn">ast</span>
+<span class="kn">import</span> <span class="nn">sys</span>
+<span class="kn">import</span> <span class="nn">shutil</span>
+<span class="kn">import</span> <span class="nn">numpy</span> <span class="k">as</span> <span class="nn">np</span>
+<span class="kn">import</span> <span class="nn">pkg_resources</span> <span class="k">as</span> <span class="nn">pkgr</span>
+<span class="kn">import</span> <span class="nn">matplotlib.artist</span> <span class="k">as</span> <span class="nn">art</span>
+
+
+<span class="n">LOG</span> <span class="o">=</span> <span class="n">logging</span><span class="o">.</span><span class="n">getLogger</span><span class="p">(</span><span class="vm">__name__</span><span class="p">)</span>
+
+
+<div class="viewcode-block" id="addtup"><a class="viewcode-back" href="../../ariaec.html#ariaec.base.addtup">[docs]</a><span class="k">def</span> <span class="nf">addtup</span><span class="p">(</span><span class="n">tup</span><span class="p">,</span> <span class="n">inc</span><span class="o">=</span><span class="mi">1</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Increment all values by 1 in a tuple</span>
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> tup :</span>
+<span class="sd"> param inc:</span>
+<span class="sd"> inc :</span>
+<span class="sd"> (Default value = 1)</span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+<span class="sd"> </span>
+<span class="sd"> """</span>
+ <span class="k">return</span> <span class="nb">tuple</span><span class="p">((</span><span class="n">val</span> <span class="o">+</span> <span class="n">inc</span> <span class="k">for</span> <span class="n">val</span> <span class="ow">in</span> <span class="n">tup</span><span class="p">))</span></div>
+
+
+<div class="viewcode-block" id="titleprint"><a class="viewcode-back" href="../../ariaec.html#ariaec.base.titleprint">[docs]</a><span class="k">def</span> <span class="nf">titleprint</span><span class="p">(</span><span class="n">outfile</span><span class="p">,</span> <span class="n">progname</span><span class="o">=</span><span class="s1">''</span><span class="p">,</span> <span class="n">desc</span><span class="o">=</span><span class="s1">''</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Init log file</span>
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> outfile :</span>
+<span class="sd"> param progname: docstring</span>
+<span class="sd"> desc :</span>
+<span class="sd"> return: (Default value = '')</span>
+<span class="sd"> progname :</span>
+<span class="sd"> (Default value = '')</span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+<span class="sd"> </span>
+<span class="sd"> """</span>
+ <span class="n">out</span> <span class="o">=</span> <span class="s1">'''</span>
+<span class="s1">================================================================================</span>
+<span class="si">{progname}</span><span class="s1"></span>
+<span class="s1"> </span><span class="si">{desc}</span><span class="s1"></span>
+<span class="s1">================================================================================</span>
+<span class="s1">'''</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">progname</span><span class="o">=</span><span class="n">progname</span><span class="p">,</span> <span class="n">desc</span><span class="o">=</span><span class="n">desc</span><span class="o">.</span><span class="n">capitalize</span><span class="p">())</span>
+ <span class="n">outfile</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">out</span><span class="p">[</span><span class="mi">1</span><span class="p">:])</span></div>
+
+
+<div class="viewcode-block" id="get_filename"><a class="viewcode-back" href="../../ariaec.html#ariaec.base.get_filename">[docs]</a><span class="k">def</span> <span class="nf">get_filename</span><span class="p">(</span><span class="n">path</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Search filename in the given path</span>
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> path :</span>
+<span class="sd"> return:</span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+<span class="sd"> </span>
+<span class="sd"> """</span>
+ <span class="k">return</span> <span class="s2">"_"</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">path</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s2">"/"</span><span class="p">)[</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s2">"."</span><span class="p">)[:</span><span class="o">-</span><span class="mi">1</span><span class="p">])</span></div>
+
+
+<div class="viewcode-block" id="reg_load"><a class="viewcode-back" href="../../ariaec.html#ariaec.base.reg_load">[docs]</a><span class="k">def</span> <span class="nf">reg_load</span><span class="p">(</span><span class="n">regex</span><span class="p">,</span> <span class="n">filepath</span><span class="p">,</span> <span class="n">sort</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> </span>
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> regex :</span>
+<span class="sd"> param filepath:</span>
+<span class="sd"> sort :</span>
+<span class="sd"> return: (Default value = None)</span>
+<span class="sd"> filepath :</span>
+<span class="sd"> </span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+<span class="sd"> </span>
+<span class="sd"> """</span>
+
+ <span class="n">lines_dict</span> <span class="o">=</span> <span class="p">{}</span>
+
+ <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">filepath</span><span class="p">)</span> <span class="k">as</span> <span class="n">infile</span><span class="p">:</span>
+ <span class="k">for</span> <span class="n">index</span><span class="p">,</span> <span class="n">line</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">infile</span><span class="p">):</span>
+ <span class="n">match</span> <span class="o">=</span> <span class="n">regex</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="n">line</span><span class="p">)</span>
+ <span class="k">if</span> <span class="n">match</span><span class="p">:</span>
+ <span class="n">lines_dict</span><span class="p">[</span><span class="n">index</span><span class="p">]</span> <span class="o">=</span> <span class="n">match</span><span class="o">.</span><span class="n">groupdict</span><span class="p">()</span>
+
+ <span class="k">if</span> <span class="n">sort</span><span class="p">:</span>
+ <span class="n">lines_dict</span> <span class="o">=</span> <span class="n">sort_2dict</span><span class="p">(</span><span class="n">lines_dict</span><span class="p">,</span> <span class="n">sort</span><span class="p">)</span>
+
+ <span class="k">return</span> <span class="n">lines_dict</span></div>
+
+
+<div class="viewcode-block" id="sort_2dict"><a class="viewcode-back" href="../../ariaec.html#ariaec.base.sort_2dict">[docs]</a><span class="k">def</span> <span class="nf">sort_2dict</span><span class="p">(</span><span class="n">unsort_dict</span><span class="p">,</span> <span class="n">key</span><span class="p">,</span> <span class="n">reverse</span><span class="o">=</span><span class="kc">True</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Sort 2d dict by key</span>
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> reverse :</span>
+<span class="sd"> param key: (Default value = True)</span>
+<span class="sd"> unsort_dict :</span>
+<span class="sd"> return: sorted dict</span>
+<span class="sd"> key :</span>
+<span class="sd"> </span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+<span class="sd"> </span>
+<span class="sd"> """</span>
+ <span class="n">sorted_index</span> <span class="o">=</span> <span class="nb">sorted</span><span class="p">(</span><span class="n">unsort_dict</span><span class="p">,</span> <span class="n">key</span><span class="o">=</span><span class="k">lambda</span> <span class="n">x</span><span class="p">:</span> <span class="nb">float</span><span class="p">(</span><span class="n">unsort_dict</span><span class="p">[</span><span class="n">x</span><span class="p">][</span><span class="n">key</span><span class="p">]),</span>
+ <span class="n">reverse</span><span class="o">=</span><span class="n">reverse</span><span class="p">)</span>
+ <span class="n">sorted_dict</span> <span class="o">=</span> <span class="p">{}</span>
+
+ <span class="k">for</span> <span class="n">rank</span><span class="p">,</span> <span class="n">ind</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">sorted_index</span><span class="p">):</span>
+ <span class="n">sorted_dict</span><span class="p">[</span><span class="n">rank</span> <span class="o">+</span> <span class="mi">1</span><span class="p">]</span> <span class="o">=</span> <span class="n">unsort_dict</span><span class="p">[</span><span class="n">ind</span><span class="p">]</span>
+
+ <span class="k">return</span> <span class="n">sorted_dict</span></div>
+
+
+<div class="viewcode-block" id="cart_dist"><a class="viewcode-back" href="../../ariaec.html#ariaec.base.cart_dist">[docs]</a><span class="k">def</span> <span class="nf">cart_dist</span><span class="p">(</span><span class="n">vectx</span><span class="p">,</span> <span class="n">vecty</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Evaluate cartesian distance beetween 2 points x, vecty</span>
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> vectx :</span>
+<span class="sd"> numpy array (len = n dimensions)</span>
+<span class="sd"> vecty :</span>
+<span class="sd"> numpy array (len = n dimensions)</span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+<span class="sd"> </span>
+<span class="sd"> """</span>
+ <span class="k">return</span> <span class="n">np</span><span class="o">.</span><span class="n">sqrt</span><span class="p">(</span><span class="nb">sum</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">power</span><span class="p">(</span><span class="n">vectx</span> <span class="o">-</span> <span class="n">vecty</span><span class="p">,</span> <span class="mi">2</span><span class="p">)))</span></div>
+
+
+<div class="viewcode-block" id="format_str"><a class="viewcode-back" href="../../ariaec.html#ariaec.base.format_str">[docs]</a><span class="k">def</span> <span class="nf">format_str</span><span class="p">(</span><span class="n">string</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Convert str in bool, float, int or str</span>
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> string :</span>
+<span class="sd"> return:</span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+<span class="sd"> </span>
+<span class="sd"> """</span>
+ <span class="k">if</span> <span class="n">re</span><span class="o">.</span><span class="n">search</span><span class="p">(</span><span class="sa">r</span><span class="s2">"^\s*(true)\s*$"</span><span class="p">,</span> <span class="n">string</span><span class="p">,</span> <span class="n">re</span><span class="o">.</span><span class="n">I</span><span class="p">):</span>
+ <span class="k">return</span> <span class="kc">True</span>
+ <span class="k">elif</span> <span class="n">re</span><span class="o">.</span><span class="n">search</span><span class="p">(</span><span class="sa">r</span><span class="s2">"^\s*(false)\s*$"</span><span class="p">,</span> <span class="n">string</span><span class="p">,</span> <span class="n">re</span><span class="o">.</span><span class="n">I</span><span class="p">):</span>
+ <span class="k">return</span> <span class="kc">False</span>
+ <span class="k">elif</span> <span class="n">re</span><span class="o">.</span><span class="n">search</span><span class="p">(</span><span class="sa">r</span><span class="s2">"^\s*\d+\s*$"</span><span class="p">,</span> <span class="n">string</span><span class="p">):</span>
+ <span class="k">return</span> <span class="nb">int</span><span class="p">(</span><span class="n">string</span><span class="p">)</span>
+ <span class="k">elif</span> <span class="n">re</span><span class="o">.</span><span class="n">search</span><span class="p">(</span><span class="sa">r</span><span class="s2">"^[\s\d-]+\.\d+\s*$"</span><span class="p">,</span> <span class="n">string</span><span class="p">):</span>
+ <span class="k">return</span> <span class="nb">float</span><span class="p">(</span><span class="n">string</span><span class="p">)</span>
+ <span class="k">elif</span> <span class="n">re</span><span class="o">.</span><span class="n">search</span><span class="p">(</span><span class="sa">r</span><span class="s1">'^".+"$'</span><span class="p">,</span> <span class="n">string</span><span class="p">):</span>
+ <span class="c1"># remove " characters</span>
+ <span class="k">return</span> <span class="n">string</span><span class="p">[</span><span class="mi">1</span><span class="p">:</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span>
+ <span class="k">elif</span> <span class="s2">","</span> <span class="ow">in</span> <span class="n">string</span><span class="p">:</span>
+ <span class="k">return</span> <span class="n">string</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">','</span><span class="p">)</span>
+ <span class="k">elif</span> <span class="s2">"+"</span> <span class="ow">in</span> <span class="n">string</span><span class="p">:</span>
+ <span class="k">return</span> <span class="n">string</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">'+'</span><span class="p">)</span>
+ <span class="k">elif</span> <span class="s2">"/"</span> <span class="ow">in</span> <span class="n">string</span> <span class="ow">and</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">(</span><span class="n">string</span><span class="p">):</span>
+ <span class="k">return</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">abspath</span><span class="p">(</span><span class="n">string</span><span class="p">)</span>
+ <span class="k">elif</span> <span class="n">re</span><span class="o">.</span><span class="n">search</span><span class="p">(</span><span class="sa">r</span><span class="s2">"[/\w]+"</span><span class="p">,</span> <span class="n">string</span><span class="p">):</span>
+ <span class="k">return</span> <span class="n">string</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">if</span> <span class="n">string</span><span class="p">:</span>
+ <span class="k">try</span><span class="p">:</span>
+ <span class="n">ev_str</span> <span class="o">=</span> <span class="n">ast</span><span class="o">.</span><span class="n">literal_eval</span><span class="p">(</span><span class="n">string</span><span class="p">)</span>
+ <span class="k">except</span> <span class="ne">ValueError</span><span class="p">:</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">error</span><span class="p">(</span><span class="s2">"Don't understand given string </span><span class="si">%s</span><span class="s2">. Please check "</span>
+ <span class="s2">"format."</span><span class="p">,</span> <span class="n">string</span><span class="p">)</span>
+ <span class="k">return</span> <span class="kc">None</span>
+ <span class="k">except</span> <span class="ne">SyntaxError</span><span class="p">:</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">error</span><span class="p">(</span><span class="s2">"Given string </span><span class="si">%s</span><span class="s2"> is not a valid expression"</span><span class="p">,</span> <span class="n">string</span><span class="p">)</span>
+ <span class="k">return</span> <span class="kc">None</span>
+ <span class="k">return</span> <span class="n">ev_str</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">return</span> <span class="kc">None</span></div>
+
+
+<div class="viewcode-block" id="format_dict"><a class="viewcode-back" href="../../ariaec.html#ariaec.base.format_dict">[docs]</a><span class="k">def</span> <span class="nf">format_dict</span><span class="p">(</span><span class="n">indict</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> </span>
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> indict :</span>
+<span class="sd"> return:</span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+<span class="sd"> </span>
+<span class="sd"> """</span>
+ <span class="k">for</span> <span class="n">key</span> <span class="ow">in</span> <span class="n">indict</span><span class="p">:</span>
+ <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">indict</span><span class="p">[</span><span class="n">key</span><span class="p">],</span> <span class="nb">str</span><span class="p">):</span>
+ <span class="n">indict</span><span class="p">[</span><span class="n">key</span><span class="p">]</span> <span class="o">=</span> <span class="n">format_str</span><span class="p">(</span><span class="n">indict</span><span class="p">[</span><span class="n">key</span><span class="p">])</span>
+ <span class="k">return</span> <span class="n">indict</span></div>
+
+
+<div class="viewcode-block" id="ppdict"><a class="viewcode-back" href="../../ariaec.html#ariaec.base.ppdict">[docs]</a><span class="k">def</span> <span class="nf">ppdict</span><span class="p">(</span><span class="n">indict</span><span class="p">,</span> <span class="n">indent</span><span class="o">=</span><span class="mi">2</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> </span>
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> indict :</span>
+<span class="sd"> param indent:</span>
+<span class="sd"> indent :</span>
+<span class="sd"> (Default value = 2)</span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+<span class="sd"> </span>
+<span class="sd"> """</span>
+ <span class="k">return</span> <span class="n">json</span><span class="o">.</span><span class="n">dumps</span><span class="p">(</span><span class="n">indict</span><span class="p">,</span> <span class="n">indent</span><span class="o">=</span><span class="n">indent</span><span class="p">)</span></div>
+
+
+<div class="viewcode-block" id="tickmin"><a class="viewcode-back" href="../../ariaec.html#ariaec.base.tickmin">[docs]</a><span class="k">def</span> <span class="nf">tickmin</span><span class="p">(</span><span class="n">pandata</span><span class="p">,</span> <span class="n">ntick</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">shift</span><span class="o">=</span><span class="mi">0</span><span class="p">,</span> <span class="n">offset</span><span class="o">=</span><span class="mi">5</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Minimise number of ticks labels for matplotlib or seaborn plot</span>
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> offset :</span>
+<span class="sd"> param shift: (Default value = 5)</span>
+<span class="sd"> pandata :</span>
+<span class="sd"> pandas dataframe</span>
+<span class="sd"> ntick :</span>
+<span class="sd"> number of ticks wanted per axes (Default value = None)</span>
+<span class="sd"> shift :</span>
+<span class="sd"> (Default value = 0)</span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+<span class="sd"> </span>
+<span class="sd"> """</span>
+ <span class="n">yticks</span> <span class="o">=</span> <span class="p">[</span><span class="n">_</span> <span class="o">+</span> <span class="n">shift</span> <span class="k">for</span> <span class="n">_</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="nb">len</span><span class="p">(</span><span class="n">pandata</span><span class="o">.</span><span class="n">index</span><span class="p">))]</span>
+ <span class="n">xticks</span> <span class="o">=</span> <span class="p">[</span><span class="n">_</span> <span class="o">+</span> <span class="n">shift</span> <span class="k">for</span> <span class="n">_</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="nb">len</span><span class="p">(</span><span class="n">pandata</span><span class="o">.</span><span class="n">columns</span><span class="p">))]</span>
+ <span class="k">if</span> <span class="n">ntick</span><span class="p">:</span>
+ <span class="n">keptticks</span> <span class="o">=</span> <span class="n">yticks</span><span class="p">[::(</span><span class="nb">len</span><span class="p">(</span><span class="n">pandata</span><span class="o">.</span><span class="n">index</span><span class="p">)</span> <span class="o">//</span> <span class="nb">int</span><span class="p">(</span><span class="n">ntick</span><span class="p">))]</span>
+ <span class="n">yticks</span> <span class="o">=</span> <span class="p">[</span><span class="n">_</span> <span class="k">if</span> <span class="n">_</span> <span class="ow">in</span> <span class="n">keptticks</span> <span class="k">else</span> <span class="s1">''</span> <span class="k">for</span> <span class="n">_</span> <span class="ow">in</span> <span class="n">yticks</span><span class="p">]</span>
+ <span class="c1"># If shift != 0, need to initialize first value of ticks</span>
+
+ <span class="n">keptticks</span> <span class="o">=</span> <span class="n">xticks</span><span class="p">[::(</span><span class="nb">len</span><span class="p">(</span><span class="n">xticks</span><span class="p">)</span> <span class="o">//</span> <span class="nb">int</span><span class="p">(</span><span class="n">ntick</span><span class="p">))]</span>
+ <span class="n">xticks</span> <span class="o">=</span> <span class="p">[</span><span class="n">_</span> <span class="k">if</span> <span class="n">_</span> <span class="ow">in</span> <span class="n">keptticks</span> <span class="k">else</span> <span class="s1">''</span> <span class="k">for</span> <span class="n">_</span> <span class="ow">in</span> <span class="n">xticks</span><span class="p">]</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="n">keptticks</span> <span class="o">=</span> <span class="p">[</span><span class="n">ytick</span> <span class="k">for</span> <span class="n">i</span><span class="p">,</span> <span class="n">ytick</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">yticks</span><span class="p">)</span>
+ <span class="k">if</span> <span class="p">(</span><span class="n">i</span> <span class="o">+</span> <span class="n">shift</span><span class="p">)</span> <span class="o">%</span> <span class="n">offset</span> <span class="o">==</span> <span class="mi">0</span><span class="p">]</span>
+ <span class="c1"># keptticks = yticks[::offset - shift]</span>
+ <span class="n">yticks</span> <span class="o">=</span> <span class="p">[</span><span class="n">_</span> <span class="k">if</span> <span class="n">_</span> <span class="ow">in</span> <span class="n">keptticks</span> <span class="k">else</span> <span class="s1">''</span> <span class="k">for</span> <span class="n">_</span> <span class="ow">in</span> <span class="n">yticks</span><span class="p">]</span>
+ <span class="c1"># If shift != 0, need to initialize first value of ticks</span>
+
+ <span class="n">keptticks</span> <span class="o">=</span> <span class="p">[</span><span class="n">xtick</span> <span class="k">for</span> <span class="n">i</span><span class="p">,</span> <span class="n">xtick</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">xticks</span><span class="p">)</span>
+ <span class="k">if</span> <span class="p">(</span><span class="n">i</span> <span class="o">+</span> <span class="n">shift</span><span class="p">)</span> <span class="o">%</span> <span class="n">offset</span> <span class="o">==</span> <span class="mi">0</span><span class="p">]</span>
+ <span class="c1"># keptticks = xticks[::offset - shift]</span>
+ <span class="n">xticks</span> <span class="o">=</span> <span class="p">[</span><span class="n">_</span> <span class="k">if</span> <span class="n">_</span> <span class="ow">in</span> <span class="n">keptticks</span> <span class="k">else</span> <span class="s1">''</span> <span class="k">for</span> <span class="n">_</span> <span class="ow">in</span> <span class="n">xticks</span><span class="p">]</span>
+ <span class="k">return</span> <span class="n">xticks</span><span class="p">,</span> <span class="n">yticks</span></div>
+
+
+<div class="viewcode-block" id="tickrot"><a class="viewcode-back" href="../../ariaec.html#ariaec.base.tickrot">[docs]</a><span class="k">def</span> <span class="nf">tickrot</span><span class="p">(</span><span class="n">axes</span><span class="p">,</span> <span class="n">figure</span><span class="p">,</span> <span class="n">rotype</span><span class="o">=</span><span class="s1">'horizontal'</span><span class="p">,</span> <span class="n">xaxis</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">yaxis</span><span class="o">=</span><span class="kc">True</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Matplot rotation of ticks labels</span>
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> axes :</span>
+<span class="sd"> param figure:</span>
+<span class="sd"> rotype :</span>
+<span class="sd"> param xaxis: (Default value = 'horizontal')</span>
+<span class="sd"> yaxis :</span>
+<span class="sd"> return: (Default value = True)</span>
+<span class="sd"> figure :</span>
+<span class="sd"> </span>
+<span class="sd"> xaxis :</span>
+<span class="sd"> (Default value = True)</span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+<span class="sd"> </span>
+<span class="sd"> """</span>
+ <span class="k">if</span> <span class="n">yaxis</span><span class="p">:</span>
+ <span class="n">art</span><span class="o">.</span><span class="n">setp</span><span class="p">(</span><span class="n">axes</span><span class="o">.</span><span class="n">get_yticklabels</span><span class="p">(),</span> <span class="n">rotation</span><span class="o">=</span><span class="n">rotype</span><span class="p">)</span>
+ <span class="k">if</span> <span class="n">xaxis</span><span class="p">:</span>
+ <span class="n">art</span><span class="o">.</span><span class="n">setp</span><span class="p">(</span><span class="n">axes</span><span class="o">.</span><span class="n">get_xticklabels</span><span class="p">(),</span> <span class="n">rotation</span><span class="o">=</span><span class="n">rotype</span><span class="p">)</span>
+ <span class="n">figure</span><span class="o">.</span><span class="n">canvas</span><span class="o">.</span><span class="n">draw</span><span class="p">()</span></div>
+
+
+<span class="c1"># TODO: Add another level when we use verbose options instead of displaying debug messages</span>
+<div class="viewcode-block" id="CustomLogging"><a class="viewcode-back" href="../../ariaec.html#ariaec.base.CustomLogging">[docs]</a><span class="k">class</span> <span class="nc">CustomLogging</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Customized python logging config</span>
+<span class="sd"> """</span>
+ <span class="c1"># default_file = os.path.join(os.path.abspath(os.path.dirname(__file__)),</span>
+ <span class="c1"># "conf/logging.json")</span>
+ <span class="n">default_file</span> <span class="o">=</span> <span class="s2">"conf/logging.json"</span>
+
+ <span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">level</span><span class="o">=</span><span class="n">logging</span><span class="o">.</span><span class="n">INFO</span><span class="p">,</span> <span class="n">desc</span><span class="o">=</span><span class="vm">__doc__</span><span class="p">):</span>
+ <span class="sd">"""</span>
+
+<span class="sd"> :param level:</span>
+<span class="sd"> :param desc:</span>
+<span class="sd"> :return:</span>
+<span class="sd"> """</span>
+ <span class="c1"># TODO: detect path log filenames and makedirs if not exists</span>
+ <span class="n">logging</span><span class="o">.</span><span class="n">basicConfig</span><span class="p">(</span><span class="n">level</span><span class="o">=</span><span class="n">level</span><span class="p">)</span>
+ <span class="k">if</span> <span class="n">desc</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">msg</span> <span class="o">=</span> <span class="n">desc</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">msg</span> <span class="o">=</span> <span class="s2">""</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">config</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">default_config</span><span class="p">()</span>
+
+<div class="viewcode-block" id="CustomLogging.update_msg"><a class="viewcode-back" href="../../ariaec.html#ariaec.base.CustomLogging.update_msg">[docs]</a> <span class="k">def</span> <span class="nf">update_msg</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">desc</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> </span>
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> desc :</span>
+<span class="sd"> return:</span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+<span class="sd"> </span>
+<span class="sd"> """</span>
+ <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">msg</span><span class="p">,</span> <span class="nb">list</span><span class="p">):</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">msg</span> <span class="o">+=</span> <span class="n">desc</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">msg</span> <span class="o">=</span> <span class="s2">" - "</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">msg</span><span class="p">)</span>
+ <span class="k">elif</span> <span class="nb">isinstance</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">msg</span><span class="p">,</span> <span class="nb">str</span><span class="p">):</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">msg</span> <span class="o">=</span> <span class="s2">" - "</span><span class="o">.</span><span class="n">join</span><span class="p">((</span><span class="bp">self</span><span class="o">.</span><span class="n">msg</span><span class="p">,</span> <span class="n">desc</span><span class="o">.</span><span class="n">capitalize</span><span class="p">()))</span></div>
+
+<div class="viewcode-block" id="CustomLogging.default_config"><a class="viewcode-back" href="../../ariaec.html#ariaec.base.CustomLogging.default_config">[docs]</a> <span class="k">def</span> <span class="nf">default_config</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="sd">""":return:"""</span>
+ <span class="c1"># with open(self.default_file, 'rt') as f:</span>
+ <span class="n">conf</span> <span class="o">=</span> <span class="n">pkgr</span><span class="o">.</span><span class="n">resource_stream</span><span class="p">(</span><span class="vm">__name__</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">default_file</span><span class="p">)</span><span class="o">.</span><span class="n">read</span><span class="p">()</span><span class="o">.</span><span class="n">decode</span><span class="p">()</span>
+ <span class="n">config</span> <span class="o">=</span> <span class="n">json</span><span class="o">.</span><span class="n">loads</span><span class="p">(</span><span class="n">conf</span><span class="p">)</span>
+ <span class="n">logging</span><span class="o">.</span><span class="n">config</span><span class="o">.</span><span class="n">dictConfig</span><span class="p">(</span><span class="n">config</span><span class="p">)</span>
+ <span class="k">return</span> <span class="n">config</span></div>
+
+<div class="viewcode-block" id="CustomLogging.set_outdir"><a class="viewcode-back" href="../../ariaec.html#ariaec.base.CustomLogging.set_outdir">[docs]</a> <span class="k">def</span> <span class="nf">set_outdir</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">outdir</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Create log directory and change log files location</span>
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> outdir :</span>
+<span class="sd"> path output directory</span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+<span class="sd"> </span>
+<span class="sd"> """</span>
+ <span class="n">outdir</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">outdir</span><span class="p">,</span>
+ <span class="s2">"log"</span><span class="p">)</span> <span class="k">if</span> <span class="s2">"log"</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">outdir</span> <span class="k">else</span> <span class="n">outdir</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">abspath</span><span class="p">(</span><span class="n">outdir</span><span class="p">)):</span>
+ <span class="n">os</span><span class="o">.</span><span class="n">makedirs</span><span class="p">(</span><span class="n">outdir</span><span class="p">)</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="c1"># Trick to avoid overwriting files with w mode after copy2 call</span>
+ <span class="n">shutil</span><span class="o">.</span><span class="n">rmtree</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">abspath</span><span class="p">(</span><span class="n">outdir</span><span class="p">))</span>
+ <span class="n">os</span><span class="o">.</span><span class="n">makedirs</span><span class="p">(</span><span class="n">outdir</span><span class="p">)</span>
+ <span class="k">if</span> <span class="n">outdir</span> <span class="ow">and</span> <span class="s2">"handlers"</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">config</span><span class="p">:</span>
+ <span class="k">for</span> <span class="n">hand</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">config</span><span class="p">[</span><span class="s2">"handlers"</span><span class="p">]:</span>
+ <span class="k">if</span> <span class="s2">"filename"</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">config</span><span class="p">[</span><span class="s2">"handlers"</span><span class="p">][</span><span class="n">hand</span><span class="p">]:</span>
+ <span class="n">oldpath</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">config</span><span class="p">[</span><span class="s2">"handlers"</span><span class="p">][</span><span class="n">hand</span><span class="p">][</span><span class="s2">"filename"</span><span class="p">]</span>
+ <span class="n">newpath</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">abspath</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span>
+ <span class="n">outdir</span><span class="p">,</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">basename</span><span class="p">(</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">config</span><span class="p">[</span><span class="s2">"handlers"</span><span class="p">][</span><span class="n">hand</span><span class="p">][</span><span class="s2">"filename"</span><span class="p">])))</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">config</span><span class="p">[</span><span class="s2">"handlers"</span><span class="p">][</span><span class="n">hand</span><span class="p">][</span><span class="s2">"filename"</span><span class="p">]</span> <span class="o">=</span> <span class="n">newpath</span>
+ <span class="n">shutil</span><span class="o">.</span><span class="n">copy2</span><span class="p">(</span><span class="n">oldpath</span><span class="p">,</span> <span class="n">newpath</span><span class="p">)</span>
+ <span class="n">logging</span><span class="o">.</span><span class="n">config</span><span class="o">.</span><span class="n">dictConfig</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">config</span><span class="p">)</span></div>
+
+<div class="viewcode-block" id="CustomLogging.welcome"><a class="viewcode-back" href="../../ariaec.html#ariaec.base.CustomLogging.welcome">[docs]</a> <span class="k">def</span> <span class="nf">welcome</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="sd">""":return:"""</span>
+ <span class="n">desc</span> <span class="o">=</span> <span class="s1">'''</span>
+<span class="s1">================================================================================</span>
+
+<span class="si">{:^80}</span><span class="s1"></span>
+
+<span class="s1">================================================================================</span>
+<span class="s1">'''</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">msg</span><span class="p">)</span>
+ <span class="nb">print</span><span class="p">(</span><span class="n">desc</span><span class="p">)</span>
+ <span class="k">for</span> <span class="n">hand</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">config</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"handlers"</span><span class="p">):</span>
+ <span class="k">if</span> <span class="s2">"filename"</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">config</span><span class="p">[</span><span class="s2">"handlers"</span><span class="p">][</span><span class="n">hand</span><span class="p">]:</span>
+ <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">config</span><span class="p">[</span><span class="s2">"handlers"</span><span class="p">][</span><span class="n">hand</span><span class="p">][</span><span class="s2">"filename"</span><span class="p">],</span>
+ <span class="s1">'w'</span><span class="p">)</span> <span class="k">as</span> <span class="n">outfile</span><span class="p">:</span>
+ <span class="n">outfile</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">desc</span><span class="p">)</span></div></div>
+
+
+<div class="viewcode-block" id="Capturing"><a class="viewcode-back" href="../../ariaec.html#ariaec.base.Capturing">[docs]</a><span class="k">class</span> <span class="nc">Capturing</span><span class="p">(</span><span class="nb">list</span><span class="p">):</span>
+ <span class="sd">"""Capture output"""</span>
+ <span class="k">def</span> <span class="nf">__enter__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="sd">"""</span>
+
+<span class="sd"> :return:</span>
+<span class="sd"> """</span>
+ <span class="c1"># Stock default stdout and redirect current stdout to this class</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_stdout</span> <span class="o">=</span> <span class="n">sys</span><span class="o">.</span><span class="n">stdout</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_stderr</span> <span class="o">=</span> <span class="n">sys</span><span class="o">.</span><span class="n">stderr</span>
+ <span class="c1"># All print calls are saved into self._stringio</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_stringio</span> <span class="o">=</span> <span class="n">six</span><span class="o">.</span><span class="n">moves</span><span class="o">.</span><span class="n">StringIO</span><span class="p">()</span>
+ <span class="n">sys</span><span class="o">.</span><span class="n">stdout</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_stringio</span>
+ <span class="n">sys</span><span class="o">.</span><span class="n">stderr</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_stringio</span>
+ <span class="k">return</span> <span class="bp">self</span>
+
+ <span class="k">def</span> <span class="nf">__exit__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">):</span>
+ <span class="sd">"""</span>
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> args</span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+<span class="sd"> """</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">extend</span><span class="p">(</span><span class="s2">"</span><span class="se">\n</span><span class="s2">"</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_stringio</span><span class="o">.</span><span class="n">getvalue</span><span class="p">()</span><span class="o">.</span><span class="n">splitlines</span><span class="p">()))</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_stringio</span><span class="o">.</span><span class="n">truncate</span><span class="p">(</span><span class="mi">0</span><span class="p">)</span>
+ <span class="k">del</span> <span class="bp">self</span><span class="o">.</span><span class="n">_stringio</span> <span class="c1"># free up some memory</span>
+ <span class="n">sys</span><span class="o">.</span><span class="n">stdout</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_stdout</span>
+ <span class="n">sys</span><span class="o">.</span><span class="n">stderr</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_stderr</span></div>
+
+
+<div class="viewcode-block" id="RedirectStdStreams"><a class="viewcode-back" href="../../ariaec.html#ariaec.base.RedirectStdStreams">[docs]</a><span class="k">class</span> <span class="nc">RedirectStdStreams</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span>
+ <span class="sd">"""Redirect standard ouput and errors"""</span>
+ <span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">stdout</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">stderr</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_stdout</span> <span class="o">=</span> <span class="n">stdout</span> <span class="ow">or</span> <span class="n">sys</span><span class="o">.</span><span class="n">stdout</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_stderr</span> <span class="o">=</span> <span class="n">stderr</span> <span class="ow">or</span> <span class="n">sys</span><span class="o">.</span><span class="n">stderr</span>
+
+ <span class="k">def</span> <span class="nf">__enter__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">old_stdout</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">old_stderr</span> <span class="o">=</span> <span class="n">sys</span><span class="o">.</span><span class="n">stdout</span><span class="p">,</span> <span class="n">sys</span><span class="o">.</span><span class="n">stderr</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">old_stdout</span><span class="o">.</span><span class="n">flush</span><span class="p">()</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">old_stderr</span><span class="o">.</span><span class="n">flush</span><span class="p">()</span>
+ <span class="n">sys</span><span class="o">.</span><span class="n">stdout</span><span class="p">,</span> <span class="n">sys</span><span class="o">.</span><span class="n">stderr</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_stdout</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">_stderr</span>
+ <span class="k">return</span> <span class="bp">self</span>
+
+ <span class="k">def</span> <span class="nf">__exit__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">exc_type</span><span class="p">,</span> <span class="n">exc_value</span><span class="p">,</span> <span class="n">traceback</span><span class="p">):</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_stdout</span><span class="o">.</span><span class="n">flush</span><span class="p">()</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_stderr</span><span class="o">.</span><span class="n">flush</span><span class="p">()</span>
+ <span class="n">sys</span><span class="o">.</span><span class="n">stdout</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">old_stdout</span>
+ <span class="n">sys</span><span class="o">.</span><span class="n">stderr</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">old_stderr</span></div>
+
+
+<div class="viewcode-block" id="CommandProtocol"><a class="viewcode-back" href="../../ariaec.html#ariaec.base.CommandProtocol">[docs]</a><span class="k">class</span> <span class="nc">CommandProtocol</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span>
+ <span class="sd">"""Abstract class for subcommand protocol"""</span>
+ <span class="n">__metaclass__</span> <span class="o">=</span> <span class="n">ABCMeta</span>
+
+ <span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">settings</span><span class="p">):</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">settings</span> <span class="o">=</span> <span class="n">settings</span>
+
+ <span class="nd">@abstractmethod</span>
+<div class="viewcode-block" id="CommandProtocol.run"><a class="viewcode-back" href="../../ariaec.html#ariaec.base.CommandProtocol.run">[docs]</a> <span class="k">def</span> <span class="nf">run</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> main method to launch protocol</span>
+<span class="sd"> :return:</span>
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+<span class="sd"> </span>
+<span class="sd"> """</span>
+ <span class="k">raise</span> <span class="ne">NotImplementedError</span></div></div>
+
+
+<div class="viewcode-block" id="NotDisordered"><a class="viewcode-back" href="../../ariaec.html#ariaec.base.NotDisordered">[docs]</a><span class="k">class</span> <span class="nc">NotDisordered</span><span class="p">(</span><span class="n">Select</span><span class="p">):</span>
+ <span class="sd">"""Define an atom as disordered or not in pdb selection"""</span>
+<div class="viewcode-block" id="NotDisordered.accept_atom"><a class="viewcode-back" href="../../ariaec.html#ariaec.base.NotDisordered.accept_atom">[docs]</a> <span class="k">def</span> <span class="nf">accept_atom</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">atom</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Accept or not the atom if it does not correspond to an alternative</span>
+<span class="sd"> location</span>
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> atom :</span>
+<span class="sd"> </span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+<span class="sd"> </span>
+<span class="sd"> """</span>
+ <span class="k">return</span> <span class="ow">not</span> <span class="n">atom</span><span class="o">.</span><span class="n">is_disordered</span><span class="p">()</span> <span class="ow">or</span> <span class="n">atom</span><span class="o">.</span><span class="n">get_altloc</span><span class="p">()</span> <span class="o">==</span> <span class="s1">'A'</span></div></div>
+
+
+<span class="k">if</span> <span class="vm">__name__</span> <span class="o">==</span> <span class="s2">"__main__"</span><span class="p">:</span>
+ <span class="c1"># Test Logger</span>
+ <span class="n">CustomLogging</span><span class="p">()</span><span class="o">.</span><span class="n">set_outdir</span><span class="p">(</span><span class="s2">"../examples/out"</span><span class="p">)</span>
+ <span class="n">LOG</span> <span class="o">=</span> <span class="n">logging</span><span class="o">.</span><span class="n">getLogger</span><span class="p">(</span><span class="s2">"TEST"</span><span class="p">)</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="nb">dir</span><span class="p">(</span><span class="n">LOG</span><span class="p">))</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s2">"Log test"</span><span class="p">)</span>
+</pre></div>
+
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diff --git a/examples-dev/olds/_build/html/_modules/ariaec/commands.html b/examples-dev/olds/_build/html/_modules/ariaec/commands.html
new file mode 100644
index 0000000000000000000000000000000000000000..85ed35df06cd48b14372aa054984b7dd3cf97c6b
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+
+ <h1>Source code for ariaec.commands</h1><div class="highlight"><pre>
+<span></span><span class="c1"># coding=utf-8</span>
+<span class="sd">"""</span>
+<span class="sd"> Input/Output aria_ec</span>
+<span class="sd">"""</span>
+<span class="kn">from</span> <span class="nn">__future__</span> <span class="k">import</span> <span class="n">absolute_import</span><span class="p">,</span> <span class="n">division</span><span class="p">,</span> <span class="n">print_function</span>
+
+<span class="kn">import</span> <span class="nn">os</span>
+<span class="kn">import</span> <span class="nn">logging</span>
+<span class="kn">import</span> <span class="nn">argparse</span> <span class="k">as</span> <span class="nn">argp</span>
+
+<span class="kn">from</span> <span class="nn">.</span> <span class="k">import</span> <span class="vm">__doc__</span>
+<span class="kn">from</span> <span class="nn">.common</span> <span class="k">import</span> <span class="n">format_dict</span><span class="p">,</span> <span class="n">CustomLogging</span>
+<span class="kn">from</span> <span class="nn">.settings</span> <span class="k">import</span> <span class="n">AriaEcSettings</span>
+<span class="kn">from</span> <span class="nn">.maplot</span> <span class="k">import</span> <span class="n">AriaEcContactMap</span>
+<span class="kn">from</span> <span class="nn">.converter</span> <span class="k">import</span> <span class="n">AriaEcBbConverter</span><span class="p">,</span> <span class="n">AriaEcXMLConverter</span>
+<span class="kn">from</span> <span class="nn">.setup</span> <span class="k">import</span> <span class="n">AriaEcSetup</span>
+<span class="kn">from</span> <span class="nn">.pdbqual</span> <span class="k">import</span> <span class="n">AriaEcPdbqual</span>
+<span class="kn">from</span> <span class="nn">.pdbdist</span> <span class="k">import</span> <span class="n">PDBDist</span>
+<span class="kn">from</span> <span class="nn">.pdbstat</span> <span class="k">import</span> <span class="n">PDBStat</span>
+<span class="kn">from</span> <span class="nn">.analysis</span> <span class="k">import</span> <span class="n">EnsembleAnalysis</span>
+
+
+<span class="n">LOG</span> <span class="o">=</span> <span class="n">logging</span><span class="o">.</span><span class="n">getLogger</span><span class="p">(</span><span class="vm">__name__</span><span class="p">)</span>
+
+
+<div class="viewcode-block" id="check_file"><a class="viewcode-back" href="../../ariaec.html#ariaec.commands.check_file">[docs]</a><span class="k">def</span> <span class="nf">check_file</span><span class="p">(</span><span class="n">prospective_file</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> </span>
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> prospective_file :</span>
+<span class="sd"> </span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+<span class="sd"> </span>
+<span class="sd"> """</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="s2">"Checking if </span><span class="si">%s</span><span class="s2"> is a readable file"</span><span class="p">,</span> <span class="n">prospective_file</span><span class="p">)</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">(</span><span class="n">prospective_file</span><span class="p">):</span>
+ <span class="k">raise</span> <span class="n">argp</span><span class="o">.</span><span class="n">ArgumentTypeError</span><span class="p">(</span><span class="s2">"readable_file:'</span><span class="si">{0}</span><span class="s2">' is not a valid "</span>
+ <span class="s2">"path"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">prospective_file</span><span class="p">))</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="n">os</span><span class="o">.</span><span class="n">access</span><span class="p">(</span><span class="n">prospective_file</span><span class="p">,</span> <span class="n">os</span><span class="o">.</span><span class="n">R_OK</span><span class="p">):</span>
+ <span class="k">raise</span> <span class="n">argp</span><span class="o">.</span><span class="n">ArgumentTypeError</span><span class="p">(</span><span class="s2">"readable_file:'</span><span class="si">{0}</span><span class="s2">' is not a readable "</span>
+ <span class="s2">"file"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">prospective_file</span><span class="p">))</span></div>
+
+
+<div class="viewcode-block" id="ReadableFile"><a class="viewcode-back" href="../../ariaec.html#ariaec.commands.ReadableFile">[docs]</a><span class="k">class</span> <span class="nc">ReadableFile</span><span class="p">(</span><span class="n">argp</span><span class="o">.</span><span class="n">Action</span><span class="p">):</span>
+ <span class="sd">"""Class used with argparse action to check if a file is readable"""</span>
+
+ <span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+ <span class="nb">super</span><span class="p">(</span><span class="n">ReadableFile</span><span class="p">,</span> <span class="bp">self</span><span class="p">)</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
+
+ <span class="k">def</span> <span class="nf">__call__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">parser</span><span class="p">,</span> <span class="n">namespace</span><span class="p">,</span> <span class="n">values</span><span class="p">,</span> <span class="n">option_string</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
+ <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">values</span><span class="p">,</span> <span class="nb">list</span><span class="p">):</span>
+ <span class="k">for</span> <span class="n">prospective_file</span> <span class="ow">in</span> <span class="n">values</span><span class="p">:</span>
+ <span class="n">check_file</span><span class="p">(</span><span class="n">prospective_file</span><span class="p">)</span>
+ <span class="nb">setattr</span><span class="p">(</span><span class="n">namespace</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">dest</span><span class="p">,</span>
+ <span class="p">[</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">abspath</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">expanduser</span><span class="p">(</span><span class="n">val</span><span class="p">))</span> <span class="k">for</span> <span class="n">val</span> <span class="ow">in</span> <span class="n">values</span><span class="p">])</span>
+ <span class="k">elif</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">values</span><span class="p">,</span> <span class="nb">str</span><span class="p">):</span>
+ <span class="n">check_file</span><span class="p">(</span><span class="n">values</span><span class="p">)</span>
+ <span class="nb">setattr</span><span class="p">(</span><span class="n">namespace</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">dest</span><span class="p">,</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">abspath</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">expanduser</span><span class="p">(</span><span class="n">values</span><span class="p">)))</span></div>
+
+
+<span class="c1"># TODO: Make parent Command class with _create_argparser, self.args,</span>
+<span class="c1"># update_logger and run</span>
+<div class="viewcode-block" id="AriaEcCommands"><a class="viewcode-back" href="../../ariaec.html#ariaec.commands.AriaEcCommands">[docs]</a><span class="k">class</span> <span class="nc">AriaEcCommands</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span>
+ <span class="sd">"""Argparse interface for aria_ec"""</span>
+
+ <span class="n">command_list</span> <span class="o">=</span> <span class="p">(</span><span class="s2">"setup"</span><span class="p">,</span> <span class="s2">"bbconv"</span><span class="p">,</span> <span class="s2">"maplot"</span><span class="p">,</span> <span class="s2">"pdbqual"</span><span class="p">,</span> <span class="s2">"analysis"</span><span class="p">,</span>
+ <span class="s2">"tbl2xml"</span><span class="p">,</span> <span class="s2">"pdbdist"</span><span class="p">,</span> <span class="s2">"pdbstat"</span><span class="p">)</span>
+ <span class="n">desc_list</span> <span class="o">=</span> <span class="p">(</span><span class="sa">u</span><span class="s2">"Setup ARIA infrastructure with contact maps translated "</span>
+ <span class="sa">u</span><span class="s2">"into ARIA restraints"</span><span class="p">,</span>
+ <span class="sa">u</span><span class="s2">"Convert a contact map in bbcontact format"</span><span class="p">,</span>
+ <span class="sa">u</span><span class="s2">"Contactmap visualization tool"</span><span class="p">,</span>
+ <span class="sa">u</span><span class="s2">"Quality tool for pdb file(s)"</span><span class="p">,</span>
+ <span class="sa">u</span><span class="s2">"Extended ARIA ensemble analysis on a specific iteration "</span><span class="p">,</span>
+ <span class="sa">u</span><span class="s2">"XML converter for tbl distance restraint"</span><span class="p">,</span>
+ <span class="sa">u</span><span class="s2">"Extract distance distribution from culled list of pdb files"</span><span class="p">,</span>
+ <span class="sa">u</span><span class="s2">"Analyze distance distribution with GMM, ..."</span><span class="p">)</span>
+ <span class="n">contact_types</span> <span class="o">=</span> <span class="p">(</span><span class="s2">"evfold"</span><span class="p">,</span> <span class="s2">"plmev"</span><span class="p">,</span> <span class="s2">"plm"</span><span class="p">,</span> <span class="s2">"plmdca"</span><span class="p">,</span> <span class="s2">"plmc"</span><span class="p">,</span> <span class="s2">"bbcontacts"</span><span class="p">,</span>
+ <span class="s2">"pconsc"</span><span class="p">,</span> <span class="s2">"pconsc1"</span><span class="p">,</span> <span class="s2">"pconsc2"</span><span class="p">,</span> <span class="s2">"psicov"</span><span class="p">,</span> <span class="s2">"metapsicovhb"</span><span class="p">,</span>
+ <span class="s2">"metapsicov_stg1"</span><span class="p">,</span> <span class="s2">"metapsicov_stg2"</span><span class="p">,</span> <span class="s2">"gremlin"</span><span class="p">,</span> <span class="s2">"pdb"</span><span class="p">,</span>
+ <span class="s2">"native"</span><span class="p">,</span> <span class="s2">"native_full"</span><span class="p">,</span> <span class="s2">"contactlist"</span><span class="p">)</span>
+ <span class="n">default_confile</span> <span class="o">=</span> <span class="s2">"conf/config.ini"</span>
+
+ <span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">custom_logging</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
+ <span class="c1"># Def Argument pdbparser</span>
+ <span class="n">parser</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_create_argparser</span><span class="p">()</span>
+ <span class="c1"># parse args</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">args</span> <span class="o">=</span> <span class="n">parser</span><span class="o">.</span><span class="n">parse_args</span><span class="p">()</span>
+ <span class="c1"># Update LOG with outdir</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_update_logger</span><span class="p">(</span><span class="n">custom_logging</span><span class="p">)</span>
+
+ <span class="k">def</span> <span class="nf">_update_logger</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">log</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> </span>
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> log :</span>
+<span class="sd"> </span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+<span class="sd"> </span>
+<span class="sd"> """</span>
+ <span class="k">if</span> <span class="n">log</span> <span class="ow">and</span> <span class="nb">hasattr</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">args</span><span class="p">,</span> <span class="s2">"output_directory"</span><span class="p">):</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">args</span><span class="o">.</span><span class="n">nolog</span><span class="p">:</span>
+ <span class="c1"># Don't generate log files</span>
+ <span class="c1"># TODO: get handler list from json file or customlogging object</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">removeHandler</span><span class="p">(</span><span class="s2">"info_file_handler"</span><span class="p">)</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">removeHandler</span><span class="p">(</span><span class="s2">"error_file_handler"</span><span class="p">)</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">removeHandler</span><span class="p">(</span><span class="s2">"debug_file_handler"</span><span class="p">)</span>
+ <span class="n">log</span><span class="o">.</span><span class="n">set_outdir</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">args</span><span class="o">.</span><span class="n">output_directory</span><span class="p">)</span>
+ <span class="n">log</span><span class="o">.</span><span class="n">update_msg</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">args</span><span class="o">.</span><span class="n">command</span><span class="p">)</span>
+ <span class="n">log</span><span class="o">.</span><span class="n">welcome</span><span class="p">()</span>
+
+ <span class="k">def</span> <span class="nf">_create_argparser</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="sd">""" """</span>
+ <span class="n">parser</span> <span class="o">=</span> <span class="n">argp</span><span class="o">.</span><span class="n">ArgumentParser</span><span class="p">(</span><span class="n">description</span><span class="o">=</span><span class="vm">__doc__</span><span class="p">,</span>
+ <span class="n">formatter_class</span><span class="o">=</span><span class="n">argp</span><span class="o">.</span><span class="n">ArgumentDefaultsHelpFormatter</span><span class="p">)</span>
+ <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s2">"-o"</span><span class="p">,</span> <span class="s2">"--output"</span><span class="p">,</span> <span class="n">dest</span><span class="o">=</span><span class="s2">"output_directory"</span><span class="p">,</span>
+ <span class="nb">type</span><span class="o">=</span><span class="nb">str</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s2">"Output directory"</span><span class="p">,</span> <span class="n">required</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
+ <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s2">"-c"</span><span class="p">,</span> <span class="s2">"--conf"</span><span class="p">,</span> <span class="n">action</span><span class="o">=</span><span class="n">ReadableFile</span><span class="p">,</span>
+ <span class="n">dest</span><span class="o">=</span><span class="s2">"conf_file"</span><span class="p">,</span>
+ <span class="n">default</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s2">"configuration file"</span><span class="p">)</span>
+ <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s2">"--nolog"</span><span class="p">,</span> <span class="n">action</span><span class="o">=</span><span class="s2">"store_true"</span><span class="p">,</span>
+ <span class="n">default</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s2">"Don't generate log files"</span><span class="p">)</span>
+ <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s2">"-d"</span><span class="p">,</span> <span class="s2">"--debug"</span><span class="p">,</span> <span class="n">dest</span><span class="o">=</span><span class="s2">"verbose"</span><span class="p">,</span> <span class="n">default</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span>
+ <span class="n">action</span><span class="o">=</span><span class="s1">'store_true'</span><span class="p">,</span>
+ <span class="n">help</span><span class="o">=</span><span class="s2">"Increase output verbosity"</span><span class="p">)</span>
+ <span class="c1"># Create subcommands</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_create_subparsers</span><span class="p">(</span><span class="n">parser</span><span class="o">.</span><span class="n">add_subparsers</span><span class="p">(</span><span class="n">dest</span><span class="o">=</span><span class="s2">"command"</span><span class="p">))</span>
+ <span class="k">return</span> <span class="n">parser</span>
+
+ <span class="k">def</span> <span class="nf">_create_subparsers</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">parser</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Generate subcommands</span>
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> parser :</span>
+<span class="sd"> argparser object</span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+<span class="sd"> </span>
+<span class="sd"> """</span>
+ <span class="k">for</span> <span class="n">index</span><span class="p">,</span> <span class="n">command</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">command_list</span><span class="p">):</span>
+ <span class="c1"># Create subparser defined in command list</span>
+ <span class="n">subcommand</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s2">"_"</span> <span class="o">+</span> <span class="n">command</span> <span class="o">+</span> <span class="s2">"_argparser"</span><span class="p">)(</span>
+ <span class="n">desc</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">desc_list</span><span class="p">[</span><span class="n">index</span><span class="p">])</span>
+ <span class="n">parser</span><span class="o">.</span><span class="n">add_parser</span><span class="p">(</span><span class="n">command</span><span class="p">,</span> <span class="n">parents</span><span class="o">=</span><span class="p">[</span><span class="n">subcommand</span><span class="p">])</span>
+
+ <span class="k">def</span> <span class="nf">_setup_argparser</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">desc</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> setup opt & args</span>
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> desc :</span>
+<span class="sd"> command descriptor (Default value = None)</span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+<span class="sd"> </span>
+<span class="sd"> """</span>
+ <span class="n">parser</span> <span class="o">=</span> <span class="n">argp</span><span class="o">.</span><span class="n">ArgumentParser</span><span class="p">(</span><span class="n">description</span><span class="o">=</span><span class="n">desc</span><span class="p">,</span>
+ <span class="n">add_help</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span>
+ <span class="c1"># Options</span>
+ <span class="c1"># Args</span>
+ <span class="n">group</span> <span class="o">=</span> <span class="n">parser</span><span class="o">.</span><span class="n">add_argument_group</span><span class="p">(</span><span class="s1">'required arguments'</span><span class="p">)</span>
+ <span class="n">group</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s2">"seq"</span><span class="p">,</span> <span class="n">action</span><span class="o">=</span><span class="n">ReadableFile</span><span class="p">,</span>
+ <span class="n">help</span><span class="o">=</span><span class="s2">"sequence file [FASTA]"</span><span class="p">)</span>
+ <span class="c1"># group.add_argument("sspred", action=ReadableFile,</span>
+ <span class="c1"># help="secondary structure prediction file")</span>
+ <span class="n">group</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s2">"infiles"</span><span class="p">,</span> <span class="n">nargs</span><span class="o">=</span><span class="s2">"+"</span><span class="p">,</span> <span class="n">metavar</span><span class="o">=</span><span class="s2">"infile"</span><span class="p">,</span>
+ <span class="n">action</span><span class="o">=</span><span class="n">ReadableFile</span><span class="p">,</span>
+ <span class="n">help</span><span class="o">=</span><span class="s2">"contact or pdb file(s) used to build aria "</span>
+ <span class="s2">"distance restraints"</span><span class="p">)</span>
+ <span class="n">group</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s2">"-d"</span><span class="p">,</span> <span class="s2">"--distfile"</span><span class="p">,</span> <span class="n">dest</span><span class="o">=</span><span class="s2">"distfile"</span><span class="p">,</span>
+ <span class="n">help</span><span class="o">=</span><span class="s2">"Pdb or distance matrix iif distance_type "</span>
+ <span class="s2">"set to distfile in conf file, "</span>
+ <span class="s2">"use distances in the given file as "</span>
+ <span class="s2">"target distance to build distance "</span>
+ <span class="s2">"restraints"</span><span class="p">)</span>
+ <span class="n">group</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s2">"-s"</span><span class="p">,</span> <span class="s2">"--ssfile"</span><span class="p">,</span> <span class="n">dest</span><span class="o">=</span><span class="s2">"sspred"</span><span class="p">,</span> <span class="n">action</span><span class="o">=</span><span class="n">ReadableFile</span><span class="p">,</span>
+ <span class="n">help</span><span class="o">=</span><span class="s2">"secondary structure prediction file"</span><span class="p">)</span>
+ <span class="n">group</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s2">"-p"</span><span class="p">,</span> <span class="s2">"--ariaproject"</span><span class="p">,</span> <span class="n">dest</span><span class="o">=</span><span class="s2">"ariaproject"</span><span class="p">,</span>
+ <span class="n">action</span><span class="o">=</span><span class="n">ReadableFile</span><span class="p">,</span>
+ <span class="n">help</span><span class="o">=</span><span class="s2">"ARIA project file. This file will be used as"</span>
+ <span class="s2">"an initialization file if"</span><span class="p">)</span>
+ <span class="n">group</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s2">"-t"</span><span class="p">,</span> <span class="s2">"--type"</span><span class="p">,</span> <span class="n">required</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span>
+ <span class="n">nargs</span><span class="o">=</span><span class="s2">"+"</span><span class="p">,</span> <span class="n">dest</span><span class="o">=</span><span class="s2">"contact_types"</span><span class="p">,</span>
+ <span class="n">choices</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">contact_types</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s2">"Infile(s) contact "</span>
+ <span class="s2">"type(s)"</span><span class="p">)</span>
+ <span class="n">group</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s2">"-r"</span><span class="p">,</span> <span class="s2">"--ref"</span><span class="p">,</span> <span class="n">dest</span><span class="o">=</span><span class="s2">"ref"</span><span class="p">,</span>
+ <span class="n">help</span><span class="o">=</span><span class="s2">"Native pdb. Allow TP/FP detection."</span><span class="p">)</span>
+ <span class="n">group</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s2">"--hb"</span><span class="p">,</span> <span class="n">dest</span><span class="o">=</span><span class="s2">"hb"</span><span class="p">,</span>
+ <span class="n">help</span><span class="o">=</span><span class="s2">"H-bonds contact file (eg: metapsicov.hb)"</span><span class="p">)</span>
+ <span class="n">group</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s2">"--ssidx"</span><span class="p">,</span> <span class="n">dest</span><span class="o">=</span><span class="s2">"ssidx"</span><span class="p">,</span> <span class="n">action</span><span class="o">=</span><span class="s2">"store_true"</span><span class="p">,</span>
+ <span class="n">default</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s2">"Use secondary structure index"</span><span class="p">)</span>
+ <span class="n">group</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s2">"--no-filter"</span><span class="p">,</span> <span class="n">dest</span><span class="o">=</span><span class="s2">"no_filter"</span><span class="p">,</span> <span class="n">action</span><span class="o">=</span><span class="s2">"store_true"</span><span class="p">,</span>
+ <span class="n">default</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s2">"Do not filter contact map."</span><span class="p">)</span>
+ <span class="n">group</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s2">"--extract-all"</span><span class="p">,</span> <span class="n">dest</span><span class="o">=</span><span class="s2">"extractall"</span><span class="p">,</span> <span class="n">action</span><span class="o">=</span><span class="s2">"store_true"</span><span class="p">,</span>
+ <span class="n">default</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s2">"Extract data or all data and"</span>
+ <span class="s2">"parameters if an ARIA project"</span>
+ <span class="s2">"is defined with -p option"</span><span class="p">)</span>
+ <span class="k">return</span> <span class="n">parser</span>
+
+ <span class="k">def</span> <span class="nf">_bbconv_argparser</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">desc</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> bbconv opt & args</span>
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> desc :</span>
+<span class="sd"> command descriptor (Default value = None)</span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+<span class="sd"> </span>
+<span class="sd"> """</span>
+ <span class="n">parser</span> <span class="o">=</span> <span class="n">argp</span><span class="o">.</span><span class="n">ArgumentParser</span><span class="p">(</span><span class="n">description</span><span class="o">=</span><span class="n">desc</span><span class="p">,</span>
+ <span class="n">add_help</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span>
+ <span class="c1"># args</span>
+ <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s2">"contactfile"</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s2">"contacts file (pconsc, plm)"</span><span class="p">,</span>
+ <span class="n">action</span><span class="o">=</span><span class="n">ReadableFile</span><span class="p">)</span>
+ <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s2">"sspred"</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s2">"psipred file"</span><span class="p">,</span>
+ <span class="n">action</span><span class="o">=</span><span class="n">ReadableFile</span><span class="p">)</span>
+ <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s2">"seq"</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s2">"sequence file [FASTA]"</span><span class="p">,</span>
+ <span class="n">action</span><span class="o">=</span><span class="n">ReadableFile</span><span class="p">)</span>
+ <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s2">"msa"</span><span class="p">,</span> <span class="n">nargs</span><span class="o">=</span><span class="s1">'?'</span><span class="p">,</span>
+ <span class="n">help</span><span class="o">=</span><span class="s2">"MSA [FASTA] for diversityvalue"</span>
+ <span class="s2">"used with bbcontacts"</span><span class="p">)</span>
+ <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s2">"-t"</span><span class="p">,</span> <span class="s2">"--type"</span><span class="p">,</span> <span class="n">required</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">dest</span><span class="o">=</span><span class="s2">"contact_type"</span><span class="p">,</span>
+ <span class="n">choices</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">contact_types</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s2">"Infile contact "</span>
+ <span class="s2">"type"</span><span class="p">)</span>
+ <span class="k">return</span> <span class="n">parser</span>
+
+ <span class="k">def</span> <span class="nf">_maplot_argparser</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">desc</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> maplot opt & args</span>
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> desc :</span>
+<span class="sd"> command descriptor (Default value = None)</span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+<span class="sd"> </span>
+<span class="sd"> """</span>
+ <span class="n">parser</span> <span class="o">=</span> <span class="n">argp</span><span class="o">.</span><span class="n">ArgumentParser</span><span class="p">(</span><span class="n">description</span><span class="o">=</span><span class="n">desc</span><span class="p">,</span>
+ <span class="n">add_help</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span>
+ <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s2">"seq"</span><span class="p">,</span> <span class="n">action</span><span class="o">=</span><span class="n">ReadableFile</span><span class="p">,</span>
+ <span class="n">help</span><span class="o">=</span><span class="s2">"sequence file [FASTA]"</span><span class="p">)</span>
+ <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s2">"sspred"</span><span class="p">,</span> <span class="n">action</span><span class="o">=</span><span class="n">ReadableFile</span><span class="p">,</span>
+ <span class="n">help</span><span class="o">=</span><span class="s2">"secondary structure prediction file"</span><span class="p">)</span>
+ <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s2">"infiles"</span><span class="p">,</span> <span class="n">nargs</span><span class="o">=</span><span class="s2">"+"</span><span class="p">,</span> <span class="n">metavar</span><span class="o">=</span><span class="s2">"infile"</span><span class="p">,</span>
+ <span class="n">action</span><span class="o">=</span><span class="n">ReadableFile</span><span class="p">,</span>
+ <span class="n">help</span><span class="o">=</span><span class="s2">"contact or pdb file(s) used to build aria "</span>
+ <span class="s2">"distance restraints"</span><span class="p">)</span>
+ <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s2">"-t"</span><span class="p">,</span> <span class="s2">"--type"</span><span class="p">,</span> <span class="n">required</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span>
+ <span class="n">nargs</span><span class="o">=</span><span class="s2">"+"</span><span class="p">,</span> <span class="n">dest</span><span class="o">=</span><span class="s2">"contact_types"</span><span class="p">,</span>
+ <span class="n">choices</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">contact_types</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s2">"Infile(s) "</span>
+ <span class="s2">"contact "</span>
+ <span class="s2">"type(s)"</span><span class="p">)</span>
+ <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s2">"--merge"</span><span class="p">,</span> <span class="n">nargs</span><span class="o">=</span><span class="s2">"+"</span><span class="p">,</span> <span class="n">dest</span><span class="o">=</span><span class="s2">"merge"</span><span class="p">,</span>
+ <span class="n">choices</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">contact_types</span><span class="p">,</span>
+ <span class="n">help</span><span class="o">=</span><span class="s2">"Merge given contact types with other maps"</span><span class="p">)</span>
+ <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s2">"--filter"</span><span class="p">,</span> <span class="n">dest</span><span class="o">=</span><span class="s2">"filter"</span><span class="p">,</span> <span class="n">action</span><span class="o">=</span><span class="s2">"store_true"</span><span class="p">,</span>
+ <span class="n">default</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s2">"Use contact list filter "</span>
+ <span class="s2">"and top n contacts selection"</span><span class="p">)</span>
+ <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s2">"--onlyreport"</span><span class="p">,</span> <span class="n">dest</span><span class="o">=</span><span class="s2">"onlyreport"</span><span class="p">,</span>
+ <span class="n">action</span><span class="o">=</span><span class="s2">"store_true"</span><span class="p">,</span>
+ <span class="n">default</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s2">"Generate only report file"</span><span class="p">)</span>
+ <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s2">"--no-filter"</span><span class="p">,</span> <span class="n">dest</span><span class="o">=</span><span class="s2">"no_filter"</span><span class="p">,</span> <span class="n">action</span><span class="o">=</span><span class="s2">"store_true"</span><span class="p">,</span>
+ <span class="n">default</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s2">"Do not filter contact map."</span><span class="p">)</span>
+ <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s2">"--ssidx"</span><span class="p">,</span> <span class="n">dest</span><span class="o">=</span><span class="s2">"ssidx"</span><span class="p">,</span> <span class="n">action</span><span class="o">=</span><span class="s2">"store_true"</span><span class="p">,</span>
+ <span class="n">default</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span>
+ <span class="n">help</span><span class="o">=</span><span class="s2">"Use secondary structure index"</span><span class="p">)</span>
+ <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s2">"--prefix"</span><span class="p">,</span> <span class="n">dest</span><span class="o">=</span><span class="s2">"prefix"</span><span class="p">,</span> <span class="n">action</span><span class="o">=</span><span class="s2">"store_true"</span><span class="p">,</span>
+ <span class="n">default</span><span class="o">=</span><span class="s2">""</span><span class="p">,</span>
+ <span class="n">help</span><span class="o">=</span><span class="s2">"Generate prefix for file names"</span><span class="p">)</span>
+ <span class="k">return</span> <span class="n">parser</span>
+
+ <span class="nd">@staticmethod</span>
+ <span class="k">def</span> <span class="nf">_pdbqual_argparser</span><span class="p">(</span><span class="n">desc</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> </span>
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> desc :</span>
+<span class="sd"> (Default value = None)</span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+<span class="sd"> </span>
+<span class="sd"> """</span>
+ <span class="n">parser</span> <span class="o">=</span> <span class="n">argp</span><span class="o">.</span><span class="n">ArgumentParser</span><span class="p">(</span><span class="n">description</span><span class="o">=</span><span class="n">desc</span><span class="p">,</span>
+ <span class="n">add_help</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span>
+ <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s2">"infiles"</span><span class="p">,</span> <span class="n">nargs</span><span class="o">=</span><span class="s2">"+"</span><span class="p">,</span> <span class="n">metavar</span><span class="o">=</span><span class="s2">"infile"</span><span class="p">,</span>
+ <span class="n">action</span><span class="o">=</span><span class="n">ReadableFile</span><span class="p">,</span>
+ <span class="n">help</span><span class="o">=</span><span class="s2">"PDB file(s) used to run quality tools with "</span>
+ <span class="s2">"aria API"</span><span class="p">)</span>
+ <span class="k">return</span> <span class="n">parser</span>
+
+ <span class="nd">@staticmethod</span>
+ <span class="k">def</span> <span class="nf">_analysis_argparser</span><span class="p">(</span><span class="n">desc</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> </span>
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> desc :</span>
+<span class="sd"> (Default value = None)</span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+<span class="sd"> </span>
+<span class="sd"> """</span>
+ <span class="n">parser</span> <span class="o">=</span> <span class="n">argp</span><span class="o">.</span><span class="n">ArgumentParser</span><span class="p">(</span><span class="n">description</span><span class="o">=</span><span class="n">desc</span><span class="p">,</span>
+ <span class="n">add_help</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span>
+ <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s2">"project"</span><span class="p">,</span> <span class="n">action</span><span class="o">=</span><span class="n">ReadableFile</span><span class="p">,</span>
+ <span class="n">help</span><span class="o">=</span><span class="s2">"ARIA project file [XML]"</span><span class="p">)</span>
+ <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s2">"iteration"</span><span class="p">,</span> <span class="n">metavar</span><span class="o">=</span><span class="s2">"iteration_path"</span><span class="p">,</span>
+ <span class="n">action</span><span class="o">=</span><span class="n">ReadableFile</span><span class="p">,</span>
+ <span class="n">help</span><span class="o">=</span><span class="s2">"Iteration path used to run violation analysis"</span><span class="p">)</span>
+ <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span>
+ <span class="s2">"listname"</span><span class="p">,</span> <span class="n">metavar</span><span class="o">=</span><span class="s2">"list_name"</span><span class="p">,</span>
+ <span class="n">help</span><span class="o">=</span><span class="s2">"Name of restraint list analyzed in the tbl file"</span><span class="p">)</span>
+ <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s2">"-r"</span><span class="p">,</span> <span class="s2">"--ref"</span><span class="p">,</span> <span class="n">dest</span><span class="o">=</span><span class="s2">"ref"</span><span class="p">,</span>
+ <span class="n">help</span><span class="o">=</span><span class="s2">"Native pdb. Allow TP/FP detection."</span><span class="p">)</span>
+ <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s2">"-d"</span><span class="p">,</span> <span class="n">dest</span><span class="o">=</span><span class="s2">"restraint"</span><span class="p">,</span> <span class="n">default</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
+ <span class="n">help</span><span class="o">=</span><span class="s2">"Distance restraint file (XML) used for "</span>
+ <span class="s2">"violation analysis. Otherwise, use restraints"</span>
+ <span class="s2">" of the current iteration"</span><span class="p">)</span>
+ <span class="k">return</span> <span class="n">parser</span>
+
+ <span class="nd">@staticmethod</span>
+ <span class="k">def</span> <span class="nf">_tbl2xml_argparser</span><span class="p">(</span><span class="n">desc</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> </span>
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> desc :</span>
+<span class="sd"> (Default value = None)</span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+<span class="sd"> </span>
+<span class="sd"> """</span>
+ <span class="n">parser</span> <span class="o">=</span> <span class="n">argp</span><span class="o">.</span><span class="n">ArgumentParser</span><span class="p">(</span><span class="n">description</span><span class="o">=</span><span class="n">desc</span><span class="p">,</span>
+ <span class="n">add_help</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span>
+ <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span>
+ <span class="s2">"molecule"</span><span class="p">,</span> <span class="n">metavar</span><span class="o">=</span><span class="s2">"molecule.xml"</span><span class="p">,</span> <span class="n">action</span><span class="o">=</span><span class="n">ReadableFile</span><span class="p">,</span>
+ <span class="n">help</span><span class="o">=</span><span class="s2">"ARIA XML molecule file"</span><span class="p">)</span>
+ <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s2">"listname"</span><span class="p">,</span> <span class="n">metavar</span><span class="o">=</span><span class="s2">"list_name"</span><span class="p">,</span>
+ <span class="n">help</span><span class="o">=</span><span class="s2">"Restraint list name in the tbl file"</span><span class="p">)</span>
+ <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s2">"infiles"</span><span class="p">,</span> <span class="n">nargs</span><span class="o">=</span><span class="s2">"+"</span><span class="p">,</span> <span class="n">metavar</span><span class="o">=</span><span class="s2">"infile.tbl"</span><span class="p">,</span>
+ <span class="n">action</span><span class="o">=</span><span class="n">ReadableFile</span><span class="p">,</span>
+ <span class="n">help</span><span class="o">=</span><span class="s2">"TBL distance restraint file(s)"</span><span class="p">)</span>
+ <span class="k">return</span> <span class="n">parser</span>
+
+ <span class="nd">@staticmethod</span>
+ <span class="k">def</span> <span class="nf">_pdbdist_argparser</span><span class="p">(</span><span class="n">desc</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> </span>
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> desc :</span>
+<span class="sd"> (Default value = None)</span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+<span class="sd"> </span>
+<span class="sd"> """</span>
+ <span class="n">parser</span> <span class="o">=</span> <span class="n">argp</span><span class="o">.</span><span class="n">ArgumentParser</span><span class="p">(</span><span class="n">description</span><span class="o">=</span><span class="n">desc</span><span class="p">,</span>
+ <span class="n">add_help</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span>
+ <span class="c1"># TODO: find a way to list all cullpdb file in package ressources</span>
+ <span class="c1"># Maybe move this args to the config file</span>
+
+ <span class="c1"># Culled pdb list are actually saved in data/cullpdb folder with yymmdd</span>
+ <span class="c1"># pattern as naming convention</span>
+ <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span>
+ <span class="s2">"--cullist"</span><span class="p">,</span> <span class="n">dest</span><span class="o">=</span><span class="s2">"cullpdbs"</span><span class="p">,</span> <span class="n">default</span><span class="o">=</span><span class="s1">''</span><span class="p">,</span>
+ <span class="n">metavar</span><span class="o">=</span><span class="s2">"CULLED_PDB_LIST"</span><span class="p">,</span> <span class="n">action</span><span class="o">=</span><span class="n">ReadableFile</span><span class="p">,</span>
+ <span class="n">help</span><span class="o">=</span><span class="s2">"Culled list of pdb files from PISCES server ["</span>
+ <span class="s2">"G. Wang and R. L. Dunbrack, Jr. PISCES: a protein sequence "</span>
+ <span class="s2">"culling server. Bioinformatics, 19:1589-1591, 2003.]"</span><span class="p">)</span>
+ <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span>
+ <span class="s2">"--pdbdir"</span><span class="p">,</span> <span class="n">dest</span><span class="o">=</span><span class="s2">"pdbdir"</span><span class="p">,</span> <span class="n">default</span><span class="o">=</span><span class="s1">''</span><span class="p">,</span>
+ <span class="n">metavar</span><span class="o">=</span><span class="s2">"PDB_FOLDER"</span><span class="p">,</span>
+ <span class="n">help</span><span class="o">=</span><span class="s2">"Folder containing pdb file entries"</span><span class="p">)</span>
+ <span class="k">return</span> <span class="n">parser</span>
+
+ <span class="nd">@staticmethod</span>
+ <span class="k">def</span> <span class="nf">_pdbstat_argparser</span><span class="p">(</span><span class="n">desc</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
+ <span class="sd">"""</span>
+
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> desc :</span>
+<span class="sd"> (Default value = None)</span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+
+<span class="sd"> """</span>
+ <span class="n">parser</span> <span class="o">=</span> <span class="n">argp</span><span class="o">.</span><span class="n">ArgumentParser</span><span class="p">(</span><span class="n">description</span><span class="o">=</span><span class="n">desc</span><span class="p">,</span>
+ <span class="n">add_help</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span>
+ <span class="c1"># TODO: find a way to list all cullpdb file in package ressources</span>
+ <span class="c1"># Maybe move this args to the config file</span>
+
+ <span class="c1"># Culled pdb list are actually saved in data/cullpdb folder with yymmdd</span>
+ <span class="c1"># pattern as naming convention</span>
+ <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span>
+ <span class="s2">"pdbdists"</span><span class="p">,</span> <span class="n">action</span><span class="o">=</span><span class="n">ReadableFile</span><span class="p">,</span>
+ <span class="n">help</span><span class="o">=</span><span class="s2">"PDB distance file in csv format"</span><span class="p">)</span>
+ <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span>
+ <span class="s2">"-j"</span><span class="p">,</span> <span class="n">dest</span><span class="o">=</span><span class="s2">"njobs"</span><span class="p">,</span> <span class="n">default</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">metavar</span><span class="o">=</span><span class="s2">"N_JOBS"</span><span class="p">,</span>
+ <span class="n">help</span><span class="o">=</span><span class="s2">"Number of cpus used to run mixture in parallel. By default,"</span>
+ <span class="s2">" use max of available cpus."</span>
+ <span class="p">)</span>
+ <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span>
+ <span class="s2">"--min"</span><span class="p">,</span> <span class="n">dest</span><span class="o">=</span><span class="s2">"minflag"</span><span class="p">,</span> <span class="n">action</span><span class="o">=</span><span class="s2">"store_true"</span><span class="p">,</span> <span class="n">default</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span>
+ <span class="n">help</span><span class="o">=</span><span class="s2">"Compute stats only on a minimized list of atom (CA, CB and 1 "</span>
+ <span class="s2">"SC)"</span><span class="p">)</span>
+ <span class="k">return</span> <span class="n">parser</span>
+
+<div class="viewcode-block" id="AriaEcCommands.create_settings"><a class="viewcode-back" href="../../ariaec.html#ariaec.commands.AriaEcCommands.create_settings">[docs]</a> <span class="k">def</span> <span class="nf">create_settings</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="sd">"""Create settings relative to args.command"""</span>
+
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">args</span><span class="o">.</span><span class="n">verbose</span><span class="p">:</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s2">"Toggle on debug mode"</span><span class="p">)</span>
+ <span class="n">logging</span><span class="o">.</span><span class="n">getLogger</span><span class="p">()</span><span class="o">.</span><span class="n">setLevel</span><span class="p">(</span><span class="n">logging</span><span class="o">.</span><span class="n">DEBUG</span><span class="p">)</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="s2">"Create AriaEcSettings"</span><span class="p">)</span>
+ <span class="n">settings</span> <span class="o">=</span> <span class="n">AriaEcSettings</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">args</span><span class="o">.</span><span class="n">command</span><span class="p">)</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s2">"Loading default config file"</span><span class="p">)</span>
+ <span class="n">settings</span><span class="o">.</span><span class="n">load_config</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">default_confile</span><span class="p">,</span> <span class="n">pkg</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">args</span><span class="o">.</span><span class="n">conf_file</span><span class="p">:</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s2">"Updating settings with conf file"</span><span class="p">)</span>
+ <span class="n">settings</span><span class="o">.</span><span class="n">load_config</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">args</span><span class="o">.</span><span class="n">conf_file</span><span class="p">)</span>
+ <span class="c1"># Update settings associated to command section</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s2">"Updating </span><span class="si">%s</span><span class="s2"> args settings"</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">args</span><span class="o">.</span><span class="n">command</span><span class="p">)</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">args</span><span class="o">.</span><span class="vm">__dict__</span><span class="p">)</span>
+ <span class="nb">getattr</span><span class="p">(</span><span class="n">settings</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">args</span><span class="o">.</span><span class="n">command</span><span class="p">)</span><span class="o">.</span><span class="n">args</span><span class="o">.</span><span class="n">update</span><span class="p">(</span><span class="n">format_dict</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">args</span><span class="o">.</span><span class="vm">__dict__</span><span class="p">))</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="nb">getattr</span><span class="p">(</span><span class="n">settings</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">args</span><span class="o">.</span><span class="n">command</span><span class="p">)</span><span class="o">.</span><span class="n">args</span><span class="p">)</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">args</span><span class="o">.</span><span class="n">output_directory</span><span class="p">:</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s2">"Updating output directory </span><span class="si">%s</span><span class="s2">"</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">args</span><span class="o">.</span><span class="n">output_directory</span><span class="p">)</span>
+ <span class="n">settings</span><span class="o">.</span><span class="n">infra</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">args</span><span class="o">.</span><span class="n">output_directory</span>
+ <span class="k">return</span> <span class="n">settings</span></div>
+
+<div class="viewcode-block" id="AriaEcCommands.run"><a class="viewcode-back" href="../../ariaec.html#ariaec.commands.AriaEcCommands.run">[docs]</a> <span class="k">def</span> <span class="nf">run</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="sd">"""call method relative to args.command"""</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s2">"Run </span><span class="si">%s</span><span class="s2"> command"</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">args</span><span class="o">.</span><span class="n">command</span><span class="p">)</span>
+ <span class="nb">getattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">args</span><span class="o">.</span><span class="n">command</span><span class="p">)()</span></div>
+
+<div class="viewcode-block" id="AriaEcCommands.setup"><a class="viewcode-back" href="../../ariaec.html#ariaec.commands.AriaEcCommands.setup">[docs]</a> <span class="k">def</span> <span class="nf">setup</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="sd">"""Setup call"""</span>
+ <span class="n">setup_inst</span> <span class="o">=</span> <span class="n">AriaEcSetup</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">create_settings</span><span class="p">())</span>
+ <span class="n">setup_inst</span><span class="o">.</span><span class="n">run</span><span class="p">()</span></div>
+
+<div class="viewcode-block" id="AriaEcCommands.bbconv"><a class="viewcode-back" href="../../ariaec.html#ariaec.commands.AriaEcCommands.bbconv">[docs]</a> <span class="k">def</span> <span class="nf">bbconv</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="sd">"""bbcontacts converter call"""</span>
+ <span class="n">bbconverter</span> <span class="o">=</span> <span class="n">AriaEcBbConverter</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">create_settings</span><span class="p">())</span>
+ <span class="n">bbconverter</span><span class="o">.</span><span class="n">run</span><span class="p">()</span></div>
+
+<div class="viewcode-block" id="AriaEcCommands.maplot"><a class="viewcode-back" href="../../ariaec.html#ariaec.commands.AriaEcCommands.maplot">[docs]</a> <span class="k">def</span> <span class="nf">maplot</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="sd">"""instantiate AriaEcContactmap with AriaSettings"""</span>
+ <span class="n">econtactmap</span> <span class="o">=</span> <span class="n">AriaEcContactMap</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">create_settings</span><span class="p">())</span>
+ <span class="n">econtactmap</span><span class="o">.</span><span class="n">run</span><span class="p">()</span></div>
+
+<div class="viewcode-block" id="AriaEcCommands.pdbqual"><a class="viewcode-back" href="../../ariaec.html#ariaec.commands.AriaEcCommands.pdbqual">[docs]</a> <span class="k">def</span> <span class="nf">pdbqual</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="sd">"""Quality run subcommand"""</span>
+ <span class="n">qualprot</span> <span class="o">=</span> <span class="n">AriaEcPdbqual</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">create_settings</span><span class="p">())</span>
+ <span class="n">qualprot</span><span class="o">.</span><span class="n">run</span><span class="p">()</span></div>
+
+<div class="viewcode-block" id="AriaEcCommands.tbl2xml"><a class="viewcode-back" href="../../ariaec.html#ariaec.commands.AriaEcCommands.tbl2xml">[docs]</a> <span class="k">def</span> <span class="nf">tbl2xml</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="sd">"""tbl2xml command"""</span>
+ <span class="n">tblconverter</span> <span class="o">=</span> <span class="n">AriaEcXMLConverter</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">create_settings</span><span class="p">())</span>
+ <span class="n">tblconverter</span><span class="o">.</span><span class="n">run_tbl2xml</span><span class="p">()</span></div>
+
+<div class="viewcode-block" id="AriaEcCommands.pdbdist"><a class="viewcode-back" href="../../ariaec.html#ariaec.commands.AriaEcCommands.pdbdist">[docs]</a> <span class="k">def</span> <span class="nf">pdbdist</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="sd">"""Extract pdb distance distributions"""</span>
+ <span class="n">inst</span> <span class="o">=</span> <span class="n">PDBDist</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">create_settings</span><span class="p">())</span>
+ <span class="n">inst</span><span class="o">.</span><span class="n">run</span><span class="p">()</span></div>
+
+<div class="viewcode-block" id="AriaEcCommands.pdbstat"><a class="viewcode-back" href="../../ariaec.html#ariaec.commands.AriaEcCommands.pdbstat">[docs]</a> <span class="k">def</span> <span class="nf">pdbstat</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="sd">"""Analyse pdb distance distribution"""</span>
+ <span class="n">inst</span> <span class="o">=</span> <span class="n">PDBStat</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">create_settings</span><span class="p">())</span>
+ <span class="n">inst</span><span class="o">.</span><span class="n">run</span><span class="p">()</span></div>
+
+<div class="viewcode-block" id="AriaEcCommands.analysis"><a class="viewcode-back" href="../../ariaec.html#ariaec.commands.AriaEcCommands.analysis">[docs]</a> <span class="k">def</span> <span class="nf">analysis</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="sd">"""Extended ensemble analysis of distance restraints"""</span>
+ <span class="n">inst</span> <span class="o">=</span> <span class="n">EnsembleAnalysis</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">create_settings</span><span class="p">())</span>
+ <span class="n">inst</span><span class="o">.</span><span class="n">run</span><span class="p">()</span></div></div>
+
+
+<div class="viewcode-block" id="main"><a class="viewcode-back" href="../../ariaec.html#ariaec.commands.main">[docs]</a><span class="k">def</span> <span class="nf">main</span><span class="p">():</span>
+ <span class="sd">"""Launch ariaec command interface"""</span>
+
+ <span class="n">mylog</span> <span class="o">=</span> <span class="n">CustomLogging</span><span class="p">(</span><span class="n">desc</span><span class="o">=</span><span class="vm">__doc__</span><span class="p">)</span>
+
+ <span class="n">command</span> <span class="o">=</span> <span class="n">AriaEcCommands</span><span class="p">(</span><span class="n">custom_logging</span><span class="o">=</span><span class="n">mylog</span><span class="p">)</span>
+
+ <span class="n">command</span><span class="o">.</span><span class="n">run</span><span class="p">()</span></div>
+
+
+<span class="k">if</span> <span class="vm">__name__</span> <span class="o">==</span> <span class="s2">"__main__"</span><span class="p">:</span>
+ <span class="c1"># Test AriaEcCommand object</span>
+ <span class="n">logging</span><span class="o">.</span><span class="n">basicConfig</span><span class="p">(</span><span class="n">level</span><span class="o">=</span><span class="n">logging</span><span class="o">.</span><span class="n">DEBUG</span><span class="p">)</span>
+ <span class="n">LOG</span> <span class="o">=</span> <span class="n">logging</span><span class="o">.</span><span class="n">getLogger</span><span class="p">(</span><span class="s2">"IO"</span><span class="p">)</span>
+ <span class="n">AriaEcCommands</span><span class="p">()</span>
+</pre></div>
+
+ </div>
+ <div class="articleComments">
+
+ </div>
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diff --git a/examples-dev/olds/_build/html/_modules/ariaec/converter.html b/examples-dev/olds/_build/html/_modules/ariaec/converter.html
new file mode 100644
index 0000000000000000000000000000000000000000..f03804a53d85e91c0d1fba5ca3507639d4b91360
--- /dev/null
+++ b/examples-dev/olds/_build/html/_modules/ariaec/converter.html
@@ -0,0 +1,2041 @@
+
+
+<!DOCTYPE html>
+<!--[if IE 8]><html class="no-js lt-ie9" lang="en" > <![endif]-->
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+ <div itemprop="articleBody">
+
+ <h1>Source code for ariaec.converter</h1><div class="highlight"><pre>
+<span></span><span class="c1"># coding=utf-8</span>
+<span class="sd">"""</span>
+<span class="sd"> Input/Output aria_ec scripts</span>
+<span class="sd">"""</span>
+<span class="kn">from</span> <span class="nn">__future__</span> <span class="k">import</span> <span class="n">absolute_import</span><span class="p">,</span> <span class="n">division</span><span class="p">,</span> <span class="n">print_function</span>
+
+<span class="kn">import</span> <span class="nn">logging</span>
+<span class="kn">import</span> <span class="nn">math</span>
+<span class="kn">import</span> <span class="nn">random</span>
+<span class="kn">import</span> <span class="nn">collections</span>
+<span class="kn">import</span> <span class="nn">itertools</span>
+<span class="kn">import</span> <span class="nn">datetime</span>
+<span class="kn">import</span> <span class="nn">os</span>
+<span class="kn">import</span> <span class="nn">json</span>
+<span class="kn">import</span> <span class="nn">re</span>
+<span class="kn">import</span> <span class="nn">textwrap</span>
+<span class="kn">import</span> <span class="nn">pickle</span>
+<span class="kn">import</span> <span class="nn">pandas</span> <span class="k">as</span> <span class="nn">pd</span>
+<span class="kn">import</span> <span class="nn">numpy</span> <span class="k">as</span> <span class="nn">np</span>
+<span class="kn">import</span> <span class="nn">pkg_resources</span> <span class="k">as</span> <span class="nn">pkgr</span>
+<span class="kn">import</span> <span class="nn">aria.legacy.AminoAcid</span> <span class="k">as</span> <span class="nn">AminoAcid</span>
+<span class="kn">from</span> <span class="nn">tqdm</span> <span class="k">import</span> <span class="n">tqdm</span>
+<span class="kn">from</span> <span class="nn">.common</span> <span class="k">import</span> <span class="n">get_filename</span><span class="p">,</span> <span class="n">TqdmToLogger</span>
+<span class="kn">from</span> <span class="nn">.protein</span> <span class="k">import</span> <span class="n">Protein</span>
+<span class="kn">from</span> <span class="nn">.reader</span> <span class="k">import</span> <span class="n">MapFileListReader</span><span class="p">,</span> <span class="n">TblDistFile</span>
+<span class="kn">from</span> <span class="nn">.protmap</span> <span class="k">import</span> <span class="p">(</span><span class="n">ResAtmMap</span><span class="p">,</span> <span class="n">ResMap</span><span class="p">,</span> <span class="n">SsAaAtmMap</span><span class="p">)</span>
+<span class="kn">from</span> <span class="nn">mako.template</span> <span class="k">import</span> <span class="n">Template</span>
+<span class="kn">from</span> <span class="nn">aria.Molecule</span> <span class="k">import</span> <span class="n">Molecule</span>
+<span class="kn">from</span> <span class="nn">aria.tools</span> <span class="k">import</span> <span class="n">string_to_segid</span>
+<span class="kn">from</span> <span class="nn">aria.AriaXML</span> <span class="k">import</span> <span class="n">AriaXMLPickler</span>
+<span class="kn">from</span> <span class="nn">aria.PDBReader</span> <span class="k">import</span> <span class="n">PDBReader</span>
+<span class="kn">from</span> <span class="nn">aria.ConversionTable</span> <span class="k">import</span> <span class="n">ConversionTable</span>
+<span class="kn">from</span> <span class="nn">future.utils</span> <span class="k">import</span> <span class="n">iteritems</span>
+<span class="kn">from</span> <span class="nn">aria.conversion</span> <span class="k">import</span> <span class="n">Converter</span><span class="p">,</span> <span class="n">SequenceList</span><span class="p">,</span> <span class="n">MoleculeSettings</span>
+<span class="kn">from</span> <span class="nn">aria.DataContainer</span> <span class="k">import</span> <span class="n">DATA_TYPES</span><span class="p">,</span> <span class="n">DATA_SEQUENCE</span><span class="p">,</span> <span class="n">DATA_RDCS</span><span class="p">,</span> \
+ <span class="n">DATA_ANNEALING_RDC</span>
+
+<span class="n">LOG</span> <span class="o">=</span> <span class="n">logging</span><span class="o">.</span><span class="n">getLogger</span><span class="p">(</span><span class="vm">__name__</span><span class="p">)</span>
+
+
+<div class="viewcode-block" id="AriaEcBbConverter"><a class="viewcode-back" href="../../ariaec.html#ariaec.converter.AriaEcBbConverter">[docs]</a><span class="k">class</span> <span class="nc">AriaEcBbConverter</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span>
+ <span class="sd">"""Bbcontacts convert main class"""</span>
+
+ <span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">settings</span><span class="p">):</span>
+ <span class="c1"># TODO: check_type settings (AriaEcSettings)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">settings</span> <span class="o">=</span> <span class="n">settings</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">protein</span> <span class="o">=</span> <span class="n">Protein</span><span class="p">(</span><span class="n">settings</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">reader</span> <span class="o">=</span> <span class="n">MapFileListReader</span><span class="p">()</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">outprefix</span> <span class="o">=</span> <span class="s1">''</span>
+
+<div class="viewcode-block" id="AriaEcBbConverter.run"><a class="viewcode-back" href="../../ariaec.html#ariaec.converter.AriaEcBbConverter.run">[docs]</a> <span class="k">def</span> <span class="nf">run</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="sd">"""BBConverter command"""</span>
+ <span class="c1"># Check input</span>
+ <span class="sd">"""</span>
+<span class="sd"> main method</span>
+<span class="sd"> """</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="s2">"Settings:</span><span class="se">\n</span><span class="s2">"</span> <span class="o">+</span> <span class="n">json</span><span class="o">.</span><span class="n">dumps</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">setup</span><span class="o">.</span><span class="n">config</span><span class="p">,</span>
+ <span class="n">indent</span><span class="o">=</span><span class="mi">4</span><span class="p">))</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="s2">"Args:</span><span class="se">\n</span><span class="s2">"</span> <span class="o">+</span> <span class="n">json</span><span class="o">.</span><span class="n">dumps</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">setup</span><span class="o">.</span><span class="n">args</span><span class="p">,</span>
+ <span class="n">indent</span><span class="o">=</span><span class="mi">4</span><span class="p">))</span>
+ <span class="c1"># TODO: redirect print output to logging ? (low priority)</span>
+ <span class="c1"># ----------------------------- Input -------------------------------- #</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">outprefix</span> <span class="o">=</span> <span class="n">get_filename</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">bbconv</span><span class="o">.</span><span class="n">args</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"seq"</span><span class="p">,</span>
+ <span class="kc">None</span><span class="p">))</span>
+ <span class="c1"># Load Sequence file</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">protein</span><span class="o">.</span><span class="n">set_aa_sequence</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">bbconv</span><span class="o">.</span><span class="n">args</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"seq"</span><span class="p">,</span> <span class="kc">None</span><span class="p">))</span>
+ <span class="c1"># Load secondary structure prediction file</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">protein</span><span class="o">.</span><span class="n">set_sec_struct</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">bbconv</span><span class="o">.</span><span class="n">args</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"sspred"</span><span class="p">,</span>
+ <span class="kc">None</span><span class="p">))</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">reader</span><span class="o">.</span><span class="n">read</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">bbconv</span><span class="o">.</span><span class="n">args</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"contactfile"</span><span class="p">),</span>
+ <span class="n">maptypes</span><span class="o">=</span><span class="p">[</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">bbconv</span><span class="o">.</span><span class="n">args</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"contact_type"</span><span class="p">)],</span>
+ <span class="n">protein</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">protein</span><span class="p">,</span>
+ <span class="n">groupby_method</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">setup</span><span class="o">.</span><span class="n">config</span><span class="p">[</span>
+ <span class="s1">'groupby_method'</span><span class="p">],</span>
+ <span class="n">scsc</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">scsc_min</span><span class="p">)</span>
+ <span class="c1"># ---------------------------- Processing ---------------------------- #</span>
+ <span class="c1"># Convert contacts into couplingmatrix file (CCMPred format)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">reader</span><span class="o">.</span><span class="n">maps</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">mapdict</span><span class="p">[</span><span class="s2">"scoremap"</span><span class="p">]</span><span class="o">.</span><span class="n">to_csv</span><span class="p">(</span>
+ <span class="s2">"</span><span class="si">%s</span><span class="s2">/</span><span class="si">%s</span><span class="s2">.mat"</span> <span class="o">%</span> <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">outdir</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">outprefix</span><span class="p">),</span>
+ <span class="n">index</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span> <span class="n">header</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span> <span class="n">sep</span><span class="o">=</span><span class="s2">"</span><span class="se">\t</span><span class="s2">"</span><span class="p">,</span> <span class="n">float_format</span><span class="o">=</span><span class="s2">"</span><span class="si">%13.10f</span><span class="s2">"</span><span class="p">)</span>
+
+ <span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">bbconv</span><span class="o">.</span><span class="n">config</span><span class="p">[</span><span class="s1">'couplingmatrix'</span><span class="p">]</span> <span class="o">=</span> <span class="s2">"</span><span class="si">%s</span><span class="s2">/</span><span class="si">%s</span><span class="s2">.mat"</span> <span class="o">%</span> <span class="p">(</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">outdir</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">outprefix</span><span class="p">)</span>
+ <span class="c1"># Convert psipred format (fasta-like)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">protein</span><span class="o">.</span><span class="n">sec_struct</span><span class="o">.</span><span class="n">write_ssfasta</span><span class="p">(</span><span class="s2">"</span><span class="si">%s</span><span class="s2">/</span><span class="si">%s</span><span class="s2">.psipred"</span> <span class="o">%</span> <span class="p">(</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">outdir</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">outprefix</span><span class="p">),</span> <span class="n">desc</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">outprefix</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">bbconv</span><span class="o">.</span><span class="n">config</span><span class="p">[</span><span class="s1">'psipredfile'</span><span class="p">]</span> <span class="o">=</span> <span class="s2">"</span><span class="si">%s</span><span class="s2">/</span><span class="si">%s</span><span class="s2">.psipred"</span> <span class="o">%</span> <span class="p">(</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">outdir</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">outprefix</span><span class="p">)</span>
+ <span class="c1"># Compute diversityvalue</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">bbconv</span><span class="o">.</span><span class="n">config</span><span class="p">[</span><span class="s1">'diversityvalue'</span><span class="p">]</span> <span class="o">=</span> \
+ <span class="bp">self</span><span class="o">.</span><span class="n">compute_diversityvalue</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">bbconv</span><span class="o">.</span><span class="n">args</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"msa"</span><span class="p">),</span>
+ <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">protein</span><span class="o">.</span><span class="n">aa_sequence</span><span class="o">.</span><span class="n">sequence</span><span class="p">))</span>
+ <span class="c1"># Generate .ini file with bbconv options (input args for bbcontacts)</span>
+ <span class="c1"># TODO: Generate with only bbconv option !</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">write_config</span><span class="p">(</span><span class="s2">"</span><span class="si">%s</span><span class="s2">/</span><span class="si">%s</span><span class="s2">_bbconv.ini"</span> <span class="o">%</span> <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">outdir</span><span class="p">,</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">outprefix</span><span class="p">))</span></div>
+
+<div class="viewcode-block" id="AriaEcBbConverter.compute_diversityvalue"><a class="viewcode-back" href="../../ariaec.html#ariaec.converter.AriaEcBbConverter.compute_diversityvalue">[docs]</a> <span class="nd">@staticmethod</span>
+ <span class="k">def</span> <span class="nf">compute_diversityvalue</span><span class="p">(</span><span class="n">msa</span><span class="p">,</span> <span class="n">seqlen</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Compute bbcontacts diversity value</span>
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> msa : `str`</span>
+<span class="sd"> multiple sequence alignment file path</span>
+<span class="sd"> seqlen : `int`</span>
+<span class="sd"> protein sequence length</span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+<span class="sd"> diversity_score : `float`</span>
+<span class="sd"> </span>
+
+<span class="sd"> Notes</span>
+<span class="sd"> -----</span>
+<span class="sd"> Diversity score correspond to the square root of the multiple</span>
+<span class="sd"> sequence alignment length (:math:`m`) over the length of the protein</span>
+<span class="sd"> sequence (:math:`l`)</span>
+<span class="sd"> </span>
+<span class="sd"> .. math:: Divscore = \frac{\sqrt{m}}{l}</span>
+<span class="sd"> """</span>
+ <span class="n">msa_reg</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span><span class="sa">r</span><span class="s2">"^>[A-Za-z0-9]+_[A-Za-z0-9]+"</span><span class="p">)</span>
+ <span class="n">msalen</span> <span class="o">=</span> <span class="mi">0</span>
+
+ <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">msa</span><span class="p">)</span> <span class="k">as</span> <span class="n">msafile</span><span class="p">:</span>
+ <span class="k">for</span> <span class="n">line</span> <span class="ow">in</span> <span class="n">msafile</span><span class="p">:</span>
+ <span class="n">match</span> <span class="o">=</span> <span class="n">msa_reg</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="n">line</span><span class="p">)</span>
+ <span class="k">if</span> <span class="n">match</span> <span class="ow">and</span> <span class="s2">"deselect"</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">line</span><span class="p">:</span>
+ <span class="n">msalen</span> <span class="o">+=</span> <span class="mi">1</span>
+
+ <span class="k">return</span> <span class="n">math</span><span class="o">.</span><span class="n">sqrt</span><span class="p">(</span><span class="n">msalen</span><span class="p">)</span> <span class="o">/</span> <span class="nb">float</span><span class="p">(</span><span class="n">seqlen</span><span class="p">)</span></div></div>
+
+
+<div class="viewcode-block" id="AriaXMLConverter"><a class="viewcode-back" href="../../ariaec.html#ariaec.converter.AriaXMLConverter">[docs]</a><span class="k">class</span> <span class="nc">AriaXMLConverter</span><span class="p">(</span><span class="n">Converter</span><span class="p">,</span> <span class="nb">object</span><span class="p">):</span>
+ <span class="sd">"""XML converter for aria files"""</span>
+
+ <span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">settings</span><span class="p">):</span>
+ <span class="n">Converter</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_mol_set</span> <span class="o">=</span> <span class="n">MoleculeSettings</span><span class="p">()</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_pickler</span> <span class="o">=</span> <span class="n">AriaXMLPickler</span><span class="p">()</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_molecule</span> <span class="o">=</span> <span class="kc">None</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_upflag</span> <span class="o">=</span> <span class="kc">False</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">outprefix</span> <span class="o">=</span> <span class="s2">""</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">settings</span> <span class="o">=</span> <span class="n">settings</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">structure</span> <span class="o">=</span> <span class="kc">None</span>
+
+ <span class="nd">@property</span>
+ <span class="k">def</span> <span class="nf">molecule</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> aria.Molecule.Molecule object or None. If a structure has been loaded,</span>
+<span class="sd"> use it to update the molecule</span>
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+<span class="sd"> </span>
+<span class="sd"> """</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">structure</span> <span class="ow">and</span> <span class="bp">self</span><span class="o">.</span><span class="n">_molecule</span> <span class="ow">and</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">_upflag</span><span class="p">:</span>
+ <span class="c1"># update self._molecule with self.structure</span>
+ <span class="c1"># change value of self._upflag</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">upd_mol</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_molecule</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">structure</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_upflag</span> <span class="o">=</span> <span class="kc">True</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_molecule</span>
+
+<div class="viewcode-block" id="AriaXMLConverter.upd_mol"><a class="viewcode-back" href="../../ariaec.html#ariaec.converter.AriaXMLConverter.upd_mol">[docs]</a> <span class="nd">@staticmethod</span>
+ <span class="k">def</span> <span class="nf">upd_mol</span><span class="p">(</span><span class="n">molecule</span><span class="p">,</span> <span class="n">structure</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Update molecule object according to pdb structure</span>
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> molecule :</span>
+<span class="sd"> </span>
+<span class="sd"> structure :</span>
+<span class="sd"> </span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+<span class="sd"> </span>
+<span class="sd"> """</span>
+ <span class="c1"># Check if pdb structure is in the same format as molecule</span>
+ <span class="c1"># Loop over pdb structure and update/remove atoms in molecule chains (cf</span>
+ <span class="c1"># aria molecule and chain methods</span>
+ <span class="c1"># TODO</span>
+ <span class="k">pass</span></div>
+
+<div class="viewcode-block" id="AriaXMLConverter.read_seq"><a class="viewcode-back" href="../../ariaec.html#ariaec.converter.AriaXMLConverter.read_seq">[docs]</a> <span class="k">def</span> <span class="nf">read_seq</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">seqpath</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Load aria Molecule object from seq file</span>
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> seqpath :</span>
+<span class="sd"> </span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+<span class="sd"> </span>
+<span class="sd"> """</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_mol_set</span><span class="p">[</span><span class="s1">'format'</span><span class="p">]</span> <span class="o">=</span> <span class="s1">'seq'</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_mol_set</span><span class="p">[</span><span class="s1">'input'</span><span class="p">]</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">abspath</span><span class="p">(</span><span class="nb">str</span><span class="p">(</span><span class="n">seqpath</span><span class="p">))</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_mol_set</span><span class="p">[</span><span class="s1">'output'</span><span class="p">]</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">infra</span><span class="p">[</span><span class="s2">"xml"</span><span class="p">],</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">outprefix</span> <span class="o">+</span> <span class="s2">".xml"</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_mol_set</span><span class="p">[</span><span class="s1">'type'</span><span class="p">]</span> <span class="o">=</span> <span class="s1">'PROTEIN'</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_mol_set</span><span class="p">[</span><span class="s1">'segid'</span><span class="p">]</span> <span class="o">=</span> <span class="s1">' A'</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_mol_set</span><span class="p">[</span><span class="s1">'first_residue_number'</span><span class="p">]</span> <span class="o">=</span> <span class="mi">1</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_mol_set</span><span class="p">[</span><span class="s1">'naming_convention'</span><span class="p">]</span> <span class="o">=</span> <span class="s1">''</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_mol_set</span><span class="p">[</span><span class="s1">'name'</span><span class="p">]</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">outprefix</span>
+
+ <span class="n">segids</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_mol_set</span><span class="p">[</span><span class="s1">'segid'</span><span class="p">]</span>
+ <span class="n">segids</span> <span class="o">=</span> <span class="n">segids</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">'/'</span><span class="p">)</span>
+
+ <span class="n">segids</span> <span class="o">=</span> <span class="p">[</span><span class="n">string_to_segid</span><span class="p">(</span><span class="n">segid</span><span class="p">)</span> <span class="k">for</span> <span class="n">segid</span> <span class="ow">in</span> <span class="n">segids</span><span class="p">]</span>
+ <span class="c1"># Fetch molecule</span>
+ <span class="n">chain_types</span> <span class="o">=</span> <span class="p">{}</span>
+ <span class="k">for</span> <span class="n">segid</span> <span class="ow">in</span> <span class="n">segids</span><span class="p">:</span>
+ <span class="n">chain_types</span><span class="p">[</span><span class="n">segid</span><span class="p">]</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_mol_set</span><span class="p">[</span><span class="s1">'type'</span><span class="p">]</span>
+
+ <span class="n">sequence</span> <span class="o">=</span> <span class="n">SequenceList</span><span class="p">(</span><span class="n">chain_types</span><span class="p">,</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_mol_set</span><span class="p">[</span><span class="s1">'first_residue_number'</span><span class="p">])</span>
+
+ <span class="c1"># with Capturing() as output:</span>
+ <span class="c1"># Initialize SequenceList object with seq file</span>
+ <span class="n">sequence</span><span class="o">.</span><span class="n">parse</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_mol_set</span><span class="p">[</span><span class="s1">'input'</span><span class="p">],</span> <span class="bp">self</span><span class="o">.</span><span class="n">_mol_set</span><span class="p">[</span><span class="s1">'format'</span><span class="p">],</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_mol_set</span><span class="p">[</span><span class="s1">'naming_convention'</span><span class="p">])</span>
+
+ <span class="c1"># LOG.info("\n" + "".join(output))</span>
+
+ <span class="c1"># Initialize aria Atom factory</span>
+ <span class="n">factory</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">create_factory</span><span class="p">()</span>
+
+ <span class="n">factory</span><span class="o">.</span><span class="n">reset</span><span class="p">()</span>
+ <span class="n">factory</span><span class="o">.</span><span class="n">unfreeze</span><span class="p">()</span>
+
+ <span class="c1"># Create chains in SequenceList object with aria atom factory</span>
+ <span class="n">chains</span> <span class="o">=</span> <span class="n">sequence</span><span class="o">.</span><span class="n">create_chains</span><span class="p">(</span><span class="n">factory</span><span class="p">)</span>
+
+ <span class="c1"># Instantiate aria molecule object</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_molecule</span> <span class="o">=</span> <span class="n">Molecule</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_mol_set</span><span class="p">[</span><span class="s1">'name'</span><span class="p">])</span>
+ <span class="k">for</span> <span class="n">segid</span> <span class="ow">in</span> <span class="n">segids</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">molecule</span><span class="o">.</span><span class="n">add_chain</span><span class="p">(</span><span class="n">chains</span><span class="p">[</span><span class="n">segid</span><span class="p">])</span></div>
+
+<div class="viewcode-block" id="AriaXMLConverter.read_pdb"><a class="viewcode-back" href="../../ariaec.html#ariaec.converter.AriaXMLConverter.read_pdb">[docs]</a> <span class="k">def</span> <span class="nf">read_pdb</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">pdbpath</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> </span>
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> pdbpath :</span>
+<span class="sd"> </span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+<span class="sd"> </span>
+<span class="sd"> """</span>
+ <span class="c1"># read pdb file with aria pdb reader and load it in self.structure</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">structure</span> <span class="o">=</span> <span class="n">PDBReader</span><span class="p">()</span><span class="o">.</span><span class="n">read</span><span class="p">(</span><span class="n">pdbpath</span><span class="p">)</span></div>
+
+<div class="viewcode-block" id="AriaXMLConverter.write_xmlseq"><a class="viewcode-back" href="../../ariaec.html#ariaec.converter.AriaXMLConverter.write_xmlseq">[docs]</a> <span class="k">def</span> <span class="nf">write_xmlseq</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="sd">"""Use aria xml pickler to generate xml molecule file"""</span>
+
+ <span class="k">try</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_pickler</span><span class="o">.</span><span class="n">dump</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">molecule</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">_mol_set</span><span class="p">[</span><span class="s1">'output'</span><span class="p">])</span>
+
+ <span class="k">except</span> <span class="ne">Exception</span> <span class="k">as</span> <span class="n">msg</span><span class="p">:</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">critical</span><span class="p">(</span><span class="s2">"Error for writing xml seq file </span><span class="si">%s</span><span class="s2">: </span><span class="si">%s</span><span class="s2">"</span><span class="p">,</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_mol_set</span><span class="p">[</span><span class="s1">'output'</span><span class="p">],</span> <span class="n">msg</span><span class="p">)</span>
+ <span class="k">raise</span>
+
+ <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_mol_set</span><span class="p">[</span><span class="s1">'output'</span><span class="p">]</span></div>
+
+<div class="viewcode-block" id="AriaXMLConverter.deff"><a class="viewcode-back" href="../../ariaec.html#ariaec.converter.AriaXMLConverter.deff">[docs]</a> <span class="nd">@staticmethod</span>
+ <span class="k">def</span> <span class="nf">deff</span><span class="p">(</span><span class="n">atm_dists</span><span class="p">,</span> <span class="n">dpow</span><span class="o">=</span><span class="mi">6</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Compute aria effective distance from input distances</span>
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> atm_dists : list</span>
+<span class="sd"> list of atm-atm distances</span>
+<span class="sd"> dpow : int</span>
+<span class="sd"> effective distance exponant (Default value = 6)</span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+<span class="sd"> </span>
+<span class="sd"> """</span>
+ <span class="k">return</span> <span class="n">math</span><span class="o">.</span><span class="n">pow</span><span class="p">(</span><span class="nb">sum</span><span class="p">([</span><span class="n">math</span><span class="o">.</span><span class="n">pow</span><span class="p">(</span><span class="n">x</span><span class="p">,</span> <span class="o">-</span><span class="nb">int</span><span class="p">(</span><span class="n">dpow</span><span class="p">))</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span>
+ <span class="n">atm_dists</span><span class="p">]),</span> <span class="o">-</span><span class="mi">1</span> <span class="o">/</span> <span class="mi">6</span><span class="p">)</span></div>
+
+ <span class="c1"># TODO: should define distance restraints in a class, not a dict</span>
+ <span class="c1"># TODO: Use mako</span>
+<div class="viewcode-block" id="AriaXMLConverter.write_dist_xml"><a class="viewcode-back" href="../../ariaec.html#ariaec.converter.AriaXMLConverter.write_dist_xml">[docs]</a> <span class="nd">@staticmethod</span>
+ <span class="k">def</span> <span class="nf">write_dist_xml</span><span class="p">(</span><span class="n">dist_restraints</span><span class="p">,</span> <span class="n">outfile</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Write aria distance restraint xml file</span>
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> dist_restraints :</span>
+<span class="sd"> </span>
+<span class="sd"> outfile :</span>
+<span class="sd"> </span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+<span class="sd"> </span>
+<span class="sd"> """</span>
+ <span class="n">xml_file</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="n">outfile</span><span class="p">,</span> <span class="s2">"w"</span><span class="p">)</span>
+ <span class="n">xml_file</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s1">'''</span><span class="se">\</span>
+<span class="s1"><!DOCTYPE distance_restraint_list SYSTEM "distance_restraint1.0.dtd"></span>
+<span class="s1"><distance_restraint_list></span>
+<span class="s1">'''</span><span class="p">)</span>
+ <span class="c1"># Pour chaque contrainte</span>
+ <span class="c1"># Pour chaque contribution</span>
+ <span class="k">for</span> <span class="n">restraint_id</span> <span class="ow">in</span> <span class="n">dist_restraints</span><span class="p">:</span>
+ <span class="n">restraint</span> <span class="o">=</span> <span class="p">{</span>
+ <span class="s1">'rest_id'</span><span class="p">:</span> <span class="n">restraint_id</span><span class="p">,</span>
+ <span class="s1">'rest_weight'</span><span class="p">:</span> <span class="n">dist_restraints</span><span class="p">[</span><span class="n">restraint_id</span><span class="p">][</span><span class="s2">"meta"</span><span class="p">][</span><span class="s2">"weight"</span><span class="p">],</span>
+ <span class="s1">'rest_dist'</span><span class="p">:</span> <span class="nb">float</span><span class="p">(</span>
+ <span class="n">dist_restraints</span><span class="p">[</span><span class="n">restraint_id</span><span class="p">][</span><span class="s2">"meta"</span><span class="p">][</span><span class="s2">"distance"</span><span class="p">]),</span>
+ <span class="s1">'lower_bound'</span><span class="p">:</span> <span class="nb">float</span><span class="p">(</span>
+ <span class="n">dist_restraints</span><span class="p">[</span><span class="n">restraint_id</span><span class="p">][</span><span class="s2">"meta"</span><span class="p">][</span><span class="s2">"lower_bound"</span><span class="p">]),</span>
+ <span class="s1">'upper_bound'</span><span class="p">:</span> <span class="nb">float</span><span class="p">(</span>
+ <span class="n">dist_restraints</span><span class="p">[</span><span class="n">restraint_id</span><span class="p">][</span><span class="s2">"meta"</span><span class="p">][</span><span class="s2">"upper_bound"</span><span class="p">]),</span>
+ <span class="s1">'reliable'</span><span class="p">:</span> <span class="n">dist_restraints</span><span class="p">[</span><span class="n">restraint_id</span><span class="p">][</span><span class="s2">"meta"</span><span class="p">][</span><span class="s2">"reliable"</span><span class="p">],</span>
+ <span class="s1">'list_name'</span><span class="p">:</span> <span class="n">dist_restraints</span><span class="p">[</span><span class="n">restraint_id</span><span class="p">][</span><span class="s2">"meta"</span><span class="p">][</span><span class="s2">"list_name"</span><span class="p">]</span>
+ <span class="p">}</span>
+ <span class="n">xml_file</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s1">'''</span><span class="se">\</span>
+<span class="s1"> <restraint id="</span><span class="si">{rest_id}</span><span class="s1">" weight="</span><span class="si">{rest_weight:.1f}</span><span class="s1">" distance="</span><span class="si">{rest_dist:.1f}</span><span class="s1">" </span><span class="se">\</span>
+<span class="s1">lower_bound="</span><span class="si">{lower_bound:.1f}</span><span class="s1">" upper_bound="</span><span class="si">{upper_bound:.1f}</span><span class="s1">" active="1" </span><span class="se">\</span>
+<span class="s1">reliable="</span><span class="si">{reliable}</span><span class="s1">" list_name="</span><span class="si">{list_name}</span><span class="s1">"></span>
+<span class="s1">'''</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="o">**</span><span class="n">restraint</span><span class="p">))</span>
+ <span class="k">for</span> <span class="n">contrib_id</span> <span class="ow">in</span> <span class="n">dist_restraints</span><span class="p">[</span><span class="n">restraint_id</span><span class="p">][</span><span class="s2">"contrib"</span><span class="p">]:</span>
+ <span class="n">res_id</span> <span class="o">=</span> <span class="n">dist_restraints</span><span class="p">[</span><span class="n">restraint_id</span><span class="p">][</span><span class="s2">"contrib"</span><span class="p">][</span><span class="n">contrib_id</span><span class="p">][</span>
+ <span class="s2">"spin_pair"</span><span class="p">]</span><span class="o">.</span><span class="n">keys</span><span class="p">()</span>
+ <span class="c1"># TODO: Get segids from molecule file instead</span>
+ <span class="n">segids</span> <span class="o">=</span> <span class="n">dist_restraints</span><span class="p">[</span><span class="n">restraint_id</span><span class="p">][</span><span class="s2">"contrib"</span><span class="p">][</span><span class="n">contrib_id</span><span class="p">][</span>
+ <span class="s2">"meta"</span><span class="p">]</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"segids"</span><span class="p">)</span>
+ <span class="n">segid1</span> <span class="o">=</span> <span class="n">segids</span><span class="p">[</span><span class="n">res_id</span><span class="p">[</span><span class="mi">0</span><span class="p">]]</span> <span class="k">if</span> <span class="n">segids</span> <span class="k">else</span> <span class="s2">" A"</span>
+ <span class="n">segid2</span> <span class="o">=</span> <span class="n">segids</span><span class="p">[</span><span class="n">res_id</span><span class="p">[</span><span class="mi">1</span><span class="p">]]</span> <span class="k">if</span> <span class="n">segids</span> <span class="k">else</span> <span class="s2">" A"</span>
+ <span class="n">xml_file</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s1">'''</span><span class="se">\</span>
+<span class="s1"> <contribution id="</span><span class="si">{id}</span><span class="s1">" weight="</span><span class="si">{weight:.8f}</span><span class="s1">"></span>
+<span class="s1"> <spin_pair></span>
+<span class="s1"> <atom segid="</span><span class="si">{res1_segid}</span><span class="s1">" residue="</span><span class="si">{res1_pos}</span><span class="s1">" name="</span><span class="si">{atm1_name}</span><span class="s1">"/></span>
+<span class="s1"> <atom segid="</span><span class="si">{res2_segid}</span><span class="s1">" residue="</span><span class="si">{res2_pos}</span><span class="s1">" name="</span><span class="si">{atm2_name}</span><span class="s1">"/></span>
+<span class="s1"> </spin_pair></span>
+<span class="s1"> </contribution></span>
+<span class="s1">'''</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="nb">id</span><span class="o">=</span><span class="n">contrib_id</span><span class="p">,</span> <span class="n">res1_segid</span><span class="o">=</span><span class="n">segid1</span><span class="p">,</span> <span class="n">res2_segid</span><span class="o">=</span><span class="n">segid2</span><span class="p">,</span>
+ <span class="n">weight</span><span class="o">=</span><span class="n">dist_restraints</span><span class="p">[</span><span class="n">restraint_id</span><span class="p">][</span><span class="s2">"contrib"</span><span class="p">][</span><span class="n">contrib_id</span><span class="p">][</span><span class="s2">"meta"</span><span class="p">][</span>
+ <span class="s2">"weight"</span><span class="p">],</span>
+ <span class="n">res1_pos</span><span class="o">=</span><span class="n">res_id</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">res2_pos</span><span class="o">=</span><span class="n">res_id</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span>
+ <span class="n">atm1_name</span><span class="o">=</span><span class="n">dist_restraints</span><span class="p">[</span><span class="n">restraint_id</span><span class="p">][</span><span class="s2">"contrib"</span><span class="p">][</span><span class="n">contrib_id</span><span class="p">][</span>
+ <span class="s2">"spin_pair"</span><span class="p">][</span><span class="n">res_id</span><span class="p">[</span><span class="mi">0</span><span class="p">]],</span>
+ <span class="n">atm2_name</span><span class="o">=</span><span class="n">dist_restraints</span><span class="p">[</span><span class="n">restraint_id</span><span class="p">][</span><span class="s2">"contrib"</span><span class="p">][</span><span class="n">contrib_id</span><span class="p">][</span>
+ <span class="s2">"spin_pair"</span><span class="p">][</span><span class="n">res_id</span><span class="p">[</span><span class="mi">1</span><span class="p">]]))</span>
+ <span class="n">xml_file</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s1">'''</span><span class="se">\</span>
+<span class="s1"> </restraint></span>
+<span class="s1">'''</span><span class="p">)</span>
+ <span class="n">xml_file</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s1">'''</span><span class="se">\</span>
+<span class="s1"></distance_restraint_list></span>
+<span class="s1">'''</span><span class="p">)</span></div>
+
+ <span class="nd">@staticmethod</span>
+ <span class="k">def</span> <span class="nf">_write_helix_hb_tbl</span><span class="p">(</span><span class="n">sec_struct</span><span class="p">,</span> <span class="n">outfile</span><span class="p">,</span> <span class="n">dminus</span><span class="p">,</span> <span class="n">dplus</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> </span>
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> sec_struct :</span>
+<span class="sd"> </span>
+<span class="sd"> outfile :</span>
+<span class="sd"> </span>
+<span class="sd"> dminus :</span>
+<span class="sd"> </span>
+<span class="sd"> dplus :</span>
+<span class="sd"> </span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+<span class="sd"> </span>
+<span class="sd"> """</span>
+ <span class="n">outfile</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">"! Short range Hbond list (Alpha helix)"</span><span class="p">)</span>
+ <span class="k">for</span> <span class="n">idx</span><span class="p">,</span> <span class="n">secstr</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">sec_struct</span><span class="p">):</span>
+ <span class="k">if</span> <span class="p">(</span><span class="n">idx</span> <span class="o">+</span> <span class="mi">4</span><span class="p">)</span> <span class="o"><</span> <span class="nb">len</span><span class="p">(</span><span class="n">sec_struct</span><span class="p">):</span>
+ <span class="k">if</span> <span class="s1">'H'</span> <span class="ow">in</span> <span class="n">secstr</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="ow">and</span> <span class="s1">'H'</span> <span class="ow">in</span> <span class="n">sec_struct</span><span class="p">[</span><span class="n">idx</span> <span class="o">+</span> <span class="mi">4</span><span class="p">][</span><span class="mi">2</span><span class="p">]:</span>
+ <span class="c1"># Si residus dans helice</span>
+ <span class="n">res1</span> <span class="o">=</span> <span class="n">idx</span> <span class="o">+</span> <span class="mi">1</span>
+ <span class="n">res2</span> <span class="o">=</span> <span class="n">idx</span> <span class="o">+</span> <span class="mi">5</span>
+ <span class="n">outfile</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s1">'''</span><span class="se">\</span>
+<span class="s1">assign (resid </span><span class="si">{res1}</span><span class="s1"> and name o) (resid </span><span class="si">{res2}</span><span class="s1"> and name n) 2.8 </span><span class="si">{dminus}</span><span class="s1"> </span><span class="si">{dplus}</span><span class="s1"></span>
+<span class="s1">assign (resid </span><span class="si">{res1}</span><span class="s1"> and name o) (resid </span><span class="si">{res2}</span><span class="s1"> and name hn) 1.8 </span><span class="si">{dminus}</span><span class="s1"> </span><span class="si">{dplus}</span><span class="s1"></span>
+<span class="s1">'''</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">res1</span><span class="o">=</span><span class="n">res1</span><span class="p">,</span> <span class="n">res2</span><span class="o">=</span><span class="n">res2</span><span class="p">,</span> <span class="n">dminus</span><span class="o">=</span><span class="n">dminus</span><span class="p">,</span> <span class="n">dplus</span><span class="o">=</span><span class="n">dplus</span><span class="p">))</span>
+
+ <span class="nd">@staticmethod</span>
+ <span class="k">def</span> <span class="nf">_write_hbmap_tbl</span><span class="p">(</span><span class="n">hbmap</span><span class="p">,</span> <span class="n">outfile</span><span class="p">,</span> <span class="n">dminus</span><span class="p">,</span> <span class="n">dplus</span><span class="p">,</span> <span class="n">n_hb</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
+ <span class="n">hb_type</span><span class="o">=</span><span class="s2">"main"</span><span class="p">,</span> <span class="n">topo</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Build hbdond distance restraints from a res-res contact map. Tbl</span>
+<span class="sd"> restraints generated use pseudoatoms since we assume we don't know</span>
+<span class="sd"> which donnor/acceptor are involved.</span>
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> hbmap :</span>
+<span class="sd"> Hbond contact map with first humanidx = ['donor',</span>
+<span class="sd"> 'acceptor'] => Non symetric matrix !!!</span>
+<span class="sd"> outfile :</span>
+<span class="sd"> param dminus:</span>
+<span class="sd"> dplus :</span>
+<span class="sd"> param n_hb:</span>
+<span class="sd"> hb_type :</span>
+<span class="sd"> Long range hbond type (Default value = "main")</span>
+<span class="sd"> dminus :</span>
+<span class="sd"> </span>
+<span class="sd"> n_hb :</span>
+<span class="sd"> (Default value = None)</span>
+<span class="sd"> topo :</span>
+<span class="sd"> (Default value = None)</span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+<span class="sd"> </span>
+<span class="sd"> """</span>
+ <span class="c1"># TODO: test with several deviation since these restraints should</span>
+ <span class="c1"># contain noise !!</span>
+ <span class="c1"># Parcourt la matrice de contact</span>
+ <span class="n">outfile</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s1">'''</span><span class="se">\</span>
+<span class="s1">! Long range Hbond list (beta sheet)</span>
+<span class="s1">'''</span><span class="p">)</span>
+ <span class="n">contacts</span> <span class="o">=</span> <span class="n">hbmap</span><span class="p">[</span><span class="s2">"scoremap"</span><span class="p">]</span><span class="o">.</span><span class="n">sortedset</span><span class="p">(</span><span class="n">human_idx</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
+ <span class="c1"># distmap = hbmap.get("distmap")</span>
+ <span class="k">if</span> <span class="n">n_hb</span><span class="p">:</span>
+ <span class="n">contacts</span> <span class="o">=</span> <span class="n">contacts</span><span class="p">[:</span><span class="n">n_hb</span><span class="p">]</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="n">contacts</span><span class="p">)</span>
+ <span class="n">donors</span> <span class="o">=</span> <span class="p">[]</span>
+ <span class="n">acces</span> <span class="o">=</span> <span class="p">[]</span>
+ <span class="k">for</span> <span class="n">contact</span> <span class="ow">in</span> <span class="n">contacts</span><span class="p">:</span>
+ <span class="c1"># The first residu represent the hydrogen bond donor and the</span>
+ <span class="c1"># second residu represent the hydrogen bond acceptor</span>
+ <span class="n">res1</span><span class="p">,</span> <span class="n">res2</span> <span class="o">=</span> <span class="n">contact</span>
+ <span class="k">if</span> <span class="n">res1</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">donors</span> <span class="o">+</span> <span class="n">acces</span> <span class="ow">and</span> <span class="n">res2</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">donors</span> <span class="o">+</span> <span class="n">acces</span><span class="p">:</span>
+ <span class="c1"># Add only if new donor and new acces don't belong to</span>
+ <span class="c1"># previous hbond restraints</span>
+ <span class="n">donors</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">res1</span><span class="p">)</span>
+ <span class="n">acces</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">res2</span><span class="p">)</span>
+ <span class="c1"># residx1, residx2 = int(res1) - 1, int(res2) - 1</span>
+ <span class="c1"># TODO: find a way to use dist</span>
+ <span class="c1"># dist = distmap.iat[(residx1, residx2)]</span>
+ <span class="k">if</span> <span class="n">hb_type</span> <span class="o">==</span> <span class="s2">"all"</span><span class="p">:</span>
+ <span class="c1"># This method is deprecated seems it should add noise ...</span>
+ <span class="c1"># if topo:</span>
+ <span class="c1"># print(topo)</span>
+ <span class="c1"># print(res1, res2)</span>
+ <span class="c1"># print(topo[residx1][1]['dono'])</span>
+ <span class="c1"># print(topo[residx2][1]['acce'])</span>
+ <span class="c1"># print([x[0] for x in topo])</span>
+ <span class="c1"># print(hbmap['maplot'].sequence[residx1])</span>
+ <span class="c1"># print(hbmap['maplot'].sequence[residx2])</span>
+ <span class="c1"># print(distmap.index[residx2])</span>
+ <span class="c1"># print(dist)</span>
+ <span class="c1"># print(hbmap["scoremap"])</span>
+ <span class="c1"># Get all donor from cns topology file and make group atom/pseudoatm</span>
+ <span class="c1"># Get all acceptor from cns topology file</span>
+ <span class="c1"># !!!! Ignore case flag !!!!!</span>
+ <span class="k">raise</span> <span class="ne">NotImplementedError</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">if</span> <span class="n">hb_type</span> <span class="o">!=</span> <span class="s2">"main"</span><span class="p">:</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">error</span><span class="p">(</span><span class="s2">"Wrong longrange hbond type given. Default "</span>
+ <span class="s2">"option used (main)"</span><span class="p">)</span>
+ <span class="c1"># First residue = donor for a backbone hydrogen bond (N-H...O=C)</span>
+ <span class="n">outfile</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s1">'''</span><span class="se">\</span>
+<span class="s1"> assign (resid </span><span class="si">{res1}</span><span class="s1"> and name o) (resid </span><span class="si">{res2}</span><span class="s1"> and name n) 2.8 </span><span class="si">{dminus}</span><span class="s1"> </span><span class="si">{dplus}</span><span class="s1"></span>
+<span class="s1"> assign (resid </span><span class="si">{res1}</span><span class="s1"> and name o) (resid </span><span class="si">{res2}</span><span class="s1"> and name hn) 1.8 </span><span class="si">{dminus}</span><span class="s1"> </span><span class="si">{dplus}</span><span class="s1"></span>
+<span class="s1"> '''</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">res1</span><span class="o">=</span><span class="n">res1</span><span class="p">,</span> <span class="n">res2</span><span class="o">=</span><span class="n">res2</span><span class="p">,</span> <span class="n">dminus</span><span class="o">=</span><span class="n">dminus</span><span class="p">,</span>
+ <span class="n">dplus</span><span class="o">=</span><span class="n">dplus</span><span class="p">))</span> <span class="c1"># , dist=dist))</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s2">"Writing </span><span class="si">%d</span><span class="s2"> hbonds from hbmap in </span><span class="si">%s</span><span class="s2">"</span><span class="p">,</span> <span class="nb">len</span><span class="p">(</span><span class="n">donors</span><span class="p">),</span>
+ <span class="n">outfile</span><span class="o">.</span><span class="n">name</span><span class="p">)</span>
+
+<div class="viewcode-block" id="AriaXMLConverter.write_hb_tbl"><a class="viewcode-back" href="../../ariaec.html#ariaec.converter.AriaXMLConverter.write_hb_tbl">[docs]</a> <span class="k">def</span> <span class="nf">write_hb_tbl</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">protein</span><span class="p">,</span> <span class="n">outfile</span><span class="p">,</span> <span class="n">hbmap</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">dminus</span><span class="o">=</span><span class="mf">0.0</span><span class="p">,</span>
+ <span class="n">dplus</span><span class="o">=</span><span class="mf">0.5</span><span class="p">,</span> <span class="n">n_hb</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">lr_type</span><span class="o">=</span><span class="s1">'main'</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> </span>
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> protein :</span>
+<span class="sd"> param outfile:</span>
+<span class="sd"> hbmap :</span>
+<span class="sd"> param dminus: (Default value = None)</span>
+<span class="sd"> dplus :</span>
+<span class="sd"> param n_hb: (Default value = 0.5)</span>
+<span class="sd"> lr_type :</span>
+<span class="sd"> return: (Default value = 'main')</span>
+<span class="sd"> outfile :</span>
+<span class="sd"> </span>
+<span class="sd"> dminus :</span>
+<span class="sd"> (Default value = 0.0)</span>
+<span class="sd"> n_hb :</span>
+<span class="sd"> (Default value = None)</span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+<span class="sd"> </span>
+<span class="sd"> """</span>
+ <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">outfile</span><span class="p">,</span> <span class="s1">'w'</span><span class="p">)</span> <span class="k">as</span> <span class="n">outfile</span><span class="p">:</span>
+ <span class="c1"># Write short range hbond tbl restraints</span>
+ <span class="k">if</span> <span class="n">protein</span><span class="o">.</span><span class="n">sec_struct</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_write_helix_hb_tbl</span><span class="p">(</span><span class="n">protein</span><span class="o">.</span><span class="n">sec_struct</span><span class="o">.</span><span class="n">ss_matrix</span><span class="p">,</span> <span class="n">outfile</span><span class="p">,</span>
+ <span class="n">dminus</span><span class="p">,</span>
+ <span class="n">dplus</span><span class="p">)</span>
+ <span class="k">if</span> <span class="n">hbmap</span><span class="p">:</span>
+ <span class="c1"># TODO: add another flag in order to generate hbmap xml</span>
+ <span class="c1"># ambig. Tbl pseudoatoms is probably not the best way to use</span>
+ <span class="c1"># hbmap</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_write_hbmap_tbl</span><span class="p">(</span><span class="n">hbmap</span><span class="p">,</span> <span class="n">outfile</span><span class="p">,</span> <span class="n">dminus</span><span class="p">,</span> <span class="n">dplus</span><span class="p">,</span>
+ <span class="n">n_hb</span><span class="o">=</span><span class="n">n_hb</span><span class="p">,</span> <span class="n">hb_type</span><span class="o">=</span><span class="n">lr_type</span><span class="p">,</span>
+ <span class="n">topo</span><span class="o">=</span><span class="n">protein</span><span class="o">.</span><span class="n">topology</span><span class="p">)</span></div>
+
+<div class="viewcode-block" id="AriaXMLConverter.write_ssdist_tbl"><a class="viewcode-back" href="../../ariaec.html#ariaec.converter.AriaXMLConverter.write_ssdist_tbl">[docs]</a> <span class="nd">@staticmethod</span>
+ <span class="k">def</span> <span class="nf">write_ssdist_tbl</span><span class="p">(</span><span class="n">sec_struct</span><span class="p">,</span> <span class="n">ss_dist</span><span class="p">,</span> <span class="n">outfile</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> </span>
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> sec_struct :</span>
+<span class="sd"> </span>
+<span class="sd"> ss_dist :</span>
+<span class="sd"> </span>
+<span class="sd"> outfile :</span>
+<span class="sd"> </span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+<span class="sd"> </span>
+<span class="sd"> """</span>
+ <span class="c1"># Build global secondary structure distance restraints (H-H+4, E-E+1,</span>
+ <span class="c1"># ...)</span>
+ <span class="sd">"""</span>
+
+<span class="sd"> :param sec_struct:</span>
+<span class="sd"> :param ss_dist:</span>
+<span class="sd"> :param outfile:</span>
+<span class="sd"> """</span>
+ <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">outfile</span><span class="p">,</span> <span class="s1">'w'</span><span class="p">)</span> <span class="k">as</span> <span class="n">outfile</span><span class="p">:</span>
+ <span class="k">for</span> <span class="n">resid1</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">sec_struct</span><span class="p">)</span> <span class="o">-</span> <span class="mi">1</span><span class="p">):</span>
+ <span class="k">for</span> <span class="n">resid2</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">resid1</span> <span class="o">+</span> <span class="mi">1</span><span class="p">,</span> <span class="nb">len</span><span class="p">(</span><span class="n">sec_struct</span><span class="p">)):</span>
+ <span class="n">ss1</span> <span class="o">=</span> <span class="n">sec_struct</span><span class="p">[</span><span class="n">resid1</span><span class="p">][</span><span class="mi">2</span><span class="p">]</span>
+ <span class="n">ss2</span> <span class="o">=</span> <span class="n">sec_struct</span><span class="p">[</span><span class="n">resid2</span><span class="p">][</span><span class="mi">2</span><span class="p">]</span>
+ <span class="k">if</span> <span class="p">(</span><span class="n">ss1</span> <span class="o">!=</span> <span class="n">ss2</span><span class="p">)</span> <span class="ow">or</span> <span class="s1">'C'</span> <span class="ow">in</span> <span class="n">ss1</span> <span class="ow">or</span> <span class="s1">'C'</span> <span class="ow">in</span> <span class="n">ss2</span><span class="p">:</span>
+ <span class="k">continue</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="n">gap</span> <span class="o">=</span> <span class="n">resid2</span> <span class="o">-</span> <span class="n">resid1</span> <span class="c1"># ecart en nombre de residus</span>
+ <span class="n">ss_dict_key</span> <span class="o">=</span> <span class="s1">'</span><span class="si">%s</span><span class="s1">,</span><span class="si">%s</span><span class="s1">+</span><span class="si">%d</span><span class="s1">'</span> <span class="o">%</span> <span class="p">(</span><span class="n">ss1</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">ss2</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">gap</span><span class="p">)</span>
+ <span class="n">ss_dist_subdict</span> <span class="o">=</span> <span class="n">ss_dist</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">ss_dict_key</span><span class="p">)</span>
+ <span class="k">if</span> <span class="n">ss_dist_subdict</span><span class="p">:</span>
+ <span class="k">for</span> <span class="n">atoms</span><span class="p">,</span> <span class="p">(</span><span class="n">dist</span><span class="p">,</span> <span class="n">sdev</span><span class="p">)</span> <span class="ow">in</span> <span class="n">ss_dist_subdict</span><span class="o">.</span><span class="n">items</span><span class="p">():</span>
+ <span class="k">if</span> <span class="n">dist</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span> <span class="ow">and</span> <span class="n">sdev</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+ <span class="n">atm1</span><span class="p">,</span> <span class="n">atm2</span> <span class="o">=</span> <span class="nb">tuple</span><span class="p">(</span><span class="n">atoms</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">'-'</span><span class="p">))</span>
+ <span class="n">res1</span> <span class="o">=</span> <span class="n">resid1</span> <span class="o">+</span> <span class="mi">1</span>
+ <span class="n">res2</span> <span class="o">=</span> <span class="n">resid2</span> <span class="o">+</span> <span class="mi">1</span>
+ <span class="n">outfile</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s1">'''</span><span class="se">\</span>
+<span class="s1">assign (resid </span><span class="si">{res1}</span><span class="s1"> and name </span><span class="si">{atm1}</span><span class="s1">) (resid </span><span class="si">{res2}</span><span class="s1"> and name </span><span class="si">{atm2}</span><span class="s1">) </span><span class="si">{dist}</span><span class="s1"> </span><span class="si">{sdev}</span><span class="s1"> </span><span class="si">{sdev}</span><span class="s1"> weight 5</span>
+<span class="s1">'''</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">res1</span><span class="o">=</span><span class="n">res1</span><span class="p">,</span> <span class="n">atm1</span><span class="o">=</span><span class="n">atm1</span><span class="p">,</span> <span class="n">res2</span><span class="o">=</span><span class="n">res2</span><span class="p">,</span> <span class="n">atm2</span><span class="o">=</span><span class="n">atm2</span><span class="p">,</span> <span class="n">dist</span><span class="o">=</span><span class="n">dist</span><span class="p">,</span> <span class="n">sdev</span><span class="o">=</span><span class="n">sdev</span><span class="p">))</span></div>
+
+<div class="viewcode-block" id="AriaXMLConverter.write_dihedral_tbl"><a class="viewcode-back" href="../../ariaec.html#ariaec.converter.AriaXMLConverter.write_dihedral_tbl">[docs]</a> <span class="nd">@staticmethod</span>
+ <span class="k">def</span> <span class="nf">write_dihedral_tbl</span><span class="p">(</span><span class="n">secstructs</span><span class="p">,</span> <span class="n">outfile</span><span class="p">,</span> <span class="n">knrj</span><span class="o">=</span><span class="mf">0.5</span><span class="p">,</span> <span class="n">exp</span><span class="o">=</span><span class="mi">2</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Build dihedral angle restraints (phi, psi) in tbl format</span>
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> secstructs :</span>
+<span class="sd"> </span>
+<span class="sd"> outfile :</span>
+<span class="sd"> </span>
+<span class="sd"> knrj :</span>
+<span class="sd"> (Default value = 0.5)</span>
+<span class="sd"> exp :</span>
+<span class="sd"> (Default value = 2)</span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+<span class="sd"> </span>
+<span class="sd"> """</span>
+ <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">outfile</span><span class="p">,</span> <span class="s2">"w"</span><span class="p">)</span> <span class="k">as</span> <span class="n">outfile</span><span class="p">:</span>
+ <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">secstructs</span><span class="p">)):</span>
+ <span class="k">if</span> <span class="p">(</span><span class="n">i</span> <span class="o">+</span> <span class="mi">1</span><span class="p">)</span> <span class="o">!=</span> <span class="nb">len</span><span class="p">(</span><span class="n">secstructs</span><span class="p">):</span>
+ <span class="k">if</span> <span class="n">secstructs</span><span class="p">[</span><span class="n">i</span><span class="p">][</span><span class="mi">2</span><span class="p">]</span> <span class="o">==</span> <span class="n">secstructs</span><span class="p">[</span><span class="n">i</span> <span class="o">+</span> <span class="mi">1</span><span class="p">][</span><span class="mi">2</span><span class="p">]:</span>
+ <span class="c1"># Si ss identique</span>
+ <span class="n">secstruct</span> <span class="o">=</span> <span class="n">secstructs</span><span class="p">[</span><span class="n">i</span><span class="p">][</span><span class="mi">2</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span>
+ <span class="n">res1</span> <span class="o">=</span> <span class="n">i</span> <span class="o">+</span> <span class="mi">1</span>
+ <span class="n">res2</span> <span class="o">=</span> <span class="n">i</span> <span class="o">+</span> <span class="mi">2</span>
+
+ <span class="k">if</span> <span class="n">secstruct</span> <span class="o">==</span> <span class="s1">'H'</span><span class="p">:</span>
+ <span class="n">phi</span> <span class="o">=</span> <span class="o">-</span><span class="mf">57.0</span>
+ <span class="n">psi</span> <span class="o">=</span> <span class="o">-</span><span class="mf">47.0</span>
+ <span class="n">anglerange</span> <span class="o">=</span> <span class="mf">7.0</span>
+ <span class="k">elif</span> <span class="n">secstruct</span> <span class="o">==</span> <span class="s1">'E'</span><span class="p">:</span>
+ <span class="n">phi</span> <span class="o">=</span> <span class="o">-</span><span class="mf">127.0</span>
+ <span class="n">psi</span> <span class="o">=</span> <span class="mf">122.0</span>
+ <span class="n">anglerange</span> <span class="o">=</span> <span class="mf">20.0</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="n">phi</span><span class="p">,</span> <span class="n">psi</span><span class="p">,</span> <span class="n">anglerange</span> <span class="o">=</span> <span class="p">(</span><span class="kc">None</span><span class="p">,</span> <span class="kc">None</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span>
+
+ <span class="k">if</span> <span class="n">phi</span> <span class="ow">and</span> <span class="n">psi</span><span class="p">:</span>
+ <span class="n">outfile</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s1">'''</span><span class="se">\</span>
+<span class="s1">assign (resid </span><span class="si">{res1}</span><span class="s1"> and name c) (resid </span><span class="si">{res2}</span><span class="s1"> and name n) (resid </span><span class="si">{res2}</span><span class="s1"> and name ca) </span><span class="se">\</span>
+<span class="s1">(resid </span><span class="si">{res2}</span><span class="s1"> and name c) </span><span class="si">{k}</span><span class="s1"> </span><span class="si">{phi}</span><span class="s1"> </span><span class="si">{anglerange}</span><span class="s1"> </span><span class="si">{e}</span><span class="s1"></span>
+<span class="s1">assign (resid </span><span class="si">{res1}</span><span class="s1"> and name n) (resid </span><span class="si">{res1}</span><span class="s1"> and name ca) (resid </span><span class="si">{res1}</span><span class="s1"> and name c) </span><span class="se">\</span>
+<span class="s1">(resid </span><span class="si">{res2}</span><span class="s1"> and name n) </span><span class="si">{k}</span><span class="s1"> </span><span class="si">{psi}</span><span class="s1"> </span><span class="si">{anglerange}</span><span class="s1"> </span><span class="si">{e}</span><span class="s1"></span>
+<span class="s1">'''</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">res1</span><span class="o">=</span><span class="n">res1</span><span class="p">,</span> <span class="n">res2</span><span class="o">=</span><span class="n">res2</span><span class="p">,</span> <span class="n">k</span><span class="o">=</span><span class="n">knrj</span><span class="p">,</span> <span class="n">phi</span><span class="o">=</span><span class="n">phi</span><span class="p">,</span> <span class="n">psi</span><span class="o">=</span><span class="n">psi</span><span class="p">,</span>
+ <span class="n">anglerange</span><span class="o">=</span><span class="n">anglerange</span><span class="p">,</span> <span class="n">e</span><span class="o">=</span><span class="n">exp</span><span class="p">))</span></div></div>
+
+
+<div class="viewcode-block" id="AriaEcXMLConverter"><a class="viewcode-back" href="../../ariaec.html#ariaec.converter.AriaEcXMLConverter">[docs]</a><span class="k">class</span> <span class="nc">AriaEcXMLConverter</span><span class="p">(</span><span class="n">AriaXMLConverter</span><span class="p">):</span>
+ <span class="sd">"""XML converter ariaec to aria"""</span>
+
+ <span class="c1"># TODO: use aria api instead to generate xml files</span>
+ <span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">restraint_list</span> <span class="o">=</span> <span class="p">[]</span>
+ <span class="nb">super</span><span class="p">(</span><span class="n">AriaEcXMLConverter</span><span class="p">,</span> <span class="bp">self</span><span class="p">)</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
+
+ <span class="nd">@staticmethod</span>
+ <span class="k">def</span> <span class="nf">_write_hbmap_tbl</span><span class="p">(</span><span class="n">hbmap</span><span class="p">,</span> <span class="n">outfile</span><span class="p">,</span> <span class="n">dminus</span><span class="p">,</span> <span class="n">dplus</span><span class="p">,</span> <span class="n">n_hb</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
+ <span class="n">hb_type</span><span class="o">=</span><span class="s2">"main"</span><span class="p">,</span> <span class="n">topo</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> </span>
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> hbmap :</span>
+<span class="sd"> </span>
+<span class="sd"> outfile :</span>
+<span class="sd"> </span>
+<span class="sd"> dminus :</span>
+<span class="sd"> </span>
+<span class="sd"> dplus :</span>
+<span class="sd"> </span>
+<span class="sd"> n_hb :</span>
+<span class="sd"> (Default value = None)</span>
+<span class="sd"> hb_type :</span>
+<span class="sd"> (Default value = "main")</span>
+<span class="sd"> topo :</span>
+<span class="sd"> (Default value = None)</span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+<span class="sd"> </span>
+<span class="sd"> """</span>
+ <span class="n">AriaXMLConverter</span><span class="o">.</span><span class="n">_write_hbmap_tbl</span><span class="p">(</span><span class="n">hbmap</span><span class="p">,</span> <span class="n">outfile</span><span class="p">,</span> <span class="n">dminus</span><span class="p">,</span> <span class="n">dplus</span><span class="p">)</span>
+
+ <span class="c1"># def atm_product(self, idx1, res1, idx2, res2, list_type="min", product=True):</span>
+ <span class="c1">#</span>
+ <span class="c1"># """</span>
+ <span class="c1">#</span>
+ <span class="c1">#</span>
+ <span class="c1"># Parameters</span>
+ <span class="c1"># ----------</span>
+ <span class="c1"># idx1 :</span>
+ <span class="c1"># res1:</span>
+ <span class="c1"># idx2 :</span>
+ <span class="c1"># res2:</span>
+ <span class="c1"># list_type :</span>
+ <span class="c1"># type of atoms in the product (Default value = "min")</span>
+ <span class="c1"># product :</span>
+ <span class="c1"># res1 :</span>
+ <span class="c1">#</span>
+ <span class="c1"># res2 :</span>
+ <span class="c1">#</span>
+ <span class="c1">#</span>
+ <span class="c1"># Returns</span>
+ <span class="c1"># -------</span>
+ <span class="c1">#</span>
+ <span class="c1">#</span>
+ <span class="c1"># """</span>
+ <span class="c1">#</span>
+ <span class="c1"># def resname(res):</span>
+ <span class="c1"># """</span>
+ <span class="c1">#</span>
+ <span class="c1">#</span>
+ <span class="c1"># Parameters</span>
+ <span class="c1"># ----------</span>
+ <span class="c1"># res :</span>
+ <span class="c1"># return:</span>
+ <span class="c1">#</span>
+ <span class="c1"># Returns</span>
+ <span class="c1"># -------</span>
+ <span class="c1">#</span>
+ <span class="c1">#</span>
+ <span class="c1"># """</span>
+ <span class="c1"># return AminoAcid.AminoAcid(res)[0]</span>
+ <span class="c1">#</span>
+ <span class="c1"># def min_filter(aa1, aa2, atms):</span>
+ <span class="c1"># """</span>
+ <span class="c1">#</span>
+ <span class="c1">#</span>
+ <span class="c1"># Parameters</span>
+ <span class="c1"># ----------</span>
+ <span class="c1"># aa1 : residue name 1</span>
+ <span class="c1">#</span>
+ <span class="c1"># aa2 : residue name 2</span>
+ <span class="c1">#</span>
+ <span class="c1"># atms : atom pair list of residue 1</span>
+ <span class="c1">#</span>
+ <span class="c1">#</span>
+ <span class="c1"># Returns</span>
+ <span class="c1"># -------</span>
+ <span class="c1">#</span>
+ <span class="c1">#</span>
+ <span class="c1"># """</span>
+ <span class="c1"># return [atm for atm in atms if atm in (</span>
+ <span class="c1"># 'CA', 'CB',</span>
+ <span class="c1"># self.settings.scsc_min[resname(aa1)][resname(aa2)][0])]</span>
+ <span class="c1">#</span>
+ <span class="c1"># atms1 = self.molecule.get_chains()[0].getResidues()[idx1].atoms.keys()</span>
+ <span class="c1"># atms2 = self.molecule.get_chains()[0].getResidues()[idx2].atoms.keys()</span>
+ <span class="c1">#</span>
+ <span class="c1"># if list_type == "min":</span>
+ <span class="c1"># atms1 = min_filter(res1, res2, atms1)</span>
+ <span class="c1"># atms2 = min_filter(res2, res1, atms2)</span>
+ <span class="c1"># elif list_type == "heavy":</span>
+ <span class="c1"># atms1 = filter(ResAtmMap.heavy_reg.match, atms1)</span>
+ <span class="c1"># atms2 = filter(ResAtmMap.heavy_reg.match, atms2)</span>
+ <span class="c1"># elif list_type != 'all':</span>
+ <span class="c1"># LOG.warning("Wrong pair_list option. Pair_list set to min")</span>
+ <span class="c1"># atms1 = min_filter(res1, res2, atms1)</span>
+ <span class="c1"># atms2 = min_filter(res2, res1, atms2)</span>
+ <span class="c1">#</span>
+ <span class="c1"># if product:</span>
+ <span class="c1"># return list(itertools.product(atms1, atms2))</span>
+ <span class="c1"># else:</span>
+ <span class="c1"># # Return atm1-atm2 list if both atoms are of the same type (except</span>
+ <span class="c1"># # for min atom list with the side chain atom</span>
+ <span class="c1"># return [</span>
+ <span class="c1"># (atm1, atm2) for (atm1, atm2) in list(itertools.product(atms1, atms2))</span>
+ <span class="c1"># if atm1 == atm2 or (</span>
+ <span class="c1"># atm1 not in ('CA', 'CB')</span>
+ <span class="c1"># and atm2 not in ('CA', 'CB'))] if list_type == 'min' else [</span>
+ <span class="c1"># (atm1, atm2) for (atm1, atm2) in list(itertools.product(atms1, atms2))</span>
+ <span class="c1"># if atm1 == atm2]</span>
+
+<div class="viewcode-block" id="AriaEcXMLConverter.atm_list"><a class="viewcode-back" href="../../ariaec.html#ariaec.converter.AriaEcXMLConverter.atm_list">[docs]</a> <span class="k">def</span> <span class="nf">atm_list</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">idx1</span><span class="p">,</span> <span class="n">res1</span><span class="p">,</span> <span class="n">idx2</span><span class="p">,</span> <span class="n">res2</span><span class="p">,</span> <span class="n">list_type</span><span class="o">=</span><span class="s2">"min"</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> </span>
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> idx1</span>
+<span class="sd"> res1</span>
+<span class="sd"> idx2</span>
+<span class="sd"> res2</span>
+<span class="sd"> list_type</span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+<span class="sd"> """</span>
+
+ <span class="k">def</span> <span class="nf">resname</span><span class="p">(</span><span class="n">res</span><span class="p">):</span>
+ <span class="sd">"""</span>
+
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> res :</span>
+<span class="sd"> return:</span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+
+<span class="sd"> """</span>
+ <span class="k">return</span> <span class="n">AminoAcid</span><span class="o">.</span><span class="n">AminoAcid</span><span class="p">(</span><span class="n">res</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span>
+
+ <span class="k">def</span> <span class="nf">min_filter</span><span class="p">(</span><span class="n">aa1</span><span class="p">,</span> <span class="n">aa2</span><span class="p">,</span> <span class="n">atms</span><span class="p">):</span>
+ <span class="sd">"""</span>
+
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> aa1 : residue name 1</span>
+
+<span class="sd"> aa2 : residue name 2</span>
+
+<span class="sd"> atms : atom pair list of residue 1</span>
+
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+
+<span class="sd"> """</span>
+ <span class="k">return</span> <span class="p">[</span><span class="n">atm</span> <span class="k">for</span> <span class="n">atm</span> <span class="ow">in</span> <span class="n">atms</span> <span class="k">if</span> <span class="n">atm</span> <span class="ow">in</span> <span class="p">(</span>
+ <span class="s1">'CA'</span><span class="p">,</span> <span class="s1">'CB'</span><span class="p">,</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">scsc_min</span><span class="p">[</span><span class="n">resname</span><span class="p">(</span><span class="n">aa1</span><span class="p">)][</span><span class="n">resname</span><span class="p">(</span><span class="n">aa2</span><span class="p">)][</span><span class="mi">0</span><span class="p">])]</span>
+
+ <span class="n">atms1</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">molecule</span><span class="o">.</span><span class="n">get_chains</span><span class="p">()[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">getResidues</span><span class="p">()[</span><span class="n">idx1</span><span class="p">]</span><span class="o">.</span><span class="n">atoms</span><span class="o">.</span><span class="n">keys</span><span class="p">()</span>
+ <span class="n">atms2</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">molecule</span><span class="o">.</span><span class="n">get_chains</span><span class="p">()[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">getResidues</span><span class="p">()[</span><span class="n">idx2</span><span class="p">]</span><span class="o">.</span><span class="n">atoms</span><span class="o">.</span><span class="n">keys</span><span class="p">()</span>
+
+ <span class="k">if</span> <span class="n">list_type</span> <span class="o">==</span> <span class="s2">"min"</span><span class="p">:</span>
+ <span class="n">atms1</span> <span class="o">=</span> <span class="n">min_filter</span><span class="p">(</span><span class="n">res1</span><span class="p">,</span> <span class="n">res2</span><span class="p">,</span> <span class="n">atms1</span><span class="p">)</span>
+ <span class="n">atms2</span> <span class="o">=</span> <span class="n">min_filter</span><span class="p">(</span><span class="n">res2</span><span class="p">,</span> <span class="n">res1</span><span class="p">,</span> <span class="n">atms2</span><span class="p">)</span>
+ <span class="k">elif</span> <span class="n">list_type</span> <span class="o">==</span> <span class="s2">"heavy"</span><span class="p">:</span>
+ <span class="n">atms1</span> <span class="o">=</span> <span class="nb">filter</span><span class="p">(</span><span class="n">ResAtmMap</span><span class="o">.</span><span class="n">heavy_reg</span><span class="o">.</span><span class="n">match</span><span class="p">,</span> <span class="n">atms1</span><span class="p">)</span>
+ <span class="n">atms2</span> <span class="o">=</span> <span class="nb">filter</span><span class="p">(</span><span class="n">ResAtmMap</span><span class="o">.</span><span class="n">heavy_reg</span><span class="o">.</span><span class="n">match</span><span class="p">,</span> <span class="n">atms2</span><span class="p">)</span>
+ <span class="k">elif</span> <span class="n">list_type</span> <span class="o">!=</span> <span class="s1">'all'</span><span class="p">:</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">warning</span><span class="p">(</span><span class="s2">"Wrong pair_list option. Pair_list set to min"</span><span class="p">)</span>
+ <span class="n">atms1</span> <span class="o">=</span> <span class="n">min_filter</span><span class="p">(</span><span class="n">res1</span><span class="p">,</span> <span class="n">res2</span><span class="p">,</span> <span class="n">atms1</span><span class="p">)</span>
+ <span class="n">atms2</span> <span class="o">=</span> <span class="n">min_filter</span><span class="p">(</span><span class="n">res2</span><span class="p">,</span> <span class="n">res1</span><span class="p">,</span> <span class="n">atms2</span><span class="p">)</span>
+
+ <span class="k">return</span> <span class="nb">tuple</span><span class="p">(</span><span class="n">atms1</span><span class="p">),</span> <span class="nb">tuple</span><span class="p">(</span><span class="n">atms2</span><span class="p">)</span></div>
+
+<div class="viewcode-block" id="AriaEcXMLConverter.atm_product"><a class="viewcode-back" href="../../ariaec.html#ariaec.converter.AriaEcXMLConverter.atm_product">[docs]</a> <span class="k">def</span> <span class="nf">atm_product</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">idx1</span><span class="p">,</span> <span class="n">res1</span><span class="p">,</span> <span class="n">idx2</span><span class="p">,</span> <span class="n">res2</span><span class="p">,</span> <span class="n">list_type</span><span class="o">=</span><span class="s2">"min"</span><span class="p">,</span>
+ <span class="n">adr_flag</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span> <span class="n">product_type</span><span class="o">=</span><span class="s2">"allvsall"</span><span class="p">):</span>
+ <span class="sd">"""</span>
+
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> product_type</span>
+<span class="sd"> adr_flag</span>
+<span class="sd"> idx1 :</span>
+<span class="sd"> res1:</span>
+<span class="sd"> idx2 :</span>
+<span class="sd"> res2:</span>
+<span class="sd"> list_type :</span>
+<span class="sd"> type of atoms in the product (Default value = "min")</span>
+<span class="sd"> res1 :</span>
+
+<span class="sd"> res2 :</span>
+
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+
+<span class="sd"> """</span>
+
+ <span class="k">def</span> <span class="nf">resname</span><span class="p">(</span><span class="n">res</span><span class="p">):</span>
+ <span class="sd">"""</span>
+
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> res :</span>
+<span class="sd"> return:</span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+
+<span class="sd"> """</span>
+ <span class="k">return</span> <span class="n">AminoAcid</span><span class="o">.</span><span class="n">AminoAcid</span><span class="p">(</span><span class="n">res</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span>
+
+ <span class="n">atms1</span><span class="p">,</span> <span class="n">atms2</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">atm_list</span><span class="p">(</span><span class="n">idx1</span><span class="p">,</span> <span class="n">res1</span><span class="p">,</span> <span class="n">idx2</span><span class="p">,</span> <span class="n">res2</span><span class="p">,</span>
+ <span class="n">list_type</span><span class="o">=</span><span class="n">list_type</span><span class="p">)</span>
+
+ <span class="k">if</span> <span class="n">adr_flag</span> <span class="ow">and</span> <span class="n">product_type</span> <span class="o">==</span> <span class="s2">"same"</span><span class="p">:</span>
+ <span class="c1"># We return here only minimized list with equal atoms</span>
+ <span class="c1"># Return atm1-atm2 list if both atoms are of the same type (except</span>
+ <span class="c1"># for min atom list with the side chain atom</span>
+ <span class="k">return</span> <span class="p">[[</span>
+ <span class="p">((</span><span class="n">idx1</span><span class="p">,</span> <span class="n">atm1</span><span class="p">),</span> <span class="p">(</span><span class="n">idx2</span><span class="p">,</span> <span class="n">atm2</span><span class="p">))</span> <span class="k">for</span> <span class="p">(</span><span class="n">atm1</span><span class="p">,</span> <span class="n">atm2</span><span class="p">)</span> <span class="ow">in</span>
+ <span class="nb">list</span><span class="p">(</span><span class="n">itertools</span><span class="o">.</span><span class="n">product</span><span class="p">(</span><span class="n">atms1</span><span class="p">,</span> <span class="n">atms2</span><span class="p">))</span>
+ <span class="k">if</span> <span class="n">atm1</span> <span class="o">==</span> <span class="n">atm2</span> <span class="ow">or</span> <span class="p">(</span>
+ <span class="n">atm1</span> <span class="ow">not</span> <span class="ow">in</span> <span class="p">(</span><span class="s1">'CA'</span><span class="p">,</span> <span class="s1">'CB'</span><span class="p">)</span>
+ <span class="ow">and</span> <span class="n">atm2</span> <span class="ow">not</span> <span class="ow">in</span> <span class="p">(</span><span class="s1">'CA'</span><span class="p">,</span> <span class="s1">'CB'</span><span class="p">)</span>
+ <span class="p">)</span> <span class="ow">or</span> <span class="p">(</span><span class="n">atm1</span><span class="p">,</span> <span class="n">atm2</span><span class="p">)</span> <span class="o">==</span> <span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">scsc_min</span><span class="p">[</span>
+ <span class="n">resname</span><span class="p">(</span><span class="n">res1</span><span class="p">)][</span><span class="n">resname</span><span class="p">(</span><span class="n">res2</span><span class="p">)]],</span> <span class="p">]</span> <span class="k">if</span> <span class="n">list_type</span> <span class="o">==</span> <span class="s1">'min'</span> \
+ <span class="k">else</span> <span class="p">[[(</span><span class="n">atm1</span><span class="p">,</span> <span class="n">atm2</span><span class="p">)</span> <span class="k">for</span> <span class="p">(</span><span class="n">atm1</span><span class="p">,</span> <span class="n">atm2</span><span class="p">)</span> <span class="ow">in</span>
+ <span class="nb">list</span><span class="p">(</span><span class="n">itertools</span><span class="o">.</span><span class="n">product</span><span class="p">(</span><span class="n">atms1</span><span class="p">,</span> <span class="n">atms2</span><span class="p">))</span>
+ <span class="k">if</span> <span class="n">atm1</span> <span class="o">==</span> <span class="n">atm2</span><span class="p">],</span> <span class="p">]</span>
+ <span class="k">elif</span> <span class="n">adr_flag</span> <span class="ow">and</span> <span class="n">product_type</span> <span class="o">==</span> <span class="s2">"onevsall"</span><span class="p">:</span>
+ <span class="c1"># Nested list with combination between one atom against all</span>
+ <span class="c1"># other atoms in the other list</span>
+ <span class="n">result</span> <span class="o">=</span> <span class="p">[]</span>
+ <span class="k">for</span> <span class="n">atm1</span> <span class="ow">in</span> <span class="n">atms1</span><span class="p">:</span>
+ <span class="n">result</span><span class="o">.</span><span class="n">append</span><span class="p">([</span>
+ <span class="p">((</span><span class="n">idx1</span><span class="p">,</span> <span class="n">atm1</span><span class="p">),</span> <span class="p">(</span><span class="n">idx2</span><span class="p">,</span> <span class="n">atm2</span><span class="p">))</span> <span class="k">for</span> <span class="p">(</span><span class="n">atm1</span><span class="p">,</span> <span class="n">atm2</span><span class="p">)</span> <span class="ow">in</span>
+ <span class="nb">list</span><span class="p">(</span><span class="n">itertools</span><span class="o">.</span><span class="n">product</span><span class="p">([</span><span class="n">atm1</span><span class="p">],</span> <span class="n">atms2</span><span class="p">))])</span>
+ <span class="k">return</span> <span class="n">result</span>
+ <span class="k">elif</span> <span class="n">adr_flag</span> <span class="ow">and</span> <span class="n">product_type</span> <span class="o">==</span> <span class="s2">"allvsall"</span><span class="p">:</span>
+ <span class="c1"># ADR with allvsall</span>
+ <span class="k">return</span> <span class="p">[[</span>
+ <span class="p">((</span><span class="n">idx1</span><span class="p">,</span> <span class="n">atm1</span><span class="p">),</span> <span class="p">(</span><span class="n">idx2</span><span class="p">,</span> <span class="n">atm2</span><span class="p">))</span> <span class="k">for</span> <span class="p">(</span><span class="n">atm1</span><span class="p">,</span> <span class="n">atm2</span><span class="p">)</span> <span class="ow">in</span>
+ <span class="nb">list</span><span class="p">(</span><span class="n">itertools</span><span class="o">.</span><span class="n">product</span><span class="p">(</span><span class="n">atms1</span><span class="p">,</span> <span class="n">atms2</span><span class="p">))],</span> <span class="p">]</span>
+ <span class="k">elif</span> <span class="ow">not</span> <span class="n">adr_flag</span> <span class="ow">and</span> <span class="n">product_type</span> <span class="o">==</span> <span class="s2">"same"</span><span class="p">:</span>
+ <span class="c1"># We return here only minimized list with equal atoms</span>
+ <span class="c1"># Return atm1-atm2 list if both atoms are of the same type (except</span>
+ <span class="c1"># for min atom list with the side chain atom</span>
+ <span class="k">return</span> <span class="p">[</span>
+ <span class="p">((</span><span class="n">idx1</span><span class="p">,</span> <span class="n">atm1</span><span class="p">),</span> <span class="p">(</span><span class="n">idx2</span><span class="p">,</span> <span class="n">atm2</span><span class="p">))</span> <span class="k">for</span> <span class="p">(</span><span class="n">atm1</span><span class="p">,</span> <span class="n">atm2</span><span class="p">)</span> <span class="ow">in</span>
+ <span class="nb">list</span><span class="p">(</span><span class="n">itertools</span><span class="o">.</span><span class="n">product</span><span class="p">(</span><span class="n">atms1</span><span class="p">,</span> <span class="n">atms2</span><span class="p">))</span>
+ <span class="k">if</span> <span class="n">atm1</span> <span class="o">==</span> <span class="n">atm2</span> <span class="ow">or</span> <span class="p">(</span>
+ <span class="n">atm1</span> <span class="ow">not</span> <span class="ow">in</span> <span class="p">(</span><span class="s1">'CA'</span><span class="p">,</span> <span class="s1">'CB'</span><span class="p">)</span>
+ <span class="ow">and</span> <span class="n">atm2</span> <span class="ow">not</span> <span class="ow">in</span> <span class="p">(</span>
+ <span class="s1">'CA'</span><span class="p">,</span> <span class="s1">'CB'</span><span class="p">))</span> <span class="ow">or</span> <span class="p">(</span><span class="n">atm1</span><span class="p">,</span> <span class="n">atm2</span><span class="p">)</span> <span class="o">==</span> <span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">scsc_min</span><span class="p">[</span>
+ <span class="n">resname</span><span class="p">(</span><span class="n">res1</span><span class="p">)][</span>
+ <span class="n">resname</span><span class="p">(</span><span class="n">res2</span><span class="p">)]]</span> <span class="k">if</span> <span class="n">list_type</span> <span class="o">==</span> <span class="s1">'min'</span> <span class="k">else</span> <span class="p">[</span>
+ <span class="p">(</span><span class="n">atm1</span><span class="p">,</span> <span class="n">atm2</span><span class="p">)</span> <span class="k">for</span> <span class="p">(</span><span class="n">atm1</span><span class="p">,</span> <span class="n">atm2</span><span class="p">)</span> <span class="ow">in</span>
+ <span class="nb">list</span><span class="p">(</span><span class="n">itertools</span><span class="o">.</span><span class="n">product</span><span class="p">(</span><span class="n">atms1</span><span class="p">,</span> <span class="n">atms2</span><span class="p">))</span>
+ <span class="k">if</span> <span class="n">atm1</span> <span class="o">==</span> <span class="n">atm2</span><span class="p">]</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="c1"># Unambig restraints, we have only one list with all possible</span>
+ <span class="c1"># combination between atoms. No matter what kind of product type, it</span>
+ <span class="c1"># will be the same</span>
+ <span class="k">return</span> <span class="p">[</span>
+ <span class="p">((</span><span class="n">idx1</span><span class="p">,</span> <span class="n">atm1</span><span class="p">),</span> <span class="p">(</span><span class="n">idx2</span><span class="p">,</span> <span class="n">atm2</span><span class="p">))</span> <span class="k">for</span> <span class="p">(</span><span class="n">atm1</span><span class="p">,</span> <span class="n">atm2</span><span class="p">)</span> <span class="ow">in</span>
+ <span class="nb">list</span><span class="p">(</span><span class="n">itertools</span><span class="o">.</span><span class="n">product</span><span class="p">(</span><span class="n">atms1</span><span class="p">,</span> <span class="n">atms2</span><span class="p">))]</span></div>
+
+ <span class="k">def</span> <span class="nf">_pdbdistmaps</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="c1"># TODO: use precision level, actually we only use SsAaAtmMaps</span>
+ <span class="n">precision_level</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">setup</span><span class="o">.</span><span class="n">config</span><span class="o">.</span><span class="n">get</span><span class="p">(</span>
+ <span class="s2">"pdbdistance_level"</span><span class="p">,</span> <span class="s2">"ss"</span><span class="p">)</span>
+ <span class="n">atom_types</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">setup</span><span class="o">.</span><span class="n">config</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"atoms_type"</span><span class="p">,</span> <span class="s2">"min"</span><span class="p">)</span>
+
+ <span class="c1"># TODO: Do the same for heavy matrices, it is actually hard coded to min</span>
+ <span class="c1"># matrices sinces we only have this kind of information in data/pdbdists</span>
+ <span class="n">pdbstasts_groups</span> <span class="o">=</span> <span class="p">(</span>
+ <span class="p">(</span><span class="s1">'INTERLOWERBOUNDS'</span><span class="p">,</span> <span class="s1">'interlowerbounds_pdbstat'</span><span class="p">),</span>
+ <span class="p">(</span><span class="s1">'INTERTARGET'</span><span class="p">,</span> <span class="s1">'intertarget_pdbstat'</span><span class="p">),</span>
+ <span class="p">(</span><span class="s1">'INTERUPPERBOUNDS'</span><span class="p">,</span> <span class="s1">'interupperbounds_pdbstat'</span><span class="p">),</span>
+ <span class="p">(</span><span class="s1">'INTRALOWERBOUNDS'</span><span class="p">,</span> <span class="s1">'intralowerbounds_pdbstat'</span><span class="p">),</span>
+ <span class="p">(</span><span class="s1">'INTRATARGET'</span><span class="p">,</span> <span class="s1">'intratarget_pdbstat'</span><span class="p">),</span>
+ <span class="p">(</span><span class="s1">'INTRAUPPERBOUNDS'</span><span class="p">,</span> <span class="s1">'intraupperbounds_pdbstat'</span><span class="p">)</span>
+ <span class="p">)</span>
+ <span class="n">pdbdistmaps</span> <span class="o">=</span> <span class="p">{}</span>
+
+ <span class="k">for</span> <span class="n">pdbstasts_group</span> <span class="ow">in</span> <span class="n">pdbstasts_groups</span><span class="p">:</span>
+ <span class="n">path</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">main</span><span class="o">.</span><span class="n">config</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">pdbstasts_group</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span>
+ <span class="n">pkgpath</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="p">,</span> <span class="n">pdbstasts_group</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span>
+ <span class="c1"># TODO: ONLY MIN PAIR ATOMS FOR TARGET PDB DIST</span>
+ <span class="n">targetmap</span> <span class="o">=</span> <span class="n">SsAaAtmMap</span><span class="p">(</span><span class="n">atom_types</span><span class="o">=</span><span class="n">atom_types</span><span class="p">)</span>
+
+ <span class="k">if</span> <span class="n">path</span> <span class="ow">and</span> <span class="ow">not</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">(</span><span class="n">path</span><span class="p">)</span> <span class="ow">or</span> <span class="ow">not</span> <span class="n">path</span><span class="p">:</span>
+ <span class="k">with</span> <span class="n">pkgr</span><span class="o">.</span><span class="n">resource_stream</span><span class="p">(</span><span class="vm">__name__</span><span class="p">,</span> <span class="n">pkgpath</span><span class="p">)</span> <span class="k">as</span> <span class="n">pkgfile</span><span class="p">:</span>
+ <span class="n">pdbdistmap</span> <span class="o">=</span> <span class="n">pickle</span><span class="o">.</span><span class="n">load</span><span class="p">(</span><span class="n">pkgfile</span><span class="p">)</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">try</span><span class="p">:</span>
+ <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">path</span><span class="p">)</span> <span class="k">as</span> <span class="n">pdbdistmapfile</span><span class="p">:</span>
+ <span class="n">pdbdistmap</span> <span class="o">=</span> <span class="n">pickle</span><span class="o">.</span><span class="n">load</span><span class="p">(</span><span class="n">pdbdistmapfile</span><span class="p">)</span>
+ <span class="k">except</span> <span class="p">(</span><span class="ne">IOError</span><span class="p">,</span> <span class="ne">KeyError</span><span class="p">,</span> <span class="ne">TypeError</span><span class="p">):</span>
+ <span class="k">with</span> <span class="n">pkgr</span><span class="o">.</span><span class="n">resource_stream</span><span class="p">(</span><span class="vm">__name__</span><span class="p">,</span> <span class="n">pkgpath</span><span class="p">)</span> <span class="k">as</span> <span class="n">pkgfile</span><span class="p">:</span>
+ <span class="n">pdbdistmap</span> <span class="o">=</span> <span class="n">pickle</span><span class="o">.</span><span class="n">load</span><span class="p">(</span><span class="n">pkgfile</span><span class="p">)</span>
+
+ <span class="n">pdbdistmap</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="o">.</span><span class="n">from_dict</span><span class="p">(</span><span class="n">pdbdistmap</span><span class="p">)</span>
+ <span class="c1"># We do not want 0. values here ...</span>
+ <span class="n">pdbdistmap</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="mf">0.</span><span class="p">,</span> <span class="n">np</span><span class="o">.</span><span class="n">NaN</span><span class="p">,</span> <span class="n">inplace</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
+ <span class="n">pdbdistmap</span><span class="o">.</span><span class="n">columns</span><span class="o">.</span><span class="n">set_names</span><span class="p">(</span>
+ <span class="p">[</span><span class="s1">'SecStruct'</span><span class="p">,</span> <span class="s1">'AminoAcid'</span><span class="p">,</span> <span class="s1">'Atom'</span><span class="p">],</span> <span class="n">inplace</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
+ <span class="n">pdbdistmap</span><span class="o">.</span><span class="n">index</span><span class="o">.</span><span class="n">set_names</span><span class="p">(</span>
+ <span class="p">[</span><span class="s1">'SecStruct'</span><span class="p">,</span> <span class="s1">'AminoAcid'</span><span class="p">,</span> <span class="s1">'Atom'</span><span class="p">],</span> <span class="n">inplace</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
+ <span class="n">pdbdistmap</span><span class="o">.</span><span class="n">sort_index</span><span class="p">(</span><span class="n">inplace</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
+ <span class="n">pdbdistmap</span><span class="o">.</span><span class="n">sort_index</span><span class="p">(</span><span class="n">axis</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span> <span class="n">inplace</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
+ <span class="n">targetmap</span><span class="o">.</span><span class="n">sort_index</span><span class="p">(</span><span class="n">inplace</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
+ <span class="n">targetmap</span><span class="o">.</span><span class="n">sort_index</span><span class="p">(</span><span class="n">axis</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span> <span class="n">inplace</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
+ <span class="n">targetmap</span><span class="p">[:]</span> <span class="o">=</span> <span class="n">pdbdistmap</span><span class="p">[:]</span>
+ <span class="c1"># # TODO: Find a way to rearrange index or</span>
+ <span class="n">pdbdistmaps</span><span class="p">[</span><span class="n">pdbstasts_group</span><span class="p">[</span><span class="mi">0</span><span class="p">]]</span> <span class="o">=</span> <span class="n">targetmap</span>
+
+ <span class="k">return</span> <span class="n">pdbdistmaps</span>
+
+<div class="viewcode-block" id="AriaEcXMLConverter.neighcontact"><a class="viewcode-back" href="../../ariaec.html#ariaec.converter.AriaEcXMLConverter.neighcontact">[docs]</a> <span class="nd">@staticmethod</span>
+ <span class="k">def</span> <span class="nf">neighcontact</span><span class="p">(</span><span class="n">contact</span><span class="p">,</span> <span class="n">maxidx</span><span class="p">,</span> <span class="n">offset</span><span class="o">=</span><span class="mi">0</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> </span>
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> contact: tuple object</span>
+<span class="sd"> maxidx: int</span>
+<span class="sd"> offset: int</span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+<span class="sd"> """</span>
+ <span class="n">neighcontacts</span> <span class="o">=</span> <span class="p">[]</span>
+ <span class="c1"># Add N - 1 contact</span>
+ <span class="k">if</span> <span class="mi">0</span> <span class="o">+</span> <span class="n">offset</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">contact</span><span class="p">:</span>
+ <span class="n">neighcontacts</span><span class="o">.</span><span class="n">append</span><span class="p">((</span><span class="n">contact</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">-</span> <span class="mi">1</span><span class="p">,</span> <span class="n">contact</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="o">-</span> <span class="mi">1</span><span class="p">))</span>
+ <span class="n">neighcontacts</span><span class="o">.</span><span class="n">append</span><span class="p">((</span><span class="n">contact</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">contact</span><span class="p">[</span><span class="mi">1</span><span class="p">]))</span>
+ <span class="c1"># Add N + 1 contact</span>
+ <span class="k">if</span> <span class="n">maxidx</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">contact</span><span class="p">:</span>
+ <span class="n">neighcontacts</span><span class="o">.</span><span class="n">append</span><span class="p">((</span><span class="n">contact</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">+</span> <span class="mi">1</span><span class="p">,</span> <span class="n">contact</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="o">+</span> <span class="mi">1</span><span class="p">))</span>
+ <span class="k">return</span> <span class="n">neighcontacts</span></div>
+
+<div class="viewcode-block" id="AriaEcXMLConverter.neighcontacts"><a class="viewcode-back" href="../../ariaec.html#ariaec.converter.AriaEcXMLConverter.neighcontacts">[docs]</a> <span class="nd">@staticmethod</span>
+ <span class="k">def</span> <span class="nf">neighcontacts</span><span class="p">(</span><span class="n">contacts</span><span class="p">,</span> <span class="n">maxidx</span><span class="p">,</span> <span class="n">offset</span><span class="o">=</span><span class="mi">0</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> </span>
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> contacts: list of tuple</span>
+<span class="sd"> maxidx: int</span>
+<span class="sd"> Maximum index value in pairs</span>
+<span class="sd"> offset: int</span>
+<span class="sd"> If indexes in pairs start by 0 or 0 + offset</span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+<span class="sd"> """</span>
+ <span class="n">neighcontacts</span> <span class="o">=</span> <span class="p">[]</span>
+
+ <span class="k">for</span> <span class="n">contact</span> <span class="ow">in</span> <span class="n">contacts</span><span class="p">:</span>
+ <span class="n">neighcontacts</span> <span class="o">+=</span> <span class="n">AriaEcXMLConverter</span><span class="o">.</span><span class="n">neighcontact</span><span class="p">(</span>
+ <span class="n">contact</span><span class="p">,</span> <span class="n">maxidx</span><span class="p">,</span> <span class="n">offset</span><span class="p">)</span>
+
+ <span class="k">return</span> <span class="n">neighcontacts</span></div>
+
+<div class="viewcode-block" id="AriaEcXMLConverter.targetdistmaps"><a class="viewcode-back" href="../../ariaec.html#ariaec.converter.AriaEcXMLConverter.targetdistmaps">[docs]</a> <span class="k">def</span> <span class="nf">targetdistmaps</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">sequence</span><span class="p">,</span> <span class="n">distfile</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> </span>
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> distfile :</span>
+<span class="sd"> param groupby: (Default value = None)</span>
+<span class="sd"> sequence :</span>
+<span class="sd"> </span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+<span class="sd"> </span>
+<span class="sd"> """</span>
+ <span class="c1"># TODO: valeur par defaut de distfile au fichier contenant les infos</span>
+ <span class="c1"># fixes</span>
+ <span class="c1"># ! target est une ResAtmMap pour les 20 aa, sinon il s'agit d'une</span>
+ <span class="c1"># carte de distance (native ou predite)</span>
+ <span class="c1"># Fixed</span>
+ <span class="c1"># -----</span>
+ <span class="c1"># => target contient des infos pour les 20 aa qui modifieront le champ</span>
+ <span class="c1"># distance de la contrainte</span>
+ <span class="c1"># => AaAtmMap (20 aa) OU AtmMap</span>
+ <span class="c1"># pdbstat</span>
+ <span class="c1"># -------</span>
+ <span class="c1"># => target contient des infos pour les 20 aa. Ces valeurs</span>
+ <span class="c1"># correspondant au mode des distribution des structures de haute</span>
+ <span class="c1"># resolution.</span>
+ <span class="c1"># => Construire Maps en fonction des modes des distribution</span>
+ <span class="c1"># => SsAaAtmMap (Ajout info structure secondaire) OU AaAtmMap (20</span>
+ <span class="c1"># aa) OU AaMap (20 aa) OU AtmMap pour les 20 aa</span>
+ <span class="c1"># distfile</span>
+ <span class="c1"># ---------</span>
+ <span class="c1"># => target contient les infos de distances predites en fonction</span>
+ <span class="c1"># des positions</span>
+ <span class="c1"># => ResMap (contacts pdb ou predits)</span>
+
+ <span class="c1"># 2 solutions when we use pdbstat:</span>
+ <span class="c1">#</span>
+ <span class="n">targetmaps</span> <span class="o">=</span> <span class="p">{</span>
+ <span class="s1">'INTERLOWERBOUNDS'</span><span class="p">:</span> <span class="kc">None</span><span class="p">,</span>
+ <span class="s1">'INTERTARGET'</span><span class="p">:</span> <span class="kc">None</span><span class="p">,</span>
+ <span class="s1">'INTERUPPERBOUNDS'</span><span class="p">:</span> <span class="kc">None</span><span class="p">,</span>
+ <span class="s1">'INTRALOWERBOUNDS'</span><span class="p">:</span> <span class="kc">None</span><span class="p">,</span>
+ <span class="s1">'INTRATARGET'</span><span class="p">:</span> <span class="kc">None</span><span class="p">,</span>
+ <span class="s1">'INTRAUPPERBOUNDS'</span><span class="p">:</span> <span class="kc">None</span>
+ <span class="p">}</span>
+ <span class="n">distype</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">setup</span><span class="o">.</span><span class="n">config</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"distance_type"</span><span class="p">,</span> <span class="s2">"fixed"</span><span class="p">)</span>
+
+ <span class="k">if</span> <span class="n">distype</span> <span class="o">==</span> <span class="s2">"distfile"</span> <span class="ow">and</span> <span class="n">distfile</span><span class="p">:</span>
+ <span class="c1"># Retourne ResAtmMap associe au fichier de distance pdb</span>
+ <span class="n">targetmaps</span><span class="p">[</span><span class="s1">'INTERTARGET'</span><span class="p">]</span> <span class="o">=</span> <span class="n">distfile</span><span class="o">.</span><span class="n">mapdict</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">'alldistmap'</span><span class="p">)</span>
+ <span class="k">elif</span> <span class="n">distype</span> <span class="o">==</span> <span class="s2">"fixed"</span><span class="p">:</span>
+ <span class="c1"># Fixed distances with bound in aria_ec.ini</span>
+ <span class="c1"># retourne ResAtmMap (20 aa)</span>
+ <span class="c1"># targetmap = ResAtmMap(sequence)</span>
+ <span class="c1"># targetmap[:] = self.settings.setup.config["restraint_distance"]</span>
+ <span class="c1"># targetmaps['INTERTARGET'] = targetmap</span>
+ <span class="n">targetmaps</span><span class="p">[</span><span class="s1">'INTERTARGET'</span><span class="p">]</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">setup</span><span class="o">.</span><span class="n">config</span><span class="p">[</span>
+ <span class="s2">"restraint_distance"</span><span class="p">]</span>
+ <span class="k">elif</span> <span class="n">distype</span> <span class="o">==</span> <span class="s2">"pdbstat"</span><span class="p">:</span>
+ <span class="c1"># TODO: pdbstats a partir d'une matrice pickle (faire une</span>
+ <span class="c1"># fonction qui genere la matrice en dehors et la sauvegarde</span>
+ <span class="c1"># dans le dossier data)</span>
+ <span class="c1"># Met a jour les valeurs de targetmaps en fonction de celles dispo</span>
+ <span class="c1"># dans pdbstat</span>
+
+ <span class="c1"># settings = self.settings.setup.config</span>
+ <span class="c1"># pdbdict = {atmbound.replace('_upper_bound', ''): settings.get(</span>
+ <span class="c1"># atmbound, None) for atmbound in (bound for bound in settings</span>
+ <span class="c1"># if '_upper_bound' in bound.lower())}</span>
+ <span class="c1"># targetmaps.subfill(pdbdict, level=1)</span>
+ <span class="c1"># targetmaps = SsAaAtmMap()</span>
+ <span class="n">targetmaps</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_pdbdistmaps</span><span class="p">()</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="c1"># retourne fixed AtmMap</span>
+ <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s2">"Unknown distance_type </span><span class="si">%s</span><span class="s2"> or wrong distance file"</span> <span class="o">%</span>
+ <span class="n">distype</span><span class="p">)</span>
+ <span class="k">return</span> <span class="n">targetmaps</span></div>
+
+<div class="viewcode-block" id="AriaEcXMLConverter.get_dist"><a class="viewcode-back" href="../../ariaec.html#ariaec.converter.AriaEcXMLConverter.get_dist">[docs]</a> <span class="k">def</span> <span class="nf">get_dist</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">distmap</span><span class="p">,</span> <span class="n">contribs</span><span class="p">,</span> <span class="n">defaultdist</span><span class="p">,</span> <span class="n">protein</span><span class="p">,</span>
+ <span class="n">groupby</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Get target distance from distance map</span>
+<span class="sd"> </span>
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> distmap</span>
+<span class="sd"> contribs</span>
+<span class="sd"> defaultdist</span>
+<span class="sd"> protein</span>
+<span class="sd"> groupby</span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+<span class="sd"> """</span>
+
+ <span class="k">def</span> <span class="nf">resname</span><span class="p">(</span><span class="n">res</span><span class="p">):</span>
+ <span class="sd">"""</span>
+
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> res :</span>
+<span class="sd"> return:</span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+
+<span class="sd"> """</span>
+ <span class="k">return</span> <span class="n">AminoAcid</span><span class="o">.</span><span class="n">AminoAcid</span><span class="p">(</span><span class="n">res</span><span class="p">)[</span><span class="mi">1</span><span class="p">]</span>
+
+ <span class="n">distype</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">setup</span><span class="o">.</span><span class="n">config</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"distance_type"</span><span class="p">,</span> <span class="s2">"fixed"</span><span class="p">)</span>
+ <span class="n">groupby</span> <span class="o">=</span> <span class="n">groupby</span> <span class="k">if</span> <span class="n">groupby</span> <span class="k">else</span> <span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">setup</span><span class="o">.</span><span class="n">config</span><span class="p">[</span>
+ <span class="s2">"groupby_method"</span><span class="p">]</span>
+ <span class="c1"># TODO: Avoid reduce call if possible (slow)</span>
+ <span class="k">if</span> <span class="n">distype</span> <span class="o">!=</span> <span class="s2">"fixed"</span><span class="p">:</span>
+ <span class="n">distmap</span> <span class="o">=</span> <span class="n">distmap</span> <span class="k">if</span> <span class="n">protein</span><span class="o">.</span><span class="n">sec_struct</span> <span class="k">else</span> <span class="n">distmap</span><span class="o">.</span><span class="n">reduce</span><span class="p">(</span>
+ <span class="n">groupby</span><span class="o">=</span><span class="n">groupby</span><span class="p">)</span>
+ <span class="c1"># Definir le type de la carte Puis</span>
+ <span class="c1"># Calculer l'index relatif a la paire ou la liste de paires d'atomes</span>
+ <span class="n">dist_list</span> <span class="o">=</span> <span class="p">[]</span>
+
+ <span class="k">if</span> <span class="nb">type</span><span class="p">(</span><span class="n">distmap</span><span class="p">)</span> <span class="o">==</span> <span class="n">ResAtmMap</span> <span class="ow">and</span> \
+ <span class="n">distmap</span><span class="o">.</span><span class="n">sequence</span> <span class="o">==</span> <span class="n">protein</span><span class="o">.</span><span class="n">aa_sequence</span><span class="o">.</span><span class="n">sequence</span><span class="p">:</span>
+ <span class="k">for</span> <span class="n">contrib</span> <span class="ow">in</span> <span class="n">contribs</span><span class="p">:</span>
+ <span class="n">mapidx_x</span> <span class="o">=</span> <span class="n">distmap</span><span class="o">.</span><span class="n">index</span><span class="o">.</span><span class="n">levels</span><span class="p">[</span><span class="mi">0</span><span class="p">][</span><span class="n">contrib</span><span class="p">[</span><span class="mi">0</span><span class="p">][</span><span class="mi">0</span><span class="p">]]</span>
+ <span class="n">mapidx_y</span> <span class="o">=</span> <span class="n">distmap</span><span class="o">.</span><span class="n">index</span><span class="o">.</span><span class="n">levels</span><span class="p">[</span><span class="mi">0</span><span class="p">][</span><span class="n">contrib</span><span class="p">[</span><span class="mi">1</span><span class="p">][</span><span class="mi">0</span><span class="p">]]</span>
+ <span class="n">dist_list</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">distmap</span><span class="o">.</span><span class="n">loc</span><span class="p">[</span>
+ <span class="n">mapidx_x</span><span class="p">,</span> <span class="n">contrib</span><span class="p">[</span><span class="mi">0</span><span class="p">][</span><span class="mi">1</span><span class="p">]][</span>
+ <span class="n">mapidx_y</span><span class="p">,</span> <span class="n">contrib</span><span class="p">[</span><span class="mi">1</span><span class="p">][</span><span class="mi">1</span><span class="p">]])</span>
+ <span class="k">elif</span> <span class="nb">type</span><span class="p">(</span><span class="n">distmap</span><span class="p">)</span> <span class="o">==</span> <span class="n">SsAaAtmMap</span> <span class="ow">and</span> <span class="ow">not</span> <span class="n">protein</span><span class="o">.</span><span class="n">sec_struct</span><span class="p">:</span>
+ <span class="c1"># TODO: Actually only inter distances used</span>
+ <span class="c1"># TODO: Works only with minimal target map (with CA, CB, SC indexes)</span>
+ <span class="k">for</span> <span class="n">contrib</span> <span class="ow">in</span> <span class="n">contribs</span><span class="p">:</span>
+ <span class="n">residx1</span> <span class="o">=</span> <span class="n">contrib</span><span class="p">[</span><span class="mi">0</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span>
+ <span class="n">res1</span> <span class="o">=</span> <span class="n">resname</span><span class="p">(</span><span class="n">protein</span><span class="o">.</span><span class="n">aa_sequence</span><span class="o">.</span><span class="n">sequence</span><span class="p">[</span><span class="n">residx1</span><span class="p">])</span>
+ <span class="n">atm1</span> <span class="o">=</span> <span class="n">contrib</span><span class="p">[</span><span class="mi">0</span><span class="p">][</span><span class="mi">1</span><span class="p">]</span>
+ <span class="n">atm1</span> <span class="o">=</span> <span class="n">atm1</span> <span class="k">if</span> <span class="n">atm1</span> <span class="ow">in</span> <span class="p">(</span><span class="s1">'CA'</span><span class="p">,</span> <span class="s1">'CB'</span><span class="p">)</span> <span class="k">else</span> <span class="s1">'SC'</span>
+ <span class="n">residx2</span> <span class="o">=</span> <span class="n">contrib</span><span class="p">[</span><span class="mi">1</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span>
+ <span class="n">res2</span> <span class="o">=</span> <span class="n">resname</span><span class="p">(</span><span class="n">protein</span><span class="o">.</span><span class="n">aa_sequence</span><span class="o">.</span><span class="n">sequence</span><span class="p">[</span><span class="n">residx2</span><span class="p">])</span>
+ <span class="n">atm2</span> <span class="o">=</span> <span class="n">contrib</span><span class="p">[</span><span class="mi">1</span><span class="p">][</span><span class="mi">1</span><span class="p">]</span>
+ <span class="n">atm2</span> <span class="o">=</span> <span class="n">atm2</span> <span class="k">if</span> <span class="n">atm2</span> <span class="ow">in</span> <span class="p">(</span><span class="s1">'CA'</span><span class="p">,</span> <span class="s1">'CB'</span><span class="p">)</span> <span class="k">else</span> <span class="s1">'SC'</span>
+ <span class="n">idx1</span> <span class="o">=</span> <span class="n">res1</span><span class="p">,</span> <span class="n">atm1</span>
+ <span class="n">idx2</span> <span class="o">=</span> <span class="n">res2</span><span class="p">,</span> <span class="n">atm2</span>
+ <span class="n">dist</span> <span class="o">=</span> <span class="n">distmap</span><span class="o">.</span><span class="n">sort_index</span><span class="p">()</span><span class="o">.</span><span class="n">loc</span><span class="p">[</span><span class="n">idx1</span><span class="p">][</span><span class="n">idx2</span><span class="p">]</span>
+ <span class="n">dist</span> <span class="o">=</span> <span class="n">dist</span> <span class="k">if</span> <span class="n">pd</span><span class="o">.</span><span class="n">notnull</span><span class="p">(</span><span class="n">dist</span><span class="p">)</span> <span class="ow">and</span> <span class="n">dist</span> <span class="o">!=</span> <span class="mf">0.</span> <span class="k">else</span> \
+ <span class="n">distmap</span><span class="o">.</span><span class="n">sort_index</span><span class="p">()</span><span class="o">.</span><span class="n">loc</span><span class="p">[</span><span class="n">idx2</span><span class="p">][</span><span class="n">idx1</span><span class="p">]</span>
+ <span class="k">if</span> <span class="n">pd</span><span class="o">.</span><span class="n">notnull</span><span class="p">(</span><span class="n">dist</span><span class="p">)</span> <span class="ow">and</span> <span class="n">dist</span> <span class="o">!=</span> <span class="mf">0.</span><span class="p">:</span>
+ <span class="n">dist_list</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">dist</span><span class="p">)</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="n">dist_list</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">defaultdist</span><span class="p">)</span>
+ <span class="k">elif</span> <span class="nb">type</span><span class="p">(</span><span class="n">distmap</span><span class="p">)</span> <span class="o">==</span> <span class="n">SsAaAtmMap</span><span class="p">:</span>
+ <span class="c1"># TODO: Actually only inter distances used</span>
+ <span class="c1"># TODO: Works only with minimal target map (with CA, CB, SC indexes)</span>
+ <span class="k">for</span> <span class="n">contrib</span> <span class="ow">in</span> <span class="n">contribs</span><span class="p">:</span>
+ <span class="n">residx1</span> <span class="o">=</span> <span class="n">contrib</span><span class="p">[</span><span class="mi">0</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span>
+ <span class="n">res1</span> <span class="o">=</span> <span class="n">resname</span><span class="p">(</span><span class="n">protein</span><span class="o">.</span><span class="n">aa_sequence</span><span class="o">.</span><span class="n">sequence</span><span class="p">[</span><span class="n">residx1</span><span class="p">])</span>
+ <span class="n">atm1</span> <span class="o">=</span> <span class="n">contrib</span><span class="p">[</span><span class="mi">0</span><span class="p">][</span><span class="mi">1</span><span class="p">]</span>
+ <span class="n">atm1</span> <span class="o">=</span> <span class="n">atm1</span> <span class="k">if</span> <span class="n">atm1</span> <span class="ow">in</span> <span class="p">(</span><span class="s1">'CA'</span><span class="p">,</span> <span class="s1">'CB'</span><span class="p">)</span> <span class="k">else</span> <span class="s1">'SC'</span>
+ <span class="n">ss1</span> <span class="o">=</span> <span class="n">protein</span><span class="o">.</span><span class="n">sec_struct</span><span class="o">.</span><span class="n">sequence</span><span class="p">[</span><span class="n">residx1</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span>
+ <span class="n">ss1</span> <span class="o">=</span> <span class="n">ss1</span> <span class="k">if</span> <span class="n">ss1</span> <span class="ow">in</span> <span class="p">(</span><span class="s1">'E'</span><span class="p">,</span> <span class="s1">'H'</span><span class="p">)</span> <span class="k">else</span> <span class="s1">'X'</span>
+ <span class="n">residx2</span> <span class="o">=</span> <span class="n">contrib</span><span class="p">[</span><span class="mi">1</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span>
+ <span class="n">res2</span> <span class="o">=</span> <span class="n">resname</span><span class="p">(</span><span class="n">protein</span><span class="o">.</span><span class="n">aa_sequence</span><span class="o">.</span><span class="n">sequence</span><span class="p">[</span><span class="n">residx2</span><span class="p">])</span>
+ <span class="n">atm2</span> <span class="o">=</span> <span class="n">contrib</span><span class="p">[</span><span class="mi">1</span><span class="p">][</span><span class="mi">1</span><span class="p">]</span>
+ <span class="n">atm2</span> <span class="o">=</span> <span class="n">atm2</span> <span class="k">if</span> <span class="n">atm2</span> <span class="ow">in</span> <span class="p">(</span><span class="s1">'CA'</span><span class="p">,</span> <span class="s1">'CB'</span><span class="p">)</span> <span class="k">else</span> <span class="s1">'SC'</span>
+ <span class="n">ss2</span> <span class="o">=</span> <span class="n">protein</span><span class="o">.</span><span class="n">sec_struct</span><span class="o">.</span><span class="n">sequence</span><span class="p">[</span><span class="n">residx2</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span>
+ <span class="n">ss2</span> <span class="o">=</span> <span class="n">ss2</span> <span class="k">if</span> <span class="n">ss2</span> <span class="ow">in</span> <span class="p">(</span><span class="s1">'E'</span><span class="p">,</span> <span class="s1">'H'</span><span class="p">)</span> <span class="k">else</span> <span class="s1">'X'</span>
+ <span class="n">idx1</span> <span class="o">=</span> <span class="n">ss1</span><span class="p">,</span> <span class="n">res1</span><span class="p">,</span> <span class="n">atm1</span>
+ <span class="n">idx2</span> <span class="o">=</span> <span class="n">ss2</span><span class="p">,</span> <span class="n">res2</span><span class="p">,</span> <span class="n">atm2</span>
+ <span class="n">dist</span> <span class="o">=</span> <span class="n">distmap</span><span class="o">.</span><span class="n">sort_index</span><span class="p">()</span><span class="o">.</span><span class="n">loc</span><span class="p">[</span><span class="n">idx1</span><span class="p">][</span><span class="n">idx2</span><span class="p">]</span>
+ <span class="n">dist</span> <span class="o">=</span> <span class="n">dist</span> <span class="k">if</span> <span class="n">pd</span><span class="o">.</span><span class="n">notnull</span><span class="p">(</span><span class="n">dist</span><span class="p">)</span> <span class="ow">and</span> <span class="n">dist</span> <span class="o">!=</span> <span class="mf">0.</span> <span class="k">else</span> \
+ <span class="n">distmap</span><span class="o">.</span><span class="n">sort_index</span><span class="p">()</span><span class="o">.</span><span class="n">loc</span><span class="p">[</span><span class="n">idx2</span><span class="p">][</span><span class="n">idx1</span><span class="p">]</span>
+ <span class="k">if</span> <span class="n">pd</span><span class="o">.</span><span class="n">notnull</span><span class="p">(</span><span class="n">dist</span><span class="p">)</span> <span class="ow">and</span> <span class="n">dist</span> <span class="o">!=</span> <span class="mf">0.</span><span class="p">:</span>
+ <span class="n">dist_list</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">dist</span><span class="p">)</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="n">dist_list</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">defaultdist</span><span class="p">)</span>
+ <span class="k">elif</span> <span class="nb">type</span><span class="p">(</span><span class="n">distmap</span><span class="p">)</span> <span class="o">==</span> <span class="n">ResMap</span> <span class="ow">and</span> \
+ <span class="n">distmap</span><span class="o">.</span><span class="n">sequence</span> <span class="o">==</span> <span class="n">protein</span><span class="o">.</span><span class="n">aa_sequence</span><span class="o">.</span><span class="n">sequence</span><span class="p">:</span>
+ <span class="k">for</span> <span class="n">contrib</span> <span class="ow">in</span> <span class="n">contribs</span><span class="p">:</span>
+ <span class="n">dist_list</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="s2">"</span><span class="si">%.2f</span><span class="s2">"</span> <span class="o">%</span> <span class="n">distmap</span><span class="o">.</span><span class="n">iat</span><span class="p">[</span>
+ <span class="n">contrib</span><span class="p">[</span><span class="mi">0</span><span class="p">][</span><span class="mi">0</span><span class="p">],</span> <span class="n">contrib</span><span class="p">[</span><span class="mi">1</span><span class="p">][</span><span class="mi">0</span><span class="p">]])</span>
+ <span class="k">elif</span> <span class="nb">type</span><span class="p">(</span><span class="n">distmap</span><span class="p">)</span> <span class="o">==</span> <span class="nb">float</span><span class="p">:</span>
+ <span class="k">return</span> <span class="n">distmap</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">return</span> <span class="n">defaultdist</span>
+
+ <span class="c1"># Retourner la distance si elle est unique ou une valeur utilisant la</span>
+ <span class="c1"># methode groupby</span>
+ <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">dist_list</span><span class="p">)</span> <span class="o">==</span> <span class="mi">1</span><span class="p">:</span>
+ <span class="k">return</span> <span class="n">dist_list</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
+ <span class="k">elif</span> <span class="n">groupby</span> <span class="o">==</span> <span class="s2">"deff"</span><span class="p">:</span>
+ <span class="c1"># Compute effective distance from distance list between</span>
+ <span class="c1"># all pairs in the adr</span>
+ <span class="k">return</span> <span class="s2">"</span><span class="si">%.2f</span><span class="s2">"</span> <span class="o">%</span> <span class="bp">self</span><span class="o">.</span><span class="n">deff</span><span class="p">(</span><span class="n">dist_list</span><span class="p">,</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">setup</span><span class="o">.</span><span class="n">config</span><span class="p">[</span><span class="s2">"deffpow"</span><span class="p">])</span>
+ <span class="k">elif</span> <span class="n">groupby</span> <span class="o">==</span> <span class="s2">"mean"</span><span class="p">:</span>
+ <span class="k">return</span> <span class="n">np</span><span class="o">.</span><span class="n">mean</span><span class="p">(</span><span class="n">dist_list</span><span class="p">)</span>
+ <span class="k">elif</span> <span class="n">groupby</span> <span class="o">==</span> <span class="s2">"min"</span><span class="p">:</span>
+ <span class="k">return</span> <span class="nb">min</span><span class="p">(</span><span class="n">dist_list</span><span class="p">)</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">return</span> <span class="n">defaultdist</span></div>
+
+<div class="viewcode-block" id="AriaEcXMLConverter.write_map_restraint"><a class="viewcode-back" href="../../ariaec.html#ariaec.converter.AriaEcXMLConverter.write_map_restraint">[docs]</a> <span class="k">def</span> <span class="nf">write_map_restraint</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">protein</span><span class="p">,</span> <span class="n">contactmap</span><span class="p">,</span> <span class="n">nb_c</span><span class="p">,</span> <span class="n">targetdists</span><span class="p">,</span>
+ <span class="n">scoremap</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">listname</span><span class="o">=</span><span class="s2">""</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Translate maplot in ARIA XML restraint</span>
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> protein</span>
+<span class="sd"> listname :</span>
+<span class="sd"> param contactmap: ResAtmMap for a protein (Default value = "")</span>
+<span class="sd"> nb_c :</span>
+<span class="sd"> Number of restraints selected</span>
+<span class="sd"> targetdists : dict</span>
+<span class="sd"> ResAtmMap for each atom for each amino acid</span>
+<span class="sd"> scoremap :</span>
+<span class="sd"> sorted list of contacts (Default value = None)</span>
+<span class="sd"> contactmap :</span>
+<span class="sd"> </span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+<span class="sd"> </span>
+<span class="sd"> """</span>
+
+ <span class="k">if</span> <span class="n">scoremap</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+ <span class="c1"># TODO: implement viterbiscore as scoremap for bbcontacts ?</span>
+ <span class="n">contacts</span> <span class="o">=</span> <span class="n">scoremap</span><span class="o">.</span><span class="n">sortedset</span><span class="p">()[:</span><span class="n">nb_c</span><span class="p">]</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="c1"># TODO: Probleme selection des contacts utilises en l'absence de</span>
+ <span class="c1"># poids:</span>
+ <span class="c1"># - aleatoire (implementation actuelle) => Tester la</span>
+ <span class="c1"># robustesse</span>
+ <span class="c1"># - trouver une maniere d'attribuer des poids dans le cas</span>
+ <span class="c1"># d'une matrice de distance d'un pdb ?</span>
+ <span class="c1"># - Def le max independent set dans le graphe (matrice de</span>
+ <span class="c1"># contacts) => utiliser tout les contact de ce set ou def des</span>
+ <span class="c1"># poids pour selectionner l * f contacts de ce set</span>
+ <span class="k">if</span> <span class="n">nb_c</span> <span class="o"><</span> <span class="nb">len</span><span class="p">(</span><span class="n">contactmap</span><span class="o">.</span><span class="n">contactset</span><span class="p">()):</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">info</span><span class="p">(</span>
+ <span class="s2">"Initialize sampling for contact selection with seed </span><span class="si">%s</span><span class="s2">"</span><span class="p">,</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">setup</span><span class="o">.</span><span class="n">config</span><span class="p">[</span><span class="s1">'seed'</span><span class="p">])</span>
+ <span class="n">random</span><span class="o">.</span><span class="n">seed</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">setup</span><span class="o">.</span><span class="n">config</span><span class="p">[</span><span class="s1">'seed'</span><span class="p">])</span>
+ <span class="n">contacts</span> <span class="o">=</span> <span class="n">random</span><span class="o">.</span><span class="n">sample</span><span class="p">(</span><span class="n">contactmap</span><span class="o">.</span><span class="n">contactset</span><span class="p">(),</span> <span class="n">nb_c</span><span class="p">)</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s2">"Using all contacts"</span><span class="p">)</span>
+ <span class="n">contacts</span> <span class="o">=</span> <span class="n">contactmap</span><span class="o">.</span><span class="n">contactset</span><span class="p">()[:]</span>
+
+ <span class="n">hum_list</span> <span class="o">=</span> <span class="p">[(</span><span class="n">con1</span> <span class="o">+</span> <span class="mi">1</span><span class="p">,</span> <span class="n">con2</span> <span class="o">+</span> <span class="mi">1</span><span class="p">)</span> <span class="k">for</span> <span class="n">con1</span><span class="p">,</span> <span class="n">con2</span> <span class="ow">in</span> <span class="n">contacts</span><span class="p">]</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s2">"Selecting </span><span class="si">%d</span><span class="s2"> contacts"</span><span class="p">,</span> <span class="n">nb_c</span><span class="p">)</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="s2">"</span><span class="se">\n</span><span class="si">%s</span><span class="s2">"</span><span class="p">,</span> <span class="s1">'</span><span class="se">\n</span><span class="s1">'</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">textwrap</span><span class="o">.</span><span class="n">wrap</span><span class="p">(</span>
+ <span class="s1">' '</span><span class="o">.</span><span class="n">join</span><span class="p">([</span><span class="s2">"(</span><span class="si">%2d</span><span class="s2">, </span><span class="si">%2d</span><span class="s2">)"</span> <span class="o">%</span> <span class="n">pair</span> <span class="k">for</span> <span class="n">pair</span> <span class="ow">in</span> <span class="n">hum_list</span><span class="p">]),</span> <span class="n">width</span><span class="o">=</span><span class="mi">80</span><span class="p">)))</span>
+
+ <span class="n">weight_list</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="nb">float</span><span class="p">(</span><span class="mf">10.0</span> <span class="o">/</span> <span class="p">(</span><span class="n">x</span> <span class="o">+</span> <span class="mi">1</span><span class="p">))</span> <span class="k">for</span> <span class="n">x</span><span class="p">,</span> <span class="n">v</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span>
+ <span class="n">contacts</span><span class="p">))</span> <span class="k">if</span> \
+ <span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">setup</span><span class="o">.</span><span class="n">config</span><span class="p">[</span><span class="s1">'evfold_weight'</span><span class="p">]</span> <span class="ow">and</span> \
+ <span class="n">scoremap</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span> <span class="k">else</span> <span class="nb">list</span><span class="p">(</span><span class="mf">1.0</span> <span class="k">for</span> <span class="n">_</span> <span class="ow">in</span> <span class="n">contacts</span><span class="p">)</span>
+
+ <span class="n">neigh_flag</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">setup</span><span class="o">.</span><span class="n">config</span><span class="p">[</span><span class="s1">'neighborhood_contact'</span><span class="p">]</span>
+ <span class="n">adr_flag</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">setup</span><span class="o">.</span><span class="n">config</span><span class="p">[</span><span class="s2">"ambiguous_distance_restraint"</span><span class="p">]</span>
+ <span class="n">contribs_type</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">setup</span><span class="o">.</span><span class="n">config</span><span class="p">[</span><span class="s2">"contributions_type"</span><span class="p">]</span>
+ <span class="n">atms_type</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">setup</span><span class="o">.</span><span class="n">config</span><span class="p">[</span><span class="s2">"atoms_type"</span><span class="p">]</span>
+ <span class="n">default_target_dist</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">setup</span><span class="o">.</span><span class="n">config</span><span class="p">[</span><span class="s2">"restraint_distance"</span><span class="p">]</span>
+ <span class="c1"># TODO: Lower bound and upper bound matrix not used actually...</span>
+ <span class="n">targetdistmap</span> <span class="o">=</span> <span class="n">targetdists</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">'INTERTARGET'</span><span class="p">)</span>
+ <span class="n">nat_reliable</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">setup</span><span class="o">.</span><span class="n">config</span><span class="p">[</span><span class="s2">"native_reliable"</span><span class="p">]</span>
+
+ <span class="k">def</span> <span class="nf">resname_3l</span><span class="p">(</span><span class="n">residx</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> </span>
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> residx :</span>
+<span class="sd"> return:</span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+<span class="sd"> </span>
+<span class="sd"> """</span>
+ <span class="k">return</span> <span class="n">AminoAcid</span><span class="o">.</span><span class="n">AminoAcid</span><span class="p">(</span><span class="n">contactmap</span><span class="o">.</span><span class="n">index</span><span class="o">.</span><span class="n">values</span><span class="p">[</span><span class="n">residx</span><span class="p">][</span><span class="o">-</span><span class="mi">3</span><span class="p">:])[</span><span class="mi">1</span><span class="p">]</span>
+
+ <span class="n">max_seqidx</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">contactmap</span><span class="o">.</span><span class="n">sequence</span><span class="p">)</span>
+ <span class="n">restraint_dict</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">OrderedDict</span><span class="p">()</span>
+ <span class="n">rest_id</span> <span class="o">=</span> <span class="mi">0</span>
+ <span class="n">contrib_id</span> <span class="o">=</span> <span class="mi">0</span>
+ <span class="n">tqdm_out</span> <span class="o">=</span> <span class="n">TqdmToLogger</span><span class="p">(</span><span class="n">LOG</span><span class="p">,</span> <span class="n">level</span><span class="o">=</span><span class="n">logging</span><span class="o">.</span><span class="n">INFO</span><span class="p">)</span>
+ <span class="k">for</span> <span class="n">contactidx</span><span class="p">,</span> <span class="n">subcontacts</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span>
+ <span class="n">tqdm</span><span class="p">(</span><span class="n">contacts</span><span class="p">,</span> <span class="n">file</span><span class="o">=</span><span class="n">tqdm_out</span><span class="p">,</span> <span class="n">mininterval</span><span class="o">=</span><span class="mf">1.</span><span class="p">)):</span>
+
+ <span class="n">LOG</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="s2">"Writing restraint related to contact </span><span class="si">%s</span><span class="s2">"</span> <span class="o">%</span>
+ <span class="nb">str</span><span class="p">((</span><span class="n">subcontacts</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">+</span> <span class="mi">1</span><span class="p">,</span> <span class="n">subcontacts</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="o">+</span> <span class="mi">1</span><span class="p">)))</span>
+ <span class="c1"># Get weight related to the contact</span>
+ <span class="n">contactweight</span> <span class="o">=</span> <span class="n">weight_list</span><span class="p">[</span><span class="n">contactidx</span><span class="p">]</span>
+
+ <span class="c1"># Define Residue lists for the contact. Those lists contains</span>
+ <span class="c1"># normally only one element by default except if we introduce</span>
+ <span class="c1"># neighbors with neigh_flag triggered</span>
+ <span class="n">subcontacts</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">neighcontact</span><span class="p">(</span><span class="n">subcontacts</span><span class="p">,</span>
+ <span class="n">max_seqidx</span> <span class="o">-</span> <span class="mi">1</span><span class="p">)</span> <span class="k">if</span> <span class="n">neigh_flag</span> \
+ <span class="k">else</span> <span class="p">[</span><span class="n">subcontacts</span><span class="p">]</span>
+
+ <span class="c1"># Define list of atom pairs</span>
+ <span class="n">contribs_lists</span> <span class="o">=</span> <span class="p">[]</span>
+ <span class="c1"># Compute all lists of atompair related to the contact</span>
+ <span class="k">for</span> <span class="n">subcontact</span> <span class="ow">in</span> <span class="n">subcontacts</span><span class="p">:</span>
+ <span class="n">contribs_lists</span> <span class="o">+=</span> <span class="bp">self</span><span class="o">.</span><span class="n">atm_product</span><span class="p">(</span>
+ <span class="n">subcontact</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">resname_3l</span><span class="p">(</span><span class="n">subcontact</span><span class="p">[</span><span class="mi">0</span><span class="p">]),</span> <span class="n">subcontact</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span>
+ <span class="n">resname_3l</span><span class="p">(</span><span class="n">subcontact</span><span class="p">[</span><span class="mi">1</span><span class="p">]),</span> <span class="n">list_type</span><span class="o">=</span><span class="n">atms_type</span><span class="p">,</span>
+ <span class="n">adr_flag</span><span class="o">=</span><span class="n">adr_flag</span><span class="p">,</span> <span class="n">product_type</span><span class="o">=</span><span class="n">contribs_type</span><span class="p">)</span>
+
+ <span class="c1"># We have a unique atmpair list, trick to have a unique loop for</span>
+ <span class="c1"># all kind of restraints in the following</span>
+ <span class="n">contribs_lists</span> <span class="o">=</span> <span class="p">[</span>
+ <span class="n">contribs_lists</span><span class="p">,</span> <span class="p">]</span> <span class="k">if</span> <span class="ow">not</span> <span class="n">adr_flag</span> <span class="k">else</span> <span class="n">contribs_lists</span>
+
+ <span class="c1"># If ADR, build a restraint with contributions containing</span>
+ <span class="c1"># all atom pair in atmpairs => Get 1 target distance related to</span>
+ <span class="c1"># atmpairs list</span>
+ <span class="c1"># Else unambig, build a restraint with one contribution get a</span>
+ <span class="c1"># target distance for each atom pair</span>
+ <span class="k">for</span> <span class="n">contribs_list</span> <span class="ow">in</span> <span class="n">contribs_lists</span><span class="p">:</span>
+ <span class="n">rest_id</span> <span class="o">+=</span> <span class="mi">1</span>
+ <span class="c1"># For each atom list (only one list normally if unambig restraints)</span>
+ <span class="c1"># If adr flag, each list is a contribution list for one restraint</span>
+
+ <span class="k">for</span> <span class="n">contrib_idx</span><span class="p">,</span> <span class="n">contrib</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">contribs_list</span><span class="p">):</span>
+
+ <span class="n">res1_idx</span><span class="p">,</span> <span class="n">atm1</span> <span class="o">=</span> <span class="n">contrib</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
+ <span class="n">res2_idx</span><span class="p">,</span> <span class="n">atm2</span> <span class="o">=</span> <span class="n">contrib</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
+
+ <span class="c1"># Increment restraint id if not adr else keep the same</span>
+ <span class="c1"># restraint id for the actual contribution list</span>
+ <span class="n">rest_id</span> <span class="o">=</span> <span class="n">rest_id</span> <span class="o">+</span> <span class="mi">1</span> <span class="k">if</span> <span class="n">contrib_idx</span> <span class="o">!=</span> <span class="mi">0</span> <span class="ow">and</span> <span class="ow">not</span> <span class="n">adr_flag</span> <span class="k">else</span> <span class="n">rest_id</span>
+ <span class="c1"># Increment contribution id if adr else reset to 1</span>
+ <span class="n">contrib_id</span> <span class="o">=</span> <span class="n">contrib_id</span> <span class="o">+</span> <span class="mi">1</span> <span class="k">if</span> <span class="n">contrib_idx</span> <span class="o">!=</span> <span class="mi">0</span> <span class="ow">and</span> <span class="n">adr_flag</span> <span class="k">else</span> <span class="mi">1</span>
+
+ <span class="n">lower_bound</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">setup</span><span class="o">.</span><span class="n">config</span><span class="p">[</span><span class="s2">"lower_bound"</span><span class="p">])</span>
+ <span class="n">targetdist</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">get_dist</span><span class="p">(</span><span class="n">targetdistmap</span><span class="p">,</span> <span class="n">contribs_list</span><span class="p">,</span>
+ <span class="n">default_target_dist</span><span class="p">,</span> <span class="n">protein</span><span class="p">))</span> <span class="k">if</span> \
+ <span class="n">adr_flag</span> <span class="k">else</span> <span class="nb">float</span><span class="p">(</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">get_dist</span><span class="p">(</span><span class="n">targetdistmap</span><span class="p">,</span> <span class="p">[</span><span class="n">contrib</span><span class="p">],</span>
+ <span class="n">default_target_dist</span><span class="p">,</span> <span class="n">protein</span><span class="p">))</span>
+ <span class="n">upper_bound</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">setup</span><span class="o">.</span><span class="n">config</span><span class="p">[</span><span class="s2">"ca_upper_bound"</span><span class="p">])</span> <span class="k">if</span> \
+ <span class="p">(</span><span class="n">atm1</span><span class="p">,</span> <span class="n">atm2</span><span class="p">)</span> <span class="o">==</span> <span class="p">(</span><span class="s2">"CA"</span><span class="p">,</span> <span class="s2">"CA"</span><span class="p">)</span> <span class="ow">and</span> <span class="ow">not</span> <span class="n">adr_flag</span> <span class="k">else</span> \
+ <span class="nb">float</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">setup</span><span class="o">.</span><span class="n">config</span><span class="p">[</span><span class="s2">"cb_upper_bound"</span><span class="p">])</span> <span class="k">if</span> \
+ <span class="p">(</span><span class="n">atm1</span><span class="p">,</span> <span class="n">atm2</span><span class="p">)</span> <span class="o">==</span> <span class="p">(</span><span class="s2">"CB"</span><span class="p">,</span> <span class="s2">"CB"</span><span class="p">)</span> <span class="ow">and</span> <span class="ow">not</span> <span class="n">adr_flag</span> <span class="k">else</span> \
+ <span class="nb">float</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">setup</span><span class="o">.</span><span class="n">config</span><span class="p">[</span><span class="s2">"def_upper_bound"</span><span class="p">])</span>
+
+ <span class="c1"># TODO: Better way to define upper_bound if target > upper ???</span>
+ <span class="n">upper_bound</span> <span class="o">=</span> <span class="n">upper_bound</span> <span class="k">if</span> <span class="n">targetdist</span> <span class="o"><=</span> <span class="n">upper_bound</span> <span class="k">else</span> \
+ <span class="n">targetdist</span> <span class="o">+</span> <span class="n">lower_bound</span>
+
+ <span class="k">if</span> <span class="n">restraint_dict</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">rest_id</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
+ <span class="n">restraint_dict</span><span class="p">[</span><span class="n">rest_id</span><span class="p">]</span> <span class="o">=</span> <span class="p">{</span>
+ <span class="s2">"meta"</span><span class="p">:</span> <span class="p">{</span>
+ <span class="s2">"weight"</span><span class="p">:</span> <span class="n">contactweight</span><span class="p">,</span>
+ <span class="s2">"distance"</span><span class="p">:</span> <span class="n">targetdist</span><span class="p">,</span>
+ <span class="s2">"lower_bound"</span><span class="p">:</span> <span class="n">lower_bound</span><span class="p">,</span>
+ <span class="s2">"upper_bound"</span><span class="p">:</span> <span class="n">upper_bound</span><span class="p">,</span>
+ <span class="s2">"active"</span><span class="p">:</span> <span class="mi">1</span><span class="p">,</span>
+ <span class="s2">"reliable"</span><span class="p">:</span> <span class="mi">1</span> <span class="k">if</span> <span class="n">nat_reliable</span> <span class="ow">and</span> <span class="n">listname</span> <span class="ow">in</span> <span class="p">(</span>
+ <span class="s2">"native"</span><span class="p">,</span> <span class="s2">"native_full"</span><span class="p">,</span> <span class="s2">"pdb"</span><span class="p">)</span> <span class="k">else</span> <span class="mi">0</span><span class="p">,</span>
+ <span class="s2">"list_name"</span><span class="p">:</span> <span class="n">listname</span>
+ <span class="p">},</span>
+ <span class="s2">"contrib"</span><span class="p">:</span> <span class="n">collections</span><span class="o">.</span><span class="n">OrderedDict</span><span class="p">()</span>
+ <span class="p">}</span>
+
+ <span class="n">restraint_dict</span><span class="p">[</span><span class="n">rest_id</span><span class="p">][</span><span class="s2">"contrib"</span><span class="p">][</span><span class="n">contrib_id</span><span class="p">]</span> <span class="o">=</span> <span class="p">{</span>
+ <span class="s2">"meta"</span><span class="p">:</span> <span class="p">{</span>
+ <span class="s2">"weight"</span><span class="p">:</span> <span class="mf">1.0</span>
+ <span class="p">},</span>
+ <span class="s2">"spin_pair"</span><span class="p">:</span> <span class="p">{</span>
+ <span class="n">res1_idx</span> <span class="o">+</span> <span class="mi">1</span><span class="p">:</span> <span class="n">atm1</span><span class="p">,</span>
+ <span class="n">res2_idx</span> <span class="o">+</span> <span class="mi">1</span><span class="p">:</span> <span class="n">atm2</span>
+ <span class="p">}</span>
+ <span class="p">}</span>
+
+ <span class="c1"># Compute xml restraint file path</span>
+ <span class="n">xml_file</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">infra</span><span class="p">[</span><span class="s2">"xml"</span><span class="p">]</span> <span class="o">+</span> <span class="s2">"/"</span> <span class="o">+</span> <span class="s2">"_"</span><span class="o">.</span><span class="n">join</span><span class="p">((</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">outprefix</span><span class="p">,</span> <span class="n">listname</span><span class="p">))</span> <span class="o">+</span> <span class="s2">".xml"</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s2">"Write </span><span class="si">%d</span><span class="s2"> xml distance restraints in </span><span class="si">%s</span><span class="s2">"</span><span class="p">,</span> <span class="n">nb_c</span><span class="p">,</span> <span class="n">xml_file</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">write_dist_xml</span><span class="p">(</span><span class="n">restraint_dict</span><span class="p">,</span> <span class="n">xml_file</span><span class="p">)</span>
+ <span class="k">return</span> <span class="n">xml_file</span><span class="p">,</span> <span class="n">contacts</span></div>
+
+<div class="viewcode-block" id="AriaEcXMLConverter.write_maplist_restraints"><a class="viewcode-back" href="../../ariaec.html#ariaec.converter.AriaEcXMLConverter.write_maplist_restraints">[docs]</a> <span class="k">def</span> <span class="nf">write_maplist_restraints</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">maplist</span><span class="p">,</span> <span class="n">targetmaps</span><span class="p">,</span> <span class="n">protein</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Generate ARIA XML restraints from maplist</span>
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> maplist : list of ResAtmMap or ResMap object</span>
+<span class="sd"> </span>
+<span class="sd"> targetmaps : dict</span>
+
+<span class="sd"> protein</span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+<span class="sd"> </span>
+<span class="sd"> """</span>
+ <span class="n">out</span> <span class="o">=</span> <span class="p">([],</span> <span class="p">[])</span>
+
+ <span class="k">for</span> <span class="n">maptype</span> <span class="ow">in</span> <span class="n">maplist</span><span class="p">:</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s2">"Writing </span><span class="si">%s</span><span class="s2"> ARIA XML distance restraints"</span><span class="p">,</span> <span class="n">maptype</span><span class="p">)</span>
+ <span class="n">outfile</span><span class="p">,</span> <span class="n">pairlist</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">write_map_restraint</span><span class="p">(</span>
+ <span class="n">protein</span><span class="p">,</span> <span class="n">maplist</span><span class="p">[</span><span class="n">maptype</span><span class="p">][</span><span class="s1">'maplot'</span><span class="p">],</span> <span class="n">maplist</span><span class="p">[</span><span class="n">maptype</span><span class="p">][</span><span class="s2">"nb_c"</span><span class="p">],</span>
+ <span class="n">targetmaps</span><span class="p">,</span> <span class="n">listname</span><span class="o">=</span><span class="n">maptype</span><span class="p">,</span>
+ <span class="n">scoremap</span><span class="o">=</span><span class="n">maplist</span><span class="p">[</span><span class="n">maptype</span><span class="p">]</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"scoremap"</span><span class="p">))</span>
+ <span class="n">out</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">outfile</span><span class="p">)</span>
+ <span class="n">maplist</span><span class="p">[</span><span class="n">maptype</span><span class="p">][</span><span class="s2">"filteredlist"</span><span class="p">]</span> <span class="o">=</span> <span class="n">pairlist</span>
+ <span class="n">out</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">pairlist</span><span class="p">)</span>
+ <span class="k">return</span> <span class="n">out</span></div>
+
+<div class="viewcode-block" id="AriaEcXMLConverter.write_tbl_restraints"><a class="viewcode-back" href="../../ariaec.html#ariaec.converter.AriaEcXMLConverter.write_tbl_restraints">[docs]</a> <span class="k">def</span> <span class="nf">write_tbl_restraints</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">protein</span><span class="p">,</span> <span class="n">hbmap</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">n_hb</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Write tbl restraints</span>
+<span class="sd"> </span>
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> protein</span>
+<span class="sd"> hbmap</span>
+<span class="sd"> Extra hbond map (eg: metapsicov hbonds) (Default value = None)</span>
+<span class="sd"> n_hb</span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+<span class="sd"> dict</span>
+<span class="sd"> {'hbond': hb_file, 'dihed': dihed_file, 'ssdist': ssdist_file}</span>
+<span class="sd"> """</span>
+ <span class="n">dihed_file</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">infra</span><span class="p">[</span><span class="s2">"tbl"</span><span class="p">],</span> <span class="bp">self</span><span class="o">.</span><span class="n">outprefix</span> <span class="o">+</span>
+ <span class="s2">"_dihed.tbl"</span><span class="p">)</span>
+ <span class="n">hb_file</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">infra</span><span class="p">[</span><span class="s2">"tbl"</span><span class="p">],</span> <span class="bp">self</span><span class="o">.</span><span class="n">outprefix</span> <span class="o">+</span>
+ <span class="s2">"_hbond.tbl"</span><span class="p">)</span>
+ <span class="n">ssdist_file</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">infra</span><span class="p">[</span><span class="s2">"tbl"</span><span class="p">],</span> <span class="bp">self</span><span class="o">.</span><span class="n">outprefix</span> <span class="o">+</span>
+ <span class="s2">"_ssdist.tbl"</span><span class="p">)</span>
+ <span class="k">if</span> <span class="n">protein</span><span class="o">.</span><span class="n">sec_struct</span><span class="p">:</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s2">" Dihedral restraints for secondary structures (</span><span class="si">%s</span><span class="s2">)"</span><span class="p">,</span>
+ <span class="n">dihed_file</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">write_dihedral_tbl</span><span class="p">(</span><span class="n">protein</span><span class="o">.</span><span class="n">sec_struct</span><span class="o">.</span><span class="n">ss_matrix</span><span class="p">,</span> <span class="n">dihed_file</span><span class="p">)</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s2">" Secondary structure restraints (</span><span class="si">%s</span><span class="s2">)"</span><span class="p">,</span>
+ <span class="n">ssdist_file</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">write_ssdist_tbl</span><span class="p">(</span><span class="n">protein</span><span class="o">.</span><span class="n">sec_struct</span><span class="o">.</span><span class="n">ss_matrix</span><span class="p">,</span>
+ <span class="n">protein</span><span class="o">.</span><span class="n">sec_struct</span><span class="o">.</span><span class="n">ssdist</span><span class="p">,</span>
+ <span class="n">ssdist_file</span><span class="p">)</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s2">" Helix bond restraints (</span><span class="si">%s</span><span class="s2">)"</span><span class="p">,</span> <span class="n">hb_file</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">write_hb_tbl</span><span class="p">(</span><span class="n">protein</span><span class="p">,</span> <span class="n">hb_file</span><span class="p">,</span>
+ <span class="n">hbmap</span><span class="o">=</span><span class="n">hbmap</span><span class="p">,</span> <span class="n">n_hb</span><span class="o">=</span><span class="n">n_hb</span><span class="p">,</span>
+ <span class="n">lr_type</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">setup</span><span class="o">.</span><span class="n">config</span><span class="p">[</span>
+ <span class="s1">'longrange_hbtype'</span><span class="p">],</span>
+ <span class="n">dminus</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">setup</span><span class="o">.</span><span class="n">config</span><span class="p">[</span><span class="s1">'hb_dminus'</span><span class="p">],</span>
+ <span class="n">dplus</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">setup</span><span class="o">.</span><span class="n">config</span><span class="p">[</span><span class="s1">'hb_dplus'</span><span class="p">])</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="n">dihed_file</span> <span class="o">=</span> <span class="kc">None</span>
+ <span class="n">ssdist_file</span> <span class="o">=</span> <span class="kc">None</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="n">hbmap</span><span class="p">:</span>
+ <span class="n">hb_file</span> <span class="o">=</span> <span class="kc">None</span>
+ <span class="k">return</span> <span class="p">{</span><span class="s1">'hbond'</span><span class="p">:</span> <span class="n">hb_file</span><span class="p">,</span> <span class="s1">'dihed'</span><span class="p">:</span> <span class="n">dihed_file</span><span class="p">,</span> <span class="s1">'ssdist'</span><span class="p">:</span> <span class="n">ssdist_file</span><span class="p">}</span></div>
+
+<div class="viewcode-block" id="AriaEcXMLConverter.write_ariaproject"><a class="viewcode-back" href="../../ariaec.html#ariaec.converter.AriaEcXMLConverter.write_ariaproject">[docs]</a> <span class="k">def</span> <span class="nf">write_ariaproject</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">aria_template</span><span class="p">,</span> <span class="n">seqfile</span><span class="p">,</span> <span class="n">dist_files</span><span class="p">,</span> <span class="n">tbl_files</span><span class="p">,</span>
+ <span class="n">desclist</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Generate ariaproject.xml file</span>
+<span class="sd"> </span>
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> aria_template: str</span>
+<span class="sd"> ariaproject.xml template path</span>
+<span class="sd"> seqfile: str</span>
+<span class="sd"> path of molecule sequence in SEQ format</span>
+<span class="sd"> dist_files: list of str</span>
+<span class="sd"> List of distance restraint files in ARIA XML format</span>
+<span class="sd"> tbl_files: dict</span>
+<span class="sd"> Distance restraint files in CNS TBL format</span>
+<span class="sd"> desclist: list of str</span>
+<span class="sd"> List of data descriptor for the actual run (Default value = None).</span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+<span class="sd"> None</span>
+<span class="sd"> """</span>
+ <span class="c1"># TODO: Use aria API to build project in the future</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s2">"Loading aria template file </span><span class="si">%s</span><span class="s2">"</span><span class="p">,</span> <span class="n">aria_template</span><span class="p">)</span>
+
+ <span class="n">molecule</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">molecule</span><span class="o">.</span><span class="n">getName</span><span class="p">()</span>
+ <span class="n">datas</span> <span class="o">=</span> <span class="n">desclist</span> <span class="k">if</span> <span class="n">desclist</span> <span class="k">else</span> <span class="s1">''</span>
+
+ <span class="n">templatepath</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">abspath</span><span class="p">(</span><span class="n">aria_template</span><span class="p">)</span>
+ <span class="n">ariaproj_template</span> <span class="o">=</span> <span class="n">Template</span><span class="p">(</span><span class="n">filename</span><span class="o">=</span><span class="n">templatepath</span><span class="p">,</span>
+ <span class="n">module_directory</span><span class="o">=</span><span class="s2">"/tmp/mako_modules"</span><span class="p">)</span>
+
+ <span class="k">try</span><span class="p">:</span>
+ <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">templatepath</span><span class="p">):</span>
+ <span class="k">pass</span>
+ <span class="k">except</span> <span class="ne">Exception</span> <span class="k">as</span> <span class="n">msg</span><span class="p">:</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">critical</span><span class="p">(</span><span class="s2">"""Can't open template file "</span><span class="si">%s</span><span class="s2">". </span><span class="si">%s</span><span class="s2">"""</span> <span class="o">%</span>
+ <span class="p">(</span><span class="n">templatepath</span><span class="p">,</span> <span class="n">msg</span><span class="p">))</span>
+ <span class="k">raise</span>
+
+ <span class="n">aria_project_dict</span> <span class="o">=</span> <span class="p">{}</span>
+
+ <span class="c1"># Check if ratio cool1 / cool2 is 5:4 ... (relevant ?)</span>
+ <span class="c1"># steps_1 = float(self.settings.setup.config['md_parameters_steps_cool1'])</span>
+ <span class="c1"># steps_2 = float(self.settings.setup.config['md_parameters_steps_cool2'])</span>
+ <span class="c1"># if steps_1 / steps_2 != float(5) / int(4):</span>
+ <span class="c1"># sys.exit(</span>
+ <span class="c1"># 'Length of first and second cooling stages must be fixed in '</span>
+ <span class="c1"># 'the ratio %.2f:%.2f' % (steps_1, steps_2))</span>
+
+ <span class="n">aria_project_dict</span><span class="o">.</span><span class="n">update</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">setup</span><span class="o">.</span><span class="n">config</span><span class="p">)</span>
+
+ <span class="n">work_dir</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">abspath</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">outdir</span><span class="p">)</span>
+ <span class="n">temp_dir</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">abspath</span><span class="p">(</span><span class="n">aria_project_dict</span><span class="p">[</span><span class="s1">'temp_root'</span><span class="p">]),</span>
+ <span class="n">molecule</span><span class="p">,</span> <span class="s2">"_"</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">datas</span><span class="p">))</span>
+
+ <span class="k">if</span> <span class="ow">not</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">(</span><span class="n">work_dir</span><span class="p">):</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s2">"Working dir </span><span class="si">%s</span><span class="s2"> doesn't exist."</span><span class="p">,</span> <span class="n">work_dir</span><span class="p">)</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s2">"Create new directory </span><span class="si">%s</span><span class="s2">"</span><span class="p">,</span> <span class="n">work_dir</span><span class="p">)</span>
+ <span class="n">os</span><span class="o">.</span><span class="n">makedirs</span><span class="p">(</span><span class="n">work_dir</span><span class="p">)</span>
+
+ <span class="k">if</span> <span class="ow">not</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">(</span><span class="n">temp_dir</span><span class="p">):</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s2">"Temp directory </span><span class="si">%s</span><span class="s2"> doesn't exist."</span><span class="p">,</span> <span class="n">temp_dir</span><span class="p">)</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s2">"Create new directory </span><span class="si">%s</span><span class="s2">"</span><span class="p">,</span> <span class="n">temp_dir</span><span class="p">)</span>
+ <span class="n">os</span><span class="o">.</span><span class="n">makedirs</span><span class="p">(</span><span class="n">temp_dir</span><span class="p">)</span>
+
+ <span class="n">aria_project_dict</span><span class="p">[</span><span class="s1">'working_directory'</span><span class="p">]</span> <span class="o">=</span> <span class="n">work_dir</span>
+ <span class="n">aria_project_dict</span><span class="p">[</span><span class="s1">'temp_root'</span><span class="p">]</span> <span class="o">=</span> <span class="n">temp_dir</span>
+
+ <span class="k">if</span> <span class="s2">"-o"</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">aria_project_dict</span><span class="p">[</span><span class="s1">'host_command'</span><span class="p">]:</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">warning</span><span class="p">(</span><span class="s2">"No output file defined in host_command. You should add"</span>
+ <span class="s2">" the output option (-o) to your command."</span><span class="p">)</span>
+
+ <span class="n">project</span> <span class="o">=</span> <span class="p">{</span><span class="s1">'project_name'</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">outprefix</span><span class="p">,</span>
+ <span class="s1">'date'</span><span class="p">:</span> <span class="n">datetime</span><span class="o">.</span><span class="n">date</span><span class="o">.</span><span class="n">today</span><span class="p">()</span><span class="o">.</span><span class="n">isoformat</span><span class="p">(),</span>
+ <span class="s1">'file_root'</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">outprefix</span><span class="p">}</span>
+ <span class="n">aria_project_dict</span><span class="o">.</span><span class="n">update</span><span class="p">(</span><span class="n">project</span><span class="p">)</span>
+
+ <span class="n">data_molecule</span> <span class="o">=</span> <span class="p">{</span><span class="s1">'molecule_file'</span><span class="p">:</span> <span class="n">seqfile</span><span class="p">}</span>
+ <span class="n">aria_project_dict</span><span class="o">.</span><span class="n">update</span><span class="p">(</span><span class="n">data_molecule</span><span class="p">)</span>
+
+ <span class="n">un_dict</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">()</span>
+ <span class="n">am_dict</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">()</span>
+
+ <span class="c1"># SS dist tbl restraint</span>
+ <span class="k">if</span> <span class="n">tbl_files</span><span class="p">[</span><span class="s2">"ssdist"</span><span class="p">]:</span>
+ <span class="n">un_dict</span><span class="p">[</span><span class="s1">'ss'</span><span class="p">]</span> <span class="o">=</span> <span class="p">{</span>
+ <span class="s1">'file'</span><span class="p">:</span> <span class="n">tbl_files</span><span class="p">[</span><span class="s2">"ssdist"</span><span class="p">],</span>
+ <span class="s1">'format'</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">setup</span><span class="o">.</span><span class="n">config</span><span class="p">[</span><span class="s1">'ss_dist_format'</span><span class="p">],</span>
+ <span class="s1">'ccpn_id'</span><span class="p">:</span> <span class="s1">''</span><span class="p">,</span>
+ <span class="s1">'enabled'</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">setup</span><span class="o">.</span><span class="n">config</span><span class="p">[</span><span class="s1">'ss_dist_enabled'</span><span class="p">],</span>
+ <span class="s1">'add_to_network'</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">setup</span><span class="o">.</span><span class="n">config</span><span class="p">[</span>
+ <span class="s1">'ss_dist_add_to_network'</span><span class="p">],</span>
+ <span class="s1">'calibrate'</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">setup</span><span class="o">.</span><span class="n">config</span><span class="p">[</span><span class="s1">'ss_dist_calibrate'</span><span class="p">],</span>
+ <span class="s1">'run_network_anchoring'</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">setup</span><span class="o">.</span><span class="n">config</span><span class="p">[</span>
+ <span class="s1">'ss_dist_run_network_anchoring'</span><span class="p">],</span>
+ <span class="s1">'filter_contributions'</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">setup</span><span class="o">.</span><span class="n">config</span><span class="p">[</span>
+ <span class="s1">'ss_dist_filter_contributions'</span><span class="p">]}</span>
+
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">setup</span><span class="o">.</span><span class="n">config</span><span class="p">[</span><span class="s2">"ambiguous_distance_restraint"</span><span class="p">]:</span>
+ <span class="c1"># Ajout dist_files a am_dict</span>
+ <span class="k">for</span> <span class="n">distfile</span> <span class="ow">in</span> <span class="n">dist_files</span><span class="p">:</span>
+ <span class="n">am_dict</span><span class="p">[</span><span class="n">distfile</span><span class="p">]</span> <span class="o">=</span> <span class="p">{</span>
+ <span class="s1">'file'</span><span class="p">:</span> <span class="n">distfile</span><span class="p">,</span>
+ <span class="s1">'format'</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">setup</span><span class="o">.</span><span class="n">config</span><span class="p">[</span><span class="s1">'dist_format'</span><span class="p">],</span>
+ <span class="s1">'ccpn_id'</span><span class="p">:</span> <span class="s1">''</span><span class="p">,</span>
+ <span class="s1">'enabled'</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">setup</span><span class="o">.</span><span class="n">config</span><span class="p">[</span><span class="s1">'dist_enabled'</span><span class="p">],</span>
+ <span class="s1">'add_to_network'</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">setup</span><span class="o">.</span><span class="n">config</span><span class="p">[</span>
+ <span class="s1">'dist_add_to_network'</span><span class="p">],</span>
+ <span class="s1">'calibrate'</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">setup</span><span class="o">.</span><span class="n">config</span><span class="p">[</span><span class="s1">'dist_calibrate'</span><span class="p">],</span>
+ <span class="s1">'run_network_anchoring'</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">setup</span><span class="o">.</span><span class="n">config</span><span class="p">[</span>
+ <span class="s1">'dist_run_network_anchoring'</span><span class="p">],</span>
+ <span class="s1">'filter_contributions'</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">setup</span><span class="o">.</span><span class="n">config</span><span class="p">[</span>
+ <span class="s1">'dist_filter_contributions'</span><span class="p">],</span>
+ <span class="s1">'avg_exponent'</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">setup</span><span class="o">.</span><span class="n">config</span><span class="p">[</span>
+ <span class="s1">'dist_avg_exponent'</span><span class="p">]</span>
+ <span class="p">}</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="c1"># Ajout dist_files a un_dict</span>
+ <span class="k">for</span> <span class="n">distfile</span> <span class="ow">in</span> <span class="n">dist_files</span><span class="p">:</span>
+ <span class="n">un_dict</span><span class="p">[</span><span class="n">distfile</span><span class="p">]</span> <span class="o">=</span> <span class="p">{</span>
+ <span class="s1">'file'</span><span class="p">:</span> <span class="n">distfile</span><span class="p">,</span>
+ <span class="s1">'format'</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">setup</span><span class="o">.</span><span class="n">config</span><span class="p">[</span><span class="s1">'dist_format'</span><span class="p">],</span>
+ <span class="s1">'ccpn_id'</span><span class="p">:</span> <span class="s1">''</span><span class="p">,</span>
+ <span class="s1">'enabled'</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">setup</span><span class="o">.</span><span class="n">config</span><span class="p">[</span><span class="s1">'dist_enabled'</span><span class="p">],</span>
+ <span class="s1">'add_to_network'</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">setup</span><span class="o">.</span><span class="n">config</span><span class="p">[</span>
+ <span class="s1">'dist_add_to_network'</span><span class="p">],</span>
+ <span class="s1">'calibrate'</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">setup</span><span class="o">.</span><span class="n">config</span><span class="p">[</span><span class="s1">'dist_calibrate'</span><span class="p">],</span>
+ <span class="s1">'run_network_anchoring'</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">setup</span><span class="o">.</span><span class="n">config</span><span class="p">[</span>
+ <span class="s1">'dist_run_network_anchoring'</span><span class="p">],</span>
+ <span class="s1">'filter_contributions'</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">setup</span><span class="o">.</span><span class="n">config</span><span class="p">[</span>
+ <span class="s1">'dist_filter_contributions'</span><span class="p">]}</span>
+
+ <span class="n">aria_project_dict</span><span class="o">.</span><span class="n">update</span><span class="p">({</span><span class="s1">'unambiguous_distance_restraints'</span><span class="p">:</span> <span class="n">un_dict</span><span class="p">})</span>
+ <span class="n">aria_project_dict</span><span class="o">.</span><span class="n">update</span><span class="p">({</span><span class="s1">'ambiguous_distance_restraints'</span><span class="p">:</span> <span class="n">am_dict</span><span class="p">})</span>
+
+ <span class="n">aria_project_dict</span><span class="o">.</span><span class="n">update</span><span class="p">({</span>
+ <span class="s1">'hbond_dist_file'</span><span class="p">:</span> <span class="n">tbl_files</span><span class="p">[</span><span class="s2">"hbond"</span><span class="p">]</span>
+ <span class="k">if</span> <span class="n">tbl_files</span><span class="p">[</span><span class="s1">'hbond'</span><span class="p">]</span> <span class="k">else</span> <span class="kc">None</span><span class="p">})</span>
+
+ <span class="n">aria_project_dict</span><span class="o">.</span><span class="n">update</span><span class="p">({</span>
+ <span class="s1">'dihed_angle_file'</span><span class="p">:</span> <span class="n">tbl_files</span><span class="p">[</span><span class="s2">"dihed"</span><span class="p">]</span>
+ <span class="k">if</span> <span class="n">tbl_files</span><span class="p">[</span><span class="s1">'dihed'</span><span class="p">]</span> <span class="k">else</span> <span class="kc">None</span><span class="p">})</span>
+
+ <span class="n">aria_project_dict</span><span class="p">[</span><span class="s1">'n_cpus'</span><span class="p">]</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">setup</span><span class="o">.</span><span class="n">config</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">'cpus'</span><span class="p">,</span>
+ <span class="s1">'20'</span><span class="p">)</span>
+
+ <span class="n">proj_file</span> <span class="o">=</span> <span class="s2">"</span><span class="si">%s</span><span class="s2">/ariaproject.xml"</span> <span class="o">%</span> <span class="n">work_dir</span>
+ <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">proj_file</span><span class="p">,</span> <span class="s1">'w'</span><span class="p">)</span> <span class="k">as</span> <span class="n">proj_xml</span><span class="p">:</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s2">"Writing ARIA project file (</span><span class="si">%s</span><span class="s2">)"</span><span class="p">,</span> <span class="n">proj_file</span><span class="p">)</span>
+ <span class="n">proj_xml</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">ariaproj_template</span><span class="o">.</span><span class="n">render</span><span class="p">(</span><span class="o">**</span><span class="n">aria_project_dict</span><span class="p">))</span>
+
+ <span class="c1"># TODO: Load aria project file if exists and extract data and rdc</span>
+ <span class="c1"># parameters (use flag in args)</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">setup</span><span class="o">.</span><span class="n">args</span><span class="p">[</span><span class="s1">'ariaproject'</span><span class="p">]:</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s2">"Reading ARIA project file"</span><span class="p">)</span>
+ <span class="n">ecproject</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_pickler</span><span class="o">.</span><span class="n">load</span><span class="p">(</span><span class="n">proj_file</span><span class="p">)</span>
+ <span class="n">project</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_pickler</span><span class="o">.</span><span class="n">load</span><span class="p">(</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">setup</span><span class="o">.</span><span class="n">args</span><span class="p">[</span><span class="s1">'ariaproject'</span><span class="p">])</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">setup</span><span class="o">.</span><span class="n">args</span><span class="p">[</span><span class="s1">'extractall'</span><span class="p">]:</span>
+ <span class="c1"># Add only data to the generated project</span>
+ <span class="k">for</span> <span class="n">datatype</span> <span class="ow">in</span> <span class="n">DATA_TYPES</span><span class="p">:</span>
+ <span class="n">datas</span> <span class="o">=</span> <span class="p">[</span><span class="n">dat</span> <span class="k">for</span> <span class="n">dat</span> <span class="ow">in</span> <span class="n">project</span><span class="o">.</span><span class="n">getData</span><span class="p">(</span><span class="n">datatype</span><span class="p">)]</span>
+ <span class="k">if</span> <span class="n">datas</span><span class="p">:</span>
+ <span class="n">ecdatas</span> <span class="o">=</span> <span class="p">[</span><span class="n">dat</span> <span class="k">for</span> <span class="n">dat</span> <span class="ow">in</span> <span class="n">ecproject</span><span class="o">.</span><span class="n">getData</span><span class="p">(</span><span class="n">datatype</span><span class="p">)]</span>
+ <span class="k">if</span> <span class="p">[</span><span class="n">dat</span><span class="o">.</span><span class="n">as_dict</span><span class="p">()</span> <span class="k">for</span> <span class="n">dat</span> <span class="ow">in</span> <span class="n">datas</span><span class="p">]</span> <span class="o">!=</span> \
+ <span class="p">[</span><span class="n">dat</span><span class="o">.</span><span class="n">as_dict</span><span class="p">()</span> <span class="k">for</span> <span class="n">dat</span> <span class="ow">in</span> <span class="n">ecdatas</span><span class="p">]:</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s2">"Update </span><span class="si">%s</span><span class="s2"> data in project"</span><span class="p">,</span> <span class="n">datatype</span><span class="p">)</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="n">datas</span><span class="p">)</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="s2">"Old </span><span class="si">%s</span><span class="s2"> section:</span><span class="se">\n</span><span class="si">%s</span><span class="s2">"</span><span class="p">,</span> <span class="n">datatype</span><span class="p">,</span>
+ <span class="n">ecproject</span><span class="o">.</span><span class="n">getData</span><span class="p">(</span><span class="n">datatype</span><span class="p">))</span>
+ <span class="c1"># TODO: check if sequence file is similar with the</span>
+ <span class="c1"># one generated</span>
+ <span class="k">if</span> <span class="n">datatype</span> <span class="o">==</span> <span class="n">DATA_SEQUENCE</span><span class="p">:</span>
+ <span class="p">[</span><span class="n">ecproject</span><span class="o">.</span><span class="n">delData</span><span class="p">(</span><span class="n">dat</span><span class="p">)</span>
+ <span class="k">for</span> <span class="n">dat</span> <span class="ow">in</span> <span class="n">ecproject</span><span class="o">.</span><span class="n">getData</span><span class="p">(</span><span class="n">datatype</span><span class="p">)]</span>
+ <span class="p">[</span><span class="n">ecproject</span><span class="o">.</span><span class="n">addData</span><span class="p">(</span><span class="n">dat</span><span class="p">)</span> <span class="k">for</span> <span class="n">dat</span> <span class="ow">in</span> <span class="n">datas</span><span class="p">]</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="s2">"Updated </span><span class="si">%s</span><span class="s2"> section:</span><span class="se">\n</span><span class="si">%s</span><span class="s2">"</span><span class="p">,</span> <span class="n">datatype</span><span class="p">,</span>
+ <span class="n">ecproject</span><span class="o">.</span><span class="n">getData</span><span class="p">(</span><span class="n">datatype</span><span class="p">))</span>
+ <span class="k">if</span> <span class="n">datatype</span> <span class="o">==</span> <span class="n">DATA_RDCS</span><span class="p">:</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s2">"Update </span><span class="si">%s</span><span class="s2"> annealing parameters"</span><span class="p">,</span>
+ <span class="n">datatype</span><span class="p">)</span>
+ <span class="n">rdc_params</span> <span class="o">=</span> <span class="n">project</span><span class="o">.</span><span class="n">getStructureEngine</span><span class="p">()</span><span class="o">.</span><span class="n">getAnnealingParameters</span><span class="p">()</span><span class="o">.</span><span class="n">get</span><span class="p">(</span>
+ <span class="n">DATA_ANNEALING_RDC</span><span class="p">)</span>
+ <span class="n">engine</span> <span class="o">=</span> <span class="n">ecproject</span><span class="o">.</span><span class="n">getStructureEngine</span><span class="p">()</span>
+ <span class="n">annealing</span> <span class="o">=</span> <span class="n">engine</span><span class="o">.</span><span class="n">getAnnealingParameters</span><span class="p">()</span>
+ <span class="n">annealing</span><span class="p">[</span><span class="n">DATA_ANNEALING_RDC</span><span class="p">]</span> <span class="o">=</span> <span class="n">rdc_params</span>
+ <span class="n">engine</span><span class="o">.</span><span class="n">setAnnealingParameters</span><span class="p">(</span><span class="n">annealing</span><span class="p">)</span>
+ <span class="n">ecproject</span><span class="o">.</span><span class="n">setStructureEngine</span><span class="p">(</span><span class="n">engine</span><span class="p">)</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">raise</span> <span class="ne">NotImplementedError</span>
+
+ <span class="n">LOG</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s2">"Writing new ARIA xml file (</span><span class="si">%s</span><span class="s2">)"</span><span class="p">,</span> <span class="n">proj_file</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_pickler</span><span class="o">.</span><span class="n">dump</span><span class="p">(</span><span class="n">ecproject</span><span class="p">,</span> <span class="n">proj_file</span><span class="p">)</span></div>
+
+<div class="viewcode-block" id="AriaEcXMLConverter.tbl2xml"><a class="viewcode-back" href="../../ariaec.html#ariaec.converter.AriaEcXMLConverter.tbl2xml">[docs]</a> <span class="nd">@staticmethod</span>
+ <span class="k">def</span> <span class="nf">tbl2xml</span><span class="p">(</span><span class="n">outdir_path</span><span class="p">,</span> <span class="n">molecule_path</span><span class="p">,</span> <span class="n">tbl_paths</span><span class="p">,</span> <span class="n">list_name</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Read cns distance restraints in TBL format and convert them into ARIA</span>
+<span class="sd"> XML format</span>
+<span class="sd"> </span>
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> outdir_path : str</span>
+<span class="sd"> Path where ARIA XML files are saved </span>
+<span class="sd"> molecule_path : str</span>
+<span class="sd"> Path of molecule file in ARIA XML format </span>
+<span class="sd"> tbl_paths : list of str</span>
+<span class="sd"> List of distance restraints paths</span>
+<span class="sd"> list_name : str</span>
+<span class="sd"> Name of spec in tbl file which will be converted into XML format</span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+<span class="sd"> xml_paths: str</span>
+<span class="sd"> List of distance restraints in ARIA XML format</span>
+<span class="sd"> </span>
+<span class="sd"> """</span>
+ <span class="n">pickler</span> <span class="o">=</span> <span class="n">AriaXMLPickler</span><span class="p">()</span>
+ <span class="n">molecule</span> <span class="o">=</span> <span class="n">pickler</span><span class="o">.</span><span class="n">load</span><span class="p">(</span><span class="n">molecule_path</span><span class="p">)</span>
+ <span class="n">convtable</span> <span class="o">=</span> <span class="n">ConversionTable</span><span class="p">()</span>
+ <span class="n">xml_paths</span> <span class="o">=</span> <span class="p">[]</span>
+
+ <span class="c1"># Read tbl file(s) and build dist_restraints dict</span>
+ <span class="k">for</span> <span class="n">tbl_path</span> <span class="ow">in</span> <span class="n">tbl_paths</span><span class="p">:</span>
+
+ <span class="n">tbl</span> <span class="o">=</span> <span class="n">TblDistFile</span><span class="p">(</span><span class="n">tbl_path</span><span class="p">)</span>
+ <span class="n">tbl</span><span class="o">.</span><span class="n">load</span><span class="p">()</span>
+ <span class="n">xml_path</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span>
+ <span class="n">outdir_path</span><span class="p">,</span>
+ <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">splitext</span><span class="p">(</span>
+ <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">basename</span><span class="p">(</span><span class="n">tbl_path</span><span class="p">))[</span><span class="mi">0</span><span class="p">]</span> <span class="o">+</span> <span class="s2">"_restraints.xml"</span><span class="p">)</span>
+
+ <span class="n">xmldists</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">OrderedDict</span><span class="p">()</span>
+ <span class="n">restno</span> <span class="o">=</span> <span class="kc">None</span>
+ <span class="n">listflag</span> <span class="o">=</span> <span class="kc">False</span>
+
+ <span class="k">for</span> <span class="n">idline</span><span class="p">,</span> <span class="n">line</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="n">tbl</span><span class="o">.</span><span class="n">lines</span><span class="p">):</span>
+
+ <span class="n">assign_flag</span> <span class="o">=</span> <span class="kc">True</span> <span class="k">if</span> <span class="s2">"assign"</span> <span class="ow">in</span> <span class="n">line</span><span class="o">.</span><span class="n">get</span><span class="p">(</span>
+ <span class="s2">"restflag"</span><span class="p">)</span> <span class="k">else</span> <span class="kc">False</span>
+ <span class="n">res1_id</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">line</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"resid1"</span><span class="p">))</span>
+ <span class="n">res2_id</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">line</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"resid2"</span><span class="p">))</span>
+ <span class="n">res1</span> <span class="o">=</span> <span class="n">molecule</span><span class="o">.</span><span class="n">getChain</span><span class="p">(</span><span class="n">line</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"segid1"</span><span class="p">))[</span><span class="n">res1_id</span><span class="p">]</span>
+ <span class="n">res2</span> <span class="o">=</span> <span class="n">molecule</span><span class="o">.</span><span class="n">getChain</span><span class="p">(</span><span class="n">line</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"segid2"</span><span class="p">))[</span><span class="n">res2_id</span><span class="p">]</span>
+
+ <span class="c1"># Convert atom name</span>
+ <span class="c1"># TBL file follow cns nomenclature for atom names</span>
+ <span class="c1"># ARIA XML distance restraints follow iupac names</span>
+ <span class="n">atm1_name</span> <span class="o">=</span> <span class="n">convtable</span><span class="o">.</span><span class="n">convert_atom</span><span class="p">(</span>
+ <span class="n">res1</span><span class="o">.</span><span class="n">getType</span><span class="p">(),</span> <span class="n">line</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"atm1"</span><span class="p">),</span> <span class="s1">'cns'</span><span class="p">,</span> <span class="s1">'iupac'</span><span class="p">,</span>
+ <span class="s1">'AMINO_ACID'</span><span class="p">)</span>
+ <span class="n">atm2_name</span> <span class="o">=</span> <span class="n">convtable</span><span class="o">.</span><span class="n">convert_atom</span><span class="p">(</span>
+ <span class="n">res2</span><span class="o">.</span><span class="n">getType</span><span class="p">(),</span> <span class="n">line</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"atm2"</span><span class="p">),</span> <span class="s1">'cns'</span><span class="p">,</span> <span class="s1">'iupac'</span><span class="p">,</span>
+ <span class="s1">'AMINO_ACID'</span><span class="p">)</span>
+
+ <span class="c1"># If assign flag, initialize a new restraint</span>
+ <span class="k">if</span> <span class="n">assign_flag</span><span class="p">:</span>
+ <span class="n">listflag</span> <span class="o">=</span> <span class="kc">False</span>
+ <span class="n">restno</span> <span class="o">=</span> <span class="n">line</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"restno"</span><span class="p">)</span>
+ <span class="n">restlistname</span> <span class="o">=</span> <span class="n">line</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"listname"</span><span class="p">)</span>
+ <span class="k">if</span> <span class="n">list_name</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span> <span class="o">==</span> <span class="n">restlistname</span><span class="o">.</span><span class="n">lower</span><span class="p">():</span>
+ <span class="n">listflag</span> <span class="o">=</span> <span class="kc">True</span>
+ <span class="n">dtarg</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">line</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"dtarget"</span><span class="p">))</span>
+ <span class="n">lwbound</span> <span class="o">=</span> <span class="n">dtarg</span> <span class="o">-</span> <span class="nb">float</span><span class="p">(</span><span class="n">line</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"dminus"</span><span class="p">))</span>
+ <span class="n">upbound</span> <span class="o">=</span> <span class="n">dtarg</span> <span class="o">+</span> <span class="nb">float</span><span class="p">(</span><span class="n">line</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"dplus"</span><span class="p">))</span>
+ <span class="n">xmldists</span><span class="p">[</span><span class="n">restno</span><span class="p">]</span> <span class="o">=</span> <span class="p">{</span>
+ <span class="s2">"meta"</span><span class="p">:</span> <span class="p">{</span>
+ <span class="s2">"weight"</span><span class="p">:</span> <span class="nb">float</span><span class="p">(</span><span class="n">line</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"weight"</span><span class="p">)),</span>
+ <span class="s2">"distance"</span><span class="p">:</span> <span class="n">dtarg</span><span class="p">,</span>
+ <span class="s2">"lower_bound"</span><span class="p">:</span> <span class="n">lwbound</span><span class="p">,</span>
+ <span class="s2">"upper_bound"</span><span class="p">:</span> <span class="n">upbound</span><span class="p">,</span>
+ <span class="s2">"active"</span><span class="p">:</span> <span class="mi">1</span><span class="p">,</span>
+ <span class="s2">"reliable"</span><span class="p">:</span> <span class="mi">1</span><span class="p">,</span>
+ <span class="s2">"list_name"</span><span class="p">:</span> <span class="n">restlistname</span>
+ <span class="p">},</span>
+ <span class="s2">"contrib"</span><span class="p">:</span> <span class="n">collections</span><span class="o">.</span><span class="n">OrderedDict</span><span class="p">()</span>
+ <span class="p">}</span>
+ <span class="n">contrib_id</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">xmldists</span><span class="p">[</span><span class="n">restno</span><span class="p">][</span><span class="s2">"contrib"</span><span class="p">])</span> <span class="o">+</span> <span class="mi">1</span>
+ <span class="n">xmldists</span><span class="p">[</span><span class="n">restno</span><span class="p">][</span><span class="s2">"contrib"</span><span class="p">][</span><span class="n">contrib_id</span><span class="p">]</span> <span class="o">=</span> <span class="p">{</span>
+ <span class="s2">"meta"</span><span class="p">:</span> <span class="p">{</span>
+ <span class="s2">"weight"</span><span class="p">:</span> <span class="mf">1.0</span>
+ <span class="p">},</span>
+ <span class="s2">"spin_pair"</span><span class="p">:</span> <span class="n">collections</span><span class="o">.</span><span class="n">OrderedDict</span><span class="p">([</span>
+ <span class="p">(</span><span class="n">res1_id</span><span class="p">,</span> <span class="n">atm1_name</span><span class="p">),</span>
+ <span class="p">(</span><span class="n">res2_id</span><span class="p">,</span> <span class="n">atm2_name</span><span class="p">)</span>
+ <span class="p">])</span>
+ <span class="p">}</span>
+ <span class="c1"># Else add contrib to restraint</span>
+ <span class="k">elif</span> <span class="n">listflag</span><span class="p">:</span>
+ <span class="n">contrib_id</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">xmldists</span><span class="p">[</span><span class="n">restno</span><span class="p">][</span><span class="s2">"contrib"</span><span class="p">])</span> <span class="o">+</span> <span class="mi">1</span>
+ <span class="n">xmldists</span><span class="p">[</span><span class="n">restno</span><span class="p">][</span><span class="s2">"contrib"</span><span class="p">][</span><span class="n">contrib_id</span><span class="p">]</span> <span class="o">=</span> <span class="p">{</span>
+ <span class="s2">"meta"</span><span class="p">:</span> <span class="p">{</span>
+ <span class="s2">"weight"</span><span class="p">:</span> <span class="mf">1.0</span>
+ <span class="p">},</span>
+ <span class="s2">"spin_pair"</span><span class="p">:</span> <span class="n">collections</span><span class="o">.</span><span class="n">OrderedDict</span><span class="p">([</span>
+ <span class="p">(</span><span class="n">res1_id</span><span class="p">,</span> <span class="n">atm1_name</span><span class="p">),</span>
+ <span class="p">(</span><span class="n">res2_id</span><span class="p">,</span> <span class="n">atm2_name</span><span class="p">)</span>
+ <span class="p">])</span>
+ <span class="p">}</span>
+
+ <span class="c1"># Generate distance restraint file using self.write_dist_xml</span>
+ <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">xmldists</span><span class="p">)</span> <span class="o">!=</span> <span class="mi">0</span><span class="p">:</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s2">"Wrote </span><span class="si">%d</span><span class="s2"> xml distance restraints in </span><span class="si">%s</span><span class="s2">"</span><span class="p">,</span>
+ <span class="nb">len</span><span class="p">(</span><span class="n">xmldists</span><span class="p">),</span>
+ <span class="n">xml_path</span><span class="p">)</span>
+ <span class="n">AriaXMLConverter</span><span class="o">.</span><span class="n">write_dist_xml</span><span class="p">(</span><span class="n">xmldists</span><span class="p">,</span> <span class="n">xml_path</span><span class="p">)</span>
+ <span class="n">xml_paths</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">xml_path</span><span class="p">)</span>
+
+ <span class="k">return</span> <span class="n">xml_paths</span></div>
+
+<div class="viewcode-block" id="AriaEcXMLConverter.run_tbl2xml"><a class="viewcode-back" href="../../ariaec.html#ariaec.converter.AriaEcXMLConverter.run_tbl2xml">[docs]</a> <span class="k">def</span> <span class="nf">run_tbl2xml</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="sd">"""Main command to convert tbl file(s) in ARIA XML Format"""</span>
+ <span class="c1"># Check if we have the correct args in self.settings</span>
+ <span class="n">outdir_path</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">tbl2xml</span><span class="o">.</span><span class="n">args</span><span class="p">[</span><span class="s2">"output_directory"</span><span class="p">]</span>
+ <span class="n">molecule_path</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">tbl2xml</span><span class="o">.</span><span class="n">args</span><span class="p">[</span><span class="s2">"molecule"</span><span class="p">]</span>
+ <span class="n">tbl_paths</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">tbl2xml</span><span class="o">.</span><span class="n">args</span><span class="p">[</span><span class="s2">"infiles"</span><span class="p">]</span>
+ <span class="n">list_name</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">tbl2xml</span><span class="o">.</span><span class="n">args</span><span class="p">[</span><span class="s2">"listname"</span><span class="p">]</span>
+
+ <span class="bp">self</span><span class="o">.</span><span class="n">tbl2xml</span><span class="p">(</span><span class="n">outdir_path</span><span class="p">,</span> <span class="n">molecule_path</span><span class="p">,</span> <span class="n">tbl_paths</span><span class="p">,</span> <span class="n">list_name</span><span class="p">)</span></div></div>
+</pre></div>
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@@ -0,0 +1,425 @@
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+
+ <h1>Source code for ariaec.maplot</h1><div class="highlight"><pre>
+<span></span><span class="c1"># coding=utf-8</span>
+<span class="sd">"""</span>
+<span class="sd"> Input/Output aria_ec scripts</span>
+<span class="sd">"""</span>
+<span class="kn">from</span> <span class="nn">__future__</span> <span class="k">import</span> <span class="n">absolute_import</span><span class="p">,</span> <span class="n">division</span><span class="p">,</span> <span class="n">print_function</span>
+
+<span class="kn">import</span> <span class="nn">sys</span>
+<span class="kn">import</span> <span class="nn">json</span>
+<span class="kn">import</span> <span class="nn">logging</span>
+<span class="kn">from</span> <span class="nn">.common</span> <span class="k">import</span> <span class="n">get_filename</span>
+<span class="kn">from</span> <span class="nn">.reader</span> <span class="k">import</span> <span class="n">MapFileListReader</span>
+<span class="kn">from</span> <span class="nn">.protmap</span> <span class="k">import</span> <span class="n">MapFilter</span>
+<span class="kn">from</span> <span class="nn">.protein</span> <span class="k">import</span> <span class="n">Protein</span>
+
+<span class="n">LOG</span> <span class="o">=</span> <span class="n">logging</span><span class="o">.</span><span class="n">getLogger</span><span class="p">(</span><span class="vm">__name__</span><span class="p">)</span>
+
+
+<div class="viewcode-block" id="AriaEcContactMap"><a class="viewcode-back" href="../../ariaec.html#ariaec.maplot.AriaEcContactMap">[docs]</a><span class="k">class</span> <span class="nc">AriaEcContactMap</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span>
+ <span class="sd">"""Contact maplot class"""</span>
+
+ <span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">settings</span><span class="p">):</span>
+ <span class="c1"># TODO: check_type settings (AriaEcSettings)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">settings</span> <span class="o">=</span> <span class="n">settings</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">protein</span> <span class="o">=</span> <span class="n">Protein</span><span class="p">(</span><span class="n">settings</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">file_reader</span> <span class="o">=</span> <span class="n">MapFileListReader</span><span class="p">(</span>
+ <span class="n">cont_def</span><span class="o">=</span><span class="n">settings</span><span class="o">.</span><span class="n">contactdef</span><span class="o">.</span><span class="n">config</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">filter</span> <span class="o">=</span> <span class="n">MapFilter</span><span class="p">(</span><span class="n">settings</span><span class="o">.</span><span class="n">setup</span><span class="o">.</span><span class="n">config</span><span class="p">,</span>
+ <span class="n">nofilter</span><span class="o">=</span><span class="n">settings</span><span class="o">.</span><span class="n">maplot</span><span class="o">.</span><span class="n">args</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"no_filter"</span><span class="p">))</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">protname</span> <span class="o">=</span> <span class="s1">''</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">allresmap</span> <span class="o">=</span> <span class="p">{}</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">refmap</span> <span class="o">=</span> <span class="kc">None</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">refname</span> <span class="o">=</span> <span class="kc">None</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">reftype</span> <span class="o">=</span> <span class="s1">''</span>
+
+<div class="viewcode-block" id="AriaEcContactMap.run"><a class="viewcode-back" href="../../ariaec.html#ariaec.maplot.AriaEcContactMap.run">[docs]</a> <span class="k">def</span> <span class="nf">run</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="sd">"""Contact map analysis command"""</span>
+ <span class="c1"># Check input</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="s2">"Settings:</span><span class="se">\n</span><span class="s2">"</span> <span class="o">+</span> <span class="n">json</span><span class="o">.</span><span class="n">dumps</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">maplot</span><span class="o">.</span><span class="n">config</span><span class="p">,</span>
+ <span class="n">indent</span><span class="o">=</span><span class="mi">4</span><span class="p">))</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="s2">"Args:</span><span class="se">\n</span><span class="s2">"</span> <span class="o">+</span> <span class="n">json</span><span class="o">.</span><span class="n">dumps</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">maplot</span><span class="o">.</span><span class="n">args</span><span class="p">,</span>
+ <span class="n">indent</span><span class="o">=</span><span class="mi">4</span><span class="p">))</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">maplot</span><span class="o">.</span><span class="n">args</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"onlyreport"</span><span class="p">,</span> <span class="kc">False</span><span class="p">):</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">make_infra</span><span class="p">()</span>
+ <span class="c1"># ----------------------------- Input -------------------------------- #</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">protname</span> <span class="o">=</span> <span class="n">get_filename</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">maplot</span><span class="o">.</span><span class="n">args</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"seq"</span><span class="p">,</span> <span class="kc">None</span><span class="p">))</span>
+ <span class="c1"># Load Sequence file</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">protein</span><span class="o">.</span><span class="n">set_aa_sequence</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">maplot</span><span class="o">.</span><span class="n">args</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"seq"</span><span class="p">,</span> <span class="kc">None</span><span class="p">))</span>
+ <span class="c1"># Load secondary structure prediction file</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">protein</span><span class="o">.</span><span class="n">set_sec_struct</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">maplot</span><span class="o">.</span><span class="n">args</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"sspred"</span><span class="p">,</span>
+ <span class="kc">None</span><span class="p">),</span>
+ <span class="n">ssdist_filename</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">ssdist</span><span class="p">,</span>
+ <span class="n">ssidx</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">maplot</span><span class="o">.</span><span class="n">args</span><span class="o">.</span><span class="n">get</span><span class="p">(</span>
+ <span class="s2">"ssidx"</span><span class="p">,</span> <span class="kc">False</span><span class="p">))</span>
+ <span class="c1"># ---------------------------- Processing ---------------------------- #</span>
+
+ <span class="c1"># Reading step</span>
+ <span class="c1"># ------------</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">file_reader</span><span class="o">.</span><span class="n">read</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">maplot</span><span class="o">.</span><span class="n">args</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"infiles"</span><span class="p">),</span>
+ <span class="n">maptypes</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">maplot</span><span class="o">.</span><span class="n">args</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"contact_types"</span><span class="p">),</span>
+ <span class="n">protein</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">protein</span><span class="p">,</span>
+ <span class="n">groupby_method</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">setup</span><span class="o">.</span><span class="n">config</span><span class="p">[</span>
+ <span class="s1">'groupby_method'</span><span class="p">],</span>
+ <span class="n">scsc</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">scsc_min</span><span class="p">)</span>
+
+ <span class="k">for</span> <span class="n">idx</span><span class="p">,</span> <span class="n">fo</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">file_reader</span><span class="o">.</span><span class="n">maps</span><span class="p">):</span>
+ <span class="c1"># fo need a maplot in order to wite XML dist restraints</span>
+ <span class="c1"># TODO: filter pour toutes les map de mapdict !! (fonction remove</span>
+ <span class="c1"># s'applique sur l'humanidx contenant les residus)</span>
+ <span class="k">if</span> <span class="n">idx</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s2">"</span><span class="si">%s</span><span class="s2"> map set as reference"</span><span class="p">,</span> <span class="n">fo</span><span class="o">.</span><span class="n">filetype</span><span class="o">.</span><span class="n">capitalize</span><span class="p">())</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">refmap</span> <span class="o">=</span> <span class="n">fo</span><span class="o">.</span><span class="n">mapdict</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">reftype</span> <span class="o">=</span> <span class="n">fo</span><span class="o">.</span><span class="n">filetype</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">refname</span> <span class="o">=</span> <span class="n">fo</span><span class="o">.</span><span class="n">filename</span> <span class="k">if</span> <span class="nb">type</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">protname</span><span class="p">)</span> <span class="o">!=</span> <span class="nb">list</span> \
+ <span class="k">else</span> <span class="bp">self</span><span class="o">.</span><span class="n">protname</span><span class="p">[</span><span class="n">idx</span><span class="p">]</span>
+
+ <span class="c1"># Filtering step</span>
+ <span class="c1"># --------------</span>
+ <span class="k">if</span> <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">maplot</span><span class="o">.</span><span class="n">args</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"filter"</span><span class="p">)</span> <span class="ow">and</span> <span class="n">idx</span> <span class="o">!=</span> <span class="mi">0</span><span class="p">)</span> <span class="ow">or</span> \
+ <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">maplot</span><span class="o">.</span><span class="n">args</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"filter"</span><span class="p">)</span>
+ <span class="ow">and</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">file_reader</span><span class="o">.</span><span class="n">maps</span><span class="p">)</span> <span class="o">==</span> <span class="mi">1</span><span class="p">):</span>
+ <span class="c1"># Filtering all maplot except the reference map</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s2">"Filtering </span><span class="si">%s</span><span class="s2"> map"</span><span class="p">,</span> <span class="n">fo</span><span class="o">.</span><span class="n">filetype</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">filter</span><span class="p">(</span><span class="n">fo</span><span class="o">.</span><span class="n">mapdict</span><span class="p">,</span> <span class="n">fo</span><span class="o">.</span><span class="n">filetype</span><span class="p">,</span> <span class="n">fo</span><span class="o">.</span><span class="n">contactlist</span><span class="p">,</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">protein</span><span class="p">,</span> <span class="n">clashlist</span><span class="o">=</span><span class="n">fo</span><span class="o">.</span><span class="n">clashlist</span><span class="p">,</span>
+ <span class="n">outprefix</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">protname</span><span class="p">[</span><span class="n">idx</span><span class="p">]</span> <span class="k">if</span> <span class="nb">type</span><span class="p">(</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">protname</span><span class="p">)</span> <span class="o">==</span> <span class="nb">list</span> <span class="k">else</span> <span class="bp">self</span><span class="o">.</span><span class="n">protname</span><span class="p">,</span>
+ <span class="n">outdir</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">outdir</span><span class="p">)</span>
+ <span class="c1"># else:</span>
+ <span class="c1"># Use only position filter</span>
+ <span class="c1"># self.filter(fo.mapdict, fo.filetype, fo.contactlist,</span>
+ <span class="c1"># self.protein, clashlist=fo.clashlist,</span>
+ <span class="c1"># protname=self.protname,</span>
+ <span class="c1"># outdir=self.settings.outdir, mapfilters="pos")</span>
+
+ <span class="c1"># Save the loaded map into allresmap dict</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">allresmap</span><span class="p">[(</span><span class="n">fo</span><span class="o">.</span><span class="n">filename</span> <span class="k">if</span> <span class="nb">type</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">protname</span><span class="p">)</span> <span class="o">!=</span> <span class="nb">list</span> <span class="k">else</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">protname</span><span class="p">[</span><span class="n">idx</span><span class="p">],</span> <span class="n">fo</span><span class="o">.</span><span class="n">filetype</span><span class="p">,</span>
+ <span class="n">fo</span><span class="o">.</span><span class="n">filepath</span><span class="p">)]</span> <span class="o">=</span> <span class="n">fo</span><span class="o">.</span><span class="n">mapdict</span>
+
+ <span class="k">try</span><span class="p">:</span>
+ <span class="n">refmap</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">refmap</span><span class="p">[</span><span class="s2">"maplot"</span><span class="p">]</span>
+ <span class="k">except</span> <span class="ne">TypeError</span><span class="p">:</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">error</span><span class="p">(</span><span class="s2">"First contact map should be a valid file"</span><span class="p">)</span>
+ <span class="n">sys</span><span class="o">.</span><span class="n">exit</span><span class="p">(</span><span class="mi">1</span><span class="p">)</span>
+
+ <span class="c1"># nb_c = int(len(self.protein.aa_sequence.sequence) *</span>
+ <span class="c1"># self.settings.setup.config.get("n_factor"))</span>
+ <span class="n">plotparams</span> <span class="o">=</span> <span class="p">{</span><span class="n">k</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">maplot</span><span class="o">.</span><span class="n">config</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">k</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span>
+ <span class="k">for</span> <span class="n">k</span> <span class="ow">in</span> <span class="p">(</span><span class="s1">'size_fig'</span><span class="p">,</span> <span class="s1">'plot_ext'</span><span class="p">,</span> <span class="s1">'plot_dpi'</span><span class="p">)}</span>
+ <span class="n">outdir</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">outdir</span>
+
+ <span class="c1"># Reference contact map plot</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">maplot</span><span class="o">.</span><span class="n">config</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"save_fig"</span><span class="p">)</span> <span class="ow">and</span> <span class="ow">not</span> \
+ <span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">maplot</span><span class="o">.</span><span class="n">args</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"onlyreport"</span><span class="p">,</span> <span class="kc">False</span><span class="p">):</span>
+ <span class="n">refmap</span><span class="o">.</span><span class="n">saveplot</span><span class="p">(</span><span class="n">outdir</span><span class="o">=</span><span class="n">outdir</span><span class="p">,</span>
+ <span class="n">outprefix</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">protname</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="k">if</span> <span class="nb">type</span><span class="p">(</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">protname</span><span class="p">)</span> <span class="o">==</span> <span class="nb">list</span> <span class="k">else</span> <span class="bp">self</span><span class="o">.</span><span class="n">protname</span><span class="p">,</span>
+ <span class="o">**</span><span class="n">plotparams</span><span class="p">)</span>
+
+ <span class="c1"># Merge maps if asked by the user</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">maplot</span><span class="o">.</span><span class="n">args</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"merge"</span><span class="p">,</span> <span class="kc">None</span><span class="p">):</span>
+ <span class="c1"># Combine map with other maps</span>
+ <span class="n">mergelist</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">maplot</span><span class="o">.</span><span class="n">args</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"merge"</span><span class="p">)</span>
+ <span class="c1"># LOG.info("Merging contact maps (%s)" % ', '.join(mergelist))</span>
+ <span class="k">for</span> <span class="n">mergetype</span> <span class="ow">in</span> <span class="n">mergelist</span><span class="p">:</span>
+ <span class="k">if</span> <span class="n">mergetype</span> <span class="ow">in</span> <span class="nb">zip</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">allresmap</span><span class="o">.</span><span class="n">keys</span><span class="p">())[</span><span class="mi">0</span><span class="p">]:</span>
+ <span class="n">mergemaps</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">allresmap</span><span class="o">.</span><span class="n">pop</span><span class="p">(</span><span class="n">mergetype</span><span class="p">)</span>
+ <span class="n">mergecontactmap</span> <span class="o">=</span> <span class="n">mergemaps</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"maplot"</span><span class="p">)</span>
+ <span class="k">for</span> <span class="n">mapname</span><span class="p">,</span> <span class="n">mapt</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">allresmap</span><span class="o">.</span><span class="n">keys</span><span class="p">():</span>
+ <span class="k">if</span> <span class="n">mapt</span> <span class="o">!=</span> <span class="bp">self</span><span class="o">.</span><span class="n">reftype</span><span class="p">:</span>
+ <span class="c1"># TODO: DON'T WORK !!!!</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s2">"Merging </span><span class="si">%s</span><span class="s2"> with </span><span class="si">%s</span><span class="s2"> map"</span><span class="p">,</span>
+ <span class="n">mergetype</span><span class="p">,</span> <span class="n">mapt</span><span class="p">)</span>
+ <span class="n">up_map</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">allresmap</span><span class="p">[</span><span class="n">mapt</span><span class="p">][</span><span class="s2">"maplot"</span><span class="p">]</span>
+ <span class="n">up_map</span><span class="p">[:]</span> <span class="o">=</span> <span class="n">up_map</span><span class="p">[:]</span> <span class="o">+</span> <span class="n">mergecontactmap</span><span class="p">[:]</span>
+ <span class="n">mergekey</span> <span class="o">=</span> <span class="s2">"</span><span class="si">%s</span><span class="s2">_</span><span class="si">%s</span><span class="s2">"</span> <span class="o">%</span> <span class="p">(</span><span class="n">mapt</span><span class="p">,</span> <span class="n">mergetype</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">allresmap</span><span class="p">[</span><span class="n">mergekey</span><span class="p">]</span> <span class="o">=</span> <span class="p">{}</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">allresmap</span><span class="p">[</span><span class="n">mergekey</span><span class="p">][</span><span class="s2">"maplot"</span><span class="p">]</span> <span class="o">=</span> <span class="n">up_map</span>
+ <span class="k">raise</span> <span class="ne">NotImplementedError</span>
+
+ <span class="c1"># ------------------------------ Output ------------------------------ #</span>
+
+ <span class="k">for</span> <span class="n">mapname</span><span class="p">,</span> <span class="n">mapt</span><span class="p">,</span> <span class="n">mapath</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">allresmap</span><span class="o">.</span><span class="n">keys</span><span class="p">():</span>
+ <span class="n">prefix</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">maplot</span><span class="o">.</span><span class="n">args</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"prefix"</span><span class="p">)</span> <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">maplot</span><span class="o">.</span><span class="n">args</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"prefix"</span><span class="p">)</span> <span class="k">else</span> <span class="s2">""</span>
+
+ <span class="k">if</span> <span class="n">mapname</span> <span class="o">==</span> <span class="bp">self</span><span class="o">.</span><span class="n">refname</span><span class="p">:</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">maplot</span><span class="o">.</span><span class="n">args</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"onlyreport"</span><span class="p">,</span> <span class="kc">False</span><span class="p">):</span>
+ <span class="n">refmap</span><span class="o">.</span><span class="n">write_contacts</span><span class="p">(</span><span class="n">mapname</span><span class="p">,</span> <span class="n">prefix</span><span class="o">=</span><span class="n">prefix</span><span class="p">,</span>
+ <span class="n">outdir</span><span class="o">=</span><span class="n">outdir</span><span class="p">,</span>
+ <span class="n">scoremap</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">refmap</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"scoremap"</span><span class="p">,</span>
+ <span class="kc">None</span><span class="p">))</span>
+ <span class="k">continue</span>
+
+ <span class="n">prefix</span> <span class="o">=</span> <span class="s2">"</span><span class="si">%s</span><span class="s2">_</span><span class="si">%s</span><span class="s2">vs</span><span class="si">%s</span><span class="s2">"</span> <span class="o">%</span> <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">protname</span><span class="p">,</span> <span class="n">mapt</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">reftype</span><span class="p">)</span> <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">maplot</span><span class="o">.</span><span class="n">args</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"prefix"</span><span class="p">)</span> <span class="k">else</span> <span class="s2">""</span>
+ <span class="n">scoremap</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">allresmap</span><span class="p">[(</span><span class="n">mapname</span><span class="p">,</span> <span class="n">mapt</span><span class="p">,</span> <span class="n">mapath</span><span class="p">)]</span><span class="o">.</span><span class="n">get</span><span class="p">(</span>
+ <span class="s1">'scoremap'</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span>
+ <span class="c1"># if self.allresmap[mapt].get("maplot") is not None and \</span>
+ <span class="c1"># self.allresmap[mapt].get("scoremap") is not None:</span>
+ <span class="c1"># Get top contact map/list</span>
+ <span class="c1"># cmpmap = self.allresmap[mapt]["maplot"].topmap(</span>
+ <span class="c1"># self.allresmap[mapt]["scoremap"], nb_c)</span>
+ <span class="c1"># cmplist = self.allresmap[mapt]['scoremap'].sortedset(</span>
+ <span class="c1"># human_idx=True)[:nb_c]</span>
+ <span class="c1"># elif self.allresmap[mapt].get("maplot") is not None:</span>
+ <span class="c1"># If no score given, use all contact list</span>
+ <span class="n">cmpmap</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">allresmap</span><span class="p">[(</span><span class="n">mapname</span><span class="p">,</span> <span class="n">mapt</span><span class="p">,</span> <span class="n">mapath</span><span class="p">)][</span><span class="s2">"maplot"</span><span class="p">]</span>
+ <span class="n">cmplist</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">allresmap</span><span class="p">[(</span><span class="n">mapname</span><span class="p">,</span> <span class="n">mapt</span><span class="p">,</span> <span class="n">mapath</span><span class="p">)][</span>
+ <span class="s1">'maplot'</span><span class="p">]</span><span class="o">.</span><span class="n">contact_list</span><span class="p">(</span><span class="n">human_idx</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
+ <span class="c1"># else:</span>
+ <span class="c1"># LOG.warning("%s map doesn't have any score related. Can't "</span>
+ <span class="c1"># "define top list related to this map", mapt)</span>
+ <span class="c1"># continue</span>
+
+ <span class="c1"># TODO: only one function for output files</span>
+ <span class="c1"># Write contact list in txt file</span>
+ <span class="n">refmap</span><span class="o">.</span><span class="n">report</span><span class="p">(</span><span class="n">cmpmap</span><span class="p">,</span> <span class="n">scoremap</span><span class="o">=</span><span class="n">scoremap</span><span class="p">,</span>
+ <span class="n">outdir</span><span class="o">=</span><span class="n">outdir</span><span class="p">,</span> <span class="n">outprefix</span><span class="o">=</span><span class="n">prefix</span><span class="p">,</span>
+ <span class="n">plotag</span><span class="o">=</span><span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">maplot</span><span class="o">.</span><span class="n">args</span><span class="o">.</span><span class="n">get</span><span class="p">(</span>
+ <span class="s2">"onlyreport"</span><span class="p">),</span>
+ <span class="n">plotdir</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">infra</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"graphics"</span><span class="p">,</span> <span class="n">outdir</span><span class="p">)</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">maplot</span><span class="o">.</span><span class="n">args</span><span class="o">.</span><span class="n">get</span><span class="p">(</span>
+ <span class="s2">"onlyreport"</span><span class="p">)</span> <span class="k">else</span> <span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">outdir</span><span class="p">)</span>
+ <span class="c1"># Contact map comparison plot</span>
+ <span class="c1"># TODO: elementwise error with compare method</span>
+ <span class="c1"># Write cmp stats</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">maplot</span><span class="o">.</span><span class="n">args</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"onlyreport"</span><span class="p">,</span> <span class="kc">False</span><span class="p">):</span>
+ <span class="n">cmpmap</span><span class="o">.</span><span class="n">write_contacts</span><span class="p">(</span><span class="n">mapname</span><span class="p">,</span>
+ <span class="n">scoremap</span><span class="o">=</span><span class="n">scoremap</span><span class="p">,</span>
+ <span class="n">outdir</span><span class="o">=</span><span class="n">outdir</span><span class="p">)</span>
+ <span class="n">cmpmap</span><span class="o">.</span><span class="n">compare_contactmap</span><span class="p">(</span><span class="n">refmap</span><span class="p">,</span> <span class="n">cmplist</span><span class="p">,</span> <span class="n">prefix</span><span class="p">,</span>
+ <span class="n">distmap</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">refmap</span><span class="p">[</span><span class="s2">"distmap"</span><span class="p">],</span>
+ <span class="n">human_idx</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span>
+ <span class="n">outdir</span><span class="o">=</span><span class="n">outdir</span><span class="p">)</span>
+ <span class="n">refmap</span><span class="o">.</span><span class="n">compareplot</span><span class="p">(</span><span class="n">cmpmap</span><span class="p">,</span> <span class="n">outprefix</span><span class="o">=</span><span class="n">prefix</span><span class="p">,</span>
+ <span class="n">outdir</span><span class="o">=</span><span class="n">outdir</span><span class="p">,</span>
+ <span class="n">save_fig</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">maplot</span><span class="o">.</span><span class="n">config</span><span class="o">.</span><span class="n">get</span><span class="p">(</span>
+ <span class="s2">"save_fig"</span><span class="p">),</span>
+ <span class="n">alpha</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">maplot</span><span class="o">.</span><span class="n">config</span><span class="o">.</span><span class="n">get</span><span class="p">(</span>
+ <span class="s2">"alpha"</span><span class="p">),</span>
+ <span class="o">**</span><span class="n">plotparams</span><span class="p">)</span></div></div>
+ <span class="c1"># Contingency table</span>
+ <span class="c1"># print(cmpmap.to_series())</span>
+ <span class="c1"># LOG.info(pd.crosstab(cmpmap.values, refmap.values,</span>
+ <span class="c1"># rownames=[mapt], colnames=[self.reftype]))</span>
+</pre></div>
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+ <h1>Source code for ariaec.ndconv</h1><div class="highlight"><pre>
+<span></span><span class="c1"># coding=utf-8</span>
+<span class="sd">"""</span>
+<span class="sd"> Network deconvolution tool</span>
+<span class="sd">"""</span>
+<span class="kn">from</span> <span class="nn">__future__</span> <span class="k">import</span> <span class="n">absolute_import</span><span class="p">,</span> <span class="n">division</span><span class="p">,</span> <span class="n">print_function</span>
+
+<span class="kn">import</span> <span class="nn">logging</span>
+<span class="kn">import</span> <span class="nn">numpy</span> <span class="k">as</span> <span class="nn">np</span>
+
+
+<span class="n">LOG</span> <span class="o">=</span> <span class="n">logging</span><span class="o">.</span><span class="n">getLogger</span><span class="p">(</span><span class="vm">__name__</span><span class="p">)</span>
+
+
+<div class="viewcode-block" id="net_deconv"><a class="viewcode-back" href="../../ariaec.html#ariaec.ndconv.net_deconv">[docs]</a><span class="k">def</span> <span class="nf">net_deconv</span><span class="p">(</span><span class="n">npmat</span><span class="p">,</span> <span class="n">beta</span><span class="o">=</span><span class="mf">0.99</span><span class="p">,</span> <span class="n">alpha</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span> <span class="n">control</span><span class="o">=</span><span class="mi">0</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> This is a python implementation/translation of network deconvolution by</span>
+<span class="sd"> MIT-KELLIS LAB</span>
+<span class="sd"> </span>
+<span class="sd"> </span>
+<span class="sd"> LICENSE: MIT-KELLIS LAB</span>
+<span class="sd"> </span>
+<span class="sd"> </span>
+<span class="sd"> AUTHORS:</span>
+<span class="sd"> Algorithm was programmed by Soheil Feizi.</span>
+<span class="sd"> Paper authors are S. Feizi, D. Marbach, M. Medard and M. Kellis</span>
+<span class="sd"> Python implementation: Gideon Rosenthal</span>
+<span class="sd"> </span>
+<span class="sd"> REFERENCES:</span>
+<span class="sd"> For more details, see the following paper:</span>
+<span class="sd"> Network Deconvolution as a General Method to Distinguish</span>
+<span class="sd"> Direct Dependencies over Networks</span>
+<span class="sd"> By: Soheil Feizi, Daniel Marbach, Muriel Medard and Manolis Kellis</span>
+<span class="sd"> Nature Biotechnology</span>
+<span class="sd"> </span>
+<span class="sd"> --------------------------------------------------------------------------</span>
+<span class="sd"> ND.m: network deconvolution</span>
+<span class="sd"> --------------------------------------------------------------------------</span>
+<span class="sd"> </span>
+<span class="sd"> DESCRIPTION:</span>
+<span class="sd"> </span>
+<span class="sd"> USAGE:</span>
+<span class="sd"> mat_nd = ND(npmat)</span>
+<span class="sd"> mat_nd = ND(npmat,beta)</span>
+<span class="sd"> mat_nd = ND(npmat,beta,alpha,control)</span>
+<span class="sd"> </span>
+<span class="sd"> </span>
+<span class="sd"> INPUT ARGUMENTS:</span>
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> npmat :</span>
+<span class="sd"> Input matrix, if it is a square matrix, the program assumes</span>
+<span class="sd"> it is a relevance matrix where npmat(i,j) represents the</span>
+<span class="sd"> similarity content between nodes i and j. Elements of</span>
+<span class="sd"> matrix should be non-negative.</span>
+<span class="sd"> optional parameters:</span>
+<span class="sd"> beta :</span>
+<span class="sd"> Scaling parameter, the program maps the largest absolute</span>
+<span class="sd"> eigenvalue of the direct dependency matrix to beta. It</span>
+<span class="sd"> should be between 0 and 1. (Default value = 0.99)</span>
+<span class="sd"> alpha :</span>
+<span class="sd"> fraction of edges of the observed dependency matrix to be</span>
+<span class="sd"> kept in deconvolution process. (Default value = 1)</span>
+<span class="sd"> control :</span>
+<span class="sd"> if 0, displaying direct weights for observed</span>
+<span class="sd"> interactions, if 1, displaying direct weights for both</span>
+<span class="sd"> observed and</span>
+<span class="sd"> non-observed interactions.</span>
+<span class="sd"> OUTPUT ARGUMENTS:</span>
+<span class="sd"> mat_nd Output deconvolved matrix (direct dependency matrix). Its</span>
+<span class="sd"> components</span>
+<span class="sd"> represent direct edge weights of observed interactions.</span>
+<span class="sd"> Choosing top direct interactions (a cut-off) depends on</span>
+<span class="sd"> the application and</span>
+<span class="sd"> is not implemented in this code.</span>
+<span class="sd"> To apply ND on regulatory networks, follow steps explained in</span>
+<span class="sd"> Supplementary notes</span>
+<span class="sd"> 1.4.1 and 2.1 and 2.3 of the paper.</span>
+<span class="sd"> In this implementation, input matrices are made symmetric.</span>
+<span class="sd"> **************************************************************************</span>
+<span class="sd"> loading scaling and thresholding parameters (Default value = 0)</span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+<span class="sd"> </span>
+<span class="sd"> """</span>
+ <span class="kn">import</span> <span class="nn">scipy.stats.mstats</span> <span class="k">as</span> <span class="nn">stat</span>
+ <span class="kn">from</span> <span class="nn">numpy</span> <span class="k">import</span> <span class="n">linalg</span> <span class="k">as</span> <span class="n">la</span>
+
+ <span class="k">if</span> <span class="n">beta</span> <span class="o">>=</span> <span class="mi">1</span> <span class="ow">or</span> <span class="n">beta</span> <span class="o"><=</span> <span class="mi">0</span><span class="p">:</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">error</span><span class="p">(</span><span class="s1">'error: beta should be in (0,1)'</span><span class="p">)</span>
+
+ <span class="k">if</span> <span class="n">alpha</span> <span class="o">></span> <span class="mi">1</span> <span class="ow">or</span> <span class="n">alpha</span> <span class="o"><=</span> <span class="mi">0</span><span class="p">:</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">error</span><span class="p">(</span><span class="s1">'error: alpha should be in (0,1)'</span><span class="p">)</span>
+
+ <span class="sd">'''</span>
+<span class="sd"> ***********************************</span>
+<span class="sd"> Processing the input matrix</span>
+<span class="sd"> diagonal values are filtered</span>
+<span class="sd"> '''</span>
+
+ <span class="c1"># n = npmat.shape[0]</span>
+ <span class="n">np</span><span class="o">.</span><span class="n">fill_diagonal</span><span class="p">(</span><span class="n">npmat</span><span class="p">,</span> <span class="mi">0</span><span class="p">)</span>
+
+ <span class="sd">'''</span>
+<span class="sd"> Thresholding the input matrix</span>
+<span class="sd"> '''</span>
+ <span class="n">y</span> <span class="o">=</span> <span class="n">stat</span><span class="o">.</span><span class="n">mquantiles</span><span class="p">(</span><span class="n">npmat</span><span class="p">[:],</span> <span class="n">prob</span><span class="o">=</span><span class="p">[</span><span class="mi">1</span> <span class="o">-</span> <span class="n">alpha</span><span class="p">])</span>
+ <span class="n">th</span> <span class="o">=</span> <span class="n">npmat</span> <span class="o">>=</span> <span class="n">y</span>
+ <span class="n">mat_th</span> <span class="o">=</span> <span class="n">npmat</span> <span class="o">*</span> <span class="n">th</span>
+
+ <span class="sd">'''</span>
+<span class="sd"> making the matrix symetric if already not</span>
+<span class="sd"> '''</span>
+ <span class="n">mat_th</span> <span class="o">=</span> <span class="p">(</span><span class="n">mat_th</span> <span class="o">+</span> <span class="n">mat_th</span><span class="o">.</span><span class="n">T</span><span class="p">)</span> <span class="o">/</span> <span class="mi">2</span>
+
+ <span class="sd">'''</span>
+<span class="sd"> ***********************************</span>
+<span class="sd"> eigen decomposition</span>
+<span class="sd"> '''</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s1">'Decomposition and deconvolution...'</span><span class="p">)</span>
+
+ <span class="c1"># noinspection PyTypeChecker</span>
+ <span class="n">dv</span><span class="p">,</span> <span class="n">u</span> <span class="o">=</span> <span class="n">la</span><span class="o">.</span><span class="n">eigh</span><span class="p">(</span><span class="n">mat_th</span><span class="p">)</span>
+ <span class="n">d</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">diag</span><span class="p">(</span><span class="n">dv</span><span class="p">)</span>
+ <span class="n">lam_n</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">abs</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">min</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">min</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">diag</span><span class="p">(</span><span class="n">d</span><span class="p">)),</span> <span class="mi">0</span><span class="p">))</span>
+ <span class="n">lam_p</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">abs</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">max</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">max</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">diag</span><span class="p">(</span><span class="n">d</span><span class="p">)),</span> <span class="mi">0</span><span class="p">))</span>
+
+ <span class="n">m1</span> <span class="o">=</span> <span class="n">lam_p</span> <span class="o">*</span> <span class="p">(</span><span class="mi">1</span> <span class="o">-</span> <span class="n">beta</span><span class="p">)</span> <span class="o">/</span> <span class="n">beta</span>
+ <span class="n">m2</span> <span class="o">=</span> <span class="n">lam_n</span> <span class="o">*</span> <span class="p">(</span><span class="mi">1</span> <span class="o">+</span> <span class="n">beta</span><span class="p">)</span> <span class="o">/</span> <span class="n">beta</span>
+ <span class="n">m</span> <span class="o">=</span> <span class="nb">max</span><span class="p">(</span><span class="n">m1</span><span class="p">,</span> <span class="n">m2</span><span class="p">)</span>
+
+ <span class="c1"># network deconvolution</span>
+ <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">d</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="mi">0</span><span class="p">]):</span>
+ <span class="n">d</span><span class="p">[</span><span class="n">i</span><span class="p">,</span> <span class="n">i</span><span class="p">]</span> <span class="o">=</span> <span class="p">(</span><span class="n">d</span><span class="p">[</span><span class="n">i</span><span class="p">,</span> <span class="n">i</span><span class="p">])</span> <span class="o">/</span> <span class="p">(</span><span class="n">m</span> <span class="o">+</span> <span class="n">d</span><span class="p">[</span><span class="n">i</span><span class="p">,</span> <span class="n">i</span><span class="p">])</span>
+
+ <span class="n">mat_new1</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">dot</span><span class="p">(</span><span class="n">u</span><span class="p">,</span> <span class="n">np</span><span class="o">.</span><span class="n">dot</span><span class="p">(</span><span class="n">d</span><span class="p">,</span> <span class="n">la</span><span class="o">.</span><span class="n">inv</span><span class="p">(</span><span class="n">u</span><span class="p">)))</span>
+
+ <span class="sd">'''</span>
+
+<span class="sd"> ***********************************</span>
+<span class="sd"> displaying direct weights</span>
+<span class="sd"> '''</span>
+ <span class="k">if</span> <span class="n">control</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
+ <span class="n">ind_edges</span> <span class="o">=</span> <span class="p">(</span><span class="n">mat_th</span> <span class="o">></span> <span class="mi">0</span><span class="p">)</span> <span class="o">*</span> <span class="mf">1.0</span>
+ <span class="n">ind_nonedges</span> <span class="o">=</span> <span class="p">(</span><span class="n">mat_th</span> <span class="o">==</span> <span class="mi">0</span><span class="p">)</span> <span class="o">*</span> <span class="mf">1.0</span>
+ <span class="n">m1</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">max</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">max</span><span class="p">(</span><span class="n">npmat</span> <span class="o">*</span> <span class="n">ind_nonedges</span><span class="p">))</span>
+ <span class="n">m2</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">min</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">min</span><span class="p">(</span><span class="n">mat_new1</span><span class="p">))</span>
+ <span class="n">mat_new2</span> <span class="o">=</span> <span class="p">(</span><span class="n">mat_new1</span> <span class="o">+</span> <span class="n">np</span><span class="o">.</span><span class="n">max</span><span class="p">(</span><span class="n">m1</span> <span class="o">-</span> <span class="n">m2</span><span class="p">,</span> <span class="mi">0</span><span class="p">))</span> <span class="o">*</span> <span class="n">ind_edges</span> <span class="o">+</span> <span class="p">(</span>
+ <span class="n">npmat</span> <span class="o">*</span> <span class="n">ind_nonedges</span><span class="p">)</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="n">m2</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">min</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">min</span><span class="p">(</span><span class="n">mat_new1</span><span class="p">))</span>
+ <span class="n">mat_new2</span> <span class="o">=</span> <span class="p">(</span><span class="n">mat_new1</span> <span class="o">+</span> <span class="n">np</span><span class="o">.</span><span class="n">max</span><span class="p">(</span><span class="o">-</span><span class="n">m2</span><span class="p">,</span> <span class="mi">0</span><span class="p">))</span>
+
+ <span class="sd">'''</span>
+<span class="sd"> ***********************************</span>
+<span class="sd"> linearly mapping the deconvolved matrix to be between 0 and 1</span>
+<span class="sd"> '''</span>
+ <span class="n">m1</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">min</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">min</span><span class="p">(</span><span class="n">mat_new2</span><span class="p">))</span>
+ <span class="n">m2</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">max</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">max</span><span class="p">(</span><span class="n">mat_new2</span><span class="p">))</span>
+ <span class="n">mat_nd</span> <span class="o">=</span> <span class="p">(</span><span class="n">mat_new2</span> <span class="o">-</span> <span class="n">m1</span><span class="p">)</span> <span class="o">/</span> <span class="p">(</span><span class="n">m2</span> <span class="o">-</span> <span class="n">m1</span><span class="p">)</span>
+
+ <span class="k">return</span> <span class="n">mat_nd</span></div>
+</pre></div>
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diff --git a/examples-dev/olds/_build/html/_modules/ariaec/pdbdist.html b/examples-dev/olds/_build/html/_modules/ariaec/pdbdist.html
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+ <h1>Source code for ariaec.pdbdist</h1><div class="highlight"><pre>
+<span></span><span class="c1"># coding=utf-8</span>
+<span class="sd">"""</span>
+<span class="sd"> PDB distance distribution generation</span>
+<span class="sd">"""</span>
+
+<span class="kn">import</span> <span class="nn">os</span>
+<span class="kn">import</span> <span class="nn">sys</span>
+<span class="kn">import</span> <span class="nn">logging</span>
+<span class="kn">import</span> <span class="nn">pandas</span> <span class="k">as</span> <span class="nn">pd</span>
+<span class="kn">import</span> <span class="nn">pbxplore</span> <span class="k">as</span> <span class="nn">pbx</span>
+<span class="kn">from</span> <span class="nn">glob</span> <span class="k">import</span> <span class="n">glob</span>
+
+<span class="kn">from</span> <span class="nn">Bio.PDB</span> <span class="k">import</span> <span class="n">PDBList</span><span class="p">,</span> <span class="n">PDBParser</span><span class="p">,</span> <span class="n">Selection</span><span class="p">,</span> <span class="n">is_aa</span><span class="p">,</span> <span class="n">NeighborSearch</span><span class="p">,</span> \
+ <span class="n">MMCIFParser</span>
+<span class="kn">from</span> <span class="nn">Bio.PDB.DSSP</span> <span class="k">import</span> <span class="n">dssp_dict_from_pdb_file</span>
+<span class="kn">from</span> <span class="nn">future.utils</span> <span class="k">import</span> <span class="n">iteritems</span>
+<span class="kn">from</span> <span class="nn">collections</span> <span class="k">import</span> <span class="n">defaultdict</span><span class="p">,</span> <span class="n">OrderedDict</span>
+
+<span class="c1"># from .base import ppdict</span>
+<span class="kn">from</span> <span class="nn">.common</span> <span class="k">import</span> <span class="n">Capturing</span>
+<span class="kn">from</span> <span class="nn">.reader</span> <span class="k">import</span> <span class="n">CulledPdbFile</span>
+<span class="kn">from</span> <span class="nn">.protmap</span> <span class="k">import</span> <span class="n">ResAtmMap</span>
+
+<span class="kn">from</span> <span class="nn">aria.legacy.AminoAcid</span> <span class="k">import</span> <span class="n">AminoAcid</span>
+
+<span class="n">LOG</span> <span class="o">=</span> <span class="n">logging</span><span class="o">.</span><span class="n">getLogger</span><span class="p">(</span><span class="vm">__name__</span><span class="p">)</span>
+
+
+<div class="viewcode-block" id="PDBDist"><a class="viewcode-back" href="../../ariaec.html#ariaec.pdbdist.PDBDist">[docs]</a><span class="k">class</span> <span class="nc">PDBDist</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Extract pdb distance distribution from culled list of pdb files provided by</span>
+<span class="sd"> PICSES server [G. Wang and R. L. Dunbrack, Jr. PISCES: a protein sequence</span>
+<span class="sd"> culling server. Bioinformatics, 19:1589-1591, 2003.] with Bio.PDB tools</span>
+<span class="sd"> [Hamelryck, T., Manderick, B. (2003) PDB pdbparser and structure class</span>
+<span class="sd"> implemented in Python. Bioinformatics 19: 2308–2310]</span>
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+<span class="sd"> </span>
+<span class="sd"> """</span>
+
+ <span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">settings</span><span class="p">):</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">settings</span> <span class="o">=</span> <span class="n">settings</span>
+
+ <span class="bp">self</span><span class="o">.</span><span class="n">_obsoletedir</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">pdbdist</span><span class="o">.</span><span class="n">config</span><span class="o">.</span><span class="n">get</span><span class="p">(</span>
+ <span class="s1">'obsolete_directory'</span><span class="p">,</span> <span class="s1">'/tmp/obsolete'</span><span class="p">)</span>
+ <span class="c1"># Setting trash directory for old downloaded pdbs</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="n">os</span><span class="o">.</span><span class="n">access</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_obsoletedir</span><span class="p">,</span> <span class="n">os</span><span class="o">.</span><span class="n">F_OK</span><span class="p">):</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">warning</span><span class="p">(</span><span class="s2">"</span><span class="si">%s</span><span class="s2"> directory does not exist. Making a new directory"</span><span class="p">,</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_obsoletedir</span><span class="p">)</span>
+ <span class="n">os</span><span class="o">.</span><span class="n">makedirs</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_obsoletedir</span><span class="p">)</span>
+
+ <span class="bp">self</span><span class="o">.</span><span class="n">pdblist</span> <span class="o">=</span> <span class="n">PDBList</span><span class="p">(</span><span class="n">obsolete_pdb</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">_obsoletedir</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">pdbparser</span> <span class="o">=</span> <span class="n">PDBParser</span><span class="p">()</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">mmcifparser</span> <span class="o">=</span> <span class="n">MMCIFParser</span><span class="p">()</span>
+
+<div class="viewcode-block" id="PDBDist.get_proteinblocks"><a class="viewcode-back" href="../../ariaec.html#ariaec.pdbdist.PDBDist.get_proteinblocks">[docs]</a> <span class="nd">@staticmethod</span>
+ <span class="k">def</span> <span class="nf">get_proteinblocks</span><span class="p">(</span><span class="n">pdb</span><span class="p">,</span> <span class="n">chain</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Get Protein Block assignment index for chain with pbxplore</span>
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> pdb : pdb file path</span>
+<span class="sd"> </span>
+<span class="sd"> chain : str</span>
+<span class="sd"> </span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+<span class="sd"> </span>
+<span class="sd"> """</span>
+ <span class="k">with</span> <span class="n">Capturing</span><span class="p">()</span> <span class="k">as</span> <span class="n">output</span><span class="p">:</span>
+ <span class="n">chain</span> <span class="o">=</span> <span class="p">[</span><span class="n">ch</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="k">for</span> <span class="n">ch</span> <span class="ow">in</span> <span class="n">pbx</span><span class="o">.</span><span class="n">chains_from_files</span><span class="p">([</span><span class="n">pdb</span><span class="p">])</span>
+ <span class="k">if</span> <span class="n">ch</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">name</span> <span class="o">==</span> <span class="n">chain</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span>
+ <span class="k">if</span> <span class="n">output</span><span class="p">:</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="n">output</span><span class="p">)</span>
+
+ <span class="c1"># Assign protein blocks</span>
+ <span class="n">tmpblocks</span> <span class="o">=</span> <span class="n">pbx</span><span class="o">.</span><span class="n">assign</span><span class="p">(</span><span class="n">chain</span><span class="o">.</span><span class="n">get_phi_psi_angles</span><span class="p">())</span>
+ <span class="c1"># Get related list of resid</span>
+ <span class="n">sequence</span> <span class="o">=</span> <span class="nb">set</span><span class="p">([</span><span class="n">atm</span><span class="o">.</span><span class="n">resid</span> <span class="k">for</span> <span class="n">atm</span> <span class="ow">in</span> <span class="n">chain</span><span class="o">.</span><span class="n">atoms</span><span class="p">])</span>
+ <span class="c1"># In case of missing residues, define result as default dict</span>
+ <span class="n">pblocks</span> <span class="o">=</span> <span class="n">defaultdict</span><span class="p">(</span><span class="k">lambda</span><span class="p">:</span> <span class="s1">''</span><span class="p">)</span>
+
+ <span class="k">for</span> <span class="n">idx</span><span class="p">,</span> <span class="n">res_id</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">sequence</span><span class="p">):</span>
+ <span class="n">pblocks</span><span class="p">[</span><span class="n">res_id</span><span class="p">]</span> <span class="o">=</span> <span class="s2">"</span><span class="si">%s</span><span class="s2">"</span> <span class="o">%</span> <span class="n">tmpblocks</span><span class="p">[</span><span class="n">idx</span><span class="p">]</span>
+
+ <span class="k">return</span> <span class="n">pblocks</span></div>
+
+ <span class="c1"># TODO: similar function in another part of the package, have to merge them</span>
+<div class="viewcode-block" id="PDBDist.get_secstructs"><a class="viewcode-back" href="../../ariaec.html#ariaec.pdbdist.PDBDist.get_secstructs">[docs]</a> <span class="nd">@staticmethod</span>
+ <span class="k">def</span> <span class="nf">get_secstructs</span><span class="p">(</span><span class="n">backbone</span><span class="p">,</span> <span class="n">dssp_dict</span><span class="p">,</span> <span class="n">chain</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Return related secondary structure dictionary for each backbone residue</span>
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> backbone : :obj: `list` of :obj: `Bio.PDB.Residue.Residue`</span>
+<span class="sd"> List of bacbkone residues</span>
+<span class="sd"> dssp_dict :</span>
+<span class="sd"> </span>
+<span class="sd"> chain :</span>
+<span class="sd"> </span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+<span class="sd"> </span>
+<span class="sd"> """</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="s2">"Computing secondary structure index"</span><span class="p">)</span>
+ <span class="n">ss_idx</span> <span class="o">=</span> <span class="n">defaultdict</span><span class="p">(</span><span class="k">lambda</span><span class="p">:</span> <span class="s1">''</span><span class="p">)</span>
+ <span class="n">ss_count</span> <span class="o">=</span> <span class="p">{</span><span class="s1">'H'</span><span class="p">:</span> <span class="mi">1</span><span class="p">,</span> <span class="s1">'E'</span><span class="p">:</span> <span class="mi">1</span><span class="p">,</span> <span class="s1">'X'</span><span class="p">:</span> <span class="mi">1</span><span class="p">}</span>
+
+ <span class="c1"># Sort backbone by resid</span>
+ <span class="n">backbone</span> <span class="o">=</span> <span class="nb">sorted</span><span class="p">(</span><span class="n">backbone</span><span class="p">,</span> <span class="n">key</span><span class="o">=</span><span class="k">lambda</span> <span class="n">resx</span><span class="p">:</span> <span class="n">resx</span><span class="o">.</span><span class="n">id</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span>
+
+ <span class="k">for</span> <span class="n">idx</span><span class="p">,</span> <span class="n">res_x</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">backbone</span><span class="p">):</span>
+
+ <span class="n">resid_x</span> <span class="o">=</span> <span class="n">res_x</span><span class="o">.</span><span class="n">id</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
+ <span class="c1"># Get secondary structure in dssp dict or set ss as X element</span>
+ <span class="n">ss_x</span> <span class="o">=</span> <span class="n">dssp_dict</span><span class="o">.</span><span class="n">get</span><span class="p">((</span><span class="n">chain</span><span class="p">,</span> <span class="p">(</span><span class="s2">" "</span><span class="p">,</span> <span class="n">resid_x</span><span class="p">,</span> <span class="s2">" "</span><span class="p">)),</span> <span class="p">(</span><span class="s2">""</span><span class="p">,</span> <span class="s2">"X"</span><span class="p">))[</span><span class="mi">1</span><span class="p">]</span>
+ <span class="n">ss_x</span> <span class="o">=</span> <span class="s2">"X"</span> <span class="k">if</span> <span class="n">ss_x</span> <span class="ow">not</span> <span class="ow">in</span> <span class="p">[</span><span class="s2">"H"</span><span class="p">,</span> <span class="s2">"E"</span><span class="p">]</span> <span class="k">else</span> <span class="n">ss_x</span>
+ <span class="c1"># Udate secondary structure index for residue x</span>
+ <span class="n">ss_idx</span><span class="p">[</span><span class="n">resid_x</span><span class="p">]</span> <span class="o">=</span> <span class="s2">"</span><span class="si">%s%d</span><span class="s2">"</span> <span class="o">%</span> <span class="p">(</span><span class="n">ss_x</span><span class="p">,</span> <span class="n">ss_count</span><span class="p">[</span><span class="n">ss_x</span><span class="p">])</span>
+
+ <span class="c1"># Check if next residue still belongs to the same secondary</span>
+ <span class="c1"># structure</span>
+ <span class="k">if</span> <span class="n">idx</span> <span class="o">!=</span> <span class="nb">len</span><span class="p">(</span><span class="n">backbone</span><span class="p">)</span> <span class="o">-</span> <span class="mi">1</span><span class="p">:</span>
+ <span class="n">resid_j</span> <span class="o">=</span> <span class="n">backbone</span><span class="p">[</span><span class="n">idx</span> <span class="o">+</span> <span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">id</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
+ <span class="n">ss_j</span> <span class="o">=</span> <span class="n">dssp_dict</span><span class="o">.</span><span class="n">get</span><span class="p">((</span><span class="n">chain</span><span class="p">,</span> <span class="p">(</span><span class="s2">" "</span><span class="p">,</span> <span class="n">resid_j</span><span class="p">,</span> <span class="s2">" "</span><span class="p">)),</span> <span class="p">(</span><span class="s2">""</span><span class="p">,</span> <span class="s2">"X"</span><span class="p">))[</span><span class="mi">1</span><span class="p">]</span>
+ <span class="n">ss_j</span> <span class="o">=</span> <span class="s2">"X"</span> <span class="k">if</span> <span class="n">ss_j</span> <span class="ow">not</span> <span class="ow">in</span> <span class="p">[</span><span class="s2">"H"</span><span class="p">,</span> <span class="s2">"E"</span><span class="p">]</span> <span class="k">else</span> <span class="n">ss_j</span>
+
+ <span class="k">if</span> <span class="n">ss_x</span> <span class="o">!=</span> <span class="n">ss_j</span><span class="p">:</span>
+ <span class="c1"># If end of secondary structure element, increase related ss</span>
+ <span class="c1"># count</span>
+ <span class="n">ss_count</span><span class="p">[</span><span class="n">ss_x</span><span class="p">]</span> <span class="o">+=</span> <span class="mi">1</span>
+
+ <span class="n">LOG</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="n">ss_idx</span><span class="p">)</span>
+ <span class="k">return</span> <span class="n">ss_idx</span></div>
+
+<div class="viewcode-block" id="PDBDist.pdbdists"><a class="viewcode-back" href="../../ariaec.html#ariaec.pdbdist.PDBDist.pdbdists">[docs]</a> <span class="k">def</span> <span class="nf">pdbdists</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">pdb</span><span class="p">,</span> <span class="n">pdbid</span><span class="p">,</span> <span class="n">chain</span><span class="p">,</span> <span class="n">pair_list</span><span class="o">=</span><span class="s2">"all"</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Get distance matrix from pdb file and write distances into output file</span>
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> pdb : str</span>
+<span class="sd"> Path of pdb file</span>
+<span class="sd"> pdbid : str</span>
+<span class="sd"> PDB id</span>
+<span class="sd"> chain : str</span>
+<span class="sd"> Chain id</span>
+<span class="sd"> pair_list : {'all', 'min', 'heavy'}</span>
+<span class="sd"> Defining if we generate a distance distribution for a minimal set</span>
+<span class="sd"> of atom pairs, heavy pairs or all atom pairs (Default value = "all")</span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+<span class="sd"> dists: :obj: `list` of :obj: `OrderedDict`</span>
+
+<span class="sd"> </span>
+<span class="sd"> """</span>
+ <span class="c1"># TODO: Do we have to take disordered atoms into account ?</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s2">"Compute atom distances for chain </span><span class="si">%s</span><span class="s2"> of </span><span class="si">%s</span><span class="s2">"</span><span class="p">,</span> <span class="n">chain</span><span class="p">,</span> <span class="n">pdbid</span><span class="p">)</span>
+ <span class="c1"># out = ""</span>
+ <span class="n">dists</span> <span class="o">=</span> <span class="p">[]</span>
+ <span class="n">cutoff</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">pdbdist</span><span class="o">.</span><span class="n">config</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"contact_cutoff"</span><span class="p">)</span>
+ <span class="c1"># Check if dssp executable exists otherwise we can't find secondary</span>
+ <span class="c1"># structures</span>
+ <span class="n">dssp_exec</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">pdbdist</span><span class="o">.</span><span class="n">config</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"dssp_exec"</span><span class="p">)</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="n">os</span><span class="o">.</span><span class="n">access</span><span class="p">(</span><span class="n">dssp_exec</span><span class="p">,</span> <span class="n">os</span><span class="o">.</span><span class="n">F_OK</span><span class="p">):</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">error</span><span class="p">(</span><span class="s2">"DSSP executable not found. Check if dssp_exec parameter"</span>
+ <span class="s2">" in config file is correct !"</span><span class="p">)</span>
+ <span class="n">sys</span><span class="o">.</span><span class="n">exit</span><span class="p">(</span><span class="mi">1</span><span class="p">)</span>
+
+ <span class="c1"># Get chain structure object with Bio.PDB pdbparser or mmcifparser</span>
+ <span class="c1"># (related to model 0)</span>
+ <span class="k">if</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">splitext</span><span class="p">(</span><span class="n">pdb</span><span class="p">)[</span><span class="mi">1</span><span class="p">]</span> <span class="ow">in</span> <span class="p">(</span><span class="s1">'.pdb'</span><span class="p">,</span> <span class="s1">'.ent'</span><span class="p">):</span>
+ <span class="n">structure</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">pdbparser</span><span class="o">.</span><span class="n">get_structure</span><span class="p">(</span><span class="n">pdbid</span><span class="p">,</span> <span class="n">pdb</span><span class="p">)[</span><span class="mi">0</span><span class="p">][</span><span class="n">chain</span><span class="p">]</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="n">structure</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">mmcifparser</span><span class="o">.</span><span class="n">get_structure</span><span class="p">(</span><span class="n">pdbid</span><span class="p">,</span> <span class="n">pdb</span><span class="p">)[</span><span class="mi">0</span><span class="p">][</span><span class="n">chain</span><span class="p">]</span>
+
+ <span class="c1"># Get list of residues by ignoring heteroatoms, water molecules</span>
+ <span class="c1"># by looking at the hetero-flag in residue id (H_ for hetero atoms or</span>
+ <span class="c1"># W_ for water molecules) with only one resx object by amino acid (ca</span>
+ <span class="c1"># filter). Also ignore insertion mutants</span>
+ <span class="n">residues</span> <span class="o">=</span> <span class="p">[</span><span class="n">res</span> <span class="k">for</span> <span class="n">res</span> <span class="ow">in</span> <span class="n">structure</span><span class="o">.</span><span class="n">get_residues</span><span class="p">()</span>
+ <span class="k">if</span> <span class="n">res</span><span class="o">.</span><span class="n">get_id</span><span class="p">()[</span><span class="mi">0</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span> <span class="ow">not</span> <span class="ow">in</span> <span class="p">[</span><span class="s1">'H'</span><span class="p">,</span> <span class="s1">'W'</span><span class="p">]</span>
+ <span class="ow">and</span> <span class="n">res</span><span class="o">.</span><span class="n">get_id</span><span class="p">()[</span><span class="mi">2</span><span class="p">]</span> <span class="o">==</span> <span class="s1">' '</span>
+ <span class="ow">and</span> <span class="n">is_aa</span><span class="p">(</span><span class="n">res</span><span class="p">)</span> <span class="ow">and</span> <span class="n">res</span><span class="o">.</span><span class="n">has_id</span><span class="p">(</span><span class="s1">'CA'</span><span class="p">)]</span>
+
+ <span class="c1"># Unfold atom list related to selected residues</span>
+ <span class="n">atoms</span> <span class="o">=</span> <span class="n">Selection</span><span class="o">.</span><span class="n">unfold_entities</span><span class="p">(</span><span class="n">residues</span><span class="p">,</span> <span class="s2">"A"</span><span class="p">)</span>
+
+ <span class="c1"># Get dssp dictionary and related dssp keys from pdb file</span>
+ <span class="n">logging</span><span class="o">.</span><span class="n">captureWarnings</span><span class="p">(</span><span class="kc">True</span><span class="p">)</span>
+
+ <span class="k">try</span><span class="p">:</span>
+ <span class="n">dssp_dict</span><span class="p">,</span> <span class="n">dssp_keys</span> <span class="o">=</span> <span class="n">dssp_dict_from_pdb_file</span><span class="p">(</span>
+ <span class="n">pdb</span><span class="p">,</span> <span class="n">DSSP</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">pdbdist</span><span class="o">.</span><span class="n">config</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"dssp_exec"</span><span class="p">))</span>
+ <span class="k">except</span> <span class="ne">Exception</span> <span class="k">as</span> <span class="n">msg</span><span class="p">:</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">error</span><span class="p">(</span><span class="s2">"</span><span class="si">%s</span><span class="s2">: </span><span class="si">%s</span><span class="s2">"</span><span class="p">,</span> <span class="ne">Exception</span><span class="p">,</span> <span class="n">msg</span><span class="p">)</span>
+ <span class="k">return</span> <span class="kc">None</span>
+
+ <span class="c1"># Compute secondary structure index</span>
+ <span class="n">ss_idx</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">get_secstructs</span><span class="p">(</span><span class="n">residues</span><span class="p">,</span> <span class="n">dssp_dict</span><span class="p">,</span> <span class="n">chain</span><span class="p">)</span>
+ <span class="n">pb_idx</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">get_proteinblocks</span><span class="p">(</span><span class="n">pdb</span><span class="p">,</span> <span class="n">chain</span><span class="p">)</span>
+
+ <span class="n">LOG</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="s2">"Protein Blocks assignment (</span><span class="si">%s</span><span class="s2">):</span><span class="se">\n</span><span class="si">%s</span><span class="s2">"</span><span class="p">,</span> <span class="nb">len</span><span class="p">(</span><span class="n">pb_idx</span><span class="p">),</span> <span class="n">pb_idx</span><span class="p">)</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="s2">"Secondary structure index (</span><span class="si">%s</span><span class="s2">):</span><span class="se">\n</span><span class="si">%s</span><span class="s2">"</span><span class="p">,</span> <span class="nb">len</span><span class="p">(</span><span class="n">ss_idx</span><span class="p">),</span> <span class="n">ss_idx</span><span class="p">)</span>
+
+ <span class="c1"># TODO: could be a better idea to use protmap.AtmMap class</span>
+ <span class="c1"># Initialize square checking matrix (if a resx has already been seen)</span>
+ <span class="n">atoms_idx</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">Index</span><span class="p">([</span><span class="n">atmx</span><span class="o">.</span><span class="n">get_serial_number</span><span class="p">()</span> <span class="k">for</span> <span class="n">atmx</span> <span class="ow">in</span> <span class="n">atoms</span><span class="p">])</span>
+ <span class="n">seen</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">(</span><span class="n">data</span><span class="o">=</span><span class="mi">0</span><span class="p">,</span> <span class="n">dtype</span><span class="o">=</span><span class="nb">int</span><span class="p">,</span> <span class="n">index</span><span class="o">=</span><span class="n">atoms_idx</span><span class="p">,</span>
+ <span class="n">columns</span><span class="o">=</span><span class="n">atoms_idx</span><span class="p">)</span>
+
+ <span class="c1"># Initialize Neighbor searching object</span>
+ <span class="n">neighsearch</span> <span class="o">=</span> <span class="n">NeighborSearch</span><span class="p">(</span><span class="n">atoms</span><span class="p">)</span>
+
+ <span class="k">for</span> <span class="n">resx</span> <span class="ow">in</span> <span class="n">residues</span><span class="p">:</span>
+
+ <span class="n">resx_name</span> <span class="o">=</span> <span class="n">AminoAcid</span><span class="p">(</span><span class="n">resx</span><span class="o">.</span><span class="n">get_resname</span><span class="p">())[</span><span class="mi">0</span><span class="p">]</span>
+ <span class="n">resx_id</span> <span class="o">=</span> <span class="n">resx</span><span class="o">.</span><span class="n">id</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
+ <span class="n">ssx</span> <span class="o">=</span> <span class="n">ss_idx</span><span class="p">[</span><span class="n">resx_id</span><span class="p">]</span>
+ <span class="n">pblocx</span> <span class="o">=</span> <span class="n">pb_idx</span><span class="p">[</span><span class="n">resx_id</span><span class="p">]</span>
+
+ <span class="n">LOG</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="s2">"Start at residue </span><span class="si">%s</span><span class="s2"> (</span><span class="si">%s</span><span class="s2">) with </span><span class="si">%s</span><span class="s2"> atoms"</span><span class="p">,</span> <span class="n">resx_id</span><span class="p">,</span>
+ <span class="n">resx_name</span><span class="p">,</span> <span class="n">resx</span><span class="o">.</span><span class="n">get_list</span><span class="p">())</span>
+
+ <span class="k">for</span> <span class="n">atmx</span> <span class="ow">in</span> <span class="n">resx</span><span class="o">.</span><span class="n">get_list</span><span class="p">():</span>
+
+ <span class="n">atmx_id</span> <span class="o">=</span> <span class="n">atmx</span><span class="o">.</span><span class="n">get_serial_number</span><span class="p">()</span>
+ <span class="n">atmx_name</span> <span class="o">=</span> <span class="n">atmx</span><span class="o">.</span><span class="n">get_name</span><span class="p">()</span>
+
+ <span class="c1"># Find neighboring res around atom in resi within defined cutoff</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="s2">"Looking for residues in contact with atom </span><span class="si">%s</span><span class="s2"> of res "</span>
+ <span class="s2">"</span><span class="si">%s</span><span class="s2"> (</span><span class="si">%s</span><span class="s2">)"</span><span class="p">,</span> <span class="n">atmx_name</span><span class="p">,</span> <span class="n">resx_name</span><span class="p">,</span> <span class="n">resx_id</span><span class="p">)</span>
+ <span class="n">neighbors</span> <span class="o">=</span> <span class="n">neighsearch</span><span class="o">.</span><span class="n">search</span><span class="p">(</span>
+ <span class="n">atmx</span><span class="o">.</span><span class="n">get_coord</span><span class="p">(),</span> <span class="n">cutoff</span><span class="p">,</span> <span class="n">level</span><span class="o">=</span><span class="s2">"R"</span><span class="p">)</span>
+ <span class="c1"># Select long range contacts</span>
+ <span class="n">longr_contacts</span> <span class="o">=</span> <span class="p">[</span><span class="n">res</span> <span class="k">for</span> <span class="n">res</span> <span class="ow">in</span> <span class="n">neighbors</span> <span class="k">if</span>
+ <span class="nb">abs</span><span class="p">(</span><span class="n">res</span><span class="o">.</span><span class="n">id</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="o">-</span> <span class="n">resx_id</span><span class="p">)</span> <span class="o">></span> <span class="mi">5</span><span class="p">]</span>
+
+ <span class="c1"># For each residue in contact with the selected atom</span>
+ <span class="k">for</span> <span class="n">resy</span> <span class="ow">in</span> <span class="n">longr_contacts</span><span class="p">:</span>
+
+ <span class="n">resy_name</span> <span class="o">=</span> <span class="n">AminoAcid</span><span class="p">(</span><span class="n">resy</span><span class="o">.</span><span class="n">get_resname</span><span class="p">())[</span><span class="mi">0</span><span class="p">]</span>
+ <span class="n">resy_id</span> <span class="o">=</span> <span class="n">resy</span><span class="o">.</span><span class="n">id</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
+ <span class="n">ssy</span> <span class="o">=</span> <span class="n">ss_idx</span><span class="p">[</span><span class="n">resy_id</span><span class="p">]</span>
+ <span class="n">pblocy</span> <span class="o">=</span> <span class="n">pb_idx</span><span class="p">[</span><span class="n">resy_id</span><span class="p">]</span>
+
+ <span class="c1"># Ignore disulfide bridges and unkonwn residues</span>
+ <span class="k">if</span> <span class="p">(</span><span class="n">resx_name</span> <span class="o">==</span> <span class="s2">"CYS"</span> <span class="ow">and</span> <span class="n">resy_name</span> <span class="o">==</span> <span class="s2">"CYS"</span><span class="p">)</span> \
+ <span class="ow">or</span> <span class="ow">not</span> <span class="n">resx_name</span> <span class="ow">or</span> <span class="ow">not</span> <span class="n">resy_name</span><span class="p">:</span>
+ <span class="k">continue</span>
+
+ <span class="n">scx_name</span><span class="p">,</span> <span class="n">scy_name</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">scsc_min</span><span class="p">[</span><span class="n">resx_name</span><span class="p">][</span>
+ <span class="n">resy_name</span><span class="p">]</span>
+
+ <span class="k">if</span> <span class="p">(</span><span class="n">pair_list</span> <span class="o">==</span> <span class="s2">"min"</span> <span class="ow">and</span>
+ <span class="n">atmx_name</span> <span class="ow">not</span> <span class="ow">in</span> <span class="p">(</span><span class="s2">"CA"</span><span class="p">,</span> <span class="s2">"CB"</span><span class="p">,</span> <span class="n">scx_name</span><span class="p">))</span> <span class="ow">or</span> \
+ <span class="p">(</span><span class="n">pair_list</span> <span class="o">==</span> <span class="s2">"heavy"</span>
+ <span class="ow">and</span> <span class="ow">not</span> <span class="n">ResAtmMap</span><span class="o">.</span><span class="n">heavy_reg</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="n">atmx_name</span><span class="p">)):</span>
+ <span class="k">continue</span>
+
+ <span class="n">LOG</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="s2">"Contact detected for atom </span><span class="si">%s</span><span class="s2"> of res </span><span class="si">%s</span><span class="s2"> (</span><span class="si">%s</span><span class="s2">) with"</span>
+ <span class="s2">" res </span><span class="si">%s</span><span class="s2"> (</span><span class="si">%s</span><span class="s2">)"</span><span class="p">,</span>
+ <span class="n">atmx_name</span><span class="p">,</span> <span class="n">resx_id</span><span class="p">,</span> <span class="n">resx_name</span><span class="p">,</span> <span class="n">resy_id</span><span class="p">,</span> <span class="n">resy_name</span><span class="p">)</span>
+
+ <span class="c1"># Define secondary structure type</span>
+ <span class="n">ss_type</span> <span class="o">=</span> <span class="n">ssx</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">+</span> <span class="n">ssy</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
+ <span class="k">if</span> <span class="n">ssx</span> <span class="o">!=</span> <span class="n">ssy</span><span class="p">:</span>
+ <span class="k">if</span> <span class="n">ss_type</span> <span class="ow">in</span> <span class="p">(</span><span class="s2">"HH"</span><span class="p">,</span> <span class="s2">"EE"</span><span class="p">,</span> <span class="s2">"HE"</span><span class="p">,</span> <span class="s2">"EH"</span><span class="p">):</span>
+ <span class="c1"># Contact between helice or beta strand</span>
+ <span class="n">ss_type</span> <span class="o">=</span> <span class="s2">"HE"</span> <span class="k">if</span> <span class="n">ss_type</span> <span class="ow">not</span> <span class="ow">in</span> <span class="p">(</span><span class="s2">"HH"</span><span class="p">,</span> <span class="s2">"EE"</span><span class="p">)</span> \
+ <span class="k">else</span> <span class="n">ss_type</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="c1"># Contact with loops or other secondary</span>
+ <span class="c1"># structure</span>
+ <span class="n">ss_type</span> <span class="o">=</span> <span class="s2">"XH"</span> <span class="k">if</span> <span class="s2">"H"</span> <span class="ow">in</span> <span class="n">ss_type</span> <span class="k">else</span> <span class="s2">"XE"</span> \
+ <span class="k">if</span> <span class="s2">"E"</span> <span class="ow">in</span> <span class="n">ss_type</span> <span class="k">else</span> <span class="s2">"XX"</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="c1"># Same secondary structure</span>
+ <span class="n">ss_type</span> <span class="o">=</span> <span class="n">ssx</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
+
+ <span class="c1"># PB type</span>
+ <span class="n">pb_type</span> <span class="o">=</span> <span class="s1">''</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="nb">sorted</span><span class="p">(</span><span class="n">pblocx</span> <span class="o">+</span> <span class="n">pblocy</span><span class="p">))</span>
+
+ <span class="k">for</span> <span class="n">atmy</span> <span class="ow">in</span> <span class="n">resy</span><span class="o">.</span><span class="n">get_list</span><span class="p">():</span>
+
+ <span class="n">atmy_id</span> <span class="o">=</span> <span class="n">atmy</span><span class="o">.</span><span class="n">get_serial_number</span><span class="p">()</span>
+ <span class="n">atmy_name</span> <span class="o">=</span> <span class="n">atmy</span><span class="o">.</span><span class="n">get_name</span><span class="p">()</span>
+ <span class="c1"># Filter atom pairs if pair_list is not equal to "all"</span>
+
+ <span class="n">LOG</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="s2">"Contact filter: </span><span class="si">%s</span><span class="s2">-</span><span class="si">%s</span><span class="s2"> (</span><span class="si">%s</span><span class="s2">,</span><span class="si">%s</span><span class="s2">) </span><span class="si">%s</span><span class="s2">-</span><span class="si">%s</span><span class="s2"> (</span><span class="si">%s</span><span class="s2">,</span><span class="si">%s</span><span class="s2">)"</span><span class="p">,</span>
+ <span class="n">resx_name</span><span class="p">,</span> <span class="n">resy_name</span><span class="p">,</span> <span class="n">resx_id</span><span class="p">,</span> <span class="n">resy_id</span><span class="p">,</span>
+ <span class="n">atmx_name</span><span class="p">,</span> <span class="n">atmy_name</span><span class="p">,</span> <span class="n">atmx_id</span><span class="p">,</span> <span class="n">atmy_id</span><span class="p">)</span>
+
+ <span class="k">if</span> <span class="p">(</span><span class="n">pair_list</span> <span class="o">==</span> <span class="s2">"min"</span> <span class="ow">and</span>
+ <span class="n">atmy_name</span> <span class="ow">not</span> <span class="ow">in</span> <span class="p">(</span><span class="s2">"CA"</span><span class="p">,</span> <span class="s2">"CB"</span><span class="p">,</span> <span class="n">scy_name</span><span class="p">))</span> <span class="ow">or</span> \
+ <span class="p">(</span><span class="n">pair_list</span> <span class="o">==</span> <span class="s2">"heavy"</span>
+ <span class="ow">and</span> <span class="ow">not</span> <span class="n">ResAtmMap</span><span class="o">.</span><span class="n">heavy_reg</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="n">atmy_name</span><span class="p">)):</span>
+ <span class="n">seen</span><span class="p">[</span><span class="n">atmx_id</span><span class="p">][</span><span class="n">atmy_id</span><span class="p">]</span> <span class="o">=</span> <span class="mi">1</span>
+ <span class="n">seen</span><span class="p">[</span><span class="n">atmy_id</span><span class="p">][</span><span class="n">atmx_id</span><span class="p">]</span> <span class="o">=</span> <span class="mi">1</span>
+ <span class="k">continue</span>
+
+ <span class="n">LOG</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="s2">"...valid"</span><span class="p">)</span>
+
+ <span class="k">if</span> <span class="ow">not</span> <span class="n">seen</span><span class="p">[</span><span class="n">atmx_id</span><span class="p">][</span><span class="n">atmy_id</span><span class="p">]:</span>
+ <span class="c1"># If contact between two atoms not already seen,</span>
+ <span class="c1"># write distance in the output file</span>
+ <span class="n">dist</span> <span class="o">=</span> <span class="n">atmx</span> <span class="o">-</span> <span class="n">atmy</span>
+
+ <span class="n">dists</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">OrderedDict</span><span class="p">([</span>
+ <span class="p">(</span><span class="s1">'pdbid'</span><span class="p">,</span> <span class="n">pdbid</span><span class="p">),</span> <span class="p">(</span><span class="s1">'ss_type'</span><span class="p">,</span> <span class="n">ss_type</span><span class="p">),</span>
+ <span class="p">(</span><span class="s1">'ssx'</span><span class="p">,</span> <span class="n">ssx</span><span class="p">),</span> <span class="p">(</span><span class="s1">'ssy'</span><span class="p">,</span> <span class="n">ssy</span><span class="p">),</span>
+ <span class="p">(</span><span class="s1">'pb_type'</span><span class="p">,</span> <span class="n">pb_type</span><span class="p">),</span> <span class="p">(</span><span class="s1">'pblocx'</span><span class="p">,</span> <span class="n">pblocx</span><span class="p">),</span>
+ <span class="p">(</span><span class="s1">'pblocy'</span><span class="p">,</span> <span class="n">pblocy</span><span class="p">),</span> <span class="p">(</span><span class="s1">'resx_id'</span><span class="p">,</span> <span class="nb">str</span><span class="p">(</span><span class="n">resx_id</span><span class="p">)),</span>
+ <span class="p">(</span><span class="s1">'resy_id'</span><span class="p">,</span> <span class="nb">str</span><span class="p">(</span><span class="n">resy_id</span><span class="p">)),</span>
+ <span class="p">(</span><span class="s1">'resx_name'</span><span class="p">,</span> <span class="n">resx_name</span><span class="p">),</span>
+ <span class="p">(</span><span class="s1">'resy_name'</span><span class="p">,</span> <span class="n">resy_name</span><span class="p">),</span>
+ <span class="p">(</span><span class="s1">'atmx_id'</span><span class="p">,</span> <span class="nb">str</span><span class="p">(</span><span class="n">atmx_id</span><span class="p">)),</span>
+ <span class="p">(</span><span class="s1">'atmy_id'</span><span class="p">,</span> <span class="nb">str</span><span class="p">(</span><span class="n">atmy_id</span><span class="p">)),</span>
+ <span class="p">(</span><span class="s1">'atmx_name'</span><span class="p">,</span> <span class="n">atmx_name</span><span class="p">),</span>
+ <span class="p">(</span><span class="s1">'atmy_name'</span><span class="p">,</span> <span class="n">atmy_name</span><span class="p">),</span>
+ <span class="p">(</span><span class="s1">'dist'</span><span class="p">,</span> <span class="nb">str</span><span class="p">(</span><span class="n">dist</span><span class="p">))</span>
+ <span class="p">]))</span>
+
+ <span class="n">seen</span><span class="p">[</span><span class="n">atmx_id</span><span class="p">][</span><span class="n">atmy_id</span><span class="p">]</span> <span class="o">=</span> <span class="mi">1</span>
+ <span class="n">seen</span><span class="p">[</span><span class="n">atmy_id</span><span class="p">][</span><span class="n">atmx_id</span><span class="p">]</span> <span class="o">=</span> <span class="mi">1</span>
+ <span class="k">return</span> <span class="n">dists</span></div>
+
+<div class="viewcode-block" id="PDBDist.run"><a class="viewcode-back" href="../../ariaec.html#ariaec.pdbdist.PDBDist.run">[docs]</a> <span class="k">def</span> <span class="nf">run</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="sd">"""main method"""</span>
+
+ <span class="c1"># Set pdb directory</span>
+ <span class="n">outdir</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">pdbdist</span><span class="o">.</span><span class="n">args</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"output_directory"</span><span class="p">,</span> <span class="n">os</span><span class="o">.</span><span class="n">getcwd</span><span class="p">())</span>
+ <span class="n">pdbdir</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">pdbdist</span><span class="o">.</span><span class="n">args</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">'pdbdir'</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">pdbdist</span><span class="o">.</span><span class="n">args</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">'pdbdir'</span><span class="p">)</span> <span class="ow">or</span> <span class="ow">not</span> <span class="n">os</span><span class="o">.</span><span class="n">access</span><span class="p">(</span><span class="n">pdbdir</span><span class="p">,</span>
+ <span class="n">os</span><span class="o">.</span><span class="n">F_OK</span><span class="p">):</span>
+
+ <span class="k">if</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">pdbdist</span><span class="o">.</span><span class="n">config</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"download_pdbs"</span><span class="p">,</span> <span class="kc">False</span><span class="p">):</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">warning</span><span class="p">(</span>
+ <span class="s2">"PDB directory not given and download inactivated."</span>
+ <span class="s2">" PDBDist command can't download pdb files."</span><span class="p">)</span>
+ <span class="k">return</span> <span class="kc">None</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="c1"># We have to download all files so we set outdir as pdbdir</span>
+ <span class="n">pdbdir</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">abspath</span><span class="p">(</span><span class="n">outdir</span><span class="p">),</span> <span class="s1">'pdbs'</span><span class="p">)</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="n">os</span><span class="o">.</span><span class="n">access</span><span class="p">(</span><span class="n">pdbdir</span><span class="p">,</span> <span class="n">os</span><span class="o">.</span><span class="n">F_OK</span><span class="p">):</span>
+ <span class="n">os</span><span class="o">.</span><span class="n">makedirs</span><span class="p">(</span><span class="n">pdbdir</span><span class="p">)</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="n">pdbdir</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">abspath</span><span class="p">(</span><span class="n">pdbdir</span><span class="p">)</span>
+
+ <span class="n">pair_flag</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">pdbdist</span><span class="o">.</span><span class="n">config</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"pair_list"</span><span class="p">,</span> <span class="s2">"all"</span><span class="p">)</span>
+ <span class="n">distpath</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">outdir</span><span class="p">,</span> <span class="s2">"pdbdists.dat"</span><span class="p">)</span>
+ <span class="n">distpath</span> <span class="o">=</span> <span class="n">distpath</span> <span class="k">if</span> <span class="n">pair_flag</span> <span class="ow">in</span> <span class="n">distpath</span> <span class="k">else</span> \
+ <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">splitext</span><span class="p">(</span><span class="n">distpath</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span> <span class="o">+</span> <span class="s2">"_"</span> <span class="o">+</span> <span class="n">pair_flag</span> <span class="o">+</span> \
+ <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">splitext</span><span class="p">(</span><span class="n">distpath</span><span class="p">)[</span><span class="mi">1</span><span class="p">]</span>
+
+ <span class="c1"># Load cullpdb file</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s2">"Loading culled list of pdb file(s)"</span><span class="p">)</span>
+ <span class="n">cullfile</span> <span class="o">=</span> <span class="n">CulledPdbFile</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">pdbdist</span><span class="o">.</span><span class="n">args</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"cullpdbs"</span><span class="p">))</span>
+ <span class="n">cullfile</span><span class="o">.</span><span class="n">load</span><span class="p">()</span>
+
+ <span class="c1"># Load all pdb files and generate distance file</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s2">"Looking for pdb entries into </span><span class="si">%s</span><span class="s2"> folder"</span><span class="p">,</span> <span class="n">pdbdir</span><span class="p">)</span>
+ <span class="n">header</span> <span class="o">=</span> <span class="s2">""</span>
+
+ <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">distpath</span><span class="p">,</span> <span class="s1">'w'</span><span class="p">)</span> <span class="k">as</span> <span class="n">distfile</span><span class="p">:</span>
+
+ <span class="k">for</span> <span class="n">idline</span><span class="p">,</span> <span class="n">pdbent</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="n">cullfile</span><span class="o">.</span><span class="n">lines</span><span class="p">):</span>
+
+ <span class="n">pdbid</span> <span class="o">=</span> <span class="n">pdbent</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"pdb_id"</span><span class="p">)</span>
+
+ <span class="c1"># Download file if necessary</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="n">glob</span><span class="p">(</span><span class="s1">'</span><span class="si">%s</span><span class="s1">/*</span><span class="si">%s</span><span class="s1">*'</span> <span class="o">%</span> <span class="p">(</span><span class="n">pdbdir</span><span class="p">,</span> <span class="n">pdbid</span><span class="o">.</span><span class="n">lower</span><span class="p">())):</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="s2">"Download pdb entry for </span><span class="si">%s</span><span class="s2"> pdb"</span><span class="p">,</span> <span class="n">pdbid</span><span class="p">)</span>
+ <span class="k">try</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">pdblist</span><span class="o">.</span><span class="n">retrieve_pdb_file</span><span class="p">(</span><span class="n">pdbid</span><span class="p">,</span> <span class="n">pdir</span><span class="o">=</span><span class="n">pdbdir</span><span class="p">,</span>
+ <span class="n">file_format</span><span class="o">=</span><span class="s2">"pdb"</span><span class="p">)</span>
+ <span class="k">except</span> <span class="ne">Exception</span> <span class="k">as</span> <span class="n">msg</span><span class="p">:</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">error</span><span class="p">(</span><span class="s2">"</span><span class="si">%s</span><span class="s2">: </span><span class="si">%s</span><span class="s2">"</span><span class="p">,</span> <span class="ne">Exception</span><span class="p">,</span> <span class="n">msg</span><span class="p">)</span>
+ <span class="k">continue</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="n">glob</span><span class="p">(</span><span class="s1">'</span><span class="si">%s</span><span class="s1">/*</span><span class="si">%s</span><span class="s1">*'</span> <span class="o">%</span> <span class="p">(</span><span class="n">pdbdir</span><span class="p">,</span> <span class="n">pdbid</span><span class="o">.</span><span class="n">lower</span><span class="p">())):</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s2">"Error during download, try to download in "</span>
+ <span class="s2">"mmCIF format"</span><span class="p">)</span>
+ <span class="k">try</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">pdblist</span><span class="o">.</span><span class="n">retrieve_pdb_file</span><span class="p">(</span><span class="n">pdbid</span><span class="p">,</span> <span class="n">pdir</span><span class="o">=</span><span class="n">pdbdir</span><span class="p">,</span>
+ <span class="n">file_format</span><span class="o">=</span><span class="s2">"mmCif"</span><span class="p">)</span>
+ <span class="k">except</span> <span class="ne">Exception</span> <span class="k">as</span> <span class="n">msg</span><span class="p">:</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">error</span><span class="p">(</span><span class="s2">"</span><span class="si">%s</span><span class="s2">: </span><span class="si">%s</span><span class="s2">"</span><span class="p">,</span> <span class="ne">Exception</span><span class="p">,</span> <span class="n">msg</span><span class="p">)</span>
+ <span class="k">continue</span>
+
+ <span class="n">pdbpaths</span> <span class="o">=</span> <span class="n">glob</span><span class="p">(</span><span class="s1">'</span><span class="si">%s</span><span class="s1">/*</span><span class="si">%s</span><span class="s1">*'</span> <span class="o">%</span> <span class="p">(</span><span class="n">pdbdir</span><span class="p">,</span> <span class="n">pdbid</span><span class="o">.</span><span class="n">lower</span><span class="p">()))</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="s2">"Found </span><span class="si">%s</span><span class="s2"> file(s) related to </span><span class="si">%s</span><span class="s2"> pdb entry into </span><span class="si">%s</span><span class="s2"> folder "</span>
+ <span class="s2">"(</span><span class="si">%s</span><span class="s2">)"</span><span class="p">,</span> <span class="nb">len</span><span class="p">(</span><span class="n">pdbpaths</span><span class="p">),</span> <span class="n">pdbid</span><span class="p">,</span> <span class="n">pdbdir</span><span class="p">,</span> <span class="n">pdbpaths</span><span class="p">)</span>
+
+ <span class="c1"># Get distance matrix from pdb file and write distances into</span>
+ <span class="c1"># output file</span>
+ <span class="n">dists</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">pdbdists</span><span class="p">(</span>
+ <span class="n">pdbpaths</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">pdbid</span><span class="p">,</span> <span class="n">pdbent</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"chain_id"</span><span class="p">),</span>
+ <span class="n">pair_list</span><span class="o">=</span><span class="n">pair_flag</span><span class="p">)</span>
+
+ <span class="k">if</span> <span class="n">idline</span> <span class="o">==</span> <span class="mi">1</span><span class="p">:</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s2">"Writing header line"</span><span class="p">)</span>
+ <span class="n">header</span> <span class="o">=</span> <span class="p">[</span><span class="n">key</span> <span class="k">for</span> <span class="n">key</span> <span class="ow">in</span> <span class="n">dists</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">keys</span><span class="p">()]</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="s2">","</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">header</span><span class="p">))</span>
+ <span class="n">distfile</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">"</span><span class="si">%s</span><span class="se">\n</span><span class="s2">"</span> <span class="o">%</span> <span class="s2">","</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">header</span><span class="p">))</span>
+
+ <span class="k">for</span> <span class="n">dist</span> <span class="ow">in</span> <span class="n">dists</span><span class="p">:</span>
+ <span class="n">distfile</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">"</span><span class="si">%s</span><span class="se">\n</span><span class="s2">"</span> <span class="o">%</span> <span class="s2">","</span><span class="o">.</span><span class="n">join</span><span class="p">([</span><span class="n">dist</span><span class="p">[</span><span class="n">key</span><span class="p">]</span> <span class="k">for</span> <span class="n">key</span> <span class="ow">in</span> <span class="n">header</span><span class="p">]))</span>
+
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">pdbdist</span><span class="o">.</span><span class="n">config</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"remove_pdbs"</span><span class="p">,</span> <span class="kc">False</span><span class="p">):</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s2">"Remove </span><span class="si">%s</span><span class="s2"> pdb file"</span><span class="p">,</span> <span class="n">pdbid</span><span class="p">)</span>
+ <span class="n">os</span><span class="o">.</span><span class="n">remove</span><span class="p">(</span><span class="n">pdbpaths</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span>
+
+ <span class="n">LOG</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s2">"PDBdist finished"</span><span class="p">)</span></div></div>
+</pre></div>
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diff --git a/examples-dev/olds/_build/html/_modules/ariaec/pdbqual.html b/examples-dev/olds/_build/html/_modules/ariaec/pdbqual.html
new file mode 100644
index 0000000000000000000000000000000000000000..2623c8eae410fa1cf21eb03659b804a7d1853578
--- /dev/null
+++ b/examples-dev/olds/_build/html/_modules/ariaec/pdbqual.html
@@ -0,0 +1,278 @@
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+ <h1>Source code for ariaec.pdbqual</h1><div class="highlight"><pre>
+<span></span><span class="c1"># coding=utf-8</span>
+<span class="sd">"""</span>
+<span class="sd">Created on 9/5/16</span>
+<span class="sd">@author: fallain</span>
+
+<span class="sd">Derived from qual.py script by Dr. Benjamin Bardiaux</span>
+<span class="sd">"""</span>
+<span class="kn">import</span> <span class="nn">os</span>
+<span class="kn">import</span> <span class="nn">shutil</span>
+<span class="kn">import</span> <span class="nn">logging</span>
+
+<span class="kn">from</span> <span class="nn">aria.legacy.QualityChecks</span> <span class="k">import</span> <span class="n">QualityChecks</span>
+<span class="kn">from</span> <span class="nn">.common</span> <span class="k">import</span> <span class="n">CommandProtocol</span>
+
+
+<span class="n">LOG</span> <span class="o">=</span> <span class="n">logging</span><span class="o">.</span><span class="n">getLogger</span><span class="p">(</span><span class="vm">__name__</span><span class="p">)</span>
+
+
+<div class="viewcode-block" id="AriaEcPdbqual"><a class="viewcode-back" href="../../ariaec.html#ariaec.pdbqual.AriaEcPdbqual">[docs]</a><span class="k">class</span> <span class="nc">AriaEcPdbqual</span><span class="p">(</span><span class="n">CommandProtocol</span><span class="p">):</span>
+ <span class="sd">"""Quality pdb tool"""</span>
+
+ <span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+ <span class="nb">super</span><span class="p">(</span><span class="n">AriaEcPdbqual</span><span class="p">,</span> <span class="bp">self</span><span class="p">)</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
+
+<div class="viewcode-block" id="AriaEcPdbqual.run"><a class="viewcode-back" href="../../ariaec.html#ariaec.pdbqual.AriaEcPdbqual.run">[docs]</a> <span class="k">def</span> <span class="nf">run</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="sd">""":return:"""</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s2">"Starting quality runs with </span><span class="si">%s</span><span class="s2"> file(s)"</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">pdbqual</span><span class="p">[</span><span class="s2">"infiles"</span><span class="p">])</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s2">"Copying file(s) to output directory"</span><span class="p">)</span>
+ <span class="k">for</span> <span class="n">infile</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">pdbqual</span><span class="p">[</span><span class="s2">"infiles"</span><span class="p">]:</span>
+ <span class="k">if</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">abspath</span><span class="p">(</span><span class="n">infile</span><span class="p">)</span> <span class="o">!=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">abspath</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">pdbqual</span><span class="p">[</span><span class="s2">"output_directory"</span><span class="p">]):</span>
+ <span class="n">shutil</span><span class="o">.</span><span class="n">copy</span><span class="p">(</span><span class="n">infile</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">pdbqual</span><span class="p">[</span><span class="s2">"output_directory"</span><span class="p">])</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">pdbqual</span><span class="p">[</span><span class="s2">"output_directory"</span><span class="p">])</span>
+ <span class="n">QualityChecks</span><span class="o">.</span><span class="n">runChecks</span><span class="p">(</span>
+ <span class="n">workingDirectory</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">pdbqual</span><span class="p">[</span><span class="s2">"output_directory"</span><span class="p">],</span>
+ <span class="n">trashDirectory</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">pdbqual</span><span class="p">[</span><span class="s2">"trash_directory"</span><span class="p">],</span>
+ <span class="n">prosaOnOff</span><span class="o">=</span><span class="mi">1</span> <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">pdbqual</span><span class="p">[</span><span class="s2">"prosa"</span><span class="p">]</span> <span class="k">else</span> <span class="mi">0</span><span class="p">,</span>
+ <span class="n">procheckExe</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">main</span><span class="p">[</span><span class="s2">"procheck_executable"</span><span class="p">],</span>
+ <span class="n">whatIfExe</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">main</span><span class="p">[</span><span class="s2">"whatif_executable"</span><span class="p">],</span>
+ <span class="n">clashlistExe</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">main</span><span class="p">[</span><span class="s2">"clashlist_executable"</span><span class="p">],</span>
+ <span class="n">prosaExe</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">main</span><span class="p">[</span><span class="s2">"prosa_executable"</span><span class="p">]</span> <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">main</span><span class="p">[</span><span class="s2">"prosa_executable"</span><span class="p">]</span> <span class="k">else</span> <span class="s2">""</span><span class="p">,</span>
+ <span class="n">cshExe</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">pdbqual</span><span class="p">[</span><span class="s2">"csh_executable"</span><span class="p">],</span>
+ <span class="n">howManyPdb</span><span class="o">=</span><span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">pdbqual</span><span class="p">[</span><span class="s2">"infiles"</span><span class="p">]),</span>
+ <span class="n">verbose</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span>
+ <span class="n">fileList</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">pdbqual</span><span class="p">[</span><span class="s2">"infiles"</span><span class="p">],</span>
+ <span class="n">skipPrefix</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">pdbqual</span><span class="p">[</span><span class="s2">"skip_prefix"</span><span class="p">]</span>
+ <span class="p">)</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s2">"</span><span class="si">%s</span><span class="s2"> generated"</span><span class="p">,</span>
+ <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">pdbqual</span><span class="p">[</span><span class="s2">"output_directory"</span><span class="p">],</span>
+ <span class="n">QualityChecks</span><span class="o">.</span><span class="n">FILENAME_REPORT</span><span class="p">))</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s2">"Removing infile(s) in output directory </span><span class="si">%s</span><span class="s2">"</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">pdbqual</span><span class="p">[</span><span class="s2">"output_directory"</span><span class="p">])</span>
+ <span class="p">[</span><span class="n">os</span><span class="o">.</span><span class="n">remove</span><span class="p">(</span>
+ <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">pdbqual</span><span class="p">[</span><span class="s2">"output_directory"</span><span class="p">],</span>
+ <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">basename</span><span class="p">(</span><span class="n">infile</span><span class="p">)))</span>
+ <span class="k">for</span> <span class="n">infile</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">pdbqual</span><span class="p">[</span><span class="s2">"infiles"</span><span class="p">]</span>
+ <span class="k">if</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">pdbqual</span><span class="p">[</span><span class="s2">"output_directory"</span><span class="p">],</span>
+ <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">basename</span><span class="p">(</span><span class="n">infile</span><span class="p">)))]</span></div></div>
+</pre></div>
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diff --git a/examples-dev/olds/_build/html/_modules/ariaec/protein.html b/examples-dev/olds/_build/html/_modules/ariaec/protein.html
new file mode 100644
index 0000000000000000000000000000000000000000..88f8a22b4bf69cedfe5d8381c252bbcdfdf5a0c8
--- /dev/null
+++ b/examples-dev/olds/_build/html/_modules/ariaec/protein.html
@@ -0,0 +1,861 @@
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+ <h1>Source code for ariaec.protein</h1><div class="highlight"><pre>
+<span></span><span class="c1"># coding=utf-8</span>
+<span class="sd">"""</span>
+<span class="sd"> Secondary structure list</span>
+<span class="sd">"""</span>
+
+<span class="kn">from</span> <span class="nn">__future__</span> <span class="k">import</span> <span class="n">absolute_import</span><span class="p">,</span> <span class="n">division</span><span class="p">,</span> <span class="n">print_function</span><span class="p">,</span> \
+ <span class="n">unicode_literals</span>
+
+<span class="kn">import</span> <span class="nn">os</span>
+<span class="kn">import</span> <span class="nn">sys</span>
+<span class="kn">import</span> <span class="nn">re</span>
+<span class="kn">import</span> <span class="nn">logging</span>
+<span class="kn">import</span> <span class="nn">pkg_resources</span> <span class="k">as</span> <span class="nn">pkgr</span>
+<span class="kn">import</span> <span class="nn">aria.legacy.SequenceList</span> <span class="k">as</span> <span class="nn">SequenceList</span>
+<span class="kn">import</span> <span class="nn">aria.legacy.AminoAcid</span> <span class="k">as</span> <span class="nn">AmnAcd</span>
+<span class="kn">from</span> <span class="nn">six</span> <span class="k">import</span> <span class="n">iteritems</span><span class="p">,</span> <span class="n">text_type</span>
+<span class="kn">from</span> <span class="nn">.common</span> <span class="k">import</span> <span class="p">(</span><span class="n">reg_load</span><span class="p">,</span> <span class="n">ppdict</span><span class="p">)</span>
+<span class="c1"># import skbio.Protein as skprot</span>
+<span class="c1"># TODO: interface skbio ??</span>
+
+
+<span class="n">LOG</span> <span class="o">=</span> <span class="n">logging</span><span class="o">.</span><span class="n">getLogger</span><span class="p">(</span><span class="vm">__name__</span><span class="p">)</span>
+
+
+<span class="c1"># TODO: implement psipred format 3.5</span>
+<div class="viewcode-block" id="SsList"><a class="viewcode-back" href="../../ariaec.html#ariaec.protein.SsList">[docs]</a><span class="k">class</span> <span class="nc">SsList</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span>
+ <span class="sd">"""Reader for secondary prediction structure files"""</span>
+ <span class="n">psipred_reg</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span><span class="sa">r</span><span class="s1">'^(?P<up_index>\d+)'</span>
+ <span class="sa">r</span><span class="s1">'\s+(?P<up_residue>[AC-IK-NP-TVWYZ])'</span>
+ <span class="sa">r</span><span class="s1">'\s+(?P<ss_pred>[HEC])'</span>
+ <span class="sa">r</span><span class="s1">'\s+(?P<ss_conf>\d?)'</span><span class="p">)</span>
+ <span class="n">psipred2_reg</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span><span class="sa">r</span><span class="s1">'^(?P<ss_pred>[HEC]+)'</span><span class="p">)</span>
+ <span class="n">indxplus_reg</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span>
+ <span class="sa">r</span><span class="s1">'^(?P<up_index>\d+)\s+(?P<up_residue>[AC-IK-NP-TVWYZ])\s+'</span>
+ <span class="sa">r</span><span class="s1">'(?P<ss_pred>[CEH])\s+(?P<ss_conf>\d)\s+(?P<msa_index>[\d\-]+)\s+'</span>
+ <span class="sa">r</span><span class="s1">'(?P<msa_consper>[\d\-]+)\s+(?P<msa_cons>[*~\-])\s+'</span>
+ <span class="sa">r</span><span class="s1">'(?P<in_const>[*~\-])\s+(?P<pdb_atom>[\d\-]+)\s+'</span>
+ <span class="sa">r</span><span class="s1">'(?P<pdb_chain>[\-\w])\s+(?P<pdb_index>[\d\-]+\w?)\s+'</span>
+ <span class="sa">r</span><span class="s1">'(?P<pdb_residue>[AC-IK-NP-TVWYZ\-])\s+(?P<pdb_x_pos>[\d.\-]+)\s+'</span>
+ <span class="sa">r</span><span class="s1">'(?P<pdb_y_pos>[\d.\-]+)\s+(?P<pdb_z_pos>[\d\-.]+)'</span><span class="p">)</span>
+ <span class="n">ss_dist_reg</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span><span class="sa">r</span><span class="s2">"\s+(\d+\.\d+) \( (\d+\.\d+)\)"</span><span class="p">)</span>
+
+ <span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">sett</span><span class="p">):</span>
+ <span class="sd">"""</span>
+
+<span class="sd"> :param sett:</span>
+<span class="sd"> :return:</span>
+<span class="sd"> """</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">settings</span> <span class="o">=</span> <span class="n">sett</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">ss_matrix</span> <span class="o">=</span> <span class="p">[]</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">ssdict</span> <span class="o">=</span> <span class="p">{}</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">ssdist</span> <span class="o">=</span> <span class="p">{}</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">filetype</span> <span class="o">=</span> <span class="s1">''</span>
+
+ <span class="k">def</span> <span class="nf">__bool__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="k">return</span> <span class="kc">True</span> <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">ss_matrix</span> <span class="k">else</span> <span class="kc">False</span>
+
+ <span class="k">def</span> <span class="nf">__nonzero__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="fm">__bool__</span><span class="p">()</span>
+
+ <span class="nd">@property</span>
+ <span class="k">def</span> <span class="nf">index</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="sd">""":return:"""</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">ss_matrix</span><span class="p">:</span>
+ <span class="c1"># Assuming human idx (1 ...) correspond to ss_matrix first column !!!</span>
+ <span class="k">return</span> <span class="p">[</span><span class="nb">int</span><span class="p">(</span><span class="n">_</span><span class="p">)</span> <span class="k">for</span> <span class="n">_</span> <span class="ow">in</span> <span class="nb">zip</span><span class="p">(</span><span class="o">*</span><span class="bp">self</span><span class="o">.</span><span class="n">ss_matrix</span><span class="p">)[</span><span class="mi">0</span><span class="p">]]</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">return</span> <span class="p">[]</span>
+
+ <span class="nd">@property</span>
+ <span class="k">def</span> <span class="nf">sequence</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> </span>
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+<span class="sd"> """</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">ss_matrix</span><span class="p">:</span>
+ <span class="k">return</span> <span class="p">[</span><span class="n">_</span> <span class="k">for</span> <span class="n">_</span> <span class="ow">in</span> <span class="nb">zip</span><span class="p">(</span><span class="o">*</span><span class="bp">self</span><span class="o">.</span><span class="n">ss_matrix</span><span class="p">)[</span><span class="mi">2</span><span class="p">]]</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">return</span> <span class="p">[]</span>
+
+<div class="viewcode-block" id="SsList.check_filetype"><a class="viewcode-back" href="../../ariaec.html#ariaec.protein.SsList.check_filetype">[docs]</a> <span class="k">def</span> <span class="nf">check_filetype</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">filename</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> </span>
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> filename :</span>
+<span class="sd"> return:</span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+<span class="sd"> </span>
+<span class="sd"> """</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">filetype</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">splitext</span><span class="p">(</span><span class="n">filename</span><span class="p">)[</span><span class="mi">1</span><span class="p">][</span><span class="mi">1</span><span class="p">:]</span></div>
+ <span class="c1"># TODO: check if given file is supported</span>
+
+<div class="viewcode-block" id="SsList.read"><a class="viewcode-back" href="../../ariaec.html#ariaec.protein.SsList.read">[docs]</a> <span class="k">def</span> <span class="nf">read</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">filename</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> </span>
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> filename :</span>
+<span class="sd"> return:</span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+<span class="sd"> </span>
+<span class="sd"> """</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">check_filetype</span><span class="p">(</span><span class="n">filename</span><span class="p">)</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s2">"Reading secondary structure file </span><span class="si">%s</span><span class="s2"> [</span><span class="si">%s</span><span class="s2">]"</span><span class="p">,</span>
+ <span class="n">filename</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">filetype</span><span class="p">)</span>
+ <span class="c1"># TODO: better read with getattr</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">filetype</span> <span class="o">==</span> <span class="s2">"indextableplus"</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">read_indextableplus</span><span class="p">(</span><span class="n">filename</span><span class="p">)</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">read_psipred</span><span class="p">(</span><span class="n">filename</span><span class="p">)</span>
+
+ <span class="n">LOG</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="s2">"Secondary structure list:</span><span class="se">\n</span><span class="si">%s</span><span class="se">\n</span><span class="s2">"</span>
+ <span class="s2">"Secondary structure dict:</span><span class="se">\n</span><span class="si">%s</span><span class="s2">"</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">ss_matrix</span><span class="p">,</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">ssdict</span><span class="p">)</span></div>
+
+<div class="viewcode-block" id="SsList.read_psipred"><a class="viewcode-back" href="../../ariaec.html#ariaec.protein.SsList.read_psipred">[docs]</a> <span class="k">def</span> <span class="nf">read_psipred</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">filename</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> </span>
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> filename :</span>
+<span class="sd"> </span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+<span class="sd"> </span>
+<span class="sd"> """</span>
+
+ <span class="bp">self</span><span class="o">.</span><span class="n">ssdict</span> <span class="o">=</span> <span class="n">reg_load</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">psipred_reg</span><span class="p">,</span> <span class="n">filename</span><span class="p">)</span>
+ <span class="c1"># TODO: supprimer psipred_list dans les futures implementations</span>
+ <span class="n">ss_index_dict</span> <span class="o">=</span> <span class="p">{</span><span class="s1">'H'</span><span class="p">:</span> <span class="mi">1</span><span class="p">,</span> <span class="s1">'C'</span><span class="p">:</span> <span class="mi">1</span><span class="p">,</span> <span class="s1">'E'</span><span class="p">:</span> <span class="mi">1</span><span class="p">}</span>
+ <span class="k">for</span> <span class="n">line_id</span> <span class="ow">in</span> <span class="nb">sorted</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">ssdict</span><span class="o">.</span><span class="n">keys</span><span class="p">()):</span>
+ <span class="c1"># Modif champ ss_pred</span>
+ <span class="c1"># Si line_id</span>
+ <span class="k">if</span> <span class="n">line_id</span> <span class="o">></span> <span class="mi">1</span> <span class="ow">and</span> <span class="bp">self</span><span class="o">.</span><span class="n">ssdict</span><span class="p">[</span><span class="n">line_id</span><span class="p">][</span><span class="s1">'ss_pred'</span><span class="p">]</span> <span class="ow">not</span> <span class="ow">in</span> \
+ <span class="bp">self</span><span class="o">.</span><span class="n">ssdict</span><span class="p">[</span><span class="n">line_id</span> <span class="o">-</span> <span class="mi">1</span><span class="p">][</span><span class="s1">'ss_pred'</span><span class="p">]:</span>
+ <span class="c1"># If next ss isn't the same, increment relative struct in</span>
+ <span class="c1"># ss_index_dict</span>
+ <span class="n">ss_index_dict</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">ssdict</span><span class="p">[</span><span class="n">line_id</span> <span class="o">-</span> <span class="mi">1</span><span class="p">][</span><span class="s1">'ss_pred'</span><span class="p">][</span><span class="mi">0</span><span class="p">]]</span> <span class="o">+=</span> <span class="mi">1</span>
+
+ <span class="bp">self</span><span class="o">.</span><span class="n">ssdict</span><span class="p">[</span><span class="n">line_id</span><span class="p">][</span><span class="s1">'ss_pred'</span><span class="p">]</span> <span class="o">=</span> <span class="s2">""</span><span class="o">.</span><span class="n">join</span><span class="p">(</span>
+ <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">ssdict</span><span class="p">[</span><span class="n">line_id</span><span class="p">][</span><span class="s1">'ss_pred'</span><span class="p">],</span>
+ <span class="nb">str</span><span class="p">(</span><span class="n">ss_index_dict</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">ssdict</span><span class="p">[</span><span class="n">line_id</span><span class="p">][</span><span class="s1">'ss_pred'</span><span class="p">]])))</span>
+
+ <span class="bp">self</span><span class="o">.</span><span class="n">ss_matrix</span><span class="o">.</span><span class="n">append</span><span class="p">([</span><span class="bp">self</span><span class="o">.</span><span class="n">ssdict</span><span class="p">[</span><span class="n">line_id</span><span class="p">][</span><span class="s1">'up_index'</span><span class="p">],</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">ssdict</span><span class="p">[</span><span class="n">line_id</span><span class="p">][</span><span class="s1">'up_residue'</span><span class="p">],</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">ssdict</span><span class="p">[</span><span class="n">line_id</span><span class="p">][</span><span class="s1">'ss_pred'</span><span class="p">],</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">ssdict</span><span class="p">[</span><span class="n">line_id</span><span class="p">][</span><span class="s1">'ss_conf'</span><span class="p">]])</span></div>
+
+<div class="viewcode-block" id="SsList.write_ssfasta"><a class="viewcode-back" href="../../ariaec.html#ariaec.protein.SsList.write_ssfasta">[docs]</a> <span class="k">def</span> <span class="nf">write_ssfasta</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">filename</span><span class="p">,</span> <span class="n">desc</span><span class="o">=</span><span class="s2">"pdbid"</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> </span>
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> filename :</span>
+<span class="sd"> param desc:</span>
+<span class="sd"> desc :</span>
+<span class="sd"> (Default value = "pdbid")</span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+<span class="sd"> </span>
+<span class="sd"> """</span>
+ <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">filename</span><span class="p">,</span> <span class="nb">str</span><span class="p">(</span><span class="s1">'w'</span><span class="p">))</span> <span class="k">as</span> <span class="n">psipred</span><span class="p">:</span>
+ <span class="n">psipred</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="nb">str</span><span class="p">(</span><span class="s2">"> </span><span class="si">%s</span><span class="se">\n</span><span class="s2">"</span> <span class="o">%</span> <span class="n">desc</span><span class="p">))</span>
+ <span class="n">psipred</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="nb">str</span><span class="p">(</span><span class="s2">""</span><span class="o">.</span><span class="n">join</span><span class="p">([</span><span class="n">_</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="k">for</span> <span class="n">_</span> <span class="ow">in</span> <span class="nb">zip</span><span class="p">(</span><span class="o">*</span><span class="bp">self</span><span class="o">.</span><span class="n">ss_matrix</span><span class="p">)[</span><span class="mi">2</span><span class="p">]])))</span></div>
+
+<div class="viewcode-block" id="SsList.read_indextableplus"><a class="viewcode-back" href="../../ariaec.html#ariaec.protein.SsList.read_indextableplus">[docs]</a> <span class="k">def</span> <span class="nf">read_indextableplus</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">filename</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> </span>
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> filename :</span>
+<span class="sd"> return:</span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+<span class="sd"> </span>
+<span class="sd"> """</span>
+ <span class="n">c</span> <span class="o">=</span> <span class="mi">0</span>
+ <span class="n">error_list</span> <span class="o">=</span> <span class="p">[]</span>
+ <span class="n">ss_index_dict</span> <span class="o">=</span> <span class="p">{</span><span class="s1">'H'</span><span class="p">:</span> <span class="mi">1</span><span class="p">,</span> <span class="s1">'C'</span><span class="p">:</span> <span class="mi">1</span><span class="p">,</span> <span class="s1">'E'</span><span class="p">:</span> <span class="mi">1</span><span class="p">}</span>
+ <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">filename</span><span class="p">)</span> <span class="k">as</span> <span class="n">f</span><span class="p">:</span>
+ <span class="k">for</span> <span class="n">line</span> <span class="ow">in</span> <span class="n">f</span><span class="p">:</span>
+ <span class="n">indxplus_match</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">indxplus_reg</span><span class="o">.</span><span class="n">search</span><span class="p">(</span><span class="n">line</span><span class="p">)</span>
+ <span class="k">if</span> <span class="n">line</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s2">"up_"</span><span class="p">):</span>
+ <span class="k">continue</span>
+ <span class="k">elif</span> <span class="n">indxplus_match</span><span class="p">:</span>
+
+ <span class="c1"># TODO: Other method to replace ss code ?</span>
+ <span class="c1"># => build indx_list with group_dict !</span>
+ <span class="n">ss</span> <span class="o">=</span> <span class="n">indxplus_match</span><span class="o">.</span><span class="n">group</span><span class="p">(</span><span class="s1">'ss_pred'</span><span class="p">)</span>
+ <span class="n">ss_start</span> <span class="o">=</span> <span class="n">indxplus_match</span><span class="o">.</span><span class="n">start</span><span class="p">(</span><span class="s1">'ss_pred'</span><span class="p">)</span>
+ <span class="n">line</span> <span class="o">=</span> <span class="s2">""</span><span class="o">.</span><span class="n">join</span><span class="p">([</span><span class="n">line</span><span class="p">[:</span><span class="n">ss_start</span><span class="p">],</span> <span class="n">ss</span><span class="p">,</span> <span class="nb">str</span><span class="p">(</span><span class="n">ss_index_dict</span><span class="p">[</span><span class="n">ss</span><span class="p">]),</span>
+ <span class="n">line</span><span class="p">[</span><span class="n">ss_start</span> <span class="o">+</span> <span class="mi">1</span><span class="p">:</span><span class="o">-</span><span class="mi">1</span><span class="p">]])</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">ss_matrix</span> <span class="ow">and</span> <span class="bp">self</span><span class="o">.</span><span class="n">ss_matrix</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">][</span><span class="mi">2</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span> <span class="o">!=</span> <span class="n">ss</span><span class="p">:</span>
+ <span class="c1"># Si ss est une structure secondaire diff, on incremente</span>
+ <span class="c1"># la valeur de l'ancienne dans ss_index_dict</span>
+ <span class="n">ss_index_dict</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">ss_matrix</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">][</span><span class="mi">2</span><span class="p">][</span><span class="mi">0</span><span class="p">]]</span> <span class="o">+=</span> <span class="mi">1</span>
+
+ <span class="bp">self</span><span class="o">.</span><span class="n">ss_matrix</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">line</span><span class="o">.</span><span class="n">split</span><span class="p">())</span>
+ <span class="n">c</span> <span class="o">+=</span> <span class="mi">1</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="n">error_list</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="nb">int</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">ss_matrix</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">][</span><span class="mi">0</span><span class="p">])</span> <span class="o">+</span> <span class="mi">1</span><span class="p">)</span>
+ <span class="k">try</span><span class="p">:</span>
+ <span class="k">assert</span> <span class="n">c</span> <span class="o">==</span> <span class="nb">int</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">ss_matrix</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">][</span><span class="mi">0</span><span class="p">])</span>
+ <span class="k">except</span> <span class="ne">AssertionError</span><span class="p">:</span>
+ <span class="n">sys</span><span class="o">.</span><span class="n">exit</span><span class="p">(</span><span class="s1">'Uneven number of matching lines (</span><span class="si">%d</span><span class="s1">) '</span>
+ <span class="s1">'vs up_index (</span><span class="si">%d</span><span class="s1">) : lines </span><span class="si">%s</span><span class="s1">'</span> <span class="o">%</span> <span class="p">(</span><span class="n">c</span><span class="p">,</span>
+ <span class="nb">int</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">ss_matrix</span><span class="p">[</span>
+ <span class="o">-</span><span class="mi">1</span><span class="p">][</span><span class="mi">0</span><span class="p">]),</span>
+ <span class="nb">str</span><span class="p">(</span><span class="n">error_list</span><span class="p">)))</span></div>
+
+ <span class="k">def</span> <span class="nf">_read_ssdist</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">infile</span><span class="p">,</span> <span class="n">filename</span><span class="o">=</span><span class="s1">''</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> </span>
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> infile :</span>
+<span class="sd"> param filename:</span>
+<span class="sd"> filename :</span>
+<span class="sd"> (Default value = '')</span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+<span class="sd"> </span>
+<span class="sd"> """</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s2">"Reading distance file </span><span class="si">{0}</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">filename</span><span class="p">))</span>
+ <span class="n">c</span> <span class="o">=</span> <span class="mi">0</span>
+ <span class="n">atom_list</span> <span class="o">=</span> <span class="p">[]</span>
+ <span class="k">for</span> <span class="n">line</span> <span class="ow">in</span> <span class="n">infile</span><span class="p">:</span>
+ <span class="n">c</span> <span class="o">+=</span> <span class="mi">1</span>
+ <span class="n">line_list</span> <span class="o">=</span> <span class="n">line</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">'</span><span class="se">\t</span><span class="s1">'</span><span class="p">)</span>
+ <span class="n">dist_sdev_list</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">ss_dist_reg</span><span class="o">.</span><span class="n">findall</span><span class="p">(</span><span class="n">line</span><span class="p">)</span>
+ <span class="k">if</span> <span class="n">line</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s1">'i'</span><span class="p">):</span>
+ <span class="n">atom_list</span> <span class="o">=</span> <span class="p">[</span><span class="n">elt</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span> <span class="k">for</span> <span class="n">elt</span> <span class="ow">in</span> <span class="n">line_list</span><span class="p">[</span><span class="mi">1</span><span class="p">:]]</span>
+ <span class="k">elif</span> <span class="n">re</span><span class="o">.</span><span class="n">search</span><span class="p">(</span><span class="sa">r</span><span class="s1">'^([HE],[HE]\+\d)'</span><span class="p">,</span> <span class="n">line</span><span class="p">):</span>
+ <span class="n">bond_type</span> <span class="o">=</span> <span class="n">line</span><span class="p">[</span><span class="mi">0</span><span class="p">:</span><span class="mi">5</span><span class="p">]</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">ssdist</span><span class="p">[</span><span class="n">bond_type</span><span class="p">]</span> <span class="o">=</span> <span class="p">{}</span>
+ <span class="k">for</span> <span class="n">i</span><span class="p">,</span> <span class="p">(</span><span class="n">dist</span><span class="p">,</span> <span class="n">sdev</span><span class="p">)</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">dist_sdev_list</span><span class="p">):</span>
+ <span class="n">dist</span><span class="p">,</span> <span class="n">sdev</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">dist</span><span class="p">),</span> <span class="nb">float</span><span class="p">(</span><span class="n">sdev</span><span class="p">)</span>
+ <span class="k">if</span> <span class="n">sdev</span> <span class="o"><</span> <span class="mf">0.1</span><span class="p">:</span>
+ <span class="c1"># TODO: explain more why we choose 0.1 as treshold !</span>
+ <span class="n">dist</span><span class="p">,</span> <span class="n">sdev</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span> <span class="kc">None</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">ssdist</span><span class="p">[</span><span class="n">bond_type</span><span class="p">][</span><span class="n">atom_list</span><span class="p">[</span><span class="n">i</span><span class="p">]]</span> <span class="o">=</span> <span class="p">(</span><span class="n">dist</span><span class="p">,</span> <span class="n">sdev</span><span class="p">)</span>
+ <span class="k">try</span><span class="p">:</span>
+ <span class="k">assert</span> <span class="nb">len</span><span class="p">(</span><span class="n">dist_sdev_list</span><span class="p">)</span> <span class="o">==</span> <span class="nb">len</span><span class="p">(</span><span class="n">atom_list</span><span class="p">)</span>
+ <span class="k">except</span> <span class="ne">AssertionError</span><span class="p">:</span>
+ <span class="n">sys</span><span class="o">.</span><span class="n">exit</span><span class="p">(</span>
+ <span class="s1">'Error at </span><span class="si">%s</span><span class="s1">, line </span><span class="si">%d</span><span class="s1"> : uneven number of columns '</span>
+ <span class="s1">'between current line and header'</span> <span class="o">%</span> <span class="p">(</span><span class="n">filename</span><span class="p">,</span> <span class="n">c</span><span class="p">))</span>
+
+<div class="viewcode-block" id="SsList.read_ssdist"><a class="viewcode-back" href="../../ariaec.html#ariaec.protein.SsList.read_ssdist">[docs]</a> <span class="k">def</span> <span class="nf">read_ssdist</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">ssdistpath</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Read average dist file generated using PDB</span>
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> ssdistpath :</span>
+<span class="sd"> return: (Default value = None)</span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+<span class="sd"> </span>
+<span class="sd"> """</span>
+ <span class="n">filename</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">abspath</span><span class="p">(</span><span class="n">ssdistpath</span><span class="p">)</span> <span class="k">if</span> <span class="n">ssdistpath</span> <span class="k">else</span> <span class="kc">None</span>
+
+ <span class="n">LOG</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s2">"Loading ss dist file"</span><span class="p">)</span>
+ <span class="k">try</span><span class="p">:</span>
+ <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">filename</span><span class="p">)</span> <span class="k">as</span> <span class="n">f</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_read_ssdist</span><span class="p">(</span><span class="n">f</span><span class="p">,</span> <span class="n">filename</span><span class="o">=</span><span class="n">filename</span><span class="p">)</span>
+ <span class="k">except</span> <span class="ne">Exception</span> <span class="k">as</span> <span class="n">message</span><span class="p">:</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">error</span><span class="p">(</span><span class="s2">"</span><span class="si">%s</span><span class="s2">"</span><span class="p">,</span> <span class="n">message</span><span class="p">)</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">error</span><span class="p">(</span><span class="s2">"Can't load given ss dist file..."</span><span class="p">)</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">error</span><span class="p">(</span><span class="s2">"Loading default ss dist file"</span><span class="p">)</span>
+ <span class="k">with</span> <span class="n">pkgr</span><span class="o">.</span><span class="n">resource_stream</span><span class="p">(</span><span class="vm">__name__</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">SS_DIST</span><span class="p">)</span> <span class="k">as</span> <span class="n">f</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_read_ssdist</span><span class="p">(</span><span class="n">f</span><span class="p">,</span> <span class="n">filename</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">SS_DIST</span><span class="p">)</span></div>
+
+<div class="viewcode-block" id="SsList.seq_sublist"><a class="viewcode-back" href="../../ariaec.html#ariaec.protein.SsList.seq_sublist">[docs]</a> <span class="k">def</span> <span class="nf">seq_sublist</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">sequence</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Check and adjust sslist with given sequence</span>
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> sequence :</span>
+<span class="sd"> input amino acid sequence (one letter format)</span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+<span class="sd"> </span>
+<span class="sd"> """</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="s2">"Adjust sslist related to sequence </span><span class="si">%s</span><span class="s2">"</span><span class="p">,</span> <span class="nb">str</span><span class="p">(</span><span class="n">sequence</span><span class="p">))</span>
+ <span class="n">tableplus_inv</span> <span class="o">=</span> <span class="nb">zip</span><span class="p">(</span><span class="o">*</span><span class="bp">self</span><span class="o">.</span><span class="n">ss_matrix</span><span class="p">)</span>
+ <span class="c1"># Get amino acid sequence related to secondary structure prediction</span>
+ <span class="n">tableplus_seq</span> <span class="o">=</span> <span class="s2">""</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">tableplus_inv</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span>
+
+ <span class="k">if</span> <span class="n">sequence</span> <span class="ow">in</span> <span class="n">tableplus_seq</span><span class="p">:</span>
+ <span class="n">imin</span> <span class="o">=</span> <span class="n">tableplus_seq</span><span class="o">.</span><span class="n">find</span><span class="p">(</span><span class="n">sequence</span><span class="p">)</span>
+ <span class="n">imax</span> <span class="o">=</span> <span class="n">imin</span> <span class="o">+</span> <span class="nb">len</span><span class="p">(</span><span class="n">sequence</span><span class="p">)</span>
+ <span class="k">try</span><span class="p">:</span>
+ <span class="k">assert</span> <span class="n">tableplus_seq</span><span class="p">[</span><span class="n">imin</span><span class="p">:</span><span class="n">imax</span><span class="p">]</span> <span class="o">==</span> <span class="n">sequence</span>
+ <span class="k">except</span> <span class="ne">AssertionError</span><span class="p">:</span>
+ <span class="n">sys</span><span class="o">.</span><span class="n">exit</span><span class="p">(</span><span class="s1">'Missing residues in indextableplus file'</span><span class="p">)</span>
+
+ <span class="bp">self</span><span class="o">.</span><span class="n">ss_matrix</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">ss_matrix</span><span class="p">[</span><span class="n">imin</span><span class="p">:</span><span class="n">imax</span><span class="p">]</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="s2">"Secondary structure matrix relative to given "</span>
+ <span class="s2">"sequence:</span><span class="se">\n</span><span class="si">%s</span><span class="s2">"</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">ss_matrix</span><span class="p">)</span></div></div>
+ <span class="c1"># TODO: read_dssp</span>
+
+
+<div class="viewcode-block" id="AminoAcidSequence"><a class="viewcode-back" href="../../ariaec.html#ariaec.protein.AminoAcidSequence">[docs]</a><span class="k">class</span> <span class="nc">AminoAcidSequence</span><span class="p">(</span><span class="n">SequenceList</span><span class="o">.</span><span class="n">SequenceList</span><span class="p">,</span> <span class="nb">object</span><span class="p">):</span>
+ <span class="sd">"""Amino acid sequence"""</span>
+ <span class="n">startres_reg</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span><span class="sa">r</span><span class="s2">"^\s*residue\s+(?P<name>[A-Za-z]{1,4})"</span><span class="p">,</span> <span class="n">flags</span><span class="o">=</span><span class="n">re</span><span class="o">.</span><span class="n">I</span><span class="p">)</span>
+ <span class="n">end_reg</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span><span class="sa">r</span><span class="s2">"^\s*end"</span><span class="p">,</span> <span class="n">flags</span><span class="o">=</span><span class="n">re</span><span class="o">.</span><span class="n">I</span><span class="p">)</span>
+ <span class="n">restatement_reg</span> <span class="o">=</span> <span class="p">{</span>
+ <span class="s2">"atom"</span><span class="p">:</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span><span class="sa">r</span><span class="s2">"atom\s+(?P<name>\w{1,4})\s*(?:.*?"</span>
+ <span class="sa">r</span><span class="s2">"(?:(?:type=(?P<type>\w{1,4}))|"</span>
+ <span class="sa">r</span><span class="s2">"(?:"</span>
+ <span class="sa">r</span><span class="s2">"(?:charge= ?)(?P<charge>-?\d\.\d{1,3}))|"</span>
+ <span class="sa">r</span><span class="s2">"(?:(?:mass=)(?P<mass>[- ]\d\.\d{1,3}))|"</span>
+ <span class="sa">r</span><span class="s2">"(?:(?:excl\s*=\s*)\((?P<exclude>[^(]+)\)))){1,4}"</span>
+ <span class="sa">r</span><span class="s2">"\s*end"</span><span class="p">,</span>
+ <span class="n">flags</span><span class="o">=</span><span class="n">re</span><span class="o">.</span><span class="n">I</span><span class="p">),</span>
+ <span class="s2">"bond"</span><span class="p">:</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span><span class="sa">r</span><span class="s2">"bond\s+(?P<atm1>\w{1,4})\s+(?P<atm2>\w{1,4})"</span><span class="p">,</span>
+ <span class="n">flags</span><span class="o">=</span><span class="n">re</span><span class="o">.</span><span class="n">I</span><span class="p">),</span>
+ <span class="s2">"improper"</span><span class="p">:</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span><span class="sa">r</span><span class="s2">"improper\s+(?P<atm1>\w{1,4})"</span>
+ <span class="sa">r</span><span class="s2">"\s+(?P<atm2>\w{1,4})\s+(?P<atm3>\w{1,4})"</span>
+ <span class="sa">r</span><span class="s2">"\s+(?P<atm4>\w{1,4})"</span><span class="p">,</span> <span class="n">flags</span><span class="o">=</span><span class="n">re</span><span class="o">.</span><span class="n">I</span><span class="p">),</span>
+ <span class="s2">"dihedral"</span><span class="p">:</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span><span class="sa">r</span><span class="s2">"dihedral\s+(?P<atm1>\w{1,4})"</span>
+ <span class="sa">r</span><span class="s2">"\s+(?P<atm2>\w{1,4})\s+(?P<atm3>\w{1,4})"</span>
+ <span class="sa">r</span><span class="s2">"\s+(?P<atm4>\w{1,4})"</span><span class="p">,</span> <span class="n">flags</span><span class="o">=</span><span class="n">re</span><span class="o">.</span><span class="n">I</span><span class="p">),</span>
+ <span class="s2">"dono"</span><span class="p">:</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span><span class="sa">r</span><span class="s2">"dono\s+(?P<hatm>\w{1,4})\s+(?:(?P<heavatm>\w{1,"</span>
+ <span class="sa">r</span><span class="s2">"4})|(?:</span><span class="se">\"</span><span class="s2">\s*</span><span class="se">\"</span><span class="s2">))?"</span><span class="p">,</span> <span class="n">flags</span><span class="o">=</span><span class="n">re</span><span class="o">.</span><span class="n">I</span><span class="p">),</span>
+ <span class="s2">"acce"</span><span class="p">:</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span><span class="sa">r</span><span class="s2">"^\s*acce\s+(?P<accatm>\w{1,4})\s+(?:(?P<antatm>\w{1,"</span>
+ <span class="sa">r</span><span class="s2">"4})|(?:</span><span class="se">\"</span><span class="s2">\s*</span><span class="se">\"</span><span class="s2">))"</span><span class="p">,</span> <span class="n">flags</span><span class="o">=</span><span class="n">re</span><span class="o">.</span><span class="n">I</span><span class="p">)</span>
+ <span class="p">}</span>
+
+ <span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">topologyfile</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+ <span class="sd">"""</span>
+
+<span class="sd"> :param topologyfile:</span>
+<span class="sd"> :param args:</span>
+<span class="sd"> :param kwargs:</span>
+<span class="sd"> :return:</span>
+<span class="sd"> """</span>
+ <span class="nb">super</span><span class="p">(</span><span class="n">AminoAcidSequence</span><span class="p">,</span> <span class="bp">self</span><span class="p">)</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_topfile</span> <span class="o">=</span> <span class="n">topologyfile</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_topology</span> <span class="o">=</span> <span class="kc">None</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_topok</span> <span class="o">=</span> <span class="kc">False</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">sequence</span> <span class="o">=</span> <span class="s1">''</span>
+
+ <span class="nd">@property</span>
+ <span class="k">def</span> <span class="nf">humanidx</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="sd">""":return:"""</span>
+ <span class="k">return</span> <span class="nb">range</span><span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">sequence</span><span class="p">)</span> <span class="o">+</span> <span class="mi">1</span><span class="p">)</span>
+
+ <span class="nd">@property</span>
+ <span class="k">def</span> <span class="nf">topology</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Topology dict with 3l code as dict key</span>
+<span class="sd"> :return:</span>
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+<span class="sd"> </span>
+<span class="sd"> """</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">_topology</span> <span class="ow">or</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">_topok</span><span class="p">:</span>
+ <span class="n">topo</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">readtopo</span><span class="p">()</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">aalist</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_topology</span> <span class="o">=</span> <span class="p">[(</span><span class="n">aa</span><span class="p">,</span> <span class="n">topo</span><span class="p">[</span><span class="n">aa</span><span class="p">])</span> <span class="k">for</span> <span class="n">aa</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">aalist</span><span class="p">]</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_topok</span> <span class="o">=</span> <span class="kc">True</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_topology</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="n">iteritems</span><span class="p">(</span><span class="n">topo</span><span class="p">))</span>
+ <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_topology</span>
+
+ <span class="k">def</span> <span class="nf">__getitem__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">key</span><span class="p">):</span>
+ <span class="sd">"""</span>
+
+<span class="sd"> :param key:</span>
+<span class="sd"> :return:</span>
+<span class="sd"> """</span>
+ <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">aalist</span><span class="p">[</span><span class="n">key</span><span class="p">]</span>
+
+ <span class="k">def</span> <span class="nf">__repr__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="sd">"""</span>
+
+<span class="sd"> :return:</span>
+<span class="sd"> """</span>
+ <span class="k">return</span> <span class="s2">"Amino Acid sequence </span><span class="si">%s</span><span class="s2"> (</span><span class="si">%d</span><span class="s2">)"</span> <span class="o">%</span> <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">sequence</span><span class="p">,</span>
+ <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">sequence</span><span class="p">))</span>
+
+<div class="viewcode-block" id="AminoAcidSequence.readtopo"><a class="viewcode-back" href="../../ariaec.html#ariaec.protein.AminoAcidSequence.readtopo">[docs]</a> <span class="k">def</span> <span class="nf">readtopo</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Parse topology file for amino acids</span>
+<span class="sd"> :return:</span>
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+<span class="sd"> </span>
+<span class="sd"> """</span>
+ <span class="n">topo</span> <span class="o">=</span> <span class="p">{}</span>
+ <span class="k">with</span> <span class="n">pkgr</span><span class="o">.</span><span class="n">resource_stream</span><span class="p">(</span><span class="vm">__name__</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">_topfile</span><span class="p">)</span> <span class="k">as</span> <span class="n">tpf</span><span class="p">:</span>
+ <span class="n">res_flag</span> <span class="o">=</span> <span class="kc">False</span>
+ <span class="n">resname</span> <span class="o">=</span> <span class="s2">""</span>
+ <span class="k">for</span> <span class="n">line</span> <span class="ow">in</span> <span class="n">tpf</span><span class="p">:</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="n">res_flag</span><span class="p">:</span>
+ <span class="n">match</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">startres_reg</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="n">line</span><span class="p">)</span>
+ <span class="k">if</span> <span class="n">match</span><span class="p">:</span>
+ <span class="n">res_flag</span> <span class="o">=</span> <span class="kc">True</span>
+ <span class="n">resname</span> <span class="o">=</span> <span class="n">match</span><span class="o">.</span><span class="n">group</span><span class="p">(</span><span class="s2">"name"</span><span class="p">)</span>
+ <span class="n">topo</span><span class="p">[</span><span class="n">resname</span><span class="p">]</span> <span class="o">=</span> <span class="p">{}</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="c1"># Check if end of residue statement</span>
+ <span class="n">match</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">end_reg</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="n">line</span><span class="p">)</span>
+ <span class="k">if</span> <span class="n">match</span><span class="p">:</span>
+ <span class="n">res_flag</span> <span class="o">=</span> <span class="kc">False</span>
+ <span class="n">resname</span> <span class="o">=</span> <span class="s2">""</span>
+ <span class="k">continue</span>
+ <span class="c1"># Walk along reg dict</span>
+ <span class="k">for</span> <span class="n">regid</span><span class="p">,</span> <span class="n">reg</span> <span class="ow">in</span> <span class="n">iteritems</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">restatement_reg</span><span class="p">):</span>
+ <span class="k">if</span> <span class="n">regid</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">topo</span><span class="p">[</span><span class="n">resname</span><span class="p">]:</span>
+ <span class="n">topo</span><span class="p">[</span><span class="n">resname</span><span class="p">][</span><span class="n">regid</span><span class="p">]</span> <span class="o">=</span> <span class="p">[]</span>
+ <span class="k">if</span> <span class="n">regid</span> <span class="o">==</span> <span class="s2">"bond"</span><span class="p">:</span>
+ <span class="n">match</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">findall</span><span class="p">(</span><span class="n">reg</span><span class="p">,</span> <span class="n">line</span><span class="p">)</span>
+ <span class="k">if</span> <span class="n">match</span><span class="p">:</span>
+ <span class="n">topo</span><span class="p">[</span><span class="n">resname</span><span class="p">][</span><span class="n">regid</span><span class="p">]</span> <span class="o">+=</span> <span class="n">match</span>
+ <span class="k">break</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="n">match</span> <span class="o">=</span> <span class="n">reg</span><span class="o">.</span><span class="n">search</span><span class="p">(</span><span class="n">line</span><span class="p">)</span>
+ <span class="k">if</span> <span class="n">match</span><span class="p">:</span>
+ <span class="k">if</span> <span class="n">regid</span> <span class="ow">in</span> <span class="p">(</span><span class="s2">"improper"</span><span class="p">,</span> <span class="s2">"dihedral"</span><span class="p">):</span>
+ <span class="c1"># Add tuple into list since we need atm order</span>
+ <span class="n">topo</span><span class="p">[</span><span class="n">resname</span><span class="p">][</span><span class="n">regid</span><span class="p">]</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">match</span><span class="o">.</span><span class="n">groups</span><span class="p">())</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="c1"># Add dict</span>
+ <span class="n">topo</span><span class="p">[</span><span class="n">resname</span><span class="p">][</span><span class="n">regid</span><span class="p">]</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">match</span><span class="o">.</span><span class="n">groupdict</span><span class="p">())</span>
+ <span class="k">break</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="s2">"Topology used:</span><span class="se">\n</span><span class="si">%s</span><span class="s2">"</span><span class="p">,</span> <span class="n">ppdict</span><span class="p">(</span><span class="n">topo</span><span class="p">))</span>
+ <span class="k">return</span> <span class="n">topo</span></div>
+
+<div class="viewcode-block" id="AminoAcidSequence.read"><a class="viewcode-back" href="../../ariaec.html#ariaec.protein.AminoAcidSequence.read">[docs]</a> <span class="k">def</span> <span class="nf">read</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">filename</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> </span>
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> filename :</span>
+<span class="sd"> return:</span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+<span class="sd"> </span>
+<span class="sd"> """</span>
+ <span class="c1"># TODO: smarter reader checking type of file (fasta, etc ...)</span>
+ <span class="c1"># TODO: capturing has some troubles with unicode ...</span>
+ <span class="c1"># with Capturing() as output:</span>
+ <span class="k">if</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">splitext</span><span class="p">(</span><span class="n">filename</span><span class="p">)[</span><span class="mi">1</span><span class="p">]</span> <span class="o">==</span> <span class="s1">'.seq'</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">ReadSeq</span><span class="p">(</span><span class="n">text_type</span><span class="p">(</span><span class="n">filename</span><span class="p">))</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">ReadFasta</span><span class="p">(</span><span class="n">text_type</span><span class="p">(</span><span class="n">filename</span><span class="p">))</span>
+ <span class="c1"># LOG.info(''.join(output))</span>
+
+ <span class="bp">self</span><span class="o">.</span><span class="n">sequence</span> <span class="o">=</span> <span class="s2">""</span><span class="o">.</span><span class="n">join</span><span class="p">((</span><span class="n">AmnAcd</span><span class="o">.</span><span class="n">AminoAcid</span><span class="p">(</span><span class="nb">str</span><span class="p">(</span><span class="n">_</span><span class="p">))[</span><span class="mi">0</span><span class="p">]</span> <span class="k">for</span> <span class="n">_</span> <span class="ow">in</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">aalist</span><span class="p">))</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s2">"Amino acid sequence:</span><span class="se">\t</span><span class="si">%s</span><span class="s2">"</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">sequence</span><span class="p">)</span></div></div>
+
+
+<div class="viewcode-block" id="Protein"><a class="viewcode-back" href="../../ariaec.html#ariaec.protein.Protein">[docs]</a><span class="k">class</span> <span class="nc">Protein</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span>
+ <span class="sd">"""Protein class"""</span>
+
+ <span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">sett</span><span class="p">):</span>
+ <span class="sd">"""</span>
+
+<span class="sd"> :param sett:</span>
+<span class="sd"> :return:</span>
+<span class="sd"> """</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">aa_sequence</span> <span class="o">=</span> <span class="n">AminoAcidSequence</span><span class="p">(</span><span class="n">sett</span><span class="o">.</span><span class="n">TOPO</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">sec_struct</span> <span class="o">=</span> <span class="n">SsList</span><span class="p">(</span><span class="n">sett</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">index</span> <span class="o">=</span> <span class="p">[]</span> <span class="c1"># Index starting from 1</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">seqfile_path</span> <span class="o">=</span> <span class="sa">u</span><span class="s1">''</span>
+
+<div class="viewcode-block" id="Protein.sync_index"><a class="viewcode-back" href="../../ariaec.html#ariaec.protein.Protein.sync_index">[docs]</a> <span class="nd">@staticmethod</span>
+ <span class="k">def</span> <span class="nf">sync_index</span><span class="p">(</span><span class="n">index1</span><span class="p">,</span> <span class="n">index2</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Return humanidx with upper min from existing humanidx</span>
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> index1 :</span>
+<span class="sd"> param index2:</span>
+<span class="sd"> index2 :</span>
+<span class="sd"> </span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+<span class="sd"> </span>
+<span class="sd"> """</span>
+ <span class="k">if</span> <span class="n">index1</span> <span class="ow">and</span> <span class="ow">not</span> <span class="n">index2</span><span class="p">:</span>
+ <span class="k">return</span> <span class="n">index1</span>
+ <span class="k">elif</span> <span class="n">index2</span> <span class="ow">and</span> <span class="ow">not</span> <span class="n">index1</span><span class="p">:</span>
+ <span class="k">return</span> <span class="n">index2</span>
+ <span class="k">elif</span> <span class="ow">not</span> <span class="n">index1</span> <span class="ow">and</span> <span class="ow">not</span> <span class="n">index2</span><span class="p">:</span>
+ <span class="k">return</span> <span class="p">[]</span>
+ <span class="k">elif</span> <span class="nb">len</span><span class="p">(</span><span class="n">index1</span><span class="p">)</span> <span class="o">==</span> <span class="nb">len</span><span class="p">(</span><span class="n">index2</span><span class="p">):</span>
+ <span class="k">if</span> <span class="nb">min</span><span class="p">(</span><span class="n">index1</span><span class="p">)</span> <span class="o"><</span> <span class="nb">min</span><span class="p">(</span><span class="n">index2</span><span class="p">):</span>
+ <span class="k">return</span> <span class="n">index2</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">return</span> <span class="n">index1</span>
+ <span class="k">elif</span> <span class="nb">len</span><span class="p">(</span><span class="n">index1</span><span class="p">)</span> <span class="o">!=</span> <span class="nb">len</span><span class="p">(</span><span class="n">index2</span><span class="p">):</span>
+ <span class="k">raise</span> <span class="ne">IndexError</span><span class="p">(</span>
+ <span class="s2">"Please check humanidx list from input files. They "</span>
+ <span class="s2">"are not the same length !"</span><span class="p">)</span></div>
+
+ <span class="nd">@property</span>
+ <span class="k">def</span> <span class="nf">topology</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="sd">""":return:"""</span>
+ <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">aa_sequence</span><span class="o">.</span><span class="n">topology</span>
+
+<div class="viewcode-block" id="Protein.set_aa_sequence"><a class="viewcode-back" href="../../ariaec.html#ariaec.protein.Protein.set_aa_sequence">[docs]</a> <span class="k">def</span> <span class="nf">set_aa_sequence</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">filename</span><span class="p">,</span> <span class="n">ssidx</span><span class="o">=</span><span class="kc">False</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> </span>
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> filename :</span>
+<span class="sd"> param ssidx:</span>
+<span class="sd"> ssidx :</span>
+<span class="sd"> (Default value = False)</span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+<span class="sd"> </span>
+<span class="sd"> """</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">aa_sequence</span><span class="o">.</span><span class="n">read</span><span class="p">(</span><span class="n">filename</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">index</span> <span class="o">=</span> <span class="nb">range</span><span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">aa_sequence</span><span class="o">.</span><span class="n">sequence</span><span class="p">)</span> <span class="o">+</span> <span class="mi">1</span><span class="p">)</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">sec_struct</span><span class="o">.</span><span class="n">ss_matrix</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">sec_struct</span><span class="o">.</span><span class="n">seq_sublist</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">aa_sequence</span><span class="o">.</span><span class="n">sequence</span><span class="p">)</span>
+ <span class="k">if</span> <span class="n">ssidx</span><span class="p">:</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s2">"Using secondary structure index for amino acid "</span>
+ <span class="s2">"sequence"</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">index</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">sync_index</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">aa_sequence</span><span class="o">.</span><span class="n">humanidx</span><span class="p">,</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">sec_struct</span><span class="o">.</span><span class="n">index</span><span class="p">)</span></div>
+
+<div class="viewcode-block" id="Protein.set_sec_struct"><a class="viewcode-back" href="../../ariaec.html#ariaec.protein.Protein.set_sec_struct">[docs]</a> <span class="k">def</span> <span class="nf">set_sec_struct</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">filename</span><span class="p">,</span> <span class="n">ssdist_filename</span><span class="o">=</span><span class="s1">''</span><span class="p">,</span> <span class="n">ssidx</span><span class="o">=</span><span class="kc">False</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> </span>
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> filename :</span>
+<span class="sd"> param ssdist_filename:</span>
+<span class="sd"> ssidx :</span>
+<span class="sd"> return: (Default value = False)</span>
+<span class="sd"> ssdist_filename :</span>
+<span class="sd"> (Default value = '')</span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+<span class="sd"> </span>
+<span class="sd"> """</span>
+ <span class="c1"># TODO: Add test checking if both amino acid and sec_struct sequence</span>
+ <span class="c1"># have the same length after seq_sublist call</span>
+ <span class="c1"># Read secondary structure prediction file</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">sec_struct</span><span class="o">.</span><span class="n">read</span><span class="p">(</span><span class="n">filename</span><span class="p">)</span>
+ <span class="k">if</span> <span class="n">ssdist_filename</span><span class="p">:</span>
+ <span class="c1"># Read secondary distance matrix</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">sec_struct</span><span class="o">.</span><span class="n">read_ssdist</span><span class="p">(</span><span class="n">ssdist_filename</span><span class="p">)</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">error</span><span class="p">(</span><span class="s2">"No secondary structure distance file found. Please "</span>
+ <span class="s2">"check configuration file"</span><span class="p">)</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">aa_sequence</span><span class="o">.</span><span class="n">sequence</span><span class="p">:</span>
+ <span class="c1"># Synchronise sec structure sequence with aa sequence</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s2">"Align secondary structure sequence with protein "</span>
+ <span class="s2">"sequence"</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">sec_struct</span><span class="o">.</span><span class="n">seq_sublist</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">aa_sequence</span><span class="o">.</span><span class="n">sequence</span><span class="p">)</span>
+ <span class="k">if</span> <span class="n">ssidx</span><span class="p">:</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s2">"Using secondary structure index for amino acid "</span>
+ <span class="s2">"sequence"</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">index</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">sync_index</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">aa_sequence</span><span class="o">.</span><span class="n">humanidx</span><span class="p">,</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">sec_struct</span><span class="o">.</span><span class="n">index</span><span class="p">)</span></div>
+
+<div class="viewcode-block" id="Protein.write_seq"><a class="viewcode-back" href="../../ariaec.html#ariaec.protein.Protein.write_seq">[docs]</a> <span class="k">def</span> <span class="nf">write_seq</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">outfile</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> </span>
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> outfile :</span>
+<span class="sd"> return:</span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+<span class="sd"> </span>
+<span class="sd"> """</span>
+ <span class="c1"># TODO: same as above, trouble with unicode calls inside capturing</span>
+ <span class="c1"># with Capturing() as output:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">aa_sequence</span><span class="o">.</span><span class="n">WriteSeq</span><span class="p">(</span><span class="n">text_type</span><span class="p">(</span><span class="n">outfile</span><span class="p">))</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">seqfile_path</span> <span class="o">=</span> <span class="s1">'</span><span class="si">%s</span><span class="s1">'</span> <span class="o">%</span> <span class="n">outfile</span></div></div>
+
+
+<span class="k">if</span> <span class="vm">__name__</span> <span class="o">==</span> <span class="s2">"__main__"</span><span class="p">:</span>
+ <span class="kn">from</span> <span class="nn">.settings</span> <span class="k">import</span> <span class="n">AriaEcSettings</span>
+ <span class="n">settings</span> <span class="o">=</span> <span class="n">AriaEcSettings</span><span class="p">(</span><span class="s2">"setup"</span><span class="p">)</span>
+ <span class="n">prot</span> <span class="o">=</span> <span class="n">Protein</span><span class="p">(</span><span class="n">settings</span><span class="p">)</span>
+ <span class="n">prot</span><span class="o">.</span><span class="n">set_aa_sequence</span><span class="p">(</span><span class="s2">"../examples/data/BPT1_BOVIN.fa"</span><span class="p">)</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="n">prot</span><span class="o">.</span><span class="n">aa_sequence</span><span class="p">)</span>
+</pre></div>
+
+ </div>
+ <div class="articleComments">
+
+ </div>
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\ No newline at end of file
diff --git a/examples-dev/olds/_build/html/_modules/ariaec/protmap.html b/examples-dev/olds/_build/html/_modules/ariaec/protmap.html
new file mode 100644
index 0000000000000000000000000000000000000000..bd9f8bd696ca8b6fba5b0c9016b3f247db5d4768
--- /dev/null
+++ b/examples-dev/olds/_build/html/_modules/ariaec/protmap.html
@@ -0,0 +1,2743 @@
+
+
+<!DOCTYPE html>
+<!--[if IE 8]><html class="no-js lt-ie9" lang="en" > <![endif]-->
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+ <div itemprop="articleBody">
+
+ <h1>Source code for ariaec.protmap</h1><div class="highlight"><pre>
+<span></span><span class="c1"># coding=utf-8</span>
+<span class="sd">"""</span>
+<span class="sd"> ARIA Evolutionary Constraints Tools</span>
+<span class="sd">"""</span>
+<span class="kn">from</span> <span class="nn">__future__</span> <span class="k">import</span> <span class="n">absolute_import</span><span class="p">,</span> <span class="n">division</span><span class="p">,</span> <span class="n">print_function</span>
+<span class="kn">from</span> <span class="nn">collections</span> <span class="k">import</span> <span class="n">defaultdict</span>
+<span class="kn">from</span> <span class="nn">copy</span> <span class="k">import</span> <span class="n">deepcopy</span>
+
+<span class="kn">import</span> <span class="nn">os</span>
+<span class="kn">import</span> <span class="nn">re</span>
+<span class="kn">import</span> <span class="nn">csv</span>
+<span class="kn">import</span> <span class="nn">six</span>
+<span class="kn">import</span> <span class="nn">string</span>
+<span class="kn">import</span> <span class="nn">logging</span>
+<span class="kn">import</span> <span class="nn">textwrap</span>
+<span class="kn">import</span> <span class="nn">datetime</span>
+<span class="kn">import</span> <span class="nn">operator</span>
+<span class="kn">import</span> <span class="nn">itertools</span>
+<span class="kn">import</span> <span class="nn">collections</span>
+
+<span class="kn">import</span> <span class="nn">matplotlib</span>
+<span class="kn">import</span> <span class="nn">numpy</span> <span class="k">as</span> <span class="nn">np</span>
+<span class="kn">import</span> <span class="nn">pandas</span> <span class="k">as</span> <span class="nn">pd</span>
+<span class="kn">import</span> <span class="nn">seaborn</span> <span class="k">as</span> <span class="nn">sns</span>
+<span class="kn">import</span> <span class="nn">sklearn.metrics</span> <span class="k">as</span> <span class="nn">skm</span>
+
+<span class="kn">import</span> <span class="nn">aria.ConversionTable</span> <span class="k">as</span> <span class="nn">ConversionTable</span>
+<span class="kn">import</span> <span class="nn">aria.legacy.AminoAcid</span> <span class="k">as</span> <span class="nn">AminoAcid</span>
+
+<span class="kn">from</span> <span class="nn">matplotlib</span> <span class="k">import</span> <span class="n">pyplot</span> <span class="k">as</span> <span class="n">plt</span>
+<span class="kn">from</span> <span class="nn">matplotlib.lines</span> <span class="k">import</span> <span class="n">Line2D</span>
+
+<span class="kn">from</span> <span class="nn">.common</span> <span class="k">import</span> <span class="p">(</span><span class="n">tickmin</span><span class="p">,</span> <span class="n">tickrot</span><span class="p">,</span> <span class="n">titleprint</span><span class="p">,</span> <span class="n">addtup</span><span class="p">)</span>
+<span class="kn">from</span> <span class="nn">.ndconv</span> <span class="k">import</span> <span class="n">net_deconv</span>
+
+
+<span class="n">matplotlib</span><span class="o">.</span><span class="n">use</span><span class="p">(</span><span class="s2">"Agg"</span><span class="p">,</span> <span class="n">warn</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span>
+<span class="n">LOG</span> <span class="o">=</span> <span class="n">logging</span><span class="o">.</span><span class="n">getLogger</span><span class="p">(</span><span class="vm">__name__</span><span class="p">)</span>
+<span class="c1"># TODO: check dataframe symmetry or always use unstack</span>
+<span class="c1"># TODO: objet MapContainer contenant les differentes maps en attributs ! (et</span>
+<span class="c1"># non en clef de dict)</span>
+
+
+<div class="viewcode-block" id="Map"><a class="viewcode-back" href="../../ariaec.html#ariaec.protmap.Map">[docs]</a><span class="k">class</span> <span class="nc">Map</span><span class="p">(</span><span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">):</span>
+ <span class="sd">"""Distance/contact matrix"""</span>
+
+ <span class="n">mtype_choices</span> <span class="o">=</span> <span class="p">{</span><span class="s1">'contact'</span><span class="p">:</span> <span class="nb">bool</span><span class="p">,</span> <span class="s1">'distance'</span><span class="p">:</span> <span class="nb">float</span><span class="p">,</span> <span class="s2">"score"</span><span class="p">:</span> <span class="nb">float</span><span class="p">}</span>
+
+<div class="viewcode-block" id="Map.update"><a class="viewcode-back" href="../../ariaec.html#ariaec.protmap.Map.update">[docs]</a> <span class="k">def</span> <span class="nf">update</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> </span>
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> args :</span>
+<span class="sd"> param kwargs:</span>
+<span class="sd"> *args :</span>
+<span class="sd"> </span>
+<span class="sd"> **kwargs :</span>
+<span class="sd"> </span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+<span class="sd"> </span>
+<span class="sd"> """</span>
+ <span class="nb">super</span><span class="p">(</span><span class="n">Map</span><span class="p">,</span> <span class="bp">self</span><span class="p">)</span><span class="o">.</span><span class="n">update</span><span class="p">(</span><span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">)</span></div>
+
+ <span class="c1"># def _constructor_expanddim(self):</span>
+ <span class="c1"># super(Map, self)._constructor_expanddim()</span>
+
+ <span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">index</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">columns</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">mtype</span><span class="o">=</span><span class="s1">'distance'</span><span class="p">,</span>
+ <span class="n">duplicate_levels</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span> <span class="n">data</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">dtype</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">sym</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span>
+ <span class="n">desc</span><span class="o">=</span><span class="s2">""</span><span class="p">,</span> <span class="n">path</span><span class="o">=</span><span class="s2">""</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> </span>
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> index</span>
+<span class="sd"> columns</span>
+<span class="sd"> mtype</span>
+<span class="sd"> duplicate_levels</span>
+<span class="sd"> Allow duplicate levels in dataframe</span>
+<span class="sd"> data</span>
+<span class="sd"> dtype</span>
+<span class="sd"> sym</span>
+<span class="sd"> desc</span>
+<span class="sd"> path</span>
+<span class="sd"> """</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="n">dtype</span><span class="p">:</span>
+ <span class="n">dtype</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">check_type</span><span class="p">(</span><span class="n">mtype</span><span class="p">)</span>
+ <span class="c1"># TODO: should probably init to np.NaN</span>
+ <span class="k">if</span> <span class="n">data</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
+ <span class="n">data</span> <span class="o">=</span> <span class="kc">False</span> <span class="k">if</span> <span class="n">dtype</span> <span class="o">==</span> <span class="nb">bool</span> <span class="k">else</span> <span class="n">np</span><span class="o">.</span><span class="n">NaN</span>
+ <span class="nb">super</span><span class="p">(</span><span class="n">Map</span><span class="p">,</span> <span class="bp">self</span><span class="p">)</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="n">data</span><span class="o">=</span><span class="n">data</span><span class="p">,</span> <span class="n">dtype</span><span class="o">=</span><span class="n">dtype</span><span class="p">,</span> <span class="n">index</span><span class="o">=</span><span class="n">index</span><span class="p">,</span>
+ <span class="n">columns</span><span class="o">=</span><span class="n">columns</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">duplicate_levels</span> <span class="o">=</span> <span class="n">duplicate_levels</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">mtype</span> <span class="o">=</span> <span class="n">mtype</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">dtype</span> <span class="o">=</span> <span class="n">dtype</span>
+ <span class="k">if</span> <span class="n">mtype</span> <span class="o">==</span> <span class="s2">"score"</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">sort_list</span> <span class="o">=</span> <span class="p">[]</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">sym</span> <span class="o">=</span> <span class="n">sym</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">desc</span> <span class="o">=</span> <span class="n">desc</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">path</span> <span class="o">=</span> <span class="n">path</span>
+
+ <span class="k">def</span> <span class="nf">__str__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="k">return</span> <span class="nb">super</span><span class="p">(</span><span class="n">Map</span><span class="p">,</span> <span class="bp">self</span><span class="p">)</span><span class="o">.</span><span class="fm">__str__</span><span class="p">()</span>
+
+<div class="viewcode-block" id="Map.sortedset"><a class="viewcode-back" href="../../ariaec.html#ariaec.protmap.Map.sortedset">[docs]</a> <span class="k">def</span> <span class="nf">sortedset</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">human_idx</span><span class="o">=</span><span class="kc">False</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> </span>
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> human_idx :</span>
+<span class="sd"> (Default value = False)</span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+<span class="sd"> </span>
+<span class="sd"> """</span>
+ <span class="c1"># Remove duplicate in sort_list</span>
+ <span class="sd">"""</span>
+
+<span class="sd"> :param human_idx:</span>
+<span class="sd"> :return:</span>
+<span class="sd"> """</span>
+ <span class="n">n</span> <span class="o">=</span> <span class="mi">1</span> <span class="k">if</span> <span class="n">human_idx</span> <span class="k">else</span> <span class="mi">0</span>
+ <span class="k">if</span> <span class="nb">hasattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s2">"sort_list"</span><span class="p">):</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">sym</span><span class="p">:</span>
+ <span class="c1"># Use OrderedDict to keep the order</span>
+ <span class="k">return</span> <span class="p">[(</span><span class="n">x</span> <span class="o">+</span> <span class="n">n</span><span class="p">,</span> <span class="n">y</span> <span class="o">+</span> <span class="n">n</span><span class="p">)</span>
+ <span class="k">for</span> <span class="n">x</span><span class="p">,</span> <span class="n">y</span> <span class="ow">in</span>
+ <span class="n">collections</span><span class="o">.</span><span class="n">OrderedDict</span><span class="o">.</span><span class="n">fromkeys</span><span class="p">(</span><span class="nb">frozenset</span><span class="p">(</span><span class="n">x</span><span class="p">)</span>
+ <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">sort_list</span><span class="p">)]</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="c1"># Asym matrix, no need to remove duplicate</span>
+ <span class="k">return</span> <span class="p">[(</span><span class="n">x</span> <span class="o">+</span> <span class="n">n</span><span class="p">,</span> <span class="n">y</span> <span class="o">+</span> <span class="n">n</span><span class="p">)</span> <span class="k">for</span> <span class="n">x</span><span class="p">,</span> <span class="n">y</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">sort_list</span><span class="p">]</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">return</span> <span class="kc">None</span></div>
+
+<div class="viewcode-block" id="Map.check_type"><a class="viewcode-back" href="../../ariaec.html#ariaec.protmap.Map.check_type">[docs]</a> <span class="k">def</span> <span class="nf">check_type</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">mtype</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> </span>
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> mtype :</span>
+<span class="sd"> return:</span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+<span class="sd"> </span>
+<span class="sd"> """</span>
+ <span class="n">value</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">mtype_choices</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">mtype</span><span class="p">)</span>
+ <span class="k">if</span> <span class="n">value</span><span class="p">:</span>
+ <span class="k">return</span> <span class="n">value</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">error</span><span class="p">(</span><span class="s2">"Map type should be in list </span><span class="si">%s</span><span class="s2">"</span><span class="p">,</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">mtype_choices</span><span class="o">.</span><span class="n">keys</span><span class="p">())</span>
+ <span class="k">return</span> <span class="kc">None</span></div>
+
+<div class="viewcode-block" id="Map.reduce"><a class="viewcode-back" href="../../ariaec.html#ariaec.protmap.Map.reduce">[docs]</a> <span class="k">def</span> <span class="nf">reduce</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="sd">"""Low complexcity dataframe"""</span>
+ <span class="k">raise</span> <span class="ne">NotImplementedError</span></div>
+
+<div class="viewcode-block" id="Map.copy"><a class="viewcode-back" href="../../ariaec.html#ariaec.protmap.Map.copy">[docs]</a> <span class="k">def</span> <span class="nf">copy</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Copy the current map</span>
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> **kwargs :</span>
+<span class="sd"> </span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+<span class="sd"> </span>
+<span class="sd"> """</span>
+ <span class="k">raise</span> <span class="ne">NotImplementedError</span></div>
+
+<div class="viewcode-block" id="Map.remove"><a class="viewcode-back" href="../../ariaec.html#ariaec.protmap.Map.remove">[docs]</a> <span class="k">def</span> <span class="nf">remove</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">rm_list</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> </span>
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> rm_list :</span>
+<span class="sd"> </span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+<span class="sd"> </span>
+<span class="sd"> """</span>
+ <span class="c1"># Reset values at positions in rm_list</span>
+ <span class="sd">"""</span>
+
+<span class="sd"> :param rm_list:</span>
+<span class="sd"> """</span>
+ <span class="n">value</span> <span class="o">=</span> <span class="kc">False</span> <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">dtype</span> <span class="o">==</span> <span class="nb">bool</span> <span class="k">else</span> <span class="n">np</span><span class="o">.</span><span class="n">NaN</span>
+ <span class="k">for</span> <span class="n">contact</span> <span class="ow">in</span> <span class="n">rm_list</span><span class="p">:</span>
+ <span class="n">idx1</span><span class="p">,</span> <span class="n">idx2</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">index</span><span class="p">[</span><span class="n">contact</span><span class="p">[</span><span class="mi">0</span><span class="p">]],</span> <span class="bp">self</span><span class="o">.</span><span class="n">index</span><span class="p">[</span><span class="n">contact</span><span class="p">[</span><span class="mi">1</span><span class="p">]]</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">set_value</span><span class="p">(</span><span class="n">idx1</span><span class="p">,</span> <span class="n">idx2</span><span class="p">,</span> <span class="n">value</span><span class="p">)</span>
+ <span class="c1"># self.iat[(contact[0], contact[1])] = value</span>
+ <span class="c1"># self.iat[(contact[1], contact[0])] = value</span>
+ <span class="k">if</span> <span class="nb">hasattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">'sort_list'</span><span class="p">):</span>
+ <span class="c1"># ! sort_list start at 1</span>
+ <span class="k">if</span> <span class="p">(</span><span class="n">contact</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">contact</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">sort_list</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">sort_list</span><span class="o">.</span><span class="n">remove</span><span class="p">((</span><span class="n">contact</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">contact</span><span class="p">[</span><span class="mi">1</span><span class="p">]))</span>
+ <span class="k">if</span> <span class="p">(</span><span class="n">contact</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="n">contact</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">sort_list</span> <span class="ow">and</span> <span class="bp">self</span><span class="o">.</span><span class="n">sym</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">sort_list</span><span class="o">.</span><span class="n">remove</span><span class="p">((</span><span class="n">contact</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="n">contact</span><span class="p">[</span><span class="mi">0</span><span class="p">]))</span></div>
+
+<div class="viewcode-block" id="Map.to_series"><a class="viewcode-back" href="../../ariaec.html#ariaec.protmap.Map.to_series">[docs]</a> <span class="k">def</span> <span class="nf">to_series</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="sd">"""Return panda series related to lower triangle values"""</span>
+ <span class="n">df</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">copy</span><span class="p">()</span>
+ <span class="n">df</span> <span class="o">=</span> <span class="n">df</span><span class="o">.</span><span class="n">astype</span><span class="p">(</span><span class="nb">float</span><span class="p">)</span>
+ <span class="c1"># remove values from upper triangle</span>
+ <span class="n">df</span><span class="o">.</span><span class="n">values</span><span class="p">[</span><span class="n">np</span><span class="o">.</span><span class="n">triu_indices_from</span><span class="p">(</span><span class="n">df</span><span class="p">,</span> <span class="n">k</span><span class="o">=</span><span class="mi">1</span><span class="p">)]</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">nan</span>
+ <span class="c1"># pd.series with only lower triangle values</span>
+ <span class="k">return</span> <span class="n">df</span><span class="o">.</span><span class="n">unstack</span><span class="p">()</span><span class="o">.</span><span class="n">dropna</span><span class="p">()</span></div>
+
+<div class="viewcode-block" id="Map.topmap"><a class="viewcode-back" href="../../ariaec.html#ariaec.protmap.Map.topmap">[docs]</a> <span class="k">def</span> <span class="nf">topmap</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">scoremap</span><span class="p">,</span> <span class="n">nb_topcontact</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> </span>
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> scoremap :</span>
+<span class="sd"> param nb_topcontact:</span>
+<span class="sd"> nb_topcontact :</span>
+<span class="sd"> </span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+<span class="sd"> </span>
+<span class="sd"> """</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">dtype</span> <span class="o">!=</span> <span class="nb">bool</span><span class="p">:</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s2">"Error when retrieving top contact map. The type of "</span>
+ <span class="s2">"the given map is not a contact type!"</span><span class="p">)</span>
+ <span class="k">return</span> <span class="bp">self</span>
+ <span class="bp">self</span><span class="p">[:]</span> <span class="o">=</span> <span class="kc">False</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">shape</span> <span class="o">==</span> <span class="n">scoremap</span><span class="o">.</span><span class="n">shape</span><span class="p">:</span>
+ <span class="n">pair_list</span> <span class="o">=</span> <span class="n">scoremap</span><span class="o">.</span><span class="n">sortedset</span><span class="p">()[:</span><span class="n">nb_topcontact</span><span class="p">]</span>
+ <span class="k">for</span> <span class="n">contact</span> <span class="ow">in</span> <span class="n">pair_list</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">iat</span><span class="p">[(</span><span class="n">contact</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="n">contact</span><span class="p">[</span><span class="mi">0</span><span class="p">])]</span> <span class="o">=</span> <span class="kc">True</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">iat</span><span class="p">[(</span><span class="n">contact</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">contact</span><span class="p">[</span><span class="mi">1</span><span class="p">])]</span> <span class="o">=</span> <span class="kc">True</span>
+ <span class="k">return</span> <span class="bp">self</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">error</span><span class="p">(</span><span class="s2">"Given scoremap has not the same dimension !"</span><span class="p">)</span>
+ <span class="k">return</span> <span class="kc">None</span></div>
+
+<div class="viewcode-block" id="Map.subfill"><a class="viewcode-back" href="../../ariaec.html#ariaec.protmap.Map.subfill">[docs]</a> <span class="k">def</span> <span class="nf">subfill</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">pairdict</span><span class="p">,</span> <span class="n">level</span><span class="o">=</span><span class="mi">0</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Fill map with dict giving</span>
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> pairdict :</span>
+<span class="sd"> param level:</span>
+<span class="sd"> level :</span>
+<span class="sd"> (Default value = 0)</span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+<span class="sd"> </span>
+<span class="sd"> """</span>
+ <span class="n">pairdict</span> <span class="o">=</span> <span class="p">{</span><span class="n">k</span><span class="o">.</span><span class="n">upper</span><span class="p">():</span> <span class="n">v</span> <span class="k">for</span> <span class="n">k</span><span class="p">,</span> <span class="n">v</span> <span class="ow">in</span> <span class="n">pairdict</span><span class="o">.</span><span class="n">items</span><span class="p">()}</span>
+ <span class="k">if</span> <span class="s2">"def"</span> <span class="ow">in</span> <span class="n">pairdict</span><span class="p">:</span>
+ <span class="bp">self</span><span class="p">[:]</span> <span class="o">=</span> <span class="n">pairdict</span><span class="p">[</span><span class="s2">"def"</span><span class="p">]</span>
+ <span class="k">for</span> <span class="n">idxval</span> <span class="ow">in</span> <span class="n">pairdict</span><span class="p">:</span>
+ <span class="n">idx</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">index</span><span class="o">.</span><span class="n">get_level_values</span><span class="p">(</span><span class="n">level</span><span class="p">)</span> <span class="o">==</span> <span class="n">idxval</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">loc</span><span class="p">[</span><span class="n">idx</span><span class="p">,</span> <span class="n">idx</span><span class="p">]</span> <span class="o">=</span> <span class="n">pairdict</span><span class="p">[</span><span class="n">idxval</span><span class="p">]</span></div>
+
+<div class="viewcode-block" id="Map.set_value"><a class="viewcode-back" href="../../ariaec.html#ariaec.protmap.Map.set_value">[docs]</a> <span class="k">def</span> <span class="nf">set_value</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">index</span><span class="p">,</span> <span class="n">col</span><span class="p">,</span> <span class="n">value</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> </span>
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> index :</span>
+<span class="sd"> param col:</span>
+<span class="sd"> value :</span>
+<span class="sd"> param kwargs:</span>
+<span class="sd"> col :</span>
+<span class="sd"> </span>
+<span class="sd"> **kwargs :</span>
+<span class="sd"> </span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+<span class="sd"> </span>
+<span class="sd"> """</span>
+ <span class="nb">super</span><span class="p">(</span><span class="n">Map</span><span class="p">,</span> <span class="bp">self</span><span class="p">)</span><span class="o">.</span><span class="n">set_value</span><span class="p">(</span><span class="n">index</span><span class="p">,</span> <span class="n">col</span><span class="p">,</span> <span class="n">value</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">sym</span><span class="p">:</span>
+ <span class="nb">super</span><span class="p">(</span><span class="n">Map</span><span class="p">,</span> <span class="bp">self</span><span class="p">)</span><span class="o">.</span><span class="n">set_value</span><span class="p">(</span><span class="n">col</span><span class="p">,</span> <span class="n">index</span><span class="p">,</span> <span class="n">value</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">)</span></div></div>
+
+
+<span class="c1"># TODO: Matrices PosAaAtmMap, AaAtmMap, AtmMap</span>
+<div class="viewcode-block" id="ProteinMap"><a class="viewcode-back" href="../../ariaec.html#ariaec.protmap.ProteinMap">[docs]</a><span class="k">class</span> <span class="nc">ProteinMap</span><span class="p">(</span><span class="n">Map</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Abstract class for protein contact map objects</span>
+<span class="sd"> """</span>
+ <span class="c1"># TODO: matrix should be not only for heavy atoms</span>
+ <span class="c1"># Matrix only for heavy atoms.</span>
+ <span class="n">heavy_reg</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span><span class="sa">r</span><span class="s2">"[CNOS][ABGDEZH][0-9]?"</span><span class="p">)</span>
+ <span class="n">all_reg</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span><span class="sa">r</span><span class="s2">"^((?!cns|dyana).*)$"</span><span class="p">)</span>
+ <span class="c1"># TODO: Autre methodes de dist</span>
+ <span class="n">distance_method</span> <span class="o">=</span> <span class="s1">'euclidean'</span>
+
+ <span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">sequence</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+ <span class="k">if</span> <span class="n">kwargs</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"index"</span><span class="p">)</span> <span class="ow">is</span> <span class="kc">None</span> <span class="ow">or</span> <span class="n">kwargs</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"columns"</span><span class="p">)</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
+ <span class="n">kwargs</span><span class="p">[</span><span class="s2">"index"</span><span class="p">],</span> <span class="n">kwargs</span><span class="p">[</span><span class="s2">"columns"</span><span class="p">]</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">create_index</span><span class="p">(</span>
+ <span class="n">sequence</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
+ <span class="nb">super</span><span class="p">(</span><span class="n">ProteinMap</span><span class="p">,</span> <span class="bp">self</span><span class="p">)</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">contact_flags</span> <span class="o">=</span> <span class="n">kwargs</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"flaglist"</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_maplot</span> <span class="o">=</span> <span class="kc">None</span>
+
+ <span class="c1"># def _constructor_expanddim(self):</span>
+ <span class="c1"># return self._constructor_expanddim()</span>
+ <span class="nd">@property</span>
+ <span class="k">def</span> <span class="nf">sequence</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Specific sequence related to the map in a string</span>
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+<span class="sd"> str</span>
+
+<span class="sd"> """</span>
+ <span class="k">raise</span> <span class="ne">NotImplementedError</span>
+
+<div class="viewcode-block" id="ProteinMap.create_heatmap"><a class="viewcode-back" href="../../ariaec.html#ariaec.protmap.ProteinMap.create_heatmap">[docs]</a> <span class="k">def</span> <span class="nf">create_heatmap</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Generate heatmap</span>
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+
+<span class="sd"> """</span>
+ <span class="k">raise</span> <span class="ne">NotImplementedError</span></div>
+
+<div class="viewcode-block" id="ProteinMap.contact_map"><a class="viewcode-back" href="../../ariaec.html#ariaec.protmap.ProteinMap.contact_map">[docs]</a> <span class="k">def</span> <span class="nf">contact_map</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">contactdef</span><span class="p">,</span> <span class="n">scsc_min</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Generate contact map</span>
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> contactdef :</span>
+<span class="sd"> param scsc_min:</span>
+<span class="sd"> scsc_min :</span>
+<span class="sd"> (Default value = None)</span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+
+<span class="sd"> """</span>
+ <span class="k">raise</span> <span class="ne">NotImplementedError</span></div>
+
+<div class="viewcode-block" id="ProteinMap.create_index"><a class="viewcode-back" href="../../ariaec.html#ariaec.protmap.ProteinMap.create_index">[docs]</a> <span class="k">def</span> <span class="nf">create_index</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">sequence</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+ <span class="sd">"""</span>
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> sequence</span>
+<span class="sd"> kwargs</span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+<span class="sd"> """</span>
+ <span class="c1"># Indexation matrice (tous les atomes ou tous les residus)</span>
+ <span class="k">raise</span> <span class="ne">NotImplementedError</span></div>
+
+<div class="viewcode-block" id="ProteinMap.reduce"><a class="viewcode-back" href="../../ariaec.html#ariaec.protmap.ProteinMap.reduce">[docs]</a> <span class="k">def</span> <span class="nf">reduce</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="sd">"""Lower index level if multi index"""</span>
+ <span class="c1"># TODO: check if multiindex</span>
+ <span class="n">columns</span> <span class="o">=</span> <span class="p">[</span><span class="s1">'-'</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">idx</span><span class="p">)</span> <span class="k">for</span> <span class="n">idx</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">columns</span><span class="p">]</span>
+ <span class="n">index</span> <span class="o">=</span> <span class="p">[</span><span class="s1">'-'</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">idx</span><span class="p">)</span> <span class="k">for</span> <span class="n">idx</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">index</span><span class="p">]</span>
+ <span class="k">return</span> <span class="nb">getattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">'__init__'</span><span class="p">)(</span><span class="bp">self</span><span class="o">.</span><span class="n">sequence</span><span class="p">,</span>
+ <span class="n">path</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">path</span><span class="p">,</span>
+ <span class="n">data</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">as_matrix</span><span class="p">(),</span>
+ <span class="n">index</span><span class="o">=</span><span class="n">index</span><span class="p">,</span> <span class="n">desc</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">desc</span><span class="p">,</span>
+ <span class="n">sym</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">sym</span><span class="p">,</span> <span class="n">mtype</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">mtype</span><span class="p">,</span>
+ <span class="n">columns</span><span class="o">=</span><span class="n">columns</span><span class="p">,</span> <span class="n">dtype</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">dtype</span><span class="p">)</span></div>
+
+<div class="viewcode-block" id="ProteinMap.copy"><a class="viewcode-back" href="../../ariaec.html#ariaec.protmap.ProteinMap.copy">[docs]</a> <span class="k">def</span> <span class="nf">copy</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Copy dataframe and related attributes of the map</span>
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> **kwargs :</span>
+<span class="sd"> </span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+<span class="sd"> </span>
+<span class="sd"> """</span>
+ <span class="n">df</span> <span class="o">=</span> <span class="nb">super</span><span class="p">(</span><span class="n">Map</span><span class="p">,</span> <span class="bp">self</span><span class="p">)</span><span class="o">.</span><span class="n">copy</span><span class="p">()</span>
+ <span class="k">return</span> <span class="n">ProteinMap</span><span class="p">(</span>
+ <span class="n">sequence</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">sequence</span><span class="p">,</span> <span class="n">path</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">path</span><span class="p">,</span> <span class="n">data</span><span class="o">=</span><span class="n">df</span><span class="p">,</span> <span class="n">desc</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">desc</span><span class="p">,</span>
+ <span class="n">sym</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">sym</span><span class="p">,</span> <span class="n">mtype</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">mtype</span><span class="p">,</span> <span class="n">dtype</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">dtype</span><span class="p">)</span></div>
+
+<div class="viewcode-block" id="ProteinMap.plotflush"><a class="viewcode-back" href="../../ariaec.html#ariaec.protmap.ProteinMap.plotflush">[docs]</a> <span class="k">def</span> <span class="nf">plotflush</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="sd">"""Flush contact map plot"""</span>
+ <span class="n">plt</span><span class="o">.</span><span class="n">clf</span><span class="p">()</span>
+ <span class="n">plt</span><span class="o">.</span><span class="n">cla</span><span class="p">()</span>
+ <span class="n">plt</span><span class="o">.</span><span class="n">close</span><span class="p">()</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_maplot</span> <span class="o">=</span> <span class="kc">None</span></div>
+
+ <span class="nd">@property</span>
+ <span class="k">def</span> <span class="nf">maplot</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">linewidths</span><span class="o">=</span><span class="mf">0.0</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Contact map plot</span>
+<span class="sd"> :return:</span>
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> linewidths :</span>
+<span class="sd"> (Default value = 0.0)</span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+<span class="sd"> </span>
+<span class="sd"> """</span>
+ <span class="c1"># Contact map Plot</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">_maplot</span><span class="p">:</span>
+ <span class="c1"># Flush matplot</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="s2">"Build maplot"</span><span class="p">)</span>
+ <span class="n">minticks</span> <span class="o">=</span> <span class="n">tickmin</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">shift</span><span class="o">=</span><span class="mi">1</span><span class="p">)</span> <span class="c1"># Nb graduations</span>
+
+ <span class="bp">self</span><span class="o">.</span><span class="n">_maplot</span> <span class="o">=</span> <span class="n">sns</span><span class="o">.</span><span class="n">heatmap</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">square</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">cbar</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span>
+ <span class="n">linewidths</span><span class="o">=</span><span class="n">linewidths</span><span class="p">,</span> <span class="n">vmax</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span> <span class="n">vmin</span><span class="o">=-</span><span class="mi">1</span><span class="p">,</span>
+ <span class="n">cmap</span><span class="o">=</span><span class="n">sns</span><span class="o">.</span><span class="n">diverging_palette</span><span class="p">(</span><span class="mi">20</span><span class="p">,</span> <span class="mi">220</span><span class="p">,</span> <span class="n">n</span><span class="o">=</span><span class="mi">7</span><span class="p">,</span>
+ <span class="n">as_cmap</span><span class="o">=</span><span class="kc">True</span><span class="p">),</span>
+ <span class="n">xticklabels</span><span class="o">=</span><span class="n">minticks</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span>
+ <span class="n">yticklabels</span><span class="o">=</span><span class="n">minticks</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span>
+ <span class="n">linecolor</span><span class="o">=</span><span class="s2">"grey"</span><span class="p">)</span>
+ <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_maplot</span>
+
+<div class="viewcode-block" id="ProteinMap.saveplot"><a class="viewcode-back" href="../../ariaec.html#ariaec.protmap.ProteinMap.saveplot">[docs]</a> <span class="k">def</span> <span class="nf">saveplot</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">outdir</span><span class="o">=</span><span class="s1">''</span><span class="p">,</span> <span class="n">outprefix</span><span class="o">=</span><span class="s2">"protein"</span><span class="p">,</span> <span class="n">size_fig</span><span class="o">=</span><span class="mi">10</span><span class="p">,</span>
+ <span class="n">plot_ext</span><span class="o">=</span><span class="s2">"pdf"</span><span class="p">,</span> <span class="n">plot_dpi</span><span class="o">=</span><span class="mi">200</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Save plot</span>
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> outdir :</span>
+<span class="sd"> param outprefix: (Default value = '')</span>
+<span class="sd"> size_fig :</span>
+<span class="sd"> param plot_ext: (Default value = 10)</span>
+<span class="sd"> plot_dpi :</span>
+<span class="sd"> (Default value = 200)</span>
+<span class="sd"> outprefix :</span>
+<span class="sd"> (Default value = "protein")</span>
+<span class="sd"> plot_ext :</span>
+<span class="sd"> (Default value = "pdf")</span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+<span class="sd"> </span>
+<span class="sd"> """</span>
+ <span class="n">plotpath</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">outdir</span><span class="p">,</span> <span class="s2">"</span><span class="si">%s</span><span class="s2">.maplot.</span><span class="si">%s</span><span class="s2">"</span> <span class="o">%</span> <span class="p">(</span>
+ <span class="n">outprefix</span><span class="p">,</span> <span class="n">plot_ext</span><span class="p">))</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s2">"Generate contact map plot (</span><span class="si">%s</span><span class="s2">)"</span><span class="p">,</span> <span class="n">plotpath</span><span class="p">)</span>
+ <span class="n">f</span><span class="p">,</span> <span class="n">ax</span> <span class="o">=</span> <span class="n">plt</span><span class="o">.</span><span class="n">subplots</span><span class="p">()</span>
+ <span class="n">tickrot</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">maplot</span><span class="o">.</span><span class="n">axes</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">maplot</span><span class="o">.</span><span class="n">figure</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">maplot</span><span class="o">.</span><span class="n">figure</span><span class="o">.</span><span class="n">set_size_inches</span><span class="p">(</span><span class="n">size_fig</span><span class="p">,</span> <span class="n">size_fig</span><span class="p">)</span>
+ <span class="n">map_title</span> <span class="o">=</span> <span class="s2">"</span><span class="si">%s</span><span class="s2"> contacts map"</span> <span class="o">%</span> <span class="n">outprefix</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">maplot</span><span class="o">.</span><span class="n">set_title</span><span class="p">(</span><span class="n">map_title</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">maplot</span><span class="o">.</span><span class="n">figure</span><span class="o">.</span><span class="n">tight_layout</span><span class="p">()</span>
+
+ <span class="n">f</span><span class="o">.</span><span class="n">tight_layout</span><span class="p">()</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">maplot</span><span class="o">.</span><span class="n">figure</span><span class="o">.</span><span class="n">savefig</span><span class="p">(</span><span class="n">plotpath</span><span class="p">,</span> <span class="n">dpi</span><span class="o">=</span><span class="n">plot_dpi</span><span class="p">)</span>
+ <span class="n">plt</span><span class="o">.</span><span class="n">close</span><span class="p">(</span><span class="s1">'all'</span><span class="p">)</span></div>
+
+<div class="viewcode-block" id="ProteinMap.contactset"><a class="viewcode-back" href="../../ariaec.html#ariaec.protmap.ProteinMap.contactset">[docs]</a> <span class="k">def</span> <span class="nf">contactset</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">human_idx</span><span class="o">=</span><span class="kc">False</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Remove duplicate in contact_list</span>
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> human_idx :</span>
+<span class="sd"> return: (Default value = False)</span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+<span class="sd"> list</span>
+<span class="sd"> </span>
+<span class="sd"> """</span>
+ <span class="n">contacts</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">contact_list</span><span class="p">(</span><span class="n">human_idx</span><span class="p">)</span>
+ <span class="k">if</span> <span class="n">contacts</span><span class="p">:</span>
+ <span class="n">contacts</span> <span class="o">=</span> <span class="nb">sorted</span><span class="p">(</span><span class="nb">set</span><span class="p">((</span><span class="nb">tuple</span><span class="p">(</span><span class="nb">sorted</span><span class="p">((</span><span class="n">x</span><span class="p">,</span> <span class="n">y</span><span class="p">)))</span>
+ <span class="k">for</span> <span class="n">x</span><span class="p">,</span> <span class="n">y</span> <span class="ow">in</span> <span class="n">contacts</span><span class="p">)))</span>
+ <span class="k">return</span> <span class="n">contacts</span></div>
+
+<div class="viewcode-block" id="ProteinMap.contact_list"><a class="viewcode-back" href="../../ariaec.html#ariaec.protmap.ProteinMap.contact_list">[docs]</a> <span class="k">def</span> <span class="nf">contact_list</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">human_idx</span><span class="o">=</span><span class="kc">False</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Return contact list</span>
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> human_idx :</span>
+<span class="sd"> return: (Default value = False)</span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+<span class="sd"> list</span>
+<span class="sd"> </span>
+<span class="sd"> """</span>
+ <span class="n">contact_list</span> <span class="o">=</span> <span class="p">[]</span>
+ <span class="n">n</span> <span class="o">=</span> <span class="mi">1</span> <span class="k">if</span> <span class="n">human_idx</span> <span class="k">else</span> <span class="mi">0</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">dtype</span> <span class="ow">is</span> <span class="nb">bool</span><span class="p">:</span>
+ <span class="c1"># for irow, row in enumerate(self):</span>
+ <span class="k">for</span> <span class="n">irow</span><span class="p">,</span> <span class="n">row</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">index</span><span class="p">):</span>
+ <span class="k">for</span> <span class="n">icol</span><span class="p">,</span> <span class="n">value</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="bp">self</span><span class="p">[</span><span class="n">row</span><span class="p">]):</span>
+ <span class="k">if</span> <span class="n">value</span><span class="p">:</span>
+ <span class="n">contact_list</span><span class="o">.</span><span class="n">append</span><span class="p">((</span><span class="n">irow</span> <span class="o">+</span> <span class="n">n</span><span class="p">,</span> <span class="n">icol</span> <span class="o">+</span> <span class="n">n</span><span class="p">))</span>
+ <span class="k">return</span> <span class="n">contact_list</span></div>
+
+<div class="viewcode-block" id="ProteinMap.compareplot"><a class="viewcode-back" href="../../ariaec.html#ariaec.protmap.ProteinMap.compareplot">[docs]</a> <span class="k">def</span> <span class="nf">compareplot</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">protmap</span><span class="p">,</span> <span class="n">save_fig</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">alpha</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Compare 2 contact map and plot differences</span>
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> protmap :</span>
+<span class="sd"> param save_fig:</span>
+<span class="sd"> alpha :</span>
+<span class="sd"> param kwargs: (Default value = None)</span>
+<span class="sd"> save_fig :</span>
+<span class="sd"> (Default value = True)</span>
+<span class="sd"> **kwargs :</span>
+<span class="sd"> </span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+<span class="sd"> </span>
+<span class="sd"> """</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">plotflush</span><span class="p">()</span>
+ <span class="c1"># Contact map plot</span>
+ <span class="k">if</span> <span class="nb">getattr</span><span class="p">(</span><span class="n">protmap</span><span class="p">,</span> <span class="s2">"shape"</span><span class="p">)</span> <span class="ow">and</span> <span class="bp">self</span><span class="o">.</span><span class="n">shape</span> <span class="o">!=</span> <span class="n">protmap</span><span class="o">.</span><span class="n">shape</span><span class="p">:</span>
+ <span class="n">logging</span><span class="o">.</span><span class="n">error</span><span class="p">(</span><span class="s2">"Cant't compare </span><span class="si">%s</span><span class="s2"> map with </span><span class="si">%s</span><span class="s2">"</span> <span class="o">%</span> <span class="p">(</span>
+ <span class="n">protmap</span><span class="o">.</span><span class="vm">__class__</span><span class="o">.</span><span class="vm">__name__</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="vm">__class__</span><span class="o">.</span><span class="vm">__name__</span><span class="p">))</span>
+ <span class="k">return</span> <span class="kc">None</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="n">cmplist</span> <span class="o">=</span> <span class="n">protmap</span><span class="o">.</span><span class="n">contact_list</span><span class="p">(</span><span class="n">human_idx</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
+
+ <span class="n">ymax</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">sequence</span><span class="p">)</span> <span class="o">-</span> <span class="mi">1</span>
+ <span class="k">if</span> <span class="n">protmap</span><span class="o">.</span><span class="n">contact_flags</span><span class="p">:</span>
+ <span class="n">flags</span> <span class="o">=</span> <span class="nb">set</span><span class="p">(</span><span class="n">protmap</span><span class="o">.</span><span class="n">contact_flags</span><span class="o">.</span><span class="n">values</span><span class="p">())</span>
+ <span class="c1"># Color palette</span>
+ <span class="n">pal</span> <span class="o">=</span> <span class="n">sns</span><span class="o">.</span><span class="n">color_palette</span><span class="p">(</span><span class="s2">"hls"</span><span class="p">,</span> <span class="nb">len</span><span class="p">(</span><span class="n">flags</span><span class="p">))</span>
+ <span class="k">for</span> <span class="n">i</span><span class="p">,</span> <span class="n">flag</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">flags</span><span class="p">):</span>
+ <span class="n">conlist</span> <span class="o">=</span> <span class="p">[</span><span class="n">contact</span> <span class="k">for</span> <span class="n">contact</span> <span class="ow">in</span> <span class="n">protmap</span><span class="o">.</span><span class="n">contact_flags</span> <span class="k">if</span>
+ <span class="n">protmap</span><span class="o">.</span><span class="n">contact_flags</span><span class="p">[</span><span class="n">contact</span><span class="p">]</span> <span class="o">==</span> <span class="n">flag</span><span class="p">]</span>
+ <span class="n">xind</span> <span class="o">=</span> <span class="p">[</span><span class="n">x</span> <span class="o">-</span> <span class="o">.</span><span class="mi">5</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span>
+ <span class="nb">zip</span><span class="p">(</span><span class="o">*</span><span class="n">conlist</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span> <span class="o">+</span> <span class="nb">zip</span><span class="p">(</span><span class="o">*</span><span class="n">conlist</span><span class="p">)[</span><span class="mi">1</span><span class="p">]]</span>
+ <span class="n">yind</span> <span class="o">=</span> <span class="p">[</span><span class="n">ymax</span> <span class="o">-</span> <span class="n">y</span> <span class="o">+</span> <span class="mf">1.5</span> <span class="k">for</span> <span class="n">y</span> <span class="ow">in</span>
+ <span class="nb">zip</span><span class="p">(</span><span class="o">*</span><span class="n">conlist</span><span class="p">)[</span><span class="mi">1</span><span class="p">]</span> <span class="o">+</span> <span class="nb">zip</span><span class="p">(</span><span class="o">*</span><span class="n">conlist</span><span class="p">)[</span><span class="mi">0</span><span class="p">]]</span>
+ <span class="n">color</span> <span class="o">=</span> <span class="n">pal</span><span class="p">[</span><span class="n">i</span><span class="p">]</span>
+ <span class="n">mark</span> <span class="o">=</span> <span class="n">Line2D</span><span class="o">.</span><span class="n">filled_markers</span><span class="p">[</span><span class="n">i</span><span class="p">]</span>
+ <span class="k">for</span> <span class="n">x</span><span class="p">,</span> <span class="n">y</span> <span class="ow">in</span> <span class="nb">zip</span><span class="p">(</span><span class="n">xind</span><span class="p">,</span> <span class="n">yind</span><span class="p">):</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">maplot</span><span class="o">.</span><span class="n">axes</span><span class="o">.</span><span class="n">scatter</span><span class="p">(</span><span class="n">x</span><span class="p">,</span> <span class="n">y</span><span class="p">,</span> <span class="n">s</span><span class="o">=</span><span class="mi">8</span><span class="p">,</span> <span class="n">c</span><span class="o">=</span><span class="n">color</span><span class="p">,</span>
+ <span class="n">linewidths</span><span class="o">=</span><span class="mf">0.1</span><span class="p">,</span> <span class="n">alpha</span><span class="o">=</span><span class="n">alpha</span><span class="p">,</span>
+ <span class="n">marker</span><span class="o">=</span><span class="n">mark</span><span class="p">)</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s2">"Contact list: </span><span class="si">%s</span><span class="s2">"</span><span class="p">,</span> <span class="n">cmplist</span><span class="p">)</span>
+ <span class="n">xind</span> <span class="o">=</span> <span class="p">[</span><span class="n">x</span> <span class="o">-</span> <span class="o">.</span><span class="mi">5</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span>
+ <span class="nb">zip</span><span class="p">(</span><span class="o">*</span><span class="n">cmplist</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span> <span class="o">+</span> <span class="nb">zip</span><span class="p">(</span><span class="o">*</span><span class="n">cmplist</span><span class="p">)[</span><span class="mi">1</span><span class="p">]]</span>
+ <span class="n">yind</span> <span class="o">=</span> <span class="p">[</span><span class="n">ymax</span> <span class="o">-</span> <span class="n">y</span> <span class="o">+</span> <span class="mf">1.5</span> <span class="k">for</span> <span class="n">y</span> <span class="ow">in</span>
+ <span class="nb">zip</span><span class="p">(</span><span class="o">*</span><span class="n">cmplist</span><span class="p">)[</span><span class="mi">1</span><span class="p">]</span> <span class="o">+</span> <span class="nb">zip</span><span class="p">(</span><span class="o">*</span><span class="n">cmplist</span><span class="p">)[</span><span class="mi">0</span><span class="p">]]</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="s2">"Xind: </span><span class="si">%s</span><span class="s2">"</span><span class="p">,</span> <span class="n">xind</span><span class="p">)</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="s2">"Yind: </span><span class="si">%s</span><span class="s2">"</span><span class="p">,</span> <span class="n">yind</span><span class="p">)</span>
+ <span class="n">color</span> <span class="o">=</span> <span class="s2">"red"</span>
+ <span class="c1"># width = [0.3 for _ in xind]</span>
+ <span class="c1"># for x, y, h in zip(xind, yind, width):</span>
+ <span class="k">for</span> <span class="n">x</span><span class="p">,</span> <span class="n">y</span> <span class="ow">in</span> <span class="nb">zip</span><span class="p">(</span><span class="n">xind</span><span class="p">,</span> <span class="n">yind</span><span class="p">):</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">maplot</span><span class="o">.</span><span class="n">axes</span><span class="o">.</span><span class="n">scatter</span><span class="p">(</span><span class="n">x</span><span class="p">,</span> <span class="n">y</span><span class="p">,</span> <span class="n">s</span><span class="o">=</span><span class="mi">30</span><span class="p">,</span> <span class="n">c</span><span class="o">=</span><span class="n">color</span><span class="p">,</span>
+ <span class="n">linewidths</span><span class="o">=</span><span class="mi">0</span><span class="p">,</span>
+ <span class="n">alpha</span><span class="o">=</span><span class="n">alpha</span><span class="p">)</span>
+ <span class="k">if</span> <span class="n">save_fig</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">saveplot</span><span class="p">(</span><span class="o">**</span><span class="n">kwargs</span><span class="p">)</span></div>
+
+ <span class="nd">@staticmethod</span>
+ <span class="k">def</span> <span class="nf">_write_report</span><span class="p">(</span><span class="n">reportpath</span><span class="p">,</span> <span class="o">**</span><span class="n">scores</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Write report file from score dict</span>
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> reportpath :</span>
+<span class="sd"> </span>
+<span class="sd"> scores :</span>
+<span class="sd"> </span>
+<span class="sd"> **scores :</span>
+<span class="sd"> </span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+<span class="sd"> </span>
+<span class="sd"> """</span>
+ <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">reportpath</span><span class="p">,</span> <span class="s1">'w'</span><span class="p">)</span> <span class="k">as</span> <span class="n">reportf</span><span class="p">:</span>
+ <span class="n">msg</span> <span class="o">=</span> <span class="n">string</span><span class="o">.</span><span class="n">Formatter</span><span class="p">()</span><span class="o">.</span><span class="n">vformat</span><span class="p">(</span><span class="s2">"""</span><span class="se">\</span>
+<span class="s2">## Report </span><span class="si">{map1name}</span><span class="s2"> vs. </span><span class="si">{map2name}</span><span class="s2"></span>
+<span class="s2">##</span>
+<span class="s2">## Date: </span><span class="si">{date}</span><span class="s2"></span>
+<span class="s2">##</span>
+<span class="s2">## Plots: </span><span class="si">{outdir}</span><span class="s2"></span>
+<span class="s2">## Reference map: </span><span class="si">{map1path}</span><span class="s2"></span>
+<span class="s2">## Contact map: </span><span class="si">{map2path}</span><span class="s2"></span>
+<span class="s2">##</span>
+<span class="s2">## -----------------------------------------------------------------------------</span>
+<span class="s2">##</span>
+<span class="s2">## Sequence:</span>
+<span class="s2">## </span><span class="si">{seq}</span><span class="s2"></span>
+<span class="s2">## Protein length: </span><span class="si">{protlen}</span><span class="s2"></span>
+<span class="s2">##</span>
+<span class="s2">## -----------------------------------------------------------------------------</span>
+<span class="s2">##</span>
+<span class="s2">## Matthews correlation coefficient (MCC): </span><span class="si">{mcc}</span><span class="s2"></span>
+<span class="s2">## F1 score: </span><span class="si">{f1s}</span><span class="s2"></span>
+<span class="s2">## F2 score: </span><span class="si">{f2s}</span><span class="s2"></span>
+<span class="s2">## F0.5 score: </span><span class="si">{f05s}</span><span class="s2"></span>
+<span class="s2">##</span>
+<span class="s2">## Precision: </span><span class="si">{precision}</span><span class="s2"></span>
+<span class="s2">## Recall (Sensibility): </span><span class="si">{recall}</span><span class="s2"></span>
+<span class="s2">## Accuracy: </span><span class="si">{accuracy}</span><span class="s2"></span>
+<span class="s2">##</span>
+<span class="s2">## Hamming loss: </span><span class="si">{hamm}</span><span class="s2"></span>
+<span class="s2">## Hinge loss: </span><span class="si">{hin}</span><span class="s2"></span>
+<span class="s2">##</span>
+<span class="s2">## -----------------------------------------------------------------------------</span>
+<span class="s2">##</span>
+<span class="s2">## Plot scores</span>
+<span class="s2">##</span>
+<span class="s2">## ROC Area Under Curve: </span><span class="si">{roc_auc}</span><span class="s2"></span>
+<span class="s2">## Average precision score: </span><span class="si">{aver_prec}</span><span class="s2"></span>
+<span class="s2">##</span>
+<span class="s2">## -----------------------------------------------------------------------------</span>
+<span class="s2">##</span>
+<span class="s2">## Precision recall curve</span>
+<span class="s2">##</span>
+<span class="s2">## Precision values:</span>
+<span class="s2">## </span><span class="si">{allprec}</span><span class="s2"></span>
+<span class="s2">## Recall values:</span>
+<span class="s2">## </span><span class="si">{allrec}</span><span class="s2"></span>
+<span class="s2">## Score tresholds (</span><span class="si">{map2name}</span><span class="s2">):</span>
+<span class="s2">## </span><span class="si">{prthres}</span><span class="s2"></span>
+<span class="s2">##</span>
+<span class="s2">## -----------------------------------------------------------------------------</span>
+<span class="s2">##</span>
+<span class="s2">## ROC curve</span>
+<span class="s2">##</span>
+<span class="s2">## True Positive Rate (Sensibility) values:</span>
+<span class="s2">## </span><span class="si">{alltpr}</span><span class="s2"></span>
+<span class="s2">## False Positive Rate (1 - Specificity) values:</span>
+<span class="s2">## </span><span class="si">{allfpr}</span><span class="s2"></span>
+<span class="s2">## Score tresholds (</span><span class="si">{map2name}</span><span class="s2">):</span>
+<span class="s2">## </span><span class="si">{rocthres}</span><span class="s2">"""</span><span class="p">,</span> <span class="p">(),</span> <span class="n">defaultdict</span><span class="p">(</span><span class="nb">str</span><span class="p">,</span> <span class="o">**</span><span class="n">scores</span><span class="p">))</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="s2">"</span><span class="se">\n</span><span class="s2">"</span> <span class="o">+</span> <span class="n">msg</span><span class="p">)</span>
+ <span class="n">reportf</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">msg</span><span class="p">)</span>
+
+<div class="viewcode-block" id="ProteinMap.classification_metrics"><a class="viewcode-back" href="../../ariaec.html#ariaec.protmap.ProteinMap.classification_metrics">[docs]</a> <span class="nd">@staticmethod</span>
+ <span class="k">def</span> <span class="nf">classification_metrics</span><span class="p">(</span><span class="n">y_true</span><span class="p">,</span> <span class="n">y_pred</span><span class="p">,</span> <span class="n">y_scores</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Compute classification metrics</span>
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> y_true : numpy array of true values</span>
+<span class="sd"> </span>
+<span class="sd"> y_pred : numpy array of predicted values</span>
+<span class="sd"> </span>
+<span class="sd"> y_scores : numpy array of prediction scores</span>
+<span class="sd"> (Default value = None)</span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+<span class="sd"> </span>
+<span class="sd"> """</span>
+ <span class="n">metrics</span> <span class="o">=</span> <span class="p">{}</span>
+
+ <span class="k">if</span> <span class="mi">1</span> <span class="ow">in</span> <span class="n">y_pred</span> <span class="ow">and</span> <span class="mi">1</span> <span class="ow">in</span> <span class="n">y_true</span><span class="p">:</span>
+ <span class="n">metrics</span><span class="o">.</span><span class="n">update</span><span class="p">({</span>
+ <span class="s1">'accuracy'</span><span class="p">:</span> <span class="n">skm</span><span class="o">.</span><span class="n">accuracy_score</span><span class="p">(</span><span class="n">y_true</span><span class="p">,</span> <span class="n">y_pred</span><span class="p">),</span>
+ <span class="s1">'precision'</span><span class="p">:</span> <span class="n">skm</span><span class="o">.</span><span class="n">precision_score</span><span class="p">(</span><span class="n">y_true</span><span class="p">,</span> <span class="n">y_pred</span><span class="p">),</span>
+ <span class="s1">'recall'</span><span class="p">:</span> <span class="n">skm</span><span class="o">.</span><span class="n">recall_score</span><span class="p">(</span><span class="n">y_true</span><span class="p">,</span> <span class="n">y_pred</span><span class="p">),</span>
+ <span class="s1">'mcc'</span><span class="p">:</span> <span class="n">skm</span><span class="o">.</span><span class="n">matthews_corrcoef</span><span class="p">(</span><span class="n">y_true</span><span class="p">,</span> <span class="n">y_pred</span><span class="p">),</span>
+ <span class="s1">'f1s'</span><span class="p">:</span> <span class="n">skm</span><span class="o">.</span><span class="n">f1_score</span><span class="p">(</span><span class="n">y_true</span><span class="p">,</span> <span class="n">y_pred</span><span class="p">),</span>
+ <span class="s1">'f2s'</span><span class="p">:</span> <span class="n">skm</span><span class="o">.</span><span class="n">fbeta_score</span><span class="p">(</span><span class="n">y_true</span><span class="p">,</span> <span class="n">y_pred</span><span class="p">,</span> <span class="mi">2</span><span class="p">),</span>
+ <span class="s1">'f05s'</span><span class="p">:</span> <span class="n">skm</span><span class="o">.</span><span class="n">fbeta_score</span><span class="p">(</span><span class="n">y_true</span><span class="p">,</span> <span class="n">y_pred</span><span class="p">,</span> <span class="mf">0.5</span><span class="p">),</span>
+ <span class="s1">'hamm'</span><span class="p">:</span> <span class="n">skm</span><span class="o">.</span><span class="n">hamming_loss</span><span class="p">(</span><span class="n">y_true</span><span class="p">,</span> <span class="n">y_pred</span><span class="p">),</span>
+ <span class="s1">'hin'</span><span class="p">:</span> <span class="n">skm</span><span class="o">.</span><span class="n">hinge_loss</span><span class="p">(</span><span class="n">y_true</span><span class="p">,</span> <span class="n">y_pred</span><span class="p">)</span>
+ <span class="p">})</span>
+
+ <span class="k">if</span> <span class="n">y_scores</span><span class="p">:</span>
+ <span class="c1"># ROC plot</span>
+ <span class="c1"># Replace nan values in y_scores</span>
+ <span class="n">y_scores</span><span class="p">[</span><span class="n">np</span><span class="o">.</span><span class="n">isnan</span><span class="p">(</span><span class="n">y_scores</span><span class="p">)]</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">floor</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">nanmin</span><span class="p">(</span><span class="n">y_scores</span><span class="p">))</span>
+ <span class="n">metrics</span><span class="o">.</span><span class="n">update</span><span class="p">({</span>
+ <span class="s1">'roc_auc'</span><span class="p">:</span> <span class="n">skm</span><span class="o">.</span><span class="n">roc_auc_score</span><span class="p">(</span><span class="n">y_true</span><span class="p">,</span> <span class="n">y_scores</span><span class="p">),</span>
+ <span class="s1">'aver_prec'</span><span class="p">:</span> <span class="n">skm</span><span class="o">.</span><span class="n">average_precision_score</span><span class="p">(</span><span class="n">y_true</span><span class="p">,</span> <span class="n">y_scores</span><span class="p">)</span>
+ <span class="p">})</span>
+ <span class="n">metrics</span><span class="p">[</span><span class="s1">'allfpr'</span><span class="p">],</span> <span class="n">metrics</span><span class="p">[</span><span class="s1">'alltpr'</span><span class="p">],</span> <span class="n">metrics</span><span class="p">[</span><span class="s1">'rocthres'</span><span class="p">]</span> <span class="o">=</span> \
+ <span class="n">skm</span><span class="o">.</span><span class="n">roc_curve</span><span class="p">(</span><span class="n">y_true</span><span class="p">,</span> <span class="n">y_scores</span><span class="p">,</span> <span class="n">pos_label</span><span class="o">=</span><span class="mi">1</span><span class="p">)</span>
+ <span class="n">metrics</span><span class="p">[</span><span class="s1">'allprec'</span><span class="p">],</span> <span class="n">metrics</span><span class="p">[</span><span class="s1">'allrec'</span><span class="p">],</span> <span class="n">metrics</span><span class="p">[</span><span class="s1">'prthres'</span><span class="p">]</span> <span class="o">=</span> \
+ <span class="n">skm</span><span class="o">.</span><span class="n">precision_recall_curve</span><span class="p">(</span><span class="n">y_true</span><span class="p">,</span> <span class="n">y_scores</span><span class="p">)</span>
+
+ <span class="k">return</span> <span class="n">metrics</span></div>
+
+ <span class="nd">@staticmethod</span>
+ <span class="k">def</span> <span class="nf">_metrics_plot</span><span class="p">(</span><span class="n">metrics</span><span class="p">,</span> <span class="n">mapnames</span><span class="o">=</span><span class="p">(</span><span class="s1">''</span><span class="p">,</span> <span class="s1">''</span><span class="p">),</span> <span class="n">plotdir</span><span class="o">=</span><span class="s2">""</span><span class="p">,</span> <span class="n">outprefix</span><span class="o">=</span><span class="s2">""</span><span class="p">,</span>
+ <span class="n">plot_ext</span><span class="o">=</span><span class="s2">"pdf"</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> </span>
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> metrics :</span>
+<span class="sd"> </span>
+<span class="sd"> mapnames :</span>
+<span class="sd"> (Default value = ('')</span>
+<span class="sd"> '' :</span>
+<span class="sd"> </span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+<span class="sd"> </span>
+<span class="sd"> """</span>
+ <span class="n">outprefix</span> <span class="o">=</span> <span class="n">outprefix</span> <span class="k">if</span> <span class="n">outprefix</span> <span class="k">else</span> <span class="s2">"maplot"</span>
+ <span class="n">csv_roc</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">plotdir</span><span class="p">,</span> <span class="s2">"</span><span class="si">%s</span><span class="s2">.roc.csv"</span> <span class="o">%</span> <span class="n">outprefix</span><span class="p">)</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s2">"Generate roc file (</span><span class="si">%s</span><span class="s2">)"</span><span class="p">,</span> <span class="n">csv_roc</span><span class="p">)</span>
+ <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">csv_roc</span><span class="p">,</span> <span class="s2">"w"</span><span class="p">)</span> <span class="k">as</span> <span class="n">f</span><span class="p">:</span>
+ <span class="n">f</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">"TPR,FPR,Treshold</span><span class="se">\n</span><span class="s2">"</span><span class="p">)</span>
+ <span class="n">writer</span> <span class="o">=</span> <span class="n">csv</span><span class="o">.</span><span class="n">writer</span><span class="p">(</span><span class="n">f</span><span class="p">)</span>
+ <span class="n">writer</span><span class="o">.</span><span class="n">writerows</span><span class="p">(</span><span class="nb">zip</span><span class="p">(</span><span class="n">metrics</span><span class="p">[</span><span class="s1">'alltpr'</span><span class="p">],</span> <span class="n">metrics</span><span class="p">[</span><span class="s1">'allfpr'</span><span class="p">],</span>
+ <span class="n">metrics</span><span class="p">[</span><span class="s1">'rocthres'</span><span class="p">]))</span>
+
+ <span class="n">plotpath</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">plotdir</span><span class="p">,</span> <span class="s2">"</span><span class="si">%s</span><span class="s2">.roc.</span><span class="si">%s</span><span class="s2">"</span> <span class="o">%</span> <span class="p">(</span><span class="n">outprefix</span><span class="p">,</span>
+ <span class="n">plot_ext</span><span class="p">))</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s2">"Generate roc plot (</span><span class="si">%s</span><span class="s2">)"</span><span class="p">,</span> <span class="n">plotpath</span><span class="p">)</span>
+ <span class="n">plt</span><span class="o">.</span><span class="n">figure</span><span class="p">()</span>
+ <span class="n">plt</span><span class="o">.</span><span class="n">plot</span><span class="p">(</span><span class="n">metrics</span><span class="p">[</span><span class="s1">'allfpr'</span><span class="p">],</span> <span class="n">metrics</span><span class="p">[</span><span class="s1">'alltpr'</span><span class="p">],</span>
+ <span class="n">label</span><span class="o">=</span><span class="s1">'ROC curve (area = </span><span class="si">%0.2f</span><span class="s1">)'</span> <span class="o">%</span> <span class="n">metrics</span><span class="p">[</span><span class="s1">'roc_auc'</span><span class="p">])</span>
+ <span class="n">plt</span><span class="o">.</span><span class="n">plot</span><span class="p">([</span><span class="mi">0</span><span class="p">,</span> <span class="mi">1</span><span class="p">],</span> <span class="p">[</span><span class="mi">0</span><span class="p">,</span> <span class="mi">1</span><span class="p">],</span> <span class="s1">'k--'</span><span class="p">)</span>
+ <span class="n">plt</span><span class="o">.</span><span class="n">xlim</span><span class="p">([</span><span class="mf">0.0</span><span class="p">,</span> <span class="mf">1.0</span><span class="p">])</span>
+ <span class="n">plt</span><span class="o">.</span><span class="n">ylim</span><span class="p">([</span><span class="mf">0.0</span><span class="p">,</span> <span class="mf">1.0</span><span class="p">])</span>
+ <span class="n">plt</span><span class="o">.</span><span class="n">xlabel</span><span class="p">(</span><span class="s1">'False Positive Rate'</span><span class="p">)</span>
+ <span class="n">plt</span><span class="o">.</span><span class="n">ylabel</span><span class="p">(</span><span class="s1">'True Positive Rate'</span><span class="p">)</span>
+ <span class="n">plt</span><span class="o">.</span><span class="n">title</span><span class="p">(</span><span class="s1">'Receiver operating characteristic </span><span class="si">%s</span><span class="s1"> vs. </span><span class="si">%s</span><span class="s1">'</span> <span class="o">%</span> <span class="p">(</span>
+ <span class="n">mapnames</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">mapnames</span><span class="p">[</span><span class="mi">1</span><span class="p">]))</span>
+ <span class="n">plt</span><span class="o">.</span><span class="n">legend</span><span class="p">(</span><span class="n">loc</span><span class="o">=</span><span class="s2">"lower right"</span><span class="p">)</span>
+ <span class="n">plt</span><span class="o">.</span><span class="n">savefig</span><span class="p">(</span><span class="n">plotpath</span><span class="p">)</span>
+
+ <span class="n">csv_precall</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">plotdir</span><span class="p">,</span> <span class="s2">"</span><span class="si">%s</span><span class="s2">.roc.csv"</span> <span class="o">%</span> <span class="n">outprefix</span><span class="p">)</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s2">"Generate precall file (</span><span class="si">%s</span><span class="s2">)"</span><span class="p">,</span> <span class="n">csv_precall</span><span class="p">)</span>
+ <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">csv_precall</span><span class="p">,</span> <span class="s2">"w"</span><span class="p">)</span> <span class="k">as</span> <span class="n">f</span><span class="p">:</span>
+ <span class="n">f</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">"Precision,Recall,Treshold</span><span class="se">\n</span><span class="s2">"</span><span class="p">)</span>
+ <span class="n">writer</span> <span class="o">=</span> <span class="n">csv</span><span class="o">.</span><span class="n">writer</span><span class="p">(</span><span class="n">f</span><span class="p">)</span>
+ <span class="n">writer</span><span class="o">.</span><span class="n">writerows</span><span class="p">(</span><span class="nb">zip</span><span class="p">(</span><span class="n">metrics</span><span class="p">[</span><span class="s1">'allprec'</span><span class="p">],</span> <span class="n">metrics</span><span class="p">[</span><span class="s1">'allrec'</span><span class="p">],</span>
+ <span class="n">metrics</span><span class="p">[</span><span class="s1">'prthres'</span><span class="p">]))</span>
+
+ <span class="n">plotpath</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">plotdir</span><span class="p">,</span> <span class="s2">"</span><span class="si">%s</span><span class="s2">.precall.</span><span class="si">%s</span><span class="s2">"</span> <span class="o">%</span> <span class="p">(</span><span class="n">outprefix</span><span class="p">,</span>
+ <span class="n">plot_ext</span><span class="p">))</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s2">"Generate precall plot (</span><span class="si">%s</span><span class="s2">)"</span><span class="p">,</span> <span class="n">plotpath</span><span class="p">)</span>
+ <span class="c1"># Precision recall curve</span>
+ <span class="n">plt</span><span class="o">.</span><span class="n">clf</span><span class="p">()</span>
+ <span class="n">plt</span><span class="o">.</span><span class="n">plot</span><span class="p">(</span><span class="n">metrics</span><span class="p">[</span><span class="s1">'allrec'</span><span class="p">],</span> <span class="n">metrics</span><span class="p">[</span><span class="s1">'allprec'</span><span class="p">],</span>
+ <span class="n">label</span><span class="o">=</span><span class="s1">'Precision-Recall curve'</span><span class="p">)</span>
+ <span class="n">plt</span><span class="o">.</span><span class="n">xlabel</span><span class="p">(</span><span class="s1">'Recall'</span><span class="p">)</span>
+ <span class="n">plt</span><span class="o">.</span><span class="n">ylabel</span><span class="p">(</span><span class="s1">'Precision'</span><span class="p">)</span>
+ <span class="n">plt</span><span class="o">.</span><span class="n">ylim</span><span class="p">([</span><span class="mf">0.0</span><span class="p">,</span> <span class="mf">1.0</span><span class="p">])</span>
+ <span class="n">plt</span><span class="o">.</span><span class="n">xlim</span><span class="p">([</span><span class="mf">0.0</span><span class="p">,</span> <span class="mf">1.0</span><span class="p">])</span>
+ <span class="n">plt</span><span class="o">.</span><span class="n">title</span><span class="p">(</span><span class="s1">'Precision-Recall </span><span class="si">{1}</span><span class="s1"> vs. </span><span class="si">{2}</span><span class="s1">: AUC=</span><span class="si">{0:0.2f}</span><span class="s1">'</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
+ <span class="n">metrics</span><span class="p">[</span><span class="s1">'aver_prec'</span><span class="p">],</span> <span class="n">mapnames</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">mapnames</span><span class="p">[</span><span class="mi">1</span><span class="p">]))</span>
+ <span class="n">plt</span><span class="o">.</span><span class="n">legend</span><span class="p">(</span><span class="n">loc</span><span class="o">=</span><span class="s2">"lower left"</span><span class="p">)</span>
+ <span class="n">plt</span><span class="o">.</span><span class="n">savefig</span><span class="p">(</span><span class="n">plotpath</span><span class="p">)</span>
+
+<div class="viewcode-block" id="ProteinMap.report"><a class="viewcode-back" href="../../ariaec.html#ariaec.protmap.ProteinMap.report">[docs]</a> <span class="k">def</span> <span class="nf">report</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">cmpmap</span><span class="p">,</span> <span class="n">scoremap</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">outprefix</span><span class="o">=</span><span class="s2">""</span><span class="p">,</span> <span class="n">outdir</span><span class="o">=</span><span class="s2">""</span><span class="p">,</span> <span class="n">plotdir</span><span class="o">=</span><span class="s2">""</span><span class="p">,</span>
+ <span class="c1"># plot_ext="pdf", plotag=True, n_factors=(0.5, 1.0, 1.5)):</span>
+ <span class="n">plot_ext</span><span class="o">=</span><span class="s2">"pdf"</span><span class="p">,</span> <span class="n">plotag</span><span class="o">=</span><span class="kc">True</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Generate contact map report file</span>
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> cmpmap :</span>
+<span class="sd"> </span>
+<span class="sd"> scoremap :</span>
+<span class="sd"> (Default value = None)</span>
+<span class="sd"> outprefix :</span>
+<span class="sd"> (Default value = "")</span>
+<span class="sd"> outdir :</span>
+<span class="sd"> (Default value = "")</span>
+<span class="sd"> plotdir :</span>
+<span class="sd"> (Default value = "")</span>
+<span class="sd"> plot_ext :</span>
+<span class="sd"> (Default value = "pdf")</span>
+<span class="sd"> plotag :</span>
+<span class="sd"> (Default value = True)</span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+<span class="sd"> """</span>
+ <span class="n">filename</span> <span class="o">=</span> <span class="s2">"."</span><span class="o">.</span><span class="n">join</span><span class="p">((</span><span class="n">outprefix</span><span class="p">,</span> <span class="s2">"mapreport"</span><span class="p">))</span> <span class="k">if</span> <span class="n">outprefix</span> <span class="k">else</span> \
+ <span class="s2">"mapreport"</span>
+ <span class="n">reportpath</span> <span class="o">=</span> <span class="s2">"</span><span class="si">%s</span><span class="s2">/</span><span class="si">%s</span><span class="s2">"</span> <span class="o">%</span> <span class="p">(</span><span class="n">outdir</span><span class="p">,</span> <span class="n">filename</span><span class="p">)</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s2">"Generate map report file (</span><span class="si">%s</span><span class="s2">)"</span><span class="p">,</span> <span class="n">reportpath</span><span class="p">)</span>
+
+ <span class="c1"># TODO: evaluate map statistics for several treshold (use submap var)</span>
+ <span class="c1"># nb_c = int(len(self.sequence) * float(n_factors[0]))</span>
+ <span class="c1"># submap = cmpmap.copy()</span>
+ <span class="c1"># print(np.array_equal(cmpmap.values.astype(int).flat,</span>
+ <span class="c1"># submap.topmap(scoremap, nb_c).values.astype(int).flat))</span>
+
+ <span class="n">y_true</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">values</span><span class="o">.</span><span class="n">astype</span><span class="p">(</span><span class="nb">int</span><span class="p">)</span><span class="o">.</span><span class="n">flat</span><span class="p">)</span>
+ <span class="n">y_pred</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="n">cmpmap</span><span class="o">.</span><span class="n">values</span><span class="o">.</span><span class="n">astype</span><span class="p">(</span><span class="nb">int</span><span class="p">)</span><span class="o">.</span><span class="n">flat</span><span class="p">)</span>
+ <span class="n">y_scores</span> <span class="o">=</span> <span class="n">scoremap</span><span class="o">.</span><span class="n">values</span><span class="o">.</span><span class="n">astype</span><span class="p">(</span><span class="nb">float</span><span class="p">)</span><span class="o">.</span><span class="n">flat</span> <span class="k">if</span> <span class="n">scoremap</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span> <span class="k">else</span> <span class="kc">None</span>
+
+ <span class="c1"># Compute classification metrics for the entire map</span>
+ <span class="n">metrics</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">classification_metrics</span><span class="p">(</span><span class="n">y_true</span><span class="p">,</span> <span class="n">y_pred</span><span class="p">,</span> <span class="n">y_scores</span><span class="p">)</span>
+
+ <span class="bp">self</span><span class="o">.</span><span class="n">_write_report</span><span class="p">(</span>
+ <span class="n">reportpath</span><span class="p">,</span> <span class="n">map1name</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">desc</span><span class="p">,</span> <span class="n">map2name</span><span class="o">=</span><span class="n">cmpmap</span><span class="o">.</span><span class="n">desc</span><span class="p">,</span>
+ <span class="n">map1path</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">path</span><span class="p">,</span> <span class="n">map2path</span><span class="o">=</span><span class="n">cmpmap</span><span class="o">.</span><span class="n">path</span><span class="p">,</span>
+ <span class="n">seq</span><span class="o">=</span><span class="s2">"</span><span class="se">\n</span><span class="s2">## "</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">textwrap</span><span class="o">.</span><span class="n">wrap</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">sequence</span><span class="p">,</span> <span class="n">width</span><span class="o">=</span><span class="mi">77</span><span class="p">)),</span>
+ <span class="n">protlen</span><span class="o">=</span><span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">sequence</span><span class="p">),</span>
+ <span class="n">date</span><span class="o">=</span><span class="n">datetime</span><span class="o">.</span><span class="n">date</span><span class="o">.</span><span class="n">today</span><span class="p">()</span><span class="o">.</span><span class="n">strftime</span><span class="p">(</span><span class="s2">"%A </span><span class="si">%d</span><span class="s2">. %B %Y"</span><span class="p">),</span>
+ <span class="n">outdir</span><span class="o">=</span><span class="n">outdir</span><span class="p">,</span> <span class="o">**</span><span class="n">metrics</span><span class="p">)</span>
+
+ <span class="k">if</span> <span class="n">plotag</span> <span class="ow">and</span> <span class="n">scoremap</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_metrics_plot</span><span class="p">(</span><span class="n">metrics</span><span class="p">,</span> <span class="n">mapnames</span><span class="o">=</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">desc</span><span class="p">,</span> <span class="n">cmpmap</span><span class="o">.</span><span class="n">desc</span><span class="p">),</span>
+ <span class="n">outprefix</span><span class="o">=</span><span class="n">outprefix</span><span class="p">,</span> <span class="n">plot_ext</span><span class="o">=</span><span class="n">plot_ext</span><span class="p">,</span>
+ <span class="n">plotdir</span><span class="o">=</span><span class="n">plotdir</span><span class="p">)</span></div>
+
+<div class="viewcode-block" id="ProteinMap.compare_contactmap"><a class="viewcode-back" href="../../ariaec.html#ariaec.protmap.ProteinMap.compare_contactmap">[docs]</a> <span class="k">def</span> <span class="nf">compare_contactmap</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">cmpmap</span><span class="p">,</span> <span class="n">contactlist</span><span class="p">,</span> <span class="n">outprefix</span><span class="p">,</span>
+ <span class="n">outdir</span><span class="o">=</span><span class="s2">""</span><span class="p">,</span> <span class="n">distmap</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">human_idx</span><span class="o">=</span><span class="kc">True</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Compare 2 contact map and plot differences</span>
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> cmpmap :</span>
+<span class="sd"> param contactlist:</span>
+<span class="sd"> outprefix :</span>
+<span class="sd"> param outdir:</span>
+<span class="sd"> distmap :</span>
+<span class="sd"> param human_idx: (Default value = None)</span>
+<span class="sd"> contactlist :</span>
+<span class="sd"> </span>
+<span class="sd"> outdir :</span>
+<span class="sd"> (Default value = "")</span>
+<span class="sd"> human_idx :</span>
+<span class="sd"> (Default value = True)</span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+<span class="sd"> </span>
+<span class="sd"> """</span>
+ <span class="c1"># CSV file giving TP/FP contacts</span>
+ <span class="n">outpath</span> <span class="o">=</span> <span class="s2">"</span><span class="si">%s</span><span class="s2">/</span><span class="si">%s</span><span class="s2">.contactcmp.csv"</span> <span class="o">%</span> <span class="p">(</span><span class="n">outdir</span><span class="p">,</span>
+ <span class="n">outprefix</span> <span class="k">if</span> <span class="n">outprefix</span> <span class="k">else</span> <span class="s2">"maplot"</span><span class="p">)</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s2">"Generate stat file (</span><span class="si">%s</span><span class="s2">)"</span><span class="p">,</span> <span class="n">outpath</span><span class="p">)</span>
+ <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">outpath</span><span class="p">,</span> <span class="s1">'w'</span><span class="p">)</span> <span class="k">as</span> <span class="n">outfile</span><span class="p">:</span>
+ <span class="n">offset</span> <span class="o">=</span> <span class="mi">1</span> <span class="k">if</span> <span class="n">human_idx</span> <span class="k">else</span> <span class="mi">0</span>
+ <span class="n">extra_header</span> <span class="o">=</span> <span class="s2">""</span> <span class="k">if</span> <span class="n">distmap</span> <span class="ow">is</span> <span class="kc">None</span> <span class="k">else</span> <span class="s2">",dmin"</span>
+ <span class="n">outfile</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">"#resid1,resid2,res1,res2,TP/FP</span><span class="si">%s</span><span class="se">\n</span><span class="s2">"</span> <span class="o">%</span> <span class="n">extra_header</span><span class="p">)</span>
+ <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">contactlist</span><span class="p">:</span>
+ <span class="k">if</span> <span class="n">extra_header</span><span class="p">:</span>
+ <span class="n">dmin</span> <span class="o">=</span> <span class="s2">","</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">distmap</span><span class="o">.</span><span class="n">iat</span><span class="p">[(</span><span class="nb">int</span><span class="p">(</span><span class="n">x</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span> <span class="o">-</span> <span class="n">offset</span><span class="p">,</span> <span class="nb">int</span><span class="p">(</span><span class="n">x</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span> <span class="o">-</span>
+ <span class="n">offset</span><span class="p">)])</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="n">dmin</span> <span class="o">=</span> <span class="s2">""</span>
+ <span class="n">contact</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">iat</span><span class="p">[(</span><span class="nb">int</span><span class="p">(</span><span class="n">x</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span> <span class="o">-</span> <span class="n">offset</span><span class="p">,</span> <span class="nb">int</span><span class="p">(</span><span class="n">x</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span> <span class="o">-</span> <span class="n">offset</span><span class="p">)]</span>
+ <span class="n">cmpcontact</span> <span class="o">=</span> <span class="n">cmpmap</span><span class="o">.</span><span class="n">iat</span><span class="p">[(</span><span class="nb">int</span><span class="p">(</span><span class="n">x</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span> <span class="o">-</span> <span class="n">offset</span><span class="p">,</span> <span class="nb">int</span><span class="p">(</span><span class="n">x</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span> <span class="o">-</span> <span class="n">offset</span><span class="p">)]</span>
+ <span class="k">if</span> <span class="n">contact</span> <span class="ow">and</span> <span class="n">cmpcontact</span><span class="p">:</span>
+ <span class="n">eq</span> <span class="o">=</span> <span class="s2">"TP"</span>
+ <span class="k">elif</span> <span class="n">contact</span> <span class="ow">and</span> <span class="ow">not</span> <span class="n">cmpcontact</span><span class="p">:</span>
+ <span class="n">eq</span> <span class="o">=</span> <span class="s2">"FP"</span>
+ <span class="k">elif</span> <span class="ow">not</span> <span class="n">contact</span> <span class="ow">and</span> <span class="n">cmpcontact</span><span class="p">:</span>
+ <span class="n">eq</span> <span class="o">=</span> <span class="s2">"FN"</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="n">eq</span> <span class="o">=</span> <span class="s2">"TN"</span>
+ <span class="n">msg</span> <span class="o">=</span> <span class="s2">"</span><span class="si">%s</span><span class="s2">,</span><span class="si">%s</span><span class="s2">,</span><span class="si">%s</span><span class="s2">,</span><span class="si">%s</span><span class="s2">,</span><span class="si">%s%s</span><span class="se">\n</span><span class="s2">"</span> <span class="o">%</span> <span class="p">(</span><span class="n">x</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">x</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">sequence</span><span class="p">[</span><span class="nb">int</span><span class="p">(</span><span class="n">x</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span> <span class="o">-</span> <span class="n">offset</span><span class="p">],</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">sequence</span><span class="p">[</span><span class="nb">int</span><span class="p">(</span><span class="n">x</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span> <span class="o">-</span> <span class="n">offset</span><span class="p">],</span>
+ <span class="n">eq</span><span class="p">,</span>
+ <span class="n">dmin</span><span class="p">)</span>
+ <span class="n">outfile</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">msg</span><span class="p">)</span></div>
+
+<div class="viewcode-block" id="ProteinMap.write_contacts"><a class="viewcode-back" href="../../ariaec.html#ariaec.protmap.ProteinMap.write_contacts">[docs]</a> <span class="k">def</span> <span class="nf">write_contacts</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">filename</span><span class="p">,</span> <span class="n">outdir</span><span class="o">=</span><span class="s2">""</span><span class="p">,</span> <span class="n">prefix</span><span class="o">=</span><span class="s2">""</span><span class="p">,</span> <span class="n">human_idx</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span>
+ <span class="n">scoremap</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> </span>
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> prefix</span>
+<span class="sd"> filename :</span>
+<span class="sd"> param outdir:</span>
+<span class="sd"> human_idx :</span>
+<span class="sd"> param scoremap: (Default value = True)</span>
+<span class="sd"> outdir :</span>
+<span class="sd"> (Default value = "")</span>
+<span class="sd"> scoremap :</span>
+<span class="sd"> (Default value = None)</span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+<span class="sd"> </span>
+<span class="sd"> """</span>
+ <span class="n">prefix</span> <span class="o">=</span> <span class="n">prefix</span> <span class="o">+</span> <span class="s2">"_"</span> <span class="k">if</span> <span class="n">prefix</span> <span class="k">else</span> <span class="n">prefix</span>
+ <span class="n">filepath</span> <span class="o">=</span> <span class="s2">"</span><span class="si">%s</span><span class="s2">/</span><span class="si">%s%s</span><span class="s2">.contact.txt"</span> <span class="o">%</span> <span class="p">(</span><span class="n">outdir</span><span class="p">,</span> <span class="n">prefix</span><span class="p">,</span> <span class="n">filename</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s2">"."</span><span class="p">,</span> <span class="s2">"_"</span><span class="p">))</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s2">"Generate contact file (</span><span class="si">%s</span><span class="s2">)"</span><span class="p">,</span> <span class="n">filepath</span><span class="p">)</span>
+ <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">filepath</span><span class="p">,</span> <span class="s1">'w'</span><span class="p">)</span> <span class="k">as</span> <span class="n">outfile</span><span class="p">:</span>
+ <span class="n">offset</span> <span class="o">=</span> <span class="mi">1</span> <span class="k">if</span> <span class="n">human_idx</span> <span class="k">else</span> <span class="mi">0</span>
+ <span class="c1"># contacts = [sorted(contact) for contact in self.contactset()]</span>
+ <span class="c1"># for contact in sorted(contacts):</span>
+ <span class="k">for</span> <span class="n">contact</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">contactset</span><span class="p">():</span>
+ <span class="n">contact</span> <span class="o">=</span> <span class="nb">sorted</span><span class="p">([</span><span class="n">contact</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">+</span> <span class="n">offset</span><span class="p">,</span> <span class="n">contact</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="o">+</span> <span class="n">offset</span><span class="p">])</span>
+ <span class="k">if</span> <span class="n">scoremap</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+ <span class="n">score</span> <span class="o">=</span> <span class="n">scoremap</span><span class="o">.</span><span class="n">iat</span><span class="p">[(</span><span class="nb">int</span><span class="p">(</span><span class="n">contact</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span> <span class="o">-</span> <span class="n">offset</span><span class="p">,</span>
+ <span class="nb">int</span><span class="p">(</span><span class="n">contact</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span> <span class="o">-</span> <span class="n">offset</span><span class="p">)]</span>
+ <span class="n">outfile</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">"</span><span class="si">%d</span><span class="s2"> </span><span class="si">%d</span><span class="s2"> </span><span class="si">%.4f</span><span class="se">\n</span><span class="s2">"</span> <span class="o">%</span>
+ <span class="p">(</span><span class="n">contact</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">contact</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="n">score</span><span class="p">))</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="n">outfile</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">"</span><span class="si">%d</span><span class="s2"> </span><span class="si">%d</span><span class="se">\n</span><span class="s2">"</span> <span class="o">%</span> <span class="p">(</span><span class="n">contact</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">contact</span><span class="p">[</span><span class="mi">1</span><span class="p">]))</span></div></div>
+
+
+<div class="viewcode-block" id="ResAtmMap"><a class="viewcode-back" href="../../ariaec.html#ariaec.protmap.ResAtmMap">[docs]</a><span class="k">class</span> <span class="nc">ResAtmMap</span><span class="p">(</span><span class="n">ProteinMap</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Protein distance/contact matrix for all atom pairs. If no sequence given,</span>
+<span class="sd"> protein distance/contact matrix for all amino acids</span>
+<span class="sd"> Ex:</span>
+<span class="sd"> residue PHE1 \</span>
+<span class="sd"> atom CD1 CD2 CB CA CG CZ</span>
+<span class="sd"> residue atom</span>
+<span class="sd"> PHE1 CD1 0.000000 2.394145 2.455440 3.269219 1.391024 2.421148</span>
+<span class="sd"> CD2 2.394145 0.000000 2.509243 3.407996 1.379875 2.401098</span>
+<span class="sd"> CB 2.455440 2.509243 0.000000 1.507025 1.478053 4.267602</span>
+<span class="sd"> CA 3.269219 3.407996 1.507025 0.000000 2.505414 5.085997</span>
+<span class="sd"> CG 1.391024 1.379875 1.478053 2.505414 0.000000 2.790403</span>
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+<span class="sd"> </span>
+<span class="sd"> """</span>
+
+ <span class="c1"># def _constructor_expanddim(self):</span>
+ <span class="c1"># super(ResAtmMap, self)._constructor_expanddim()</span>
+
+ <span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">sequence</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+ <span class="c1"># Sequence: 1L string or MultiIndex object</span>
+ <span class="c1"># Dataframe is in 3L code</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="n">sequence</span><span class="p">:</span>
+ <span class="n">sequence</span> <span class="o">=</span> <span class="n">ConversionTable</span><span class="o">.</span><span class="n">ConversionTable</span><span class="p">()</span><span class="o">.</span><span class="n">table</span><span class="p">[</span><span class="s1">'AMINO_ACID'</span><span class="p">][</span>
+ <span class="s1">'iupac'</span><span class="p">]</span><span class="o">.</span><span class="n">keys</span><span class="p">()</span>
+ <span class="c1"># Super call will initialize index and columns with self.create_index()</span>
+ <span class="nb">super</span><span class="p">(</span><span class="n">ResAtmMap</span><span class="p">,</span> <span class="bp">self</span><span class="p">)</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="n">sequence</span><span class="o">=</span><span class="n">sequence</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_sequence</span> <span class="o">=</span> <span class="n">sequence</span>
+
+ <span class="nd">@property</span>
+ <span class="k">def</span> <span class="nf">sequence</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Amino Acid sequence string in humanidx</span>
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+<span class="sd"> </span>
+<span class="sd"> """</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">_sequence</span><span class="p">:</span>
+ <span class="c1"># If non empty string</span>
+ <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_sequence</span>
+ <span class="k">elif</span> <span class="bp">self</span><span class="o">.</span><span class="n">index</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_sequence</span> <span class="o">=</span> <span class="s2">""</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">AminoAcid</span><span class="o">.</span><span class="n">AminoAcid</span><span class="p">(</span><span class="n">_</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s2">"-"</span><span class="p">)[</span><span class="mi">1</span><span class="p">])[</span><span class="mi">0</span><span class="p">]</span>
+ <span class="k">for</span> <span class="n">_</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">index</span><span class="o">.</span><span class="n">levels</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="c1"># No information given</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_sequence</span> <span class="o">=</span> <span class="s2">""</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="nb">sorted</span><span class="p">(</span><span class="n">ConversionTable</span><span class="o">.</span><span class="n">ConversionTable</span><span class="p">()</span><span class="o">.</span><span class="n">table</span><span class="p">[</span>
+ <span class="s1">'AMINO_ACID'</span><span class="p">][</span><span class="s1">'iupac'</span><span class="p">]</span><span class="o">.</span><span class="n">keys</span><span class="p">()))</span>
+ <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_sequence</span>
+
+<div class="viewcode-block" id="ResAtmMap.create_index"><a class="viewcode-back" href="../../ariaec.html#ariaec.protmap.ResAtmMap.create_index">[docs]</a> <span class="k">def</span> <span class="nf">create_index</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">sequence</span><span class="p">,</span> <span class="n">seq_pos</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">seqidx</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">idxnames</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
+ <span class="n">colnames</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> </span>
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> sequence</span>
+<span class="sd"> seq_pos</span>
+<span class="sd"> seqidx: pandas.MultiIndex, optional</span>
+<span class="sd"> idxnames</span>
+<span class="sd"> colnames</span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+<span class="sd"> tuple of pandas.MultiIndex objects</span>
+<span class="sd"> """</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="s2">"Indexing ResAtm - ResAtm dataframe"</span><span class="p">)</span>
+ <span class="c1"># Atom table for residues (keys are in 3L code)</span>
+ <span class="n">seqidx</span> <span class="o">=</span> <span class="n">seqidx</span> <span class="k">if</span> <span class="n">seqidx</span> <span class="ow">and</span> <span class="nb">len</span><span class="p">(</span><span class="n">seqidx</span><span class="p">)</span> <span class="o">==</span> <span class="nb">len</span><span class="p">(</span><span class="n">sequence</span><span class="p">)</span> <span class="k">else</span> <span class="kc">None</span>
+ <span class="n">iupac_aa</span> <span class="o">=</span> <span class="n">ConversionTable</span><span class="o">.</span><span class="n">ConversionTable</span><span class="p">()</span><span class="o">.</span><span class="n">table</span><span class="p">[</span><span class="s1">'AMINO_ACID'</span><span class="p">][</span>
+ <span class="s1">'iupac'</span><span class="p">]</span>
+ <span class="c1"># Amino acid conversion table 1L -> 3L</span>
+ <span class="c1"># Making humanidx list for pandas dataframe</span>
+ <span class="n">seq</span> <span class="o">=</span> <span class="p">[</span><span class="n">AminoAcid</span><span class="o">.</span><span class="n">AminoAcid</span><span class="p">(</span><span class="n">aa</span><span class="p">)[</span><span class="mi">1</span><span class="p">]</span> <span class="k">for</span> <span class="n">aa</span> <span class="ow">in</span> <span class="n">sequence</span><span class="p">]</span>
+ <span class="c1"># Repeat each res for each heavy atm (humanidx value + 1 in order to</span>
+ <span class="c1"># start at 1 as in pdb file)</span>
+ <span class="k">if</span> <span class="nb">set</span><span class="p">(</span><span class="n">sequence</span><span class="p">)</span> <span class="o">==</span> <span class="n">sequence</span><span class="p">:</span>
+ <span class="c1"># General ResAtmMap for 20 aminoacid</span>
+ <span class="n">res_list</span> <span class="o">=</span> <span class="p">[</span><span class="s2">"</span><span class="si">%s</span><span class="s2">"</span> <span class="o">%</span> <span class="n">aa</span> <span class="k">for</span> <span class="n">aa</span> <span class="ow">in</span> <span class="n">seq</span> <span class="k">for</span> <span class="n">_</span> <span class="ow">in</span>
+ <span class="p">(</span><span class="nb">filter</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">heavy_reg</span><span class="o">.</span><span class="n">match</span><span class="p">,</span> <span class="n">iupac_aa</span><span class="p">[</span><span class="n">aa</span><span class="p">]</span><span class="o">.</span><span class="n">keys</span><span class="p">()))]</span>
+ <span class="k">elif</span> <span class="n">seqidx</span><span class="p">:</span>
+ <span class="c1"># If we already have an index related to the sequence</span>
+ <span class="n">res_list</span> <span class="o">=</span> <span class="p">[</span>
+ <span class="s2">"</span><span class="si">%03d</span><span class="s2">-</span><span class="si">%s</span><span class="s2">"</span> <span class="o">%</span> <span class="p">(</span><span class="n">seqidx</span><span class="p">[</span><span class="n">i</span><span class="p">],</span> <span class="n">aa</span><span class="p">)</span> <span class="k">for</span> <span class="n">i</span><span class="p">,</span> <span class="n">aa</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">seq</span><span class="p">)</span>
+ <span class="k">for</span> <span class="n">_</span> <span class="ow">in</span> <span class="nb">filter</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">heavy_reg</span><span class="o">.</span><span class="n">match</span><span class="p">,</span> <span class="n">iupac_aa</span><span class="p">[</span><span class="n">aa</span><span class="p">]</span><span class="o">.</span><span class="n">keys</span><span class="p">())]</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="c1"># If no index related to the sequence</span>
+ <span class="n">res_list</span> <span class="o">=</span> <span class="p">[</span>
+ <span class="s2">"</span><span class="si">%03d</span><span class="s2">-</span><span class="si">%s</span><span class="s2">"</span> <span class="o">%</span> <span class="p">(</span><span class="n">i</span> <span class="o">+</span> <span class="mi">1</span><span class="p">,</span> <span class="n">aa</span><span class="p">)</span> <span class="k">for</span> <span class="n">i</span><span class="p">,</span> <span class="n">aa</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">seq</span><span class="p">)</span>
+ <span class="k">for</span> <span class="n">_</span> <span class="ow">in</span> <span class="nb">filter</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">heavy_reg</span><span class="o">.</span><span class="n">match</span><span class="p">,</span> <span class="n">iupac_aa</span><span class="p">[</span><span class="n">aa</span><span class="p">]</span><span class="o">.</span><span class="n">keys</span><span class="p">())]</span>
+ <span class="c1"># TODO: Inutile de repeter a chaque fois le calcul des listes</span>
+ <span class="c1"># d'atomes lourd pour chaque residu -> Deplacer au niveau de l'init</span>
+ <span class="n">atm_list</span> <span class="o">=</span> <span class="p">[</span><span class="n">atm</span> <span class="k">for</span> <span class="n">aa</span> <span class="ow">in</span> <span class="n">seq</span> <span class="k">for</span> <span class="n">atm</span> <span class="ow">in</span> <span class="nb">filter</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">heavy_reg</span><span class="o">.</span><span class="n">match</span><span class="p">,</span>
+ <span class="n">iupac_aa</span><span class="p">[</span><span class="n">aa</span><span class="p">]</span><span class="o">.</span><span class="n">keys</span><span class="p">())]</span>
+ <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">atm_list</span><span class="p">)</span> <span class="o">!=</span> <span class="nb">len</span><span class="p">(</span><span class="n">res_list</span><span class="p">):</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">error</span><span class="p">(</span><span class="s2">"Index lists aren't the same size</span><span class="se">\n</span><span class="si">%s</span><span class="se">\n</span><span class="si">%s</span><span class="s2">"</span><span class="p">,</span>
+ <span class="n">res_list</span><span class="p">,</span> <span class="n">atm_list</span><span class="p">)</span>
+
+ <span class="n">idxnames</span> <span class="o">=</span> <span class="n">idxnames</span> <span class="k">if</span> <span class="n">idxnames</span> <span class="ow">and</span> <span class="nb">len</span><span class="p">(</span><span class="n">idxnames</span><span class="p">)</span> <span class="o">==</span> <span class="mi">2</span> <span class="k">else</span> <span class="p">[</span>
+ <span class="s2">"residuex"</span><span class="p">,</span> <span class="s2">"atomx"</span><span class="p">]</span>
+ <span class="n">colnames</span> <span class="o">=</span> <span class="n">colnames</span> <span class="k">if</span> <span class="n">colnames</span> <span class="ow">and</span> <span class="nb">len</span><span class="p">(</span><span class="n">colnames</span><span class="p">)</span> <span class="o">==</span> <span class="mi">2</span> <span class="k">else</span> <span class="p">[</span>
+ <span class="s2">"residuey"</span><span class="p">,</span> <span class="s2">"atomy"</span><span class="p">]</span>
+ <span class="n">index</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">MultiIndex</span><span class="o">.</span><span class="n">from_tuples</span><span class="p">(</span><span class="nb">list</span><span class="p">(</span><span class="nb">zip</span><span class="p">(</span><span class="o">*</span><span class="p">[</span><span class="n">res_list</span><span class="p">,</span> <span class="n">atm_list</span><span class="p">])),</span>
+ <span class="n">names</span><span class="o">=</span><span class="n">idxnames</span><span class="p">)</span>
+ <span class="n">columns</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">MultiIndex</span><span class="o">.</span><span class="n">from_tuples</span><span class="p">(</span><span class="nb">list</span><span class="p">(</span><span class="nb">zip</span><span class="p">(</span><span class="o">*</span><span class="p">[</span><span class="n">res_list</span><span class="p">,</span>
+ <span class="n">atm_list</span><span class="p">])),</span>
+ <span class="n">names</span><span class="o">=</span><span class="n">colnames</span><span class="p">)</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="s2">"Index:</span><span class="se">\n</span><span class="si">%s</span><span class="s2">"</span><span class="p">,</span> <span class="n">index</span><span class="p">)</span>
+ <span class="k">return</span> <span class="n">index</span><span class="p">,</span> <span class="n">columns</span></div>
+
+<div class="viewcode-block" id="ResAtmMap.create_heatmap"><a class="viewcode-back" href="../../ariaec.html#ariaec.protmap.ResAtmMap.create_heatmap">[docs]</a> <span class="k">def</span> <span class="nf">create_heatmap</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="sd">""":return:"""</span>
+ <span class="n">unidf</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">reduce</span><span class="p">()</span>
+ <span class="k">if</span> <span class="n">unidf</span><span class="o">.</span><span class="n">isnull</span><span class="p">()</span><span class="o">.</span><span class="n">values</span><span class="o">.</span><span class="n">sum</span><span class="p">()</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
+ <span class="c1"># If there's no nan values</span>
+ <span class="k">return</span> <span class="n">sns</span><span class="o">.</span><span class="n">heatmap</span><span class="p">(</span><span class="n">unidf</span><span class="p">)</span>
+ <span class="k">return</span> <span class="kc">None</span></div>
+
+<div class="viewcode-block" id="ResAtmMap.reduce"><a class="viewcode-back" href="../../ariaec.html#ariaec.protmap.ResAtmMap.reduce">[docs]</a> <span class="k">def</span> <span class="nf">reduce</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">groupby</span><span class="o">=</span><span class="s2">"min"</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> </span>
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> groupby :</span>
+<span class="sd"> return: (Default value = "min")</span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+<span class="sd"> </span>
+<span class="sd"> """</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">index</span><span class="o">.</span><span class="n">nlevels</span> <span class="o">==</span> <span class="mi">1</span> <span class="ow">or</span> <span class="ow">not</span> <span class="n">groupby</span><span class="p">:</span>
+ <span class="k">return</span> <span class="bp">self</span>
+ <span class="n">newmap</span> <span class="o">=</span> <span class="n">ResMap</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">sequence</span><span class="p">,</span> <span class="n">dtype</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">dtype</span><span class="p">,</span> <span class="n">desc</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">desc</span><span class="p">,</span>
+ <span class="n">sym</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">sym</span><span class="p">,</span> <span class="n">path</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">path</span><span class="p">)</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">dtype</span> <span class="o">==</span> <span class="nb">bool</span><span class="p">:</span>
+ <span class="n">newmap</span><span class="p">[:]</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">copy</span><span class="p">()</span><span class="o">.</span><span class="n">stack</span><span class="p">(</span><span class="n">dropna</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span><span class="o">.</span><span class="n">groupby</span><span class="p">(</span><span class="n">level</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span><span class="o">.</span><span class="n">any</span><span class="p">()</span>
+ <span class="k">elif</span> <span class="n">groupby</span> <span class="o">==</span> <span class="s2">"mean"</span><span class="p">:</span>
+ <span class="n">newmap</span><span class="p">[:]</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">copy</span><span class="p">()</span><span class="o">.</span><span class="n">stack</span><span class="p">(</span><span class="n">dropna</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span><span class="o">.</span><span class="n">groupby</span><span class="p">(</span><span class="n">level</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span><span class="o">.</span><span class="n">mean</span><span class="p">()</span>
+ <span class="k">elif</span> <span class="n">groupby</span> <span class="o">==</span> <span class="s2">"min"</span><span class="p">:</span>
+ <span class="n">newmap</span><span class="p">[:]</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">copy</span><span class="p">()</span><span class="o">.</span><span class="n">stack</span><span class="p">(</span><span class="n">dropna</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span><span class="o">.</span><span class="n">groupby</span><span class="p">(</span><span class="n">level</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span><span class="o">.</span><span class="n">min</span><span class="p">()</span>
+ <span class="k">return</span> <span class="n">newmap</span></div>
+
+<div class="viewcode-block" id="ResAtmMap.contact_map"><a class="viewcode-back" href="../../ariaec.html#ariaec.protmap.ResAtmMap.contact_map">[docs]</a> <span class="k">def</span> <span class="nf">contact_map</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">contactdef</span><span class="p">,</span> <span class="n">scsc_min</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">def_cut</span><span class="o">=</span><span class="mf">5.0</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Contact map generator from all atoms distance map. There's a contact</span>
+<span class="sd"> with 2 residues iff dist between 2 atoms are below the given treshold</span>
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> def_cut :</span>
+<span class="sd"> (Default value = 5.0)</span>
+<span class="sd"> contactdef :</span>
+<span class="sd"> for all atom pair </span>
+<span class="sd"> scsc_min :</span>
+<span class="sd"> (Default value = None)</span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+<span class="sd"> </span>
+<span class="sd"> """</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">dtype</span> <span class="o">==</span> <span class="nb">bool</span><span class="p">:</span>
+ <span class="c1"># If self is already a contact map</span>
+ <span class="k">return</span> <span class="kc">None</span>
+ <span class="c1"># TODO: issue with sc_sc treshold !!!!!</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s2">"Generate contact map using contact definition </span><span class="si">%s</span><span class="s2">"</span><span class="p">,</span>
+ <span class="n">contactdef</span><span class="p">)</span>
+ <span class="c1"># Initialize contact map to a boolean matrix filled with False as values</span>
+ <span class="n">contact_map</span> <span class="o">=</span> <span class="n">ResAtmMap</span><span class="p">(</span><span class="n">sequence</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">sequence</span><span class="p">,</span> <span class="n">mtype</span><span class="o">=</span><span class="s2">"contact"</span><span class="p">,</span>
+ <span class="n">desc</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">desc</span><span class="p">,</span> <span class="n">sym</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">sym</span><span class="p">,</span> <span class="n">path</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">path</span><span class="p">)</span>
+ <span class="n">def_cutoff</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">contactdef</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"default_cutoff"</span><span class="p">))</span> <span class="k">if</span> <span class="nb">float</span><span class="p">(</span>
+ <span class="n">contactdef</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"default_cutoff"</span><span class="p">))</span> <span class="k">else</span> <span class="n">def_cut</span>
+ <span class="n">treshold</span> <span class="o">=</span> <span class="kc">None</span>
+
+ <span class="k">if</span> <span class="nb">type</span><span class="p">(</span><span class="n">contactdef</span><span class="p">)</span> <span class="o">==</span> <span class="nb">float</span><span class="p">:</span>
+ <span class="c1"># ???</span>
+ <span class="n">contact_map</span><span class="p">[:]</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">applymap</span><span class="p">(</span><span class="k">lambda</span> <span class="n">x</span><span class="p">:</span> <span class="n">x</span> <span class="o"><</span> <span class="n">contactdef</span><span class="p">)</span>
+
+ <span class="k">elif</span> <span class="nb">sum</span><span class="p">(</span><span class="n">x</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">contactdef</span><span class="o">.</span><span class="n">values</span><span class="p">())</span> <span class="o">==</span> <span class="mi">1</span> \
+ <span class="ow">and</span> <span class="n">def_cutoff</span><span class="p">:</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s2">"Using default cutoff"</span><span class="p">)</span>
+ <span class="n">contact_map</span><span class="p">[:]</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">applymap</span><span class="p">(</span>
+ <span class="k">lambda</span> <span class="n">x</span><span class="p">:</span> <span class="n">x</span> <span class="o"><</span> <span class="n">contactdef</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"default_cutoff"</span><span class="p">))</span>
+
+ <span class="k">elif</span> <span class="nb">sum</span><span class="p">(</span><span class="n">x</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">contactdef</span><span class="o">.</span><span class="n">values</span><span class="p">())</span> <span class="o">></span> <span class="mi">1</span><span class="p">:</span>
+ <span class="c1"># treshconv = lambda x: x < contactdef.get("default_cutoff")</span>
+ <span class="c1"># contact_map[:] = self.applymap(treshconv)</span>
+ <span class="n">atm_list</span> <span class="o">=</span> <span class="nb">set</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">index</span><span class="o">.</span><span class="n">get_level_values</span><span class="p">(</span><span class="mi">1</span><span class="p">))</span>
+ <span class="n">atms_list</span> <span class="o">=</span> <span class="nb">set</span><span class="p">([(</span><span class="n">a</span><span class="p">,</span> <span class="n">b</span><span class="p">)</span> <span class="k">for</span> <span class="n">a</span> <span class="ow">in</span> <span class="n">atm_list</span> <span class="k">for</span> <span class="n">b</span> <span class="ow">in</span> <span class="n">atm_list</span><span class="p">])</span>
+ <span class="k">for</span> <span class="n">pair</span> <span class="ow">in</span> <span class="n">contactdef</span><span class="o">.</span><span class="n">keys</span><span class="p">():</span>
+ <span class="n">treshold</span> <span class="o">=</span> <span class="n">contactdef</span><span class="p">[</span><span class="n">pair</span><span class="p">]</span>
+ <span class="k">if</span> <span class="n">pair</span> <span class="o">==</span> <span class="s2">"default_cutoff"</span><span class="p">:</span>
+ <span class="c1"># Since there is more than one treshold, we do not take</span>
+ <span class="c1"># default cutoff into account</span>
+ <span class="k">continue</span>
+ <span class="k">if</span> <span class="n">pair</span> <span class="o">==</span> <span class="s2">"all"</span><span class="p">:</span>
+ <span class="n">tmp</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">applymap</span><span class="p">(</span><span class="k">lambda</span> <span class="n">x</span><span class="p">:</span> <span class="n">x</span> <span class="o"><</span> <span class="n">treshold</span><span class="p">)</span>
+ <span class="n">contact_map</span><span class="o">.</span><span class="n">update</span><span class="p">(</span><span class="n">tmp</span><span class="p">)</span>
+ <span class="k">continue</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="n">pair</span> <span class="o">=</span> <span class="nb">tuple</span><span class="p">(</span><span class="n">pair</span><span class="o">.</span><span class="n">upper</span><span class="p">()</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s2">"_"</span><span class="p">))</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">info</span><span class="p">(</span>
+ <span class="s2">"Filtering values in matrix related to </span><span class="si">%s</span><span class="s2"> (</span><span class="si">%s</span><span class="s2">)"</span><span class="p">,</span>
+ <span class="nb">str</span><span class="p">(</span><span class="n">pair</span><span class="p">),</span> <span class="nb">str</span><span class="p">(</span><span class="n">treshold</span><span class="p">))</span>
+ <span class="k">if</span> <span class="n">pair</span> <span class="ow">in</span> <span class="p">((</span><span class="s2">"SC"</span><span class="p">,</span> <span class="s2">"SC"</span><span class="p">),</span> <span class="p">(</span><span class="s2">"sc"</span><span class="p">,</span> <span class="s2">"sc"</span><span class="p">)):</span>
+ <span class="c1"># Use scsc_min to apply treshold updateonly for selected atom</span>
+ <span class="c1"># sidechain</span>
+ <span class="n">idx_list</span> <span class="o">=</span> <span class="p">[]</span>
+ <span class="n">col_list</span> <span class="o">=</span> <span class="p">[]</span>
+ <span class="k">for</span> <span class="n">res1</span> <span class="ow">in</span> <span class="n">scsc_min</span><span class="p">:</span>
+ <span class="k">for</span> <span class="n">res2</span> <span class="ow">in</span> <span class="n">scsc_min</span><span class="p">[</span><span class="n">res1</span><span class="p">]:</span>
+ <span class="n">pair</span> <span class="o">=</span> <span class="p">(</span><span class="n">AminoAcid</span><span class="o">.</span><span class="n">AminoAcid</span><span class="p">(</span><span class="n">res1</span><span class="p">)[</span><span class="mi">1</span><span class="p">],</span>
+ <span class="n">AminoAcid</span><span class="o">.</span><span class="n">AminoAcid</span><span class="p">(</span><span class="n">res2</span><span class="p">)[</span><span class="mi">1</span><span class="p">])</span>
+ <span class="n">atm1</span><span class="p">,</span> <span class="n">atm2</span> <span class="o">=</span> <span class="n">scsc_min</span><span class="p">[</span><span class="n">res1</span><span class="p">][</span><span class="n">res2</span><span class="p">]</span>
+ <span class="n">idx_list</span><span class="o">.</span><span class="n">append</span><span class="p">(</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">index</span><span class="o">.</span><span class="n">map</span><span class="p">(</span><span class="k">lambda</span> <span class="n">x</span><span class="p">:</span> <span class="n">x</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">endswith</span><span class="p">(</span>
+ <span class="n">pair</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span> <span class="ow">and</span> <span class="n">x</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="o">==</span> <span class="n">atm1</span><span class="p">))</span>
+ <span class="n">col_list</span><span class="o">.</span><span class="n">append</span><span class="p">(</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">index</span><span class="o">.</span><span class="n">map</span><span class="p">(</span><span class="k">lambda</span> <span class="n">x</span><span class="p">:</span> <span class="n">x</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">endswith</span><span class="p">(</span>
+ <span class="n">pair</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span> <span class="ow">and</span> <span class="n">x</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="o">==</span> <span class="n">atm2</span><span class="p">))</span>
+ <span class="n">mask</span> <span class="o">=</span> <span class="p">([</span><span class="nb">any</span><span class="p">(</span><span class="n">tup</span><span class="p">)</span> <span class="k">for</span> <span class="n">tup</span> <span class="ow">in</span> <span class="nb">zip</span><span class="p">(</span><span class="o">*</span><span class="n">idx_list</span><span class="p">)],</span>
+ <span class="p">[</span><span class="nb">any</span><span class="p">(</span><span class="n">tup</span><span class="p">)</span> <span class="k">for</span> <span class="n">tup</span> <span class="ow">in</span> <span class="nb">zip</span><span class="p">(</span><span class="o">*</span><span class="n">col_list</span><span class="p">)])</span>
+ <span class="k">elif</span> <span class="n">pair</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">atms_list</span><span class="p">:</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">error</span><span class="p">(</span><span class="s2">"Pair </span><span class="si">%s</span><span class="s2"> doesn't exist ..."</span><span class="p">,</span> <span class="nb">str</span><span class="p">(</span><span class="n">pair</span><span class="p">))</span>
+ <span class="c1"># Already applied a treshold for this pair</span>
+ <span class="k">continue</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="s2">"Apply treshold for </span><span class="si">%s</span><span class="s2">"</span><span class="p">,</span> <span class="nb">str</span><span class="p">(</span><span class="n">pair</span><span class="p">))</span>
+ <span class="n">atms_list</span><span class="o">.</span><span class="n">discard</span><span class="p">(</span><span class="n">pair</span><span class="p">)</span>
+ <span class="c1"># Selecting rows for each atom</span>
+ <span class="n">mask</span> <span class="o">=</span> <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">index</span><span class="o">.</span><span class="n">get_level_values</span><span class="p">(</span><span class="mi">1</span><span class="p">)</span> <span class="o">==</span> <span class="n">pair</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">index</span><span class="o">.</span><span class="n">get_level_values</span><span class="p">(</span><span class="mi">1</span><span class="p">)</span> <span class="o">==</span> <span class="n">pair</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span>
+ <span class="n">tmp</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">loc</span><span class="p">[</span><span class="n">mask</span><span class="p">]</span><span class="o">.</span><span class="n">apply</span><span class="p">(</span><span class="k">lambda</span> <span class="n">x</span><span class="p">:</span> <span class="n">x</span> <span class="o"><</span> <span class="nb">float</span><span class="p">(</span><span class="n">treshold</span><span class="p">))</span>
+ <span class="n">contact_map</span><span class="o">.</span><span class="n">update</span><span class="p">(</span><span class="n">tmp</span><span class="p">)</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">error</span><span class="p">(</span><span class="s2">"Missing values in contact definition section. Add "</span>
+ <span class="s2">"at least a default_cutoff value."</span><span class="p">)</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="s2">"Contact map</span><span class="se">\n</span><span class="si">%s</span><span class="s2">"</span><span class="p">,</span> <span class="n">contact_map</span><span class="o">.</span><span class="n">head</span><span class="p">())</span>
+ <span class="k">return</span> <span class="n">contact_map</span></div>
+
+<div class="viewcode-block" id="ResAtmMap.copy"><a class="viewcode-back" href="../../ariaec.html#ariaec.protmap.ResAtmMap.copy">[docs]</a> <span class="k">def</span> <span class="nf">copy</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Copy dataframe and related attributes of the map</span>
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> **kwargs :</span>
+<span class="sd"> </span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+<span class="sd"> </span>
+<span class="sd"> """</span>
+ <span class="n">df</span> <span class="o">=</span> <span class="nb">super</span><span class="p">(</span><span class="n">Map</span><span class="p">,</span> <span class="bp">self</span><span class="p">)</span><span class="o">.</span><span class="n">copy</span><span class="p">()</span>
+ <span class="k">return</span> <span class="n">ResAtmMap</span><span class="p">(</span>
+ <span class="n">sequence</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">sequence</span><span class="p">,</span> <span class="n">path</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">path</span><span class="p">,</span> <span class="n">data</span><span class="o">=</span><span class="n">df</span><span class="p">,</span> <span class="n">desc</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">desc</span><span class="p">,</span>
+ <span class="n">sym</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">sym</span><span class="p">,</span> <span class="n">mtype</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">mtype</span><span class="p">,</span> <span class="n">dtype</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">dtype</span><span class="p">)</span></div></div>
+
+
+<div class="viewcode-block" id="ResMap"><a class="viewcode-back" href="../../ariaec.html#ariaec.protmap.ResMap">[docs]</a><span class="k">class</span> <span class="nc">ResMap</span><span class="p">(</span><span class="n">ResAtmMap</span><span class="p">):</span>
+ <span class="sd">"""Res - res distance/contact matrix"""</span>
+
+ <span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">sequence</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="n">sequence</span><span class="p">:</span>
+ <span class="n">sequence</span> <span class="o">=</span> <span class="n">ConversionTable</span><span class="o">.</span><span class="n">ConversionTable</span><span class="p">()</span><span class="o">.</span><span class="n">table</span><span class="p">[</span><span class="s1">'AMINO_ACID'</span><span class="p">][</span>
+ <span class="s1">'iupac'</span><span class="p">]</span><span class="o">.</span><span class="n">keys</span><span class="p">()</span>
+ <span class="nb">super</span><span class="p">(</span><span class="n">ResMap</span><span class="p">,</span> <span class="bp">self</span><span class="p">)</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="n">sequence</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
+
+ <span class="c1"># def _constructor_expanddim(self):</span>
+ <span class="c1"># super(ResMap, self)._constructor_expanddim()</span>
+
+ <span class="nd">@property</span>
+ <span class="k">def</span> <span class="nf">sequence</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Amino Acid sequence string in humanidx</span>
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+<span class="sd"> </span>
+<span class="sd"> """</span>
+ <span class="c1"># return "".join(AminoAcid.AminoAcid(aa.split("-")[1])[0] for aa in</span>
+ <span class="c1"># self.index)</span>
+ <span class="k">return</span> <span class="nb">super</span><span class="p">(</span><span class="n">ResMap</span><span class="p">,</span> <span class="bp">self</span><span class="p">)</span><span class="o">.</span><span class="n">sequence</span>
+
+<div class="viewcode-block" id="ResMap.create_index"><a class="viewcode-back" href="../../ariaec.html#ariaec.protmap.ResMap.create_index">[docs]</a> <span class="k">def</span> <span class="nf">create_index</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">sequence</span><span class="p">,</span> <span class="n">seqidx</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">idxnames</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
+ <span class="n">colnames</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> </span>
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> sequence</span>
+<span class="sd"> seqidx: pandas.Index</span>
+<span class="sd"> idxnames</span>
+<span class="sd"> colnames</span>
+<span class="sd"> kwargs</span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+<span class="sd"> """</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="s2">"Indexing Res - Res dataframe"</span><span class="p">)</span>
+ <span class="n">seq</span> <span class="o">=</span> <span class="p">[</span><span class="n">AminoAcid</span><span class="o">.</span><span class="n">AminoAcid</span><span class="p">(</span><span class="n">aa</span><span class="p">)[</span><span class="mi">1</span><span class="p">]</span> <span class="k">for</span> <span class="n">aa</span> <span class="ow">in</span> <span class="n">sequence</span><span class="p">]</span>
+ <span class="n">seqidx</span> <span class="o">=</span> <span class="n">seqidx</span> <span class="k">if</span> <span class="n">seqidx</span> <span class="ow">and</span> <span class="nb">len</span><span class="p">(</span><span class="n">seqidx</span><span class="p">)</span> <span class="o">==</span> <span class="nb">len</span><span class="p">(</span><span class="n">sequence</span><span class="p">)</span> <span class="k">else</span> <span class="kc">None</span>
+ <span class="k">if</span> <span class="n">seqidx</span><span class="p">:</span>
+ <span class="n">res_list</span> <span class="o">=</span> <span class="p">[</span><span class="s2">"</span><span class="si">%03d</span><span class="s2">-</span><span class="si">%s</span><span class="s2">"</span> <span class="o">%</span> <span class="p">(</span><span class="n">seqidx</span><span class="p">[</span><span class="n">i</span><span class="p">],</span> <span class="n">aa</span><span class="p">)</span> <span class="k">for</span> <span class="n">i</span><span class="p">,</span> <span class="n">aa</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">seq</span><span class="p">)]</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="n">res_list</span> <span class="o">=</span> <span class="p">[</span><span class="s2">"</span><span class="si">%03d</span><span class="s2">-</span><span class="si">%s</span><span class="s2">"</span> <span class="o">%</span> <span class="p">(</span><span class="n">i</span> <span class="o">+</span> <span class="mi">1</span><span class="p">,</span> <span class="n">aa</span><span class="p">)</span> <span class="k">for</span> <span class="n">i</span><span class="p">,</span> <span class="n">aa</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">seq</span><span class="p">)]</span>
+ <span class="n">idxnames</span> <span class="o">=</span> <span class="n">idxnames</span> <span class="k">if</span> <span class="n">idxnames</span> <span class="ow">and</span> <span class="nb">len</span><span class="p">(</span><span class="n">idxnames</span><span class="p">)</span> <span class="o">==</span> <span class="mi">1</span> <span class="k">else</span> <span class="s2">"residuex"</span>
+ <span class="n">colnames</span> <span class="o">=</span> <span class="n">colnames</span> <span class="k">if</span> <span class="n">colnames</span> <span class="ow">and</span> <span class="nb">len</span><span class="p">(</span><span class="n">colnames</span><span class="p">)</span> <span class="o">==</span> <span class="mi">1</span> <span class="k">else</span> <span class="s2">"residuey"</span>
+ <span class="n">index</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">Index</span><span class="p">(</span><span class="n">res_list</span><span class="p">,</span> <span class="n">name</span><span class="o">=</span><span class="n">idxnames</span><span class="p">)</span>
+ <span class="n">col</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">Index</span><span class="p">(</span><span class="n">res_list</span><span class="p">,</span> <span class="n">name</span><span class="o">=</span><span class="n">colnames</span><span class="p">)</span>
+ <span class="k">return</span> <span class="n">index</span><span class="p">,</span> <span class="n">col</span></div>
+
+<div class="viewcode-block" id="ResMap.create_heatmap"><a class="viewcode-back" href="../../ariaec.html#ariaec.protmap.ResMap.create_heatmap">[docs]</a> <span class="k">def</span> <span class="nf">create_heatmap</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="sd">""":return:"""</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">as_matrix</span><span class="p">()</span><span class="o">.</span><span class="n">isnull</span><span class="p">()</span><span class="o">.</span><span class="n">values</span><span class="o">.</span><span class="n">sum</span><span class="p">()</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
+ <span class="c1"># If there's no nan values</span>
+ <span class="k">return</span> <span class="n">sns</span><span class="o">.</span><span class="n">heatmap</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">as_matrix</span><span class="p">())</span>
+ <span class="k">return</span> <span class="kc">None</span></div>
+
+<div class="viewcode-block" id="ResMap.contact_map"><a class="viewcode-back" href="../../ariaec.html#ariaec.protmap.ResMap.contact_map">[docs]</a> <span class="k">def</span> <span class="nf">contact_map</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">contactdef</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> </span>
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> contactdef :</span>
+<span class="sd"> param kwargs:</span>
+<span class="sd"> **kwargs :</span>
+<span class="sd"> </span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+<span class="sd"> </span>
+<span class="sd"> """</span>
+ <span class="n">contact_map</span> <span class="o">=</span> <span class="n">ResMap</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">sequence</span><span class="p">,</span> <span class="n">mtype</span><span class="o">=</span><span class="s2">"contact"</span><span class="p">,</span> <span class="n">desc</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">desc</span><span class="p">,</span>
+ <span class="n">sym</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">sym</span><span class="p">)</span>
+
+ <span class="k">def</span> <span class="nf">treshconv</span><span class="p">(</span><span class="n">x</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> </span>
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> x :</span>
+<span class="sd"> return:</span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+<span class="sd"> </span>
+<span class="sd"> """</span>
+ <span class="k">return</span> <span class="n">x</span> <span class="o"><=</span> <span class="n">treshold</span>
+
+ <span class="c1"># Applique treshold sur la matrice ssi c'est une matrice de distance</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">dtype</span> <span class="o">==</span> <span class="nb">bool</span><span class="p">:</span>
+ <span class="c1"># If self is already a contact map</span>
+ <span class="k">return</span> <span class="kc">None</span>
+ <span class="n">treshold</span> <span class="o">=</span> <span class="n">contactdef</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"default_cutoff"</span><span class="p">,</span> <span class="mi">5</span><span class="p">)</span>
+ <span class="n">contact_map</span><span class="p">[:]</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">applymap</span><span class="p">(</span><span class="n">treshconv</span><span class="p">)</span>
+ <span class="k">return</span> <span class="n">contact_map</span></div>
+
+ <span class="k">def</span> <span class="nf">__deepcopy__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="n">deepcopy_method</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">__deepcopy__</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">__deepcopy__</span> <span class="o">=</span> <span class="kc">None</span>
+ <span class="n">cp</span> <span class="o">=</span> <span class="n">deepcopy</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">__deepcopy__</span> <span class="o">=</span> <span class="n">deepcopy_method</span>
+
+ <span class="n">cp</span><span class="o">.</span><span class="n">dtype</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">dtype</span>
+ <span class="c1"># custom treatments</span>
+ <span class="c1"># for instance: cp.id = None</span>
+
+ <span class="k">return</span> <span class="n">cp</span>
+
+<div class="viewcode-block" id="ResMap.copy"><a class="viewcode-back" href="../../ariaec.html#ariaec.protmap.ResMap.copy">[docs]</a> <span class="k">def</span> <span class="nf">copy</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Copy dataframe and related attributes of the map</span>
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> **kwargs :</span>
+<span class="sd"> </span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+<span class="sd"> </span>
+<span class="sd"> """</span>
+ <span class="n">df</span> <span class="o">=</span> <span class="nb">super</span><span class="p">(</span><span class="n">Map</span><span class="p">,</span> <span class="bp">self</span><span class="p">)</span><span class="o">.</span><span class="n">copy</span><span class="p">()</span>
+ <span class="k">return</span> <span class="n">ResMap</span><span class="p">(</span>
+ <span class="n">sequence</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">sequence</span><span class="p">,</span> <span class="n">path</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">path</span><span class="p">,</span> <span class="n">data</span><span class="o">=</span><span class="n">df</span><span class="p">,</span> <span class="n">desc</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">desc</span><span class="p">,</span>
+ <span class="n">sym</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">sym</span><span class="p">,</span> <span class="n">mtype</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">mtype</span><span class="p">,</span> <span class="n">dtype</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">dtype</span><span class="p">)</span></div></div>
+
+
+<div class="viewcode-block" id="AaMap"><a class="viewcode-back" href="../../ariaec.html#ariaec.protmap.AaMap">[docs]</a><span class="k">class</span> <span class="nc">AaMap</span><span class="p">(</span><span class="n">ProteinMap</span><span class="p">):</span>
+ <span class="sd">"""Amino Acid Distance Matrix"""</span>
+
+<div class="viewcode-block" id="AaMap.contact_map"><a class="viewcode-back" href="../../ariaec.html#ariaec.protmap.AaMap.contact_map">[docs]</a> <span class="k">def</span> <span class="nf">contact_map</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">contactdef</span><span class="p">,</span> <span class="n">scsc_min</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> </span>
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> contactdef</span>
+<span class="sd"> scsc_min</span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+<span class="sd"> """</span>
+ <span class="k">raise</span> <span class="ne">NotImplementedError</span></div>
+
+<div class="viewcode-block" id="AaMap.create_heatmap"><a class="viewcode-back" href="../../ariaec.html#ariaec.protmap.AaMap.create_heatmap">[docs]</a> <span class="k">def</span> <span class="nf">create_heatmap</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> </span>
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+<span class="sd"> """</span>
+ <span class="k">raise</span> <span class="ne">NotImplementedError</span></div>
+
+ <span class="c1"># def _constructor_expanddim(self):</span>
+ <span class="c1"># super(AaMap, self)._constructor_expanddim()</span>
+
+ <span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+ <span class="c1"># if ("index", "columns") not in kwargs:</span>
+ <span class="c1"># idx, col = self.create_index()</span>
+ <span class="c1"># kwargs["index"] = idx</span>
+ <span class="c1"># kwargs["columns"] = col</span>
+ <span class="nb">super</span><span class="p">(</span><span class="n">AaMap</span><span class="p">,</span> <span class="bp">self</span><span class="p">)</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="n">sequence</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">sequence</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
+
+ <span class="c1"># TODO: Actually useless since it raised an notimplemented error</span>
+<div class="viewcode-block" id="AaMap.reduce"><a class="viewcode-back" href="../../ariaec.html#ariaec.protmap.AaMap.reduce">[docs]</a> <span class="k">def</span> <span class="nf">reduce</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="sd">"""Reduce level of the contactmap"""</span>
+ <span class="k">return</span> <span class="nb">super</span><span class="p">(</span><span class="n">AaMap</span><span class="p">,</span> <span class="bp">self</span><span class="p">)</span><span class="o">.</span><span class="n">reduce</span><span class="p">()</span></div>
+
+ <span class="nd">@property</span>
+ <span class="k">def</span> <span class="nf">sequence</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+<span class="sd"> str</span>
+<span class="sd"> String containing all amino acid 1L code</span>
+<span class="sd"> """</span>
+ <span class="k">return</span> <span class="s1">''</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="nb">sorted</span><span class="p">([</span>
+ <span class="n">AminoAcid</span><span class="o">.</span><span class="n">AminoAcid</span><span class="p">(</span><span class="n">aa</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span>
+ <span class="k">for</span> <span class="n">aa</span> <span class="ow">in</span> <span class="n">ConversionTable</span><span class="o">.</span><span class="n">ConversionTable</span><span class="p">()</span><span class="o">.</span><span class="n">table</span><span class="p">[</span>
+ <span class="s1">'AMINO_ACID'</span><span class="p">][</span><span class="s1">'iupac'</span><span class="p">]</span><span class="o">.</span><span class="n">keys</span><span class="p">()]))</span>
+
+<div class="viewcode-block" id="AaMap.copy"><a class="viewcode-back" href="../../ariaec.html#ariaec.protmap.AaMap.copy">[docs]</a> <span class="k">def</span> <span class="nf">copy</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> </span>
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> kwargs :</span>
+<span class="sd"> </span>
+<span class="sd"> **kwargs :</span>
+<span class="sd"> </span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+<span class="sd"> </span>
+<span class="sd"> """</span>
+ <span class="n">df</span> <span class="o">=</span> <span class="nb">super</span><span class="p">(</span><span class="n">Map</span><span class="p">,</span> <span class="bp">self</span><span class="p">)</span><span class="o">.</span><span class="n">copy</span><span class="p">()</span>
+ <span class="k">return</span> <span class="n">AaMap</span><span class="p">(</span>
+ <span class="n">path</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">path</span><span class="p">,</span> <span class="n">data</span><span class="o">=</span><span class="n">df</span><span class="p">,</span> <span class="n">desc</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">desc</span><span class="p">,</span>
+ <span class="n">sym</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">sym</span><span class="p">,</span> <span class="n">mtype</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">mtype</span><span class="p">,</span> <span class="n">dtype</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">dtype</span><span class="p">)</span></div>
+
+<div class="viewcode-block" id="AaMap.create_index"><a class="viewcode-back" href="../../ariaec.html#ariaec.protmap.AaMap.create_index">[docs]</a> <span class="k">def</span> <span class="nf">create_index</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">sequence</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> </span>
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+<span class="sd"> """</span>
+ <span class="n">res_list</span> <span class="o">=</span> <span class="p">[</span><span class="n">AminoAcid</span><span class="o">.</span><span class="n">AminoAcid</span><span class="p">(</span><span class="n">aa</span><span class="p">)[</span><span class="mi">1</span><span class="p">]</span> <span class="k">for</span> <span class="n">aa</span> <span class="ow">in</span> <span class="n">sequence</span><span class="p">]</span>
+ <span class="n">index</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">Index</span><span class="p">(</span><span class="n">res_list</span><span class="p">,</span> <span class="n">name</span><span class="o">=</span><span class="s2">"aax"</span><span class="p">)</span>
+ <span class="n">col</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">Index</span><span class="p">(</span><span class="n">res_list</span><span class="p">,</span> <span class="n">name</span><span class="o">=</span><span class="s2">"aay"</span><span class="p">)</span>
+ <span class="k">return</span> <span class="n">index</span><span class="p">,</span> <span class="n">col</span></div></div>
+
+
+<div class="viewcode-block" id="AaAtmMap"><a class="viewcode-back" href="../../ariaec.html#ariaec.protmap.AaAtmMap">[docs]</a><span class="k">class</span> <span class="nc">AaAtmMap</span><span class="p">(</span><span class="n">AaMap</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Amino acid map with atom levels</span>
+<span class="sd"> """</span>
+
+<div class="viewcode-block" id="AaAtmMap.create_heatmap"><a class="viewcode-back" href="../../ariaec.html#ariaec.protmap.AaAtmMap.create_heatmap">[docs]</a> <span class="k">def</span> <span class="nf">create_heatmap</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> </span>
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+<span class="sd"> """</span>
+ <span class="k">raise</span> <span class="ne">NotImplementedError</span></div>
+
+<div class="viewcode-block" id="AaAtmMap.contact_map"><a class="viewcode-back" href="../../ariaec.html#ariaec.protmap.AaAtmMap.contact_map">[docs]</a> <span class="k">def</span> <span class="nf">contact_map</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">contactdef</span><span class="p">,</span> <span class="n">scsc_min</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> </span>
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> contactdef</span>
+<span class="sd"> scsc_min</span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+<span class="sd"> """</span>
+ <span class="k">raise</span> <span class="ne">NotImplementedError</span></div>
+
+ <span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+ <span class="nb">super</span><span class="p">(</span><span class="n">AaAtmMap</span><span class="p">,</span> <span class="bp">self</span><span class="p">)</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">atom_types</span> <span class="o">=</span> <span class="n">kwargs</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"atom_types"</span><span class="p">,</span> <span class="s2">"min"</span><span class="p">)</span>
+
+<div class="viewcode-block" id="AaAtmMap.create_index"><a class="viewcode-back" href="../../ariaec.html#ariaec.protmap.AaAtmMap.create_index">[docs]</a> <span class="k">def</span> <span class="nf">create_index</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">sequence</span><span class="p">,</span> <span class="n">atom_types</span><span class="o">=</span><span class="s2">"min"</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Update Aa index with atoms</span>
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+<span class="sd"> """</span>
+ <span class="c1"># TODO: better way to define indexs</span>
+ <span class="c1"># idx, col = super(AaAtmMap, self).create_index()</span>
+ <span class="n">atomtable</span> <span class="o">=</span> <span class="n">ConversionTable</span><span class="o">.</span><span class="n">ConversionTable</span><span class="p">()</span><span class="o">.</span><span class="n">table</span><span class="p">[</span><span class="s1">'AMINO_ACID'</span><span class="p">][</span>
+ <span class="s1">'iupac'</span><span class="p">]</span>
+ <span class="n">seq</span> <span class="o">=</span> <span class="p">[</span><span class="n">AminoAcid</span><span class="o">.</span><span class="n">AminoAcid</span><span class="p">(</span><span class="n">aa</span><span class="p">)[</span><span class="mi">1</span><span class="p">]</span> <span class="k">for</span> <span class="n">aa</span> <span class="ow">in</span> <span class="n">sequence</span><span class="p">]</span>
+ <span class="n">res_list</span> <span class="o">=</span> <span class="p">[</span>
+ <span class="s2">"</span><span class="si">%s</span><span class="s2">"</span> <span class="o">%</span> <span class="n">aa</span> <span class="k">for</span> <span class="n">i</span><span class="p">,</span> <span class="n">aa</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">seq</span><span class="p">)</span>
+ <span class="k">for</span> <span class="n">_</span> <span class="ow">in</span> <span class="nb">filter</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">heavy_reg</span><span class="o">.</span><span class="n">match</span><span class="p">,</span> <span class="n">atomtable</span><span class="p">[</span><span class="n">aa</span><span class="p">]</span><span class="o">.</span><span class="n">keys</span><span class="p">())]</span>
+ <span class="n">atm_list</span> <span class="o">=</span> <span class="p">[</span>
+ <span class="n">atm</span> <span class="k">for</span> <span class="n">aa</span> <span class="ow">in</span> <span class="n">seq</span> <span class="k">for</span> <span class="n">atm</span> <span class="ow">in</span> <span class="p">(</span><span class="s1">'CA'</span><span class="p">,</span> <span class="s1">'CB'</span><span class="p">,</span> <span class="s1">'SC'</span><span class="p">)]</span> \
+ <span class="k">if</span> <span class="n">atom_types</span> <span class="o">==</span> <span class="s2">"min"</span> <span class="k">else</span> <span class="p">[</span>
+ <span class="n">atm</span> <span class="k">for</span> <span class="n">aa</span> <span class="ow">in</span> <span class="n">seq</span> <span class="k">for</span> <span class="n">atm</span> <span class="ow">in</span> <span class="nb">filter</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">heavy_reg</span><span class="o">.</span><span class="n">match</span><span class="p">,</span>
+ <span class="n">atomtable</span><span class="p">[</span><span class="n">aa</span><span class="p">]</span><span class="o">.</span><span class="n">keys</span><span class="p">())]</span> \
+ <span class="k">if</span> <span class="n">atom_types</span> <span class="o">==</span> <span class="s2">"heavy"</span> <span class="k">else</span> <span class="p">[</span>
+ <span class="n">atm</span> <span class="k">for</span> <span class="n">aa</span> <span class="ow">in</span> <span class="n">seq</span> <span class="k">for</span> <span class="n">atm</span> <span class="ow">in</span> <span class="n">atomtable</span><span class="p">[</span><span class="n">aa</span><span class="p">]</span><span class="o">.</span><span class="n">keys</span><span class="p">()]</span>
+ <span class="n">idx</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">MultiIndex</span><span class="o">.</span><span class="n">from_tuples</span><span class="p">(</span><span class="nb">list</span><span class="p">(</span><span class="nb">zip</span><span class="p">(</span><span class="o">*</span><span class="p">[</span><span class="n">res_list</span><span class="p">,</span> <span class="n">atm_list</span><span class="p">])),</span>
+ <span class="n">names</span><span class="o">=</span><span class="p">(</span><span class="s1">'AminoAcid'</span><span class="p">,</span> <span class="s1">'Atom'</span><span class="p">))</span>
+ <span class="n">col</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">MultiIndex</span><span class="o">.</span><span class="n">from_tuples</span><span class="p">(</span><span class="nb">list</span><span class="p">(</span><span class="nb">zip</span><span class="p">(</span><span class="o">*</span><span class="p">[</span><span class="n">res_list</span><span class="p">,</span> <span class="n">atm_list</span><span class="p">])),</span>
+ <span class="n">names</span><span class="o">=</span><span class="p">(</span><span class="s1">'AminoAcid'</span><span class="p">,</span> <span class="s1">'Atom'</span><span class="p">))</span>
+ <span class="k">return</span> <span class="n">idx</span><span class="p">,</span> <span class="n">col</span></div>
+
+<div class="viewcode-block" id="AaAtmMap.copy"><a class="viewcode-back" href="../../ariaec.html#ariaec.protmap.AaAtmMap.copy">[docs]</a> <span class="k">def</span> <span class="nf">copy</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+ <span class="sd">"""</span>
+
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> kwargs :</span>
+
+<span class="sd"> **kwargs :</span>
+
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+
+<span class="sd"> """</span>
+ <span class="n">df</span> <span class="o">=</span> <span class="nb">super</span><span class="p">(</span><span class="n">Map</span><span class="p">,</span> <span class="bp">self</span><span class="p">)</span><span class="o">.</span><span class="n">copy</span><span class="p">()</span>
+ <span class="k">return</span> <span class="n">AaAtmMap</span><span class="p">(</span>
+ <span class="n">path</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">path</span><span class="p">,</span> <span class="n">data</span><span class="o">=</span><span class="n">df</span><span class="p">,</span> <span class="n">desc</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">desc</span><span class="p">,</span>
+ <span class="n">sym</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">sym</span><span class="p">,</span> <span class="n">mtype</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">mtype</span><span class="p">,</span> <span class="n">dtype</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">dtype</span><span class="p">,</span>
+ <span class="n">atom_types</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">atom_types</span><span class="p">)</span></div></div>
+
+
+<div class="viewcode-block" id="SsAaAtmMap"><a class="viewcode-back" href="../../ariaec.html#ariaec.protmap.SsAaAtmMap">[docs]</a><span class="k">class</span> <span class="nc">SsAaAtmMap</span><span class="p">(</span><span class="n">AaAtmMap</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Amino acid map with atom and secondary structure levels</span>
+<span class="sd"> """</span>
+ <span class="n">ss_types</span> <span class="o">=</span> <span class="p">(</span><span class="s2">"H"</span><span class="p">,</span> <span class="s2">"E"</span><span class="p">,</span> <span class="s2">"X"</span><span class="p">)</span>
+
+<div class="viewcode-block" id="SsAaAtmMap.contact_map"><a class="viewcode-back" href="../../ariaec.html#ariaec.protmap.SsAaAtmMap.contact_map">[docs]</a> <span class="k">def</span> <span class="nf">contact_map</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">contactdef</span><span class="p">,</span> <span class="n">scsc_min</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> </span>
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> contactdef</span>
+<span class="sd"> scsc_min</span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+<span class="sd"> """</span>
+ <span class="k">pass</span></div>
+
+<div class="viewcode-block" id="SsAaAtmMap.create_heatmap"><a class="viewcode-back" href="../../ariaec.html#ariaec.protmap.SsAaAtmMap.create_heatmap">[docs]</a> <span class="k">def</span> <span class="nf">create_heatmap</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> </span>
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+<span class="sd"> """</span>
+ <span class="k">pass</span></div>
+
+ <span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+ <span class="nb">super</span><span class="p">(</span><span class="n">SsAaAtmMap</span><span class="p">,</span> <span class="bp">self</span><span class="p">)</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">atom_types</span> <span class="o">=</span> <span class="n">kwargs</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"atom_types"</span><span class="p">,</span> <span class="s2">"min"</span><span class="p">)</span>
+
+<div class="viewcode-block" id="SsAaAtmMap.create_index"><a class="viewcode-back" href="../../ariaec.html#ariaec.protmap.SsAaAtmMap.create_index">[docs]</a> <span class="k">def</span> <span class="nf">create_index</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">sequence</span><span class="p">,</span> <span class="n">atom_types</span><span class="o">=</span><span class="s2">"min"</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> </span>
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> atom_types</span>
+<span class="sd"> sequence</span>
+<span class="sd"> kwargs</span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+<span class="sd"> """</span>
+ <span class="c1"># TODO: better way to define indexs, duplicated code here !!!</span>
+ <span class="c1"># idx, col = super(AaAtmMap, self).create_index()</span>
+ <span class="n">atomtable</span> <span class="o">=</span> <span class="n">ConversionTable</span><span class="o">.</span><span class="n">ConversionTable</span><span class="p">()</span><span class="o">.</span><span class="n">table</span><span class="p">[</span><span class="s1">'AMINO_ACID'</span><span class="p">][</span>
+ <span class="s1">'iupac'</span><span class="p">]</span>
+ <span class="n">seq</span> <span class="o">=</span> <span class="p">[</span><span class="n">AminoAcid</span><span class="o">.</span><span class="n">AminoAcid</span><span class="p">(</span><span class="n">aa</span><span class="p">)[</span><span class="mi">1</span><span class="p">]</span> <span class="k">for</span> <span class="n">aa</span> <span class="ow">in</span> <span class="n">sequence</span><span class="p">]</span>
+ <span class="n">ss_list</span><span class="p">,</span> <span class="n">res_list</span><span class="p">,</span> <span class="n">atm_list</span> <span class="o">=</span> <span class="p">[],</span> <span class="p">[],</span> <span class="p">[]</span>
+
+ <span class="k">for</span> <span class="n">ss</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">ss_types</span><span class="p">:</span>
+ <span class="k">for</span> <span class="n">aa</span> <span class="ow">in</span> <span class="n">seq</span><span class="p">:</span>
+ <span class="n">atms</span> <span class="o">=</span> <span class="p">(</span><span class="s1">'CA'</span><span class="p">,</span> <span class="s1">'CB'</span><span class="p">,</span> <span class="s1">'SC'</span><span class="p">)</span> <span class="k">if</span> <span class="n">atom_types</span> <span class="o">==</span> <span class="s2">"min"</span> <span class="k">else</span> <span class="nb">filter</span><span class="p">(</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">heavy_reg</span><span class="o">.</span><span class="n">match</span><span class="p">,</span> <span class="n">atomtable</span><span class="p">[</span><span class="n">aa</span><span class="p">]</span><span class="o">.</span><span class="n">keys</span><span class="p">())</span> <span class="k">if</span> <span class="n">atom_types</span> <span class="o">==</span> <span class="s2">"heavy"</span> <span class="k">else</span> <span class="n">atomtable</span><span class="p">[</span><span class="n">aa</span><span class="p">]</span><span class="o">.</span><span class="n">keys</span><span class="p">()</span>
+ <span class="k">for</span> <span class="n">atm</span> <span class="ow">in</span> <span class="n">atms</span><span class="p">:</span>
+ <span class="n">ss_list</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">ss</span><span class="p">)</span>
+ <span class="n">res_list</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">aa</span><span class="p">)</span>
+ <span class="n">atm_list</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">atm</span><span class="p">)</span>
+ <span class="n">idx</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">MultiIndex</span><span class="o">.</span><span class="n">from_tuples</span><span class="p">(</span>
+ <span class="nb">list</span><span class="p">(</span><span class="nb">zip</span><span class="p">(</span><span class="o">*</span><span class="p">[</span><span class="n">ss_list</span><span class="p">,</span> <span class="n">res_list</span><span class="p">,</span> <span class="n">atm_list</span><span class="p">])),</span>
+ <span class="n">names</span><span class="o">=</span><span class="p">(</span><span class="s1">'SecStruct'</span><span class="p">,</span> <span class="s1">'AminoAcid'</span><span class="p">,</span> <span class="s1">'Atom'</span><span class="p">))</span>
+ <span class="n">col</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">MultiIndex</span><span class="o">.</span><span class="n">from_tuples</span><span class="p">(</span>
+ <span class="nb">list</span><span class="p">(</span><span class="nb">zip</span><span class="p">(</span><span class="o">*</span><span class="p">[</span><span class="n">ss_list</span><span class="p">,</span> <span class="n">res_list</span><span class="p">,</span> <span class="n">atm_list</span><span class="p">])),</span>
+ <span class="n">names</span><span class="o">=</span><span class="p">(</span><span class="s1">'SecStruct'</span><span class="p">,</span> <span class="s1">'AminoAcid'</span><span class="p">,</span> <span class="s1">'Atom'</span><span class="p">))</span>
+ <span class="k">return</span> <span class="n">idx</span><span class="p">,</span> <span class="n">col</span></div>
+
+<div class="viewcode-block" id="SsAaAtmMap.reduce"><a class="viewcode-back" href="../../ariaec.html#ariaec.protmap.SsAaAtmMap.reduce">[docs]</a> <span class="k">def</span> <span class="nf">reduce</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">groupby</span><span class="o">=</span><span class="s2">"min"</span><span class="p">):</span>
+ <span class="sd">"""</span>
+
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> groupby :</span>
+<span class="sd"> return: (Default value = "min")</span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+
+<span class="sd"> """</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">index</span><span class="o">.</span><span class="n">nlevels</span> <span class="o">==</span> <span class="mi">1</span> <span class="ow">or</span> <span class="ow">not</span> <span class="n">groupby</span><span class="p">:</span>
+ <span class="k">return</span> <span class="bp">self</span>
+ <span class="n">newmap</span> <span class="o">=</span> <span class="n">AaAtmMap</span><span class="p">(</span><span class="n">path</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">path</span><span class="p">,</span> <span class="n">desc</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">desc</span><span class="p">,</span>
+ <span class="n">sym</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">sym</span><span class="p">,</span> <span class="n">mtype</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">mtype</span><span class="p">,</span> <span class="n">dtype</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">dtype</span><span class="p">,</span>
+ <span class="n">atom_types</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">atom_types</span><span class="p">)</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">dtype</span> <span class="o">==</span> <span class="nb">bool</span><span class="p">:</span>
+ <span class="n">newmap</span><span class="p">[:]</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">copy</span><span class="p">()</span><span class="o">.</span><span class="n">stack</span><span class="p">(</span><span class="s1">'SecStruct'</span><span class="p">,</span> <span class="n">dropna</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span><span class="o">.</span><span class="n">groupby</span><span class="p">(</span>
+ <span class="n">level</span><span class="o">=</span><span class="p">[</span><span class="mi">1</span><span class="p">,</span> <span class="mi">2</span><span class="p">])</span><span class="o">.</span><span class="n">any</span><span class="p">()</span>
+ <span class="k">elif</span> <span class="n">groupby</span> <span class="o">==</span> <span class="s2">"mean"</span><span class="p">:</span>
+ <span class="n">newmap</span><span class="p">[:]</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">copy</span><span class="p">()</span><span class="o">.</span><span class="n">stack</span><span class="p">(</span><span class="s1">'SecStruct'</span><span class="p">,</span> <span class="n">dropna</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span><span class="o">.</span><span class="n">groupby</span><span class="p">(</span>
+ <span class="n">level</span><span class="o">=</span><span class="p">[</span><span class="mi">1</span><span class="p">,</span> <span class="mi">2</span><span class="p">])</span><span class="o">.</span><span class="n">mean</span><span class="p">()</span>
+ <span class="k">elif</span> <span class="n">groupby</span> <span class="o">==</span> <span class="s2">"min"</span><span class="p">:</span>
+ <span class="n">newmap</span><span class="p">[:]</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">copy</span><span class="p">()</span><span class="o">.</span><span class="n">stack</span><span class="p">(</span><span class="s1">'SecStruct'</span><span class="p">,</span> <span class="n">dropna</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span><span class="o">.</span><span class="n">groupby</span><span class="p">(</span>
+ <span class="n">level</span><span class="o">=</span><span class="p">[</span><span class="mi">1</span><span class="p">,</span> <span class="mi">2</span><span class="p">])</span><span class="o">.</span><span class="n">min</span><span class="p">()</span>
+ <span class="k">return</span> <span class="n">newmap</span></div>
+
+<div class="viewcode-block" id="SsAaAtmMap.copy"><a class="viewcode-back" href="../../ariaec.html#ariaec.protmap.SsAaAtmMap.copy">[docs]</a> <span class="k">def</span> <span class="nf">copy</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+ <span class="sd">"""</span>
+
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> kwargs :</span>
+
+<span class="sd"> **kwargs :</span>
+
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+
+<span class="sd"> """</span>
+ <span class="n">df</span> <span class="o">=</span> <span class="nb">super</span><span class="p">(</span><span class="n">Map</span><span class="p">,</span> <span class="bp">self</span><span class="p">)</span><span class="o">.</span><span class="n">copy</span><span class="p">()</span>
+ <span class="k">return</span> <span class="n">SsAaAtmMap</span><span class="p">(</span>
+ <span class="n">path</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">path</span><span class="p">,</span> <span class="n">data</span><span class="o">=</span><span class="n">df</span><span class="p">,</span> <span class="n">desc</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">desc</span><span class="p">,</span>
+ <span class="n">sym</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">sym</span><span class="p">,</span> <span class="n">mtype</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">mtype</span><span class="p">,</span> <span class="n">dtype</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">dtype</span><span class="p">)</span></div></div>
+
+
+<div class="viewcode-block" id="AtmMap"><a class="viewcode-back" href="../../ariaec.html#ariaec.protmap.AtmMap">[docs]</a><span class="k">class</span> <span class="nc">AtmMap</span><span class="p">(</span><span class="n">Map</span><span class="p">):</span>
+ <span class="sd">"""Atom Distance Matrix"""</span>
+
+ <span class="c1"># def _constructor_expanddim(self):</span>
+ <span class="c1"># super(AtmMap, self)._constructor_expanddim()</span>
+
+ <span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+ <span class="nb">super</span><span class="p">(</span><span class="n">AtmMap</span><span class="p">,</span> <span class="bp">self</span><span class="p">)</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
+
+<div class="viewcode-block" id="AtmMap.reduce"><a class="viewcode-back" href="../../ariaec.html#ariaec.protmap.AtmMap.reduce">[docs]</a> <span class="k">def</span> <span class="nf">reduce</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="sd">"""Reduce level of the contactmap"""</span>
+ <span class="k">return</span> <span class="nb">super</span><span class="p">(</span><span class="n">AtmMap</span><span class="p">,</span> <span class="bp">self</span><span class="p">)</span><span class="o">.</span><span class="n">reduce</span><span class="p">()</span></div>
+
+<div class="viewcode-block" id="AtmMap.copy"><a class="viewcode-back" href="../../ariaec.html#ariaec.protmap.AtmMap.copy">[docs]</a> <span class="k">def</span> <span class="nf">copy</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> </span>
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> kwargs :</span>
+<span class="sd"> </span>
+<span class="sd"> **kwargs :</span>
+<span class="sd"> </span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+<span class="sd"> </span>
+<span class="sd"> """</span>
+ <span class="n">df</span> <span class="o">=</span> <span class="nb">super</span><span class="p">(</span><span class="n">Map</span><span class="p">,</span> <span class="bp">self</span><span class="p">)</span><span class="o">.</span><span class="n">copy</span><span class="p">()</span>
+ <span class="k">return</span> <span class="n">AtmMap</span><span class="p">(</span>
+ <span class="n">path</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">path</span><span class="p">,</span> <span class="n">data</span><span class="o">=</span><span class="n">df</span><span class="p">,</span> <span class="n">desc</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">desc</span><span class="p">,</span>
+ <span class="n">sym</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">sym</span><span class="p">,</span> <span class="n">mtype</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">mtype</span><span class="p">,</span> <span class="n">dtype</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">dtype</span><span class="p">)</span></div>
+
+<div class="viewcode-block" id="AtmMap.create_index"><a class="viewcode-back" href="../../ariaec.html#ariaec.protmap.AtmMap.create_index">[docs]</a> <span class="k">def</span> <span class="nf">create_index</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="sd">""":return:"""</span>
+ <span class="k">raise</span> <span class="ne">NotImplementedError</span></div></div>
+
+
+<div class="viewcode-block" id="ProtMapCollection"><a class="viewcode-back" href="../../ariaec.html#ariaec.protmap.ProtMapCollection">[docs]</a><span class="k">class</span> <span class="nc">ProtMapCollection</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span>
+ <span class="sd">"""Group all protein maps"""</span>
+
+ <span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">settings</span><span class="p">):</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_alldistmap</span> <span class="o">=</span> <span class="kc">None</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_allscoremap</span> <span class="o">=</span> <span class="kc">None</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_allcontactmap</span> <span class="o">=</span> <span class="kc">None</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_distmap</span> <span class="o">=</span> <span class="kc">None</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_scoremap</span> <span class="o">=</span> <span class="kc">None</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_contactmap</span> <span class="o">=</span> <span class="kc">None</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">settings</span> <span class="o">=</span> <span class="n">settings</span>
+
+ <span class="nd">@property</span>
+ <span class="k">def</span> <span class="nf">alldistmap</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Atom level distance map.</span>
+<span class="sd"> :return:</span>
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+<span class="sd"> </span>
+<span class="sd"> """</span>
+ <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_alldistmap</span>
+
+ <span class="nd">@alldistmap</span><span class="o">.</span><span class="n">setter</span>
+ <span class="k">def</span> <span class="nf">alldistmap</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">resatmap</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Atom level distance map setter. The only way is to give resatmmap object</span>
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> resatmap :</span>
+<span class="sd"> type resatmap: ResAtmMap</span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+<span class="sd"> </span>
+<span class="sd"> """</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_alldistmap</span> <span class="o">=</span> <span class="n">resatmap</span>
+
+ <span class="nd">@property</span>
+ <span class="k">def</span> <span class="nf">allcontactmap</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Atom level contact map. If alldistmap exists, return the maplot</span>
+<span class="sd"> form</span>
+<span class="sd"> :return:</span>
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+<span class="sd"> </span>
+<span class="sd"> """</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">_alldistmap</span><span class="p">:</span>
+ <span class="c1"># settings.contactdef.config</span>
+ <span class="c1"># settings.main.scsc_min_file</span>
+ <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_alldistmap</span><span class="o">.</span><span class="n">contact_map</span><span class="p">(</span><span class="n">contactdef</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="p">[</span>
+ <span class="s2">"contactdef"</span><span class="p">],</span> <span class="n">scsc_min</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="p">[</span><span class="s2">"scsc_min_file"</span><span class="p">])</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_allcontactmap</span>
+
+ <span class="nd">@allcontactmap</span><span class="o">.</span><span class="n">setter</span>
+ <span class="k">def</span> <span class="nf">allcontactmap</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">resatmap</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Atom level contact map setter</span>
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> resatmap :</span>
+<span class="sd"> binary res atm map</span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+<span class="sd"> </span>
+<span class="sd"> """</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_allcontactmap</span> <span class="o">=</span> <span class="n">resatmap</span>
+
+ <span class="nd">@property</span>
+ <span class="k">def</span> <span class="nf">allscoremap</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Atom level score map</span>
+<span class="sd"> :return:</span>
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+<span class="sd"> </span>
+<span class="sd"> """</span>
+ <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_allscoremap</span>
+
+ <span class="nd">@allscoremap</span><span class="o">.</span><span class="n">setter</span>
+ <span class="k">def</span> <span class="nf">allscoremap</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">resatmap</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Atom level score map setter</span>
+<span class="sd"> :return:</span>
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> resatmap :</span>
+<span class="sd"> </span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+<span class="sd"> </span>
+<span class="sd"> """</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_allscoremap</span> <span class="o">=</span> <span class="n">resatmap</span>
+
+ <span class="nd">@property</span>
+ <span class="k">def</span> <span class="nf">distmap</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="sd">""":return:"""</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">_alldistmap</span><span class="p">:</span>
+ <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_alldistmap</span><span class="o">.</span><span class="n">reduce</span><span class="p">(</span><span class="n">groupby</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="p">[</span>
+ <span class="s2">"groupby_method"</span><span class="p">])</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_distmap</span>
+
+ <span class="nd">@distmap</span><span class="o">.</span><span class="n">setter</span>
+ <span class="k">def</span> <span class="nf">distmap</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">resmap</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> </span>
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> resmap :</span>
+<span class="sd"> </span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+<span class="sd"> </span>
+<span class="sd"> """</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_distmap</span> <span class="o">=</span> <span class="n">resmap</span></div>
+
+
+<div class="viewcode-block" id="MapFilter"><a class="viewcode-back" href="../../ariaec.html#ariaec.protmap.MapFilter">[docs]</a><span class="k">class</span> <span class="nc">MapFilter</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Filter maplot/distancemap</span>
+<span class="sd"> nd : Network deconvolution</span>
+<span class="sd"> pos : remove close contacts</span>
+<span class="sd"> cons : remove contacts with highly conservated residues</span>
+<span class="sd"> cys-cys : unicity of ss contacts</span>
+<span class="sd"> ssclash : secondary structure conflict</span>
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+<span class="sd"> </span>
+<span class="sd"> """</span>
+ <span class="n">filter_types</span> <span class="o">=</span> <span class="p">(</span><span class="s2">"pos"</span><span class="p">,</span> <span class="s2">"cons"</span><span class="p">,</span> <span class="s2">"ssclash"</span><span class="p">,</span> <span class="s2">"cys"</span><span class="p">)</span>
+ <span class="n">clash_dict</span> <span class="o">=</span> <span class="p">{</span>
+ <span class="s2">"pos"</span><span class="p">:</span> <span class="p">{</span>
+ <span class="s2">"clash"</span><span class="p">:</span> <span class="s2">"physical proximity"</span><span class="p">,</span>
+ <span class="s2">"desc"</span><span class="p">:</span> <span class="s2">"sequence position"</span><span class="p">},</span>
+ <span class="s2">"cons"</span><span class="p">:</span> <span class="p">{</span>
+ <span class="s2">"clash"</span><span class="p">:</span> <span class="s2">"888"</span><span class="p">,</span>
+ <span class="s2">"desc"</span><span class="p">:</span> <span class="s2">"high conservation"</span><span class="p">},</span>
+ <span class="s2">"ssclash"</span><span class="p">:</span> <span class="p">{</span>
+ <span class="s2">"clash"</span><span class="p">:</span> <span class="s2">"999"</span><span class="p">,</span>
+ <span class="s2">"desc"</span><span class="p">:</span> <span class="s2">"secondary structure prediction conflict"</span><span class="p">},</span>
+ <span class="s2">"cys"</span><span class="p">:</span> <span class="p">{</span>
+ <span class="s2">"clash"</span><span class="p">:</span> <span class="s2">"222"</span><span class="p">,</span>
+ <span class="s2">"desc"</span><span class="p">:</span> <span class="s2">"disulfide bond unicity"</span><span class="p">}}</span>
+
+ <span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">settings</span><span class="p">,</span> <span class="n">nofilter</span><span class="o">=</span><span class="kc">False</span><span class="p">):</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">settings</span> <span class="o">=</span> <span class="n">settings</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">nofilter</span> <span class="o">=</span> <span class="n">nofilter</span>
+
+<div class="viewcode-block" id="MapFilter.nd_filter"><a class="viewcode-back" href="../../ariaec.html#ariaec.protmap.MapFilter.nd_filter">[docs]</a> <span class="k">def</span> <span class="nf">nd_filter</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">mapdict</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> </span>
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> mapdict :</span>
+<span class="sd"> </span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+<span class="sd"> </span>
+<span class="sd"> """</span>
+ <span class="c1"># TODO: build ROC curve with number of top contacts as the parameter</span>
+ <span class="sd">"""</span>
+
+<span class="sd"> :param mapdict:</span>
+<span class="sd"> :return:</span>
+<span class="sd"> """</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s2">"...Network deconvolution filter (alpha=</span><span class="si">%.2f</span><span class="s2">, beta=</span><span class="si">%.2f</span><span class="s2">)"</span><span class="p">,</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="p">[</span><span class="s2">"nd_beta"</span><span class="p">],</span> <span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="p">[</span><span class="s2">"nd_alpha"</span><span class="p">])</span>
+ <span class="n">scoremap</span> <span class="o">=</span> <span class="n">mapdict</span><span class="p">[</span><span class="s2">"scoremap"</span><span class="p">]</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="n">net_deconv</span><span class="p">(</span><span class="n">mapdict</span><span class="p">[</span><span class="s2">"scoremap"</span><span class="p">]</span><span class="o">.</span><span class="n">as_matrix</span><span class="p">(),</span>
+ <span class="n">beta</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="p">[</span><span class="s2">"nd_beta"</span><span class="p">],</span>
+ <span class="n">alpha</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="p">[</span><span class="s2">"nd_alpha"</span><span class="p">]))</span>
+ <span class="c1"># TODO: MAJ score map avec matrice obtenue !!!</span>
+ <span class="c1"># !!!! Verifier que scoremap est bien maj et UTILISEE !!</span>
+ <span class="k">return</span> <span class="n">scoremap</span></div>
+
+<div class="viewcode-block" id="MapFilter.pos_filter"><a class="viewcode-back" href="../../ariaec.html#ariaec.protmap.MapFilter.pos_filter">[docs]</a> <span class="k">def</span> <span class="nf">pos_filter</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">mapdict</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Position filter on maplot</span>
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> kwargs :</span>
+<span class="sd"> param mapdict: dict with maplot key</span>
+<span class="sd"> mapdict :</span>
+<span class="sd"> </span>
+<span class="sd"> **kwargs :</span>
+<span class="sd"> </span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+<span class="sd"> </span>
+<span class="sd"> """</span>
+ <span class="c1"># Liste les contacts proches</span>
+ <span class="n">clash_list</span> <span class="o">=</span> <span class="n">kwargs</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"clash_list"</span><span class="p">)</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s2">"...Position filter"</span><span class="p">)</span>
+ <span class="n">close_list</span> <span class="o">=</span> <span class="p">[]</span>
+ <span class="n">contact_list</span> <span class="o">=</span> <span class="n">mapdict</span><span class="p">[</span><span class="s2">"maplot"</span><span class="p">]</span><span class="o">.</span><span class="n">contact_list</span><span class="p">()</span>
+
+ <span class="k">for</span> <span class="n">contact</span> <span class="ow">in</span> <span class="n">contact_list</span><span class="p">:</span>
+ <span class="n">gap</span> <span class="o">=</span> <span class="nb">abs</span><span class="p">(</span><span class="nb">int</span><span class="p">(</span><span class="n">contact</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span> <span class="o">-</span> <span class="nb">int</span><span class="p">(</span><span class="n">contact</span><span class="p">[</span><span class="mi">1</span><span class="p">]))</span>
+ <span class="k">if</span> <span class="n">gap</span> <span class="o"><=</span> <span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="p">[</span><span class="s1">'position_treshold'</span><span class="p">]:</span>
+ <span class="k">if</span> <span class="n">clash_list</span> <span class="ow">and</span> <span class="n">contact</span> <span class="ow">in</span> <span class="n">clash_list</span><span class="p">:</span>
+ <span class="k">continue</span>
+ <span class="n">close_list</span><span class="o">.</span><span class="n">append</span><span class="p">((</span><span class="n">contact</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">contact</span><span class="p">[</span><span class="mi">1</span><span class="p">]))</span>
+ <span class="k">return</span> <span class="p">{</span><span class="s1">'clash'</span><span class="p">:</span> <span class="n">close_list</span><span class="p">,</span> <span class="s1">'desc'</span><span class="p">:</span> <span class="kc">None</span><span class="p">}</span></div>
+
+<div class="viewcode-block" id="MapFilter.cons_filter"><a class="viewcode-back" href="../../ariaec.html#ariaec.protmap.MapFilter.cons_filter">[docs]</a> <span class="k">def</span> <span class="nf">cons_filter</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">mapdict</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> </span>
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> mapdict :</span>
+<span class="sd"> </span>
+<span class="sd"> **kwargs :</span>
+<span class="sd"> </span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+<span class="sd"> </span>
+<span class="sd"> """</span>
+ <span class="c1"># Liste les contacts aves des residus fortement conserves</span>
+ <span class="sd">"""</span>
+
+<span class="sd"> :param mapdict:</span>
+<span class="sd"> :param kwargs:</span>
+<span class="sd"> :return:</span>
+<span class="sd"> """</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s2">"...Conservation filter"</span><span class="p">)</span>
+ <span class="n">sec_struct</span> <span class="o">=</span> <span class="n">kwargs</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"sec_struct"</span><span class="p">)</span>
+ <span class="n">clash_list</span> <span class="o">=</span> <span class="n">kwargs</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"clash_list"</span><span class="p">)</span>
+ <span class="n">cons_pair</span> <span class="o">=</span> <span class="p">[]</span>
+ <span class="n">cons_res</span> <span class="o">=</span> <span class="p">[]</span>
+ <span class="n">contact_list</span> <span class="o">=</span> <span class="n">mapdict</span><span class="p">[</span><span class="s2">"maplot"</span><span class="p">]</span><span class="o">.</span><span class="n">contact_list</span><span class="p">()</span>
+
+ <span class="k">if</span> <span class="ow">not</span> <span class="n">sec_struct</span><span class="p">:</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">warning</span><span class="p">(</span>
+ <span class="s2">"No conservation information. Can't use related filter"</span><span class="p">)</span>
+ <span class="k">return</span> <span class="p">{</span><span class="s1">'clash'</span><span class="p">:</span> <span class="kc">None</span><span class="p">,</span> <span class="s1">'desc'</span><span class="p">:</span> <span class="kc">None</span><span class="p">}</span>
+
+ <span class="k">if</span> <span class="n">sec_struct</span><span class="o">.</span><span class="n">filetype</span> <span class="o">!=</span> <span class="s2">"indextableplus"</span><span class="p">:</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s2">"Conservation filter only works with indextableplus "</span>
+ <span class="s2">"files !"</span><span class="p">)</span>
+ <span class="k">return</span> <span class="p">{</span><span class="s1">'clash'</span><span class="p">:</span> <span class="kc">None</span><span class="p">,</span> <span class="s1">'desc'</span><span class="p">:</span> <span class="kc">None</span><span class="p">}</span>
+
+ <span class="c1"># parcours la liste de paires dans la matrice struct secondaire</span>
+ <span class="k">for</span> <span class="n">index</span><span class="p">,</span> <span class="n">reslist</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">sec_struct</span><span class="o">.</span><span class="n">ss_matrix</span><span class="p">):</span>
+ <span class="c1"># TODO: Initialize conservation score if other value than int</span>
+ <span class="n">cons_score</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">reslist</span><span class="p">[</span><span class="mi">5</span><span class="p">])</span> <span class="k">if</span> <span class="n">reslist</span><span class="p">[</span><span class="mi">5</span><span class="p">]</span> <span class="o">!=</span> <span class="s2">"-"</span> <span class="k">else</span> <span class="mi">0</span>
+ <span class="k">if</span> <span class="n">cons_score</span> <span class="o">></span> <span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="p">[</span><span class="s2">"conservation_treshold"</span><span class="p">]</span> \
+ <span class="ow">and</span> <span class="n">reslist</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="o">!=</span> <span class="s1">'C'</span><span class="p">:</span>
+ <span class="n">cons_res</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">index</span><span class="p">)</span>
+
+ <span class="k">for</span> <span class="n">contact</span> <span class="ow">in</span> <span class="n">contact_list</span><span class="p">:</span>
+ <span class="k">if</span> <span class="n">contact</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="ow">in</span> <span class="n">cons_res</span> <span class="ow">or</span> <span class="n">contact</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="ow">in</span> <span class="n">cons_res</span><span class="p">:</span>
+ <span class="k">if</span> <span class="n">clash_list</span> <span class="ow">and</span> <span class="n">contact</span> <span class="ow">in</span> <span class="n">clash_list</span><span class="p">:</span>
+ <span class="c1"># If this clash already exist</span>
+ <span class="k">continue</span>
+ <span class="n">cons_pair</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">contact</span><span class="p">)</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="s2">"Highly conserved residue list: </span><span class="si">%s</span><span class="s2">"</span><span class="p">,</span> <span class="n">cons_res</span><span class="p">)</span>
+ <span class="k">return</span> <span class="p">{</span><span class="s1">'clash'</span><span class="p">:</span> <span class="n">cons_pair</span><span class="p">,</span> <span class="s1">'desc'</span><span class="p">:</span> <span class="kc">None</span><span class="p">}</span></div>
+
+<div class="viewcode-block" id="MapFilter.cys_filter"><a class="viewcode-back" href="../../ariaec.html#ariaec.protmap.MapFilter.cys_filter">[docs]</a> <span class="nd">@staticmethod</span>
+ <span class="k">def</span> <span class="nf">cys_filter</span><span class="p">(</span><span class="n">mapdict</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> </span>
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> mapdict :</span>
+<span class="sd"> </span>
+<span class="sd"> **kwargs :</span>
+<span class="sd"> </span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+<span class="sd"> </span>
+<span class="sd"> """</span>
+ <span class="c1"># Si scoremap existe, selectionner les contacts cys-cys qui ont les</span>
+ <span class="c1"># meilleurs scores, fournit une liste des contacts disulfures qui</span>
+ <span class="c1"># possedent des scores plus faibles</span>
+ <span class="sd">"""</span>
+
+<span class="sd"> :param mapdict:</span>
+<span class="sd"> :param kwargs:</span>
+<span class="sd"> :return:</span>
+<span class="sd"> """</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s2">"...Disulfure bridge unicity filter"</span><span class="p">)</span>
+ <span class="n">clash_list</span> <span class="o">=</span> <span class="n">kwargs</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"clash_list"</span><span class="p">)</span>
+ <span class="n">unidisbridge_list</span> <span class="o">=</span> <span class="p">[]</span> <span class="c1"># Liste les ponts disulfures uniques</span>
+ <span class="n">clashdisbridge_list</span> <span class="o">=</span> <span class="p">[]</span> <span class="c1"># Liste les ponts disulfures incompatibles</span>
+ <span class="n">desc</span> <span class="o">=</span> <span class="p">[]</span>
+
+ <span class="k">if</span> <span class="n">mapdict</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"scoremap"</span><span class="p">)</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+ <span class="n">scoremap</span> <span class="o">=</span> <span class="n">mapdict</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"scoremap"</span><span class="p">)</span>
+ <span class="c1"># List of all cysteine</span>
+ <span class="n">cys_list</span> <span class="o">=</span> <span class="p">[</span><span class="n">idx</span> <span class="k">for</span> <span class="n">idx</span><span class="p">,</span> <span class="n">val</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">scoremap</span><span class="o">.</span><span class="n">index</span><span class="o">.</span><span class="n">values</span><span class="p">)</span>
+ <span class="k">if</span> <span class="n">val</span><span class="o">.</span><span class="n">endswith</span><span class="p">(</span><span class="s1">'CYS'</span><span class="p">)]</span>
+ <span class="n">dis_bridge_list</span> <span class="o">=</span> <span class="p">{</span><span class="n">ss</span><span class="p">:</span> <span class="n">scoremap</span><span class="o">.</span><span class="n">iat</span><span class="p">[</span><span class="n">ss</span><span class="p">]</span> <span class="k">for</span> <span class="n">ss</span>
+ <span class="ow">in</span> <span class="nb">list</span><span class="p">(</span><span class="n">itertools</span><span class="o">.</span><span class="n">combinations</span><span class="p">(</span><span class="n">cys_list</span><span class="p">,</span> <span class="mi">2</span><span class="p">))}</span>
+ <span class="k">if</span> <span class="n">dis_bridge_list</span><span class="p">:</span>
+ <span class="c1"># Get list of all disulfure bridges sorted</span>
+ <span class="n">sorted_ss</span> <span class="o">=</span> <span class="nb">zip</span><span class="p">(</span><span class="o">*</span><span class="nb">sorted</span><span class="p">(</span><span class="n">dis_bridge_list</span><span class="o">.</span><span class="n">items</span><span class="p">(),</span>
+ <span class="n">key</span><span class="o">=</span><span class="n">operator</span><span class="o">.</span><span class="n">itemgetter</span><span class="p">(</span><span class="mi">1</span><span class="p">),</span>
+ <span class="n">reverse</span><span class="o">=</span><span class="kc">True</span><span class="p">))[</span><span class="mi">0</span><span class="p">]</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">return</span> <span class="p">{</span><span class="s1">'clash'</span><span class="p">:</span> <span class="kc">None</span><span class="p">,</span> <span class="s1">'desc'</span><span class="p">:</span> <span class="kc">None</span><span class="p">}</span>
+ <span class="k">for</span> <span class="n">dis_bridge</span> <span class="ow">in</span> <span class="n">sorted_ss</span><span class="p">:</span>
+ <span class="c1"># foreach disulfure bridge</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="s1">'Checking </span><span class="si">%s</span><span class="s1"> </span><span class="si">%s</span><span class="s1">'</span><span class="p">,</span> <span class="n">addtup</span><span class="p">(</span><span class="n">dis_bridge</span><span class="p">),</span>
+ <span class="n">scoremap</span><span class="o">.</span><span class="n">iat</span><span class="p">[</span><span class="n">dis_bridge</span><span class="p">])</span>
+ <span class="k">if</span> <span class="n">dis_bridge</span> <span class="ow">in</span> <span class="n">clash_list</span><span class="p">:</span>
+ <span class="c1"># given contact already removed with previous filters</span>
+ <span class="k">continue</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="c1"># Check for each cys in dis_bridge if they aready exists</span>
+ <span class="c1"># in unidisbridge_list</span>
+ <span class="n">exdis</span> <span class="o">=</span> <span class="kc">None</span>
+ <span class="k">if</span> <span class="n">unidisbridge_list</span><span class="p">:</span>
+ <span class="k">for</span> <span class="n">cys</span> <span class="ow">in</span> <span class="n">dis_bridge</span><span class="p">:</span>
+ <span class="k">for</span> <span class="n">unidis</span> <span class="ow">in</span> <span class="n">unidisbridge_list</span><span class="p">:</span>
+ <span class="k">if</span> <span class="n">cys</span> <span class="ow">in</span> <span class="n">unidis</span><span class="p">:</span>
+ <span class="n">exdis</span> <span class="o">=</span> <span class="n">unidis</span>
+ <span class="k">break</span>
+ <span class="k">if</span> <span class="n">exdis</span><span class="p">:</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="s2">"Ss bridge </span><span class="si">%s</span><span class="s2"> have at least one cys in "</span>
+ <span class="s2">"common with previous ss filtered (</span><span class="si">%s</span><span class="s2">). "</span><span class="p">,</span>
+ <span class="n">addtup</span><span class="p">(</span><span class="n">dis_bridge</span><span class="p">),</span>
+ <span class="nb">map</span><span class="p">(</span><span class="n">addtup</span><span class="p">,</span> <span class="n">unidisbridge_list</span><span class="p">))</span>
+ <span class="k">if</span> <span class="n">scoremap</span><span class="o">.</span><span class="n">iat</span><span class="p">[</span><span class="n">dis_bridge</span><span class="p">]</span> <span class="o">></span> <span class="n">scoremap</span><span class="o">.</span><span class="n">iat</span><span class="p">[</span><span class="n">exdis</span><span class="p">]:</span>
+ <span class="c1"># Better cys--cys contact</span>
+ <span class="c1"># List cys-cys contacts that will be removed in</span>
+ <span class="c1"># unidisbridge_list</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="s2">"</span><span class="si">%s</span><span class="s2"> has better score than </span><span class="si">%s</span><span class="s2">"</span><span class="p">,</span>
+ <span class="n">addtup</span><span class="p">(</span><span class="n">dis_bridge</span><span class="p">),</span>
+ <span class="n">addtup</span><span class="p">(</span><span class="n">exdis</span><span class="p">))</span>
+ <span class="n">remcys</span> <span class="o">=</span> <span class="p">(</span><span class="n">unidis</span> <span class="k">for</span> <span class="n">cys</span> <span class="ow">in</span> <span class="n">dis_bridge</span> <span class="k">for</span> <span class="n">unidis</span>
+ <span class="ow">in</span> <span class="n">unidisbridge_list</span> <span class="k">if</span> <span class="n">cys</span> <span class="ow">in</span> <span class="n">unidis</span><span class="p">)</span>
+ <span class="k">for</span> <span class="n">dis</span> <span class="ow">in</span> <span class="n">remcys</span><span class="p">:</span>
+ <span class="c1"># PB si un des dis supprime est</span>
+ <span class="n">clashdisbridge_list</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">dis</span><span class="p">)</span>
+ <span class="n">clashdisbridge_list</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">dis</span><span class="p">[::</span><span class="o">-</span><span class="mi">1</span><span class="p">])</span>
+ <span class="n">unidisbridge_list</span><span class="o">.</span><span class="n">remove</span><span class="p">(</span><span class="n">dis</span><span class="p">)</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="s2">"Added </span><span class="si">%s</span><span class="s2"> to clashlist </span><span class="si">%s</span><span class="s2">"</span><span class="p">,</span>
+ <span class="n">addtup</span><span class="p">(</span><span class="n">dis</span><span class="p">),</span>
+ <span class="nb">map</span><span class="p">(</span><span class="n">addtup</span><span class="p">,</span> <span class="n">clashdisbridge_list</span><span class="p">))</span>
+ <span class="n">unidisbridge_list</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">dis_bridge</span><span class="p">)</span>
+ <span class="k">continue</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="n">clashdisbridge_list</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">dis_bridge</span><span class="p">)</span>
+ <span class="n">clashdisbridge_list</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">dis_bridge</span><span class="p">[::</span><span class="o">-</span><span class="mi">1</span><span class="p">])</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="s2">"Added </span><span class="si">%s</span><span class="s2"> to ss clashlist </span><span class="si">%s</span><span class="s2">"</span><span class="p">,</span>
+ <span class="n">addtup</span><span class="p">(</span><span class="n">dis_bridge</span><span class="p">),</span>
+ <span class="nb">map</span><span class="p">(</span><span class="n">addtup</span><span class="p">,</span> <span class="n">clashdisbridge_list</span><span class="p">))</span>
+ <span class="k">continue</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="s1">'Adding bridge </span><span class="si">%s</span><span class="s1"> to ss filtered list'</span><span class="p">,</span> <span class="n">dis_bridge</span><span class="p">)</span>
+ <span class="n">unidisbridge_list</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">dis_bridge</span><span class="p">)</span>
+ <span class="k">return</span> <span class="p">{</span><span class="s1">'clash'</span><span class="p">:</span> <span class="n">clashdisbridge_list</span><span class="p">,</span> <span class="s1">'desc'</span><span class="p">:</span> <span class="n">desc</span><span class="p">}</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="c1"># If no score given, return empty list</span>
+ <span class="k">return</span> <span class="p">{</span><span class="s1">'clash'</span><span class="p">:</span> <span class="kc">None</span><span class="p">,</span> <span class="s1">'desc'</span><span class="p">:</span> <span class="kc">None</span><span class="p">}</span></div>
+
+<div class="viewcode-block" id="MapFilter.ssclash_filter"><a class="viewcode-back" href="../../ariaec.html#ariaec.protmap.MapFilter.ssclash_filter">[docs]</a> <span class="nd">@staticmethod</span>
+ <span class="k">def</span> <span class="nf">ssclash_filter</span><span class="p">(</span><span class="n">mapdict</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+
+ <span class="sd">"""</span>
+<span class="sd"> </span>
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> mapdict :</span>
+<span class="sd"> param kwargs:</span>
+<span class="sd"> **kwargs :</span>
+<span class="sd"> </span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+<span class="sd"> </span>
+<span class="sd"> """</span>
+
+ <span class="k">def</span> <span class="nf">hum_contact</span><span class="p">(</span><span class="n">xy</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> </span>
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> xy :</span>
+<span class="sd"> return:</span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+<span class="sd"> </span>
+<span class="sd"> """</span>
+ <span class="k">return</span> <span class="n">xy</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">+</span> <span class="mi">1</span><span class="p">,</span> <span class="n">xy</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="o">+</span> <span class="mi">1</span>
+
+ <span class="c1"># TODO: better add clash list and sec_struct as object attribute</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s2">"...Secondary structure clash filter"</span><span class="p">)</span>
+ <span class="n">sec_struct</span> <span class="o">=</span> <span class="n">kwargs</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"sec_struct"</span><span class="p">)</span>
+ <span class="n">clash_list</span> <span class="o">=</span> <span class="n">kwargs</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"clash_list"</span><span class="p">)</span>
+ <span class="n">ssclash_pair</span> <span class="o">=</span> <span class="p">[]</span>
+ <span class="n">desc_dict</span> <span class="o">=</span> <span class="p">{}</span>
+
+ <span class="k">if</span> <span class="ow">not</span> <span class="n">sec_struct</span><span class="p">:</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">warning</span><span class="p">(</span><span class="s2">"No secondary structure information. Can't use secondary"</span>
+ <span class="s2">" structure filter"</span><span class="p">)</span>
+ <span class="k">return</span> <span class="p">{</span><span class="s1">'clash'</span><span class="p">:</span> <span class="kc">None</span><span class="p">,</span> <span class="s1">'desc'</span><span class="p">:</span> <span class="kc">None</span><span class="p">}</span>
+
+ <span class="n">ss_matrix</span> <span class="o">=</span> <span class="n">sec_struct</span><span class="o">.</span><span class="n">ss_matrix</span>
+ <span class="n">ss_list</span> <span class="o">=</span> <span class="nb">zip</span><span class="p">(</span><span class="o">*</span><span class="n">ss_matrix</span><span class="p">)[</span><span class="mi">2</span><span class="p">]</span>
+ <span class="c1"># contact_list from contact map start at 0 !!</span>
+ <span class="n">contact_list</span> <span class="o">=</span> <span class="n">mapdict</span><span class="p">[</span><span class="s2">"maplot"</span><span class="p">]</span><span class="o">.</span><span class="n">contact_list</span><span class="p">()</span>
+
+ <span class="n">ss_start_end</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">defaultdict</span><span class="p">(</span><span class="k">lambda</span><span class="p">:</span> <span class="p">[</span><span class="kc">None</span><span class="p">,</span> <span class="kc">None</span><span class="p">])</span>
+
+ <span class="c1"># TODO: deplacer construction du dic ss_start_end dans SsList</span>
+ <span class="k">for</span> <span class="n">res_ind</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">ss_matrix</span><span class="p">)):</span>
+ <span class="c1"># Construction du dict ss_start_end</span>
+ <span class="k">if</span> <span class="n">res_ind</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
+ <span class="c1"># If first residue</span>
+ <span class="c1"># Save ss start humanidx related to res_ind</span>
+ <span class="n">ss_start_end</span><span class="p">[</span><span class="n">ss_matrix</span><span class="p">[</span><span class="n">res_ind</span><span class="p">][</span><span class="mi">2</span><span class="p">]][</span><span class="mi">0</span><span class="p">]</span> <span class="o">=</span> <span class="n">res_ind</span>
+ <span class="k">if</span> <span class="n">ss_matrix</span><span class="p">[</span><span class="n">res_ind</span><span class="p">][</span><span class="mi">2</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span> <span class="o">!=</span> <span class="n">ss_matrix</span><span class="p">[</span><span class="n">res_ind</span> <span class="o">+</span> <span class="mi">1</span><span class="p">][</span><span class="mi">2</span><span class="p">][</span><span class="mi">0</span><span class="p">]:</span>
+ <span class="c1"># If next res is not in the same ss</span>
+ <span class="n">ss_start_end</span><span class="p">[</span><span class="n">ss_matrix</span><span class="p">[</span><span class="n">res_ind</span><span class="p">][</span><span class="mi">2</span><span class="p">]][</span><span class="mi">1</span><span class="p">]</span> <span class="o">=</span> <span class="n">res_ind</span>
+ <span class="n">ss_start_end</span><span class="p">[</span><span class="n">ss_matrix</span><span class="p">[</span><span class="n">res_ind</span> <span class="o">+</span> <span class="mi">1</span><span class="p">][</span><span class="mi">2</span><span class="p">]][</span><span class="mi">0</span><span class="p">]</span> <span class="o">=</span> <span class="n">res_ind</span> <span class="o">+</span> <span class="mi">1</span>
+ <span class="k">elif</span> <span class="n">res_ind</span> <span class="o">==</span> <span class="nb">len</span><span class="p">(</span><span class="n">ss_matrix</span><span class="p">)</span> <span class="o">-</span> <span class="mi">1</span><span class="p">:</span>
+ <span class="c1"># Si dernier res</span>
+ <span class="n">ss_start_end</span><span class="p">[</span><span class="n">ss_matrix</span><span class="p">[</span><span class="n">res_ind</span><span class="p">][</span><span class="mi">2</span><span class="p">]][</span><span class="mi">1</span><span class="p">]</span> <span class="o">=</span> <span class="n">res_ind</span>
+ <span class="k">elif</span> <span class="n">ss_matrix</span><span class="p">[</span><span class="n">res_ind</span><span class="p">][</span><span class="mi">2</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span> <span class="o">!=</span> <span class="n">ss_matrix</span><span class="p">[</span><span class="n">res_ind</span> <span class="o">+</span> <span class="mi">1</span><span class="p">][</span><span class="mi">2</span><span class="p">][</span><span class="mi">0</span><span class="p">]:</span>
+ <span class="c1"># If next res not in the same ss</span>
+ <span class="n">ss_start_end</span><span class="p">[</span><span class="n">ss_matrix</span><span class="p">[</span><span class="n">res_ind</span><span class="p">][</span><span class="mi">2</span><span class="p">]][</span><span class="mi">1</span><span class="p">]</span> <span class="o">=</span> <span class="n">res_ind</span>
+ <span class="n">ss_start_end</span><span class="p">[</span><span class="n">ss_matrix</span><span class="p">[</span><span class="n">res_ind</span> <span class="o">+</span> <span class="mi">1</span><span class="p">][</span><span class="mi">2</span><span class="p">]][</span><span class="mi">0</span><span class="p">]</span> <span class="o">=</span> <span class="n">res_ind</span> <span class="o">+</span> <span class="mi">1</span>
+
+ <span class="n">start_list</span> <span class="o">=</span> <span class="p">[</span><span class="n">ss_start_end</span><span class="p">[</span><span class="n">elm</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span> <span class="k">for</span> <span class="n">elm</span> <span class="ow">in</span> <span class="n">ss_start_end</span><span class="p">]</span>
+ <span class="n">end_list</span> <span class="o">=</span> <span class="p">[</span><span class="n">ss_start_end</span><span class="p">[</span><span class="n">elm</span><span class="p">][</span><span class="mi">1</span><span class="p">]</span> <span class="k">for</span> <span class="n">elm</span> <span class="ow">in</span> <span class="n">ss_start_end</span><span class="p">]</span>
+
+ <span class="k">for</span> <span class="n">icontact</span><span class="p">,</span> <span class="n">contact</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">contact_list</span><span class="p">):</span>
+ <span class="c1"># For each res-res contact</span>
+ <span class="n">outcontact</span> <span class="o">=</span> <span class="nb">str</span><span class="p">(</span><span class="n">hum_contact</span><span class="p">(</span><span class="n">contact</span><span class="p">))</span>
+ <span class="k">if</span> <span class="n">contact</span> <span class="ow">in</span> <span class="n">clash_list</span><span class="p">:</span>
+ <span class="k">continue</span>
+ <span class="n">resi</span> <span class="o">=</span> <span class="n">contact</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="c1"># Pos number (0...n-1)</span>
+ <span class="n">resj</span> <span class="o">=</span> <span class="n">contact</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
+ <span class="n">ssi</span> <span class="o">=</span> <span class="n">ss_list</span><span class="p">[</span><span class="n">resi</span><span class="p">]</span>
+ <span class="n">ssj</span> <span class="o">=</span> <span class="n">ss_list</span><span class="p">[</span><span class="n">resj</span><span class="p">]</span>
+
+ <span class="k">if</span> <span class="n">ssi</span> <span class="o">==</span> <span class="n">ssj</span> <span class="ow">and</span> <span class="p">(</span><span class="n">ssi</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">ssj</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span> <span class="ow">in</span> <span class="p">((</span><span class="s2">"H"</span><span class="p">,</span> <span class="s2">"H"</span><span class="p">),</span> <span class="p">(</span><span class="s2">"E"</span><span class="p">,</span> <span class="s2">"E"</span><span class="p">)):</span>
+ <span class="c1"># If both residues are in same helix or strand</span>
+ <span class="n">desc</span> <span class="o">=</span> <span class="s2">"</span><span class="si">%s</span><span class="s2">,</span><span class="si">%s</span><span class="s2">"</span> <span class="o">%</span> <span class="p">(</span><span class="n">ssi</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">ssj</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span>
+ <span class="n">desc_dict</span><span class="p">[</span><span class="n">contact</span><span class="p">]</span> <span class="o">=</span> <span class="n">desc</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="s2">"Ss conflict for contact </span><span class="si">%d</span><span class="s2"> </span><span class="si">%s</span><span class="s2"> (</span><span class="si">%s</span><span class="s2">)"</span><span class="p">,</span>
+ <span class="n">icontact</span><span class="p">,</span> <span class="n">outcontact</span><span class="p">,</span> <span class="n">desc</span><span class="p">)</span>
+ <span class="n">ssclash_pair</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">contact</span><span class="p">)</span>
+ <span class="c1"># ELIF encadre H ou E</span>
+ <span class="k">elif</span> <span class="n">ssi</span> <span class="o">!=</span> <span class="n">ssj</span><span class="p">:</span>
+ <span class="c1"># If both residues are not in the same ss</span>
+ <span class="n">ssclash</span> <span class="o">=</span> <span class="kc">None</span>
+ <span class="k">for</span> <span class="n">n</span> <span class="ow">in</span> <span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="mi">2</span><span class="p">,</span> <span class="mi">3</span><span class="p">,</span> <span class="mi">4</span><span class="p">):</span>
+
+ <span class="c1"># Search type of the bond (H-1 H, E-2 E, ...)</span>
+ <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">2</span><span class="p">):</span>
+ <span class="c1"># Test both sides</span>
+
+ <span class="n">resi</span> <span class="o">=</span> <span class="n">contact</span><span class="p">[</span><span class="n">i</span><span class="p">]</span>
+ <span class="n">resj</span> <span class="o">=</span> <span class="n">contact</span><span class="p">[</span><span class="n">i</span> <span class="o">-</span> <span class="mi">1</span><span class="p">]</span>
+ <span class="n">ssi</span> <span class="o">=</span> <span class="n">ss_list</span><span class="p">[</span><span class="n">resi</span><span class="p">]</span>
+ <span class="n">ssj</span> <span class="o">=</span> <span class="n">ss_list</span><span class="p">[</span><span class="n">resj</span><span class="p">]</span>
+
+ <span class="k">try</span><span class="p">:</span>
+ <span class="n">ssi_pn</span> <span class="o">=</span> <span class="n">ss_list</span><span class="p">[</span><span class="n">resi</span> <span class="o">+</span> <span class="n">n</span><span class="p">]</span>
+ <span class="n">ssi_mn</span> <span class="o">=</span> <span class="n">ss_list</span><span class="p">[</span><span class="n">resi</span> <span class="o">-</span> <span class="n">n</span><span class="p">]</span>
+ <span class="n">ssj_pn</span> <span class="o">=</span> <span class="n">ss_list</span><span class="p">[</span><span class="n">resj</span> <span class="o">+</span> <span class="n">n</span><span class="p">]</span>
+ <span class="n">ssj_mn</span> <span class="o">=</span> <span class="n">ss_list</span><span class="p">[</span><span class="n">resj</span> <span class="o">-</span> <span class="n">n</span><span class="p">]</span>
+ <span class="k">except</span> <span class="ne">IndexError</span><span class="p">:</span>
+ <span class="k">continue</span>
+
+ <span class="c1"># (E-n, E) OR (H-n, H)</span>
+ <span class="k">if</span> <span class="n">ssj</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="ow">in</span> <span class="p">(</span><span class="s2">"H"</span><span class="p">,</span> <span class="s2">"E"</span><span class="p">)</span> \
+ <span class="ow">and</span> <span class="n">resi</span> <span class="o">+</span> <span class="n">n</span> <span class="ow">in</span> <span class="n">start_list</span> \
+ <span class="ow">and</span> <span class="n">ssi_pn</span> <span class="o">==</span> <span class="n">ssj</span><span class="p">:</span>
+ <span class="c1"># --i**[-----j-----]--- (n: **)</span>
+ <span class="c1"># E/H</span>
+ <span class="n">ssclash</span> <span class="o">=</span> <span class="s2">"</span><span class="si">%s</span><span class="s2">-</span><span class="si">%d</span><span class="s2">,</span><span class="si">%s</span><span class="s2">"</span> <span class="o">%</span> <span class="p">(</span><span class="n">ssi_pn</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">n</span><span class="p">,</span> <span class="n">ssj</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span>
+ <span class="k">break</span>
+ <span class="k">if</span> <span class="n">ssj</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="ow">in</span> <span class="p">(</span><span class="s2">"H"</span><span class="p">,</span> <span class="s2">"E"</span><span class="p">)</span> \
+ <span class="ow">and</span> <span class="n">resi</span> <span class="o">-</span> <span class="n">n</span> <span class="ow">in</span> <span class="n">end_list</span> \
+ <span class="ow">and</span> <span class="n">ssi_mn</span> <span class="o">==</span> <span class="n">ssj</span><span class="p">:</span>
+ <span class="c1"># -----[-----j-----]**i--- (n: **)</span>
+ <span class="c1"># E/H</span>
+ <span class="n">ssclash</span> <span class="o">=</span> <span class="s2">"</span><span class="si">%s</span><span class="s2">+</span><span class="si">%d</span><span class="s2">,</span><span class="si">%s</span><span class="s2">"</span> <span class="o">%</span> <span class="p">(</span><span class="n">ssi_mn</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">n</span><span class="p">,</span> <span class="n">ssj</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span>
+ <span class="k">break</span>
+ <span class="k">if</span> <span class="n">ssi</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="ow">in</span> <span class="p">(</span><span class="s2">"H"</span><span class="p">,</span> <span class="s2">"E"</span><span class="p">)</span> \
+ <span class="ow">and</span> <span class="n">resj</span> <span class="o">+</span> <span class="n">n</span> <span class="ow">in</span> <span class="n">start_list</span> \
+ <span class="ow">and</span> <span class="n">ssj_pn</span> <span class="o">==</span> <span class="n">ssi</span><span class="p">:</span>
+ <span class="c1"># --j**[-----i-----]--- (n: **)</span>
+ <span class="c1"># E/H</span>
+ <span class="n">ssclash</span> <span class="o">=</span> <span class="s2">"</span><span class="si">%s</span><span class="s2">-</span><span class="si">%d</span><span class="s2">,</span><span class="si">%s</span><span class="s2">"</span> <span class="o">%</span> <span class="p">(</span><span class="n">ssj_pn</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">n</span><span class="p">,</span> <span class="n">ssi</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span>
+ <span class="k">break</span>
+ <span class="k">if</span> <span class="n">ssi</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="ow">in</span> <span class="p">(</span><span class="s2">"H"</span><span class="p">,</span> <span class="s2">"E"</span><span class="p">)</span> \
+ <span class="ow">and</span> <span class="n">resj</span> <span class="o">-</span> <span class="n">n</span> <span class="ow">in</span> <span class="n">end_list</span> \
+ <span class="ow">and</span> <span class="n">ssj_mn</span> <span class="o">==</span> <span class="n">ssi</span><span class="p">:</span>
+ <span class="c1"># -----[-----i-----]**j--- (n: **)</span>
+ <span class="c1"># E/H</span>
+ <span class="n">ssclash</span> <span class="o">=</span> <span class="s2">"</span><span class="si">%s</span><span class="s2">+</span><span class="si">%d</span><span class="s2">,</span><span class="si">%s</span><span class="s2">"</span> <span class="o">%</span> <span class="p">(</span><span class="n">ssj_mn</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">n</span><span class="p">,</span> <span class="n">ssi</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span>
+ <span class="k">break</span>
+
+ <span class="c1"># (E+n, E-n), (H+n, H-n)</span>
+ <span class="k">if</span> <span class="n">ssi_mn</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="ow">in</span> <span class="p">(</span><span class="s2">"H"</span><span class="p">,</span> <span class="s2">"E"</span><span class="p">)</span> \
+ <span class="ow">and</span> <span class="n">resi</span> <span class="o">-</span> <span class="n">n</span> <span class="ow">in</span> <span class="n">end_list</span> \
+ <span class="ow">and</span> <span class="n">resj</span> <span class="o">+</span> <span class="n">n</span> <span class="ow">in</span> <span class="n">start_list</span> \
+ <span class="ow">and</span> <span class="n">ssi_mn</span> <span class="o">==</span> <span class="n">ssj_pn</span><span class="p">:</span>
+ <span class="c1"># --j**[-----H/E-----]**i-- (n: **)</span>
+ <span class="n">ssclash</span> <span class="o">=</span> <span class="s2">"</span><span class="si">%s</span><span class="s2">+</span><span class="si">%d</span><span class="s2">,</span><span class="si">%s</span><span class="s2">-</span><span class="si">%d</span><span class="s2">"</span> <span class="o">%</span> <span class="p">(</span><span class="n">ssi_mn</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">n</span><span class="p">,</span>
+ <span class="n">ssj_pn</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">n</span><span class="p">)</span>
+ <span class="k">break</span>
+ <span class="k">if</span> <span class="n">ssi_pn</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="ow">in</span> <span class="p">(</span><span class="s2">"H"</span><span class="p">,</span> <span class="s2">"E"</span><span class="p">)</span> \
+ <span class="ow">and</span> <span class="n">resi</span> <span class="o">+</span> <span class="n">n</span> <span class="ow">in</span> <span class="n">start_list</span> \
+ <span class="ow">and</span> <span class="n">resj</span> <span class="o">-</span> <span class="n">n</span> <span class="ow">in</span> <span class="n">end_list</span> \
+ <span class="ow">and</span> <span class="n">ssi_pn</span> <span class="o">==</span> <span class="n">ssj_mn</span><span class="p">:</span>
+ <span class="c1"># --i**[-----H/E-----]**j-- (n: **)</span>
+ <span class="n">ssclash</span> <span class="o">=</span> <span class="s2">"</span><span class="si">%s</span><span class="s2">-</span><span class="si">%d</span><span class="s2">,</span><span class="si">%s</span><span class="s2">+</span><span class="si">%d</span><span class="s2">"</span> <span class="o">%</span> <span class="p">(</span><span class="n">ssi_pn</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">n</span><span class="p">,</span>
+ <span class="n">ssj_mn</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">n</span><span class="p">)</span>
+ <span class="k">break</span>
+
+ <span class="k">if</span> <span class="n">ssclash</span><span class="p">:</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="s2">"Ss clash for contact </span><span class="si">%d</span><span class="s2"> </span><span class="si">%s</span><span class="s2"> (</span><span class="si">%s</span><span class="s2">)"</span><span class="p">,</span>
+ <span class="n">icontact</span><span class="p">,</span> <span class="n">outcontact</span><span class="p">,</span> <span class="n">ssclash</span><span class="p">)</span>
+ <span class="k">if</span> <span class="n">ssclash</span> <span class="ow">in</span> <span class="p">(</span><span class="s2">"H-2,H"</span><span class="p">,</span> <span class="s2">"H+2,H"</span><span class="p">)</span> \
+ <span class="ow">and</span> <span class="nb">abs</span><span class="p">(</span><span class="n">resi</span> <span class="o">-</span> <span class="n">resj</span><span class="p">)</span> <span class="o">==</span> <span class="mi">6</span><span class="p">:</span>
+ <span class="c1"># Allow contact to the fifth residue in the</span>
+ <span class="c1"># helix</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="s2">"Found (H-2, H) for contact </span><span class="si">%s</span><span class="s2"> clash "</span>
+ <span class="s2">"but contact with fifth residue is "</span>
+ <span class="s2">"actually allowed"</span><span class="p">,</span>
+ <span class="n">outcontact</span><span class="p">)</span>
+ <span class="n">ssclash</span> <span class="o">=</span> <span class="kc">None</span>
+ <span class="k">elif</span> <span class="n">ssclash</span> <span class="ow">in</span> <span class="p">(</span><span class="s2">"H-3,H"</span><span class="p">,</span> <span class="s2">"H+3,H"</span><span class="p">)</span> \
+ <span class="ow">and</span> <span class="nb">abs</span><span class="p">(</span><span class="n">resi</span> <span class="o">-</span> <span class="n">resj</span><span class="p">)</span> <span class="o"><</span> <span class="mi">12</span><span class="p">:</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="s2">"Found (H-3, H) for contact </span><span class="si">%s</span><span class="s2"> clash "</span>
+ <span class="s2">"but contact between 3rd and 10th "</span>
+ <span class="s2">"residues are actually allowed"</span><span class="p">,</span>
+ <span class="n">outcontact</span><span class="p">)</span>
+ <span class="c1"># Allow contact between 3rd residue and 10th</span>
+ <span class="n">ssclash</span> <span class="o">=</span> <span class="kc">None</span>
+ <span class="k">elif</span> <span class="n">ssclash</span> <span class="ow">in</span> <span class="p">(</span><span class="s2">"H-4,H"</span><span class="p">,</span> <span class="s2">"H+4,H"</span><span class="p">):</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="s2">"H-4,H are actually allowed"</span><span class="p">)</span>
+ <span class="n">ssclash</span> <span class="o">=</span> <span class="kc">None</span>
+ <span class="k">elif</span> <span class="n">ssclash</span> <span class="ow">in</span> <span class="p">(</span><span class="s2">"H-2,H+2"</span><span class="p">,</span> <span class="s2">"H+2,H-2"</span><span class="p">):</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="s2">"H-2,H+2 are actually allowed"</span><span class="p">)</span>
+ <span class="n">ssclash</span> <span class="o">=</span> <span class="kc">None</span>
+ <span class="k">elif</span> <span class="n">ssclash</span> <span class="ow">in</span> <span class="p">(</span><span class="s2">"H-3,H+3"</span><span class="p">,</span> <span class="s2">"H+3,H-3"</span><span class="p">):</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="s2">"H-3,H+3 are actually allowed"</span><span class="p">)</span>
+ <span class="n">ssclash</span> <span class="o">=</span> <span class="kc">None</span>
+ <span class="k">elif</span> <span class="n">ssclash</span> <span class="ow">in</span> <span class="p">(</span><span class="s2">"H-4,H+4"</span><span class="p">,</span> <span class="s2">"H+4,H-4"</span><span class="p">):</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="s2">"H-4,H+4 are actually allowed"</span><span class="p">)</span>
+ <span class="n">ssclash</span> <span class="o">=</span> <span class="kc">None</span>
+ <span class="k">elif</span> <span class="n">ssclash</span> <span class="o">==</span> <span class="s2">"E-2,E+2"</span><span class="p">:</span>
+ <span class="n">strand</span> <span class="o">=</span> <span class="n">ssj</span> <span class="k">if</span> <span class="n">ssj</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">==</span> <span class="s2">"E"</span> <span class="k">else</span> <span class="n">ssi</span>
+ <span class="n">start</span> <span class="o">=</span> <span class="n">ss_start_end</span><span class="p">[</span><span class="n">strand</span><span class="p">][</span><span class="mi">1</span><span class="p">]</span>
+ <span class="n">end</span> <span class="o">=</span> <span class="n">ss_start_end</span><span class="p">[</span><span class="n">strand</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span>
+ <span class="k">if</span> <span class="nb">abs</span><span class="p">(</span><span class="n">start</span> <span class="o">-</span> <span class="n">end</span> <span class="o">+</span> <span class="mi">1</span><span class="p">)</span> <span class="o"><=</span> <span class="mi">5</span><span class="p">:</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="s2">"Found (E-2, E+2) for contact "</span>
+ <span class="s2">"</span><span class="si">%s</span><span class="s2"> clash but strand "</span>
+ <span class="s2">"is < 5 residues"</span><span class="p">,</span> <span class="n">outcontact</span><span class="p">)</span>
+ <span class="c1"># Allow contact if strand < 5 residues (gap <8)</span>
+ <span class="n">ssclash</span> <span class="o">=</span> <span class="kc">None</span>
+ <span class="k">elif</span> <span class="n">ssclash</span> <span class="ow">in</span> <span class="p">(</span><span class="s2">"E-3,E+3"</span><span class="p">,</span> <span class="s2">"E+3,E-3"</span><span class="p">):</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="s2">"E-3,E+3 are actually allowed"</span><span class="p">)</span>
+ <span class="n">ssclash</span> <span class="o">=</span> <span class="kc">None</span>
+ <span class="k">elif</span> <span class="n">ssclash</span> <span class="ow">in</span> <span class="p">(</span><span class="s2">"E-4,E+4"</span><span class="p">,</span> <span class="s2">"E+4,E-4"</span><span class="p">):</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="s2">"E-4,E+4 are actually allowed"</span><span class="p">)</span>
+ <span class="n">ssclash</span> <span class="o">=</span> <span class="kc">None</span>
+ <span class="k">elif</span> <span class="n">ssclash</span> <span class="ow">in</span> <span class="p">(</span><span class="s2">"E-4,E"</span><span class="p">,</span> <span class="s2">"E+4,E"</span><span class="p">)</span> \
+ <span class="ow">and</span> <span class="nb">abs</span><span class="p">(</span><span class="n">resi</span> <span class="o">-</span> <span class="n">resj</span><span class="p">)</span> <span class="o"><</span> <span class="mi">8</span><span class="p">:</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="s2">"Found (E-4, E) for contact </span><span class="si">%s</span><span class="s2"> clash "</span>
+ <span class="s2">"but contacts below 4th residue are "</span>
+ <span class="s2">"actually allowed"</span><span class="p">,</span> <span class="n">outcontact</span><span class="p">)</span>
+ <span class="n">ssclash</span> <span class="o">=</span> <span class="kc">None</span>
+ <span class="k">if</span> <span class="n">ssclash</span><span class="p">:</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span>
+ <span class="s2">"Ss conflict for contact </span><span class="si">%d</span><span class="s2"> </span><span class="si">%s</span><span class="s2"> (</span><span class="si">%s</span><span class="s2">)"</span><span class="p">,</span>
+ <span class="n">icontact</span><span class="p">,</span> <span class="n">outcontact</span><span class="p">,</span> <span class="n">ssclash</span><span class="p">)</span>
+ <span class="n">desc_dict</span><span class="p">[</span><span class="n">contact</span><span class="p">]</span> <span class="o">=</span> <span class="n">ssclash</span>
+ <span class="n">ssclash_pair</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">contact</span><span class="p">)</span>
+ <span class="k">break</span>
+ <span class="k">return</span> <span class="p">{</span><span class="s1">'clash'</span><span class="p">:</span> <span class="n">ssclash_pair</span><span class="p">,</span> <span class="s1">'desc'</span><span class="p">:</span> <span class="n">desc_dict</span><span class="p">}</span></div>
+
+ <span class="k">def</span> <span class="nf">__call__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">mapdict</span><span class="p">,</span> <span class="n">mtype</span><span class="p">,</span> <span class="n">contactlist</span><span class="p">,</span> <span class="n">inprot</span><span class="p">,</span>
+ <span class="n">mapfilters</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">outprefix</span><span class="o">=</span><span class="s2">""</span><span class="p">,</span> <span class="n">outdir</span><span class="o">=</span><span class="s2">""</span><span class="p">,</span> <span class="n">clashlist</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Filter contact map</span>
+<span class="sd"> :param mapdict: dict containing ResMap and ResAtmMap for contacts,</span>
+<span class="sd"> distances and scores</span>
+<span class="sd"> :return:</span>
+<span class="sd"> """</span>
+ <span class="n">clash_list</span> <span class="o">=</span> <span class="p">[]</span>
+ <span class="n">desc_dict</span> <span class="o">=</span> <span class="p">{}</span>
+ <span class="n">clash_dict</span> <span class="o">=</span> <span class="p">{}</span>
+ <span class="n">mapfilters</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"contactfilter"</span><span class="p">)</span> <span class="k">if</span> <span class="n">mapfilters</span> <span class="ow">is</span> <span class="kc">None</span> \
+ <span class="k">else</span> <span class="n">mapfilters</span>
+
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="p">[</span><span class="s2">"net_deconv"</span><span class="p">]:</span>
+ <span class="c1"># TODO: maj scoremap ou maj mapcollection</span>
+ <span class="n">mapdict</span><span class="p">[</span><span class="s2">"scoremap"</span><span class="p">]</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">nd_filter</span><span class="p">(</span><span class="n">mapdict</span><span class="p">)</span>
+
+ <span class="k">if</span> <span class="n">mapfilters</span> <span class="o">==</span> <span class="s2">"all"</span> <span class="ow">and</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">nofilter</span><span class="p">:</span>
+ <span class="n">mapfilters</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">filter_types</span>
+ <span class="k">elif</span> <span class="bp">self</span><span class="o">.</span><span class="n">nofilter</span> <span class="ow">or</span> <span class="n">mapfilters</span> <span class="o">==</span> <span class="s2">"none"</span><span class="p">:</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s2">"Filtering steps removed"</span><span class="p">)</span>
+ <span class="n">mapfilters</span> <span class="o">=</span> <span class="p">[]</span>
+ <span class="k">elif</span> <span class="ow">not</span> <span class="n">mapfilters</span> <span class="ow">and</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">nofilter</span><span class="p">:</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s2">"No filtering steps. Will only use default filter (closed "</span>
+ <span class="s2">"contact filter)"</span><span class="p">)</span>
+ <span class="n">mapfilters</span> <span class="o">=</span> <span class="p">[</span><span class="s2">"pos"</span><span class="p">]</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">if</span> <span class="nb">type</span><span class="p">(</span><span class="n">mapfilters</span><span class="p">)</span> <span class="o">==</span> <span class="nb">list</span><span class="p">:</span>
+ <span class="n">mapfilters</span> <span class="o">=</span> <span class="p">[</span><span class="n">elm</span> <span class="k">for</span> <span class="n">elm</span> <span class="ow">in</span> <span class="n">mapfilters</span> <span class="k">if</span> <span class="n">elm</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">filter_types</span><span class="p">]</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="n">mapfilters</span> <span class="o">=</span> <span class="p">[</span><span class="n">mapfilters</span><span class="p">]</span>
+ <span class="k">if</span> <span class="s2">"pos"</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">mapfilters</span><span class="p">:</span>
+ <span class="n">mapfilters</span><span class="o">.</span><span class="n">insert</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="s2">"pos"</span><span class="p">)</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s2">"Filtering </span><span class="si">%s</span><span class="s2"> contact map"</span><span class="p">,</span> <span class="n">mtype</span><span class="p">)</span>
+ <span class="k">for</span> <span class="n">flt</span> <span class="ow">in</span> <span class="n">mapfilters</span><span class="p">:</span>
+ <span class="c1"># /!\ cys unicity filter must be the last filter !</span>
+ <span class="c1"># TODO: contacts_flt.out checking if given clash in coupling</span>
+ <span class="c1"># matrix are the same</span>
+ <span class="c1"># Filter on maplot for nd or contact_list</span>
+ <span class="n">kw</span> <span class="o">=</span> <span class="p">{</span><span class="s2">"clash_list"</span><span class="p">:</span> <span class="n">clash_list</span><span class="p">,</span>
+ <span class="s2">"sec_struct"</span><span class="p">:</span> <span class="n">inprot</span><span class="o">.</span><span class="n">sec_struct</span><span class="p">}</span>
+ <span class="n">flt_res</span> <span class="o">=</span> <span class="nb">getattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s2">"</span><span class="si">%s</span><span class="s2">_filter"</span> <span class="o">%</span> <span class="n">flt</span><span class="p">)(</span><span class="n">mapdict</span><span class="p">,</span> <span class="o">**</span><span class="n">kw</span><span class="p">)</span>
+ <span class="k">if</span> <span class="n">flt_res</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"clash"</span><span class="p">):</span>
+ <span class="n">clash_list</span><span class="o">.</span><span class="n">extend</span><span class="p">(</span><span class="n">flt_res</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"clash"</span><span class="p">))</span>
+ <span class="n">hum_list</span> <span class="o">=</span> <span class="p">[(</span><span class="n">x</span> <span class="o">+</span> <span class="mi">1</span><span class="p">,</span> <span class="n">y</span> <span class="o">+</span> <span class="mi">1</span><span class="p">)</span> <span class="k">for</span> <span class="n">x</span><span class="p">,</span> <span class="n">y</span> <span class="ow">in</span> <span class="n">flt_res</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"clash"</span><span class="p">)]</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s2">"Removed </span><span class="si">%d</span><span class="s2"> contacts."</span><span class="p">,</span> <span class="nb">len</span><span class="p">(</span><span class="n">flt_res</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"clash"</span><span class="p">))</span> <span class="o">/</span> <span class="mi">2</span><span class="p">)</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="s2">":</span><span class="se">\n</span><span class="si">%s</span><span class="s2">"</span><span class="p">,</span> <span class="s1">'</span><span class="se">\n</span><span class="s1">'</span><span class="o">.</span><span class="n">join</span><span class="p">(</span>
+ <span class="n">textwrap</span><span class="o">.</span><span class="n">wrap</span><span class="p">(</span><span class="s1">' '</span><span class="o">.</span><span class="n">join</span><span class="p">(</span>
+ <span class="p">[</span><span class="s2">"(</span><span class="si">%2d</span><span class="s2">, </span><span class="si">%2d</span><span class="s2">)"</span> <span class="o">%</span> <span class="n">pair</span> <span class="k">for</span> <span class="n">pair</span> <span class="ow">in</span> <span class="n">hum_list</span><span class="p">]),</span>
+ <span class="n">width</span><span class="o">=</span><span class="mi">80</span><span class="p">)))</span>
+ <span class="n">clash_dict</span><span class="p">[</span><span class="n">flt</span><span class="p">]</span> <span class="o">=</span> <span class="n">flt_res</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"clash"</span><span class="p">)</span>
+ <span class="k">if</span> <span class="n">flt_res</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"desc"</span><span class="p">):</span>
+ <span class="n">desc_dict</span><span class="o">.</span><span class="n">update</span><span class="p">(</span><span class="n">flt_res</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"desc"</span><span class="p">))</span>
+
+ <span class="c1"># write filter.out</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">write_filtout</span><span class="p">(</span><span class="n">clash_dict</span><span class="p">,</span> <span class="n">desc_dict</span><span class="p">,</span> <span class="n">contactlist</span><span class="p">,</span> <span class="n">outdir</span><span class="o">=</span><span class="n">outdir</span><span class="p">,</span>
+ <span class="n">outprefix</span><span class="o">=</span><span class="n">outprefix</span> <span class="o">+</span> <span class="s1">'.'</span> <span class="o">+</span> <span class="n">mtype</span><span class="p">,</span> <span class="n">clashlist</span><span class="o">=</span><span class="n">clashlist</span><span class="p">)</span>
+
+ <span class="c1"># Contactmap always filtered</span>
+ <span class="c1"># TODO: could set a treshold instead of n_factor</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s2">"Setting contact number with treshold </span><span class="si">%s</span><span class="s2">"</span><span class="p">,</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"n_factor"</span><span class="p">))</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"n_factor"</span><span class="p">)</span> <span class="o">==</span> <span class="s2">"all"</span><span class="p">:</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">warning</span><span class="p">(</span><span class="s2">"Factor set to all. All the contacts will be used !"</span><span class="p">)</span>
+ <span class="n">nb_c</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">mapdict</span><span class="p">[</span><span class="s2">"maplot"</span><span class="p">]</span><span class="o">.</span><span class="n">contactset</span><span class="p">())</span>
+ <span class="k">elif</span> <span class="nb">isinstance</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"n_factor"</span><span class="p">),</span> <span class="n">six</span><span class="o">.</span><span class="n">string_types</span><span class="p">)</span> \
+ <span class="ow">and</span> <span class="s2">"%"</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"n_factor"</span><span class="p">):</span>
+ <span class="n">reg</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span><span class="sa">r</span><span class="s2">"([0-9]+\.?[0-9]*)%"</span><span class="p">)</span>
+ <span class="n">perc</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">reg</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"n_factor"</span><span class="p">))</span><span class="o">.</span><span class="n">group</span><span class="p">(</span><span class="mi">1</span><span class="p">))</span>
+
+ <span class="n">nb_c</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">perc</span><span class="o">/</span><span class="mi">100</span> <span class="o">*</span> <span class="nb">len</span><span class="p">(</span><span class="n">mapdict</span><span class="p">[</span><span class="s2">"maplot"</span><span class="p">]</span><span class="o">.</span><span class="n">contactset</span><span class="p">()))</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">warning</span><span class="p">(</span><span class="s2">"Factor set as </span><span class="si">%.2f</span><span class="s2"> percentage of all the contacts "</span>
+ <span class="s2">"(random selection)."</span><span class="p">,</span> <span class="n">perc</span><span class="p">)</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="n">nb_c</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">mapdict</span><span class="p">[</span><span class="s2">"maplot"</span><span class="p">]</span><span class="o">.</span><span class="n">sequence</span><span class="p">)</span> <span class="o">*</span> <span class="nb">float</span><span class="p">(</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"n_factor"</span><span class="p">)))</span>
+ <span class="c1"># Number of selected contact</span>
+ <span class="c1"># If there isn't enough contacts in input contact map after filtering</span>
+ <span class="c1"># step, change nb_c</span>
+ <span class="n">nb_c</span> <span class="o">=</span> <span class="n">nb_c</span> <span class="k">if</span> <span class="n">nb_c</span> <span class="o"><</span> <span class="nb">len</span><span class="p">(</span><span class="n">mapdict</span><span class="p">[</span><span class="s2">"maplot"</span><span class="p">]</span><span class="o">.</span><span class="n">contactset</span><span class="p">())</span> <span class="k">else</span> <span class="nb">len</span><span class="p">(</span>
+ <span class="n">mapdict</span><span class="p">[</span><span class="s2">"maplot"</span><span class="p">]</span><span class="o">.</span><span class="n">contactset</span><span class="p">())</span>
+ <span class="n">mapdict</span><span class="p">[</span><span class="s2">"nb_c"</span><span class="p">]</span> <span class="o">=</span> <span class="n">nb_c</span>
+
+ <span class="n">LOG</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s2">"Update </span><span class="si">%s</span><span class="s2"> maplot"</span><span class="p">,</span> <span class="n">mtype</span><span class="p">)</span>
+ <span class="n">mapdict</span><span class="p">[</span><span class="s2">"maplot"</span><span class="p">]</span><span class="o">.</span><span class="n">remove</span><span class="p">(</span><span class="n">clash_list</span><span class="p">)</span>
+
+ <span class="k">if</span> <span class="n">mapdict</span><span class="p">[</span><span class="s2">"scoremap"</span><span class="p">]</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s2">"Update </span><span class="si">%s</span><span class="s2"> scoremap"</span><span class="p">,</span> <span class="n">mtype</span><span class="p">)</span>
+ <span class="n">mapdict</span><span class="p">[</span><span class="s2">"scoremap"</span><span class="p">]</span><span class="o">.</span><span class="n">remove</span><span class="p">(</span><span class="n">clash_list</span><span class="p">)</span>
+ <span class="c1"># Get nb_c top maps</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s2">"Select top </span><span class="si">%d</span><span class="s2"> contacts according to scoremap"</span><span class="p">,</span> <span class="n">nb_c</span><span class="p">)</span>
+ <span class="c1"># TODO: deplacer cette partie dans l'appel de maplot une fois</span>
+ <span class="c1"># la classe mapcollections utilisee</span>
+ <span class="n">mapdict</span><span class="p">[</span><span class="s2">"maplot"</span><span class="p">]</span> <span class="o">=</span> <span class="n">mapdict</span><span class="p">[</span><span class="s2">"maplot"</span><span class="p">]</span><span class="o">.</span><span class="n">topmap</span><span class="p">(</span>
+ <span class="n">mapdict</span><span class="p">[</span><span class="s2">"scoremap"</span><span class="p">],</span> <span class="n">nb_c</span><span class="p">)</span>
+ <span class="k">if</span> <span class="n">mapdict</span><span class="p">[</span><span class="s2">"distmap"</span><span class="p">]</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s2">"Update </span><span class="si">%s</span><span class="s2"> distmap"</span><span class="p">,</span> <span class="n">mtype</span><span class="p">)</span>
+ <span class="n">mapdict</span><span class="p">[</span><span class="s2">"distmap"</span><span class="p">]</span><span class="o">.</span><span class="n">remove</span><span class="p">(</span><span class="n">clash_list</span><span class="p">)</span>
+
+ <span class="k">return</span> <span class="n">mapdict</span>
+
+<div class="viewcode-block" id="MapFilter.write_filtout"><a class="viewcode-back" href="../../ariaec.html#ariaec.protmap.MapFilter.write_filtout">[docs]</a> <span class="nd">@staticmethod</span>
+ <span class="k">def</span> <span class="nf">write_filtout</span><span class="p">(</span><span class="n">clash_dict</span><span class="p">,</span> <span class="n">desc_dict</span><span class="p">,</span> <span class="n">contactlist</span><span class="p">,</span> <span class="n">outdir</span><span class="o">=</span><span class="s2">""</span><span class="p">,</span>
+ <span class="n">outprefix</span><span class="o">=</span><span class="s2">"protein"</span><span class="p">,</span> <span class="n">clashlist</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">human_idx</span><span class="o">=</span><span class="kc">True</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> </span>
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> clash_dict :</span>
+<span class="sd"> </span>
+<span class="sd"> desc_dict :</span>
+<span class="sd"> </span>
+<span class="sd"> contactlist :</span>
+<span class="sd"> </span>
+<span class="sd"> outdir :</span>
+<span class="sd"> (Default value = "")</span>
+<span class="sd"> outprefix :</span>
+<span class="sd"> (Default value = "protein")</span>
+<span class="sd"> clashlist :</span>
+<span class="sd"> (Default value = None)</span>
+<span class="sd"> human_idx :</span>
+<span class="sd"> (Default value = True)</span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+<span class="sd"> </span>
+<span class="sd"> """</span>
+ <span class="c1"># TODO: utiliser self.clash_dict au lieu de meta_clash</span>
+ <span class="sd">"""</span>
+
+<span class="sd"> :param clash_dict:</span>
+<span class="sd"> :param desc_dict:</span>
+<span class="sd"> :param contactlist:</span>
+<span class="sd"> :param outdir:</span>
+<span class="sd"> :param outprefix:</span>
+<span class="sd"> :param clashlist:</span>
+<span class="sd"> :param human_idx:</span>
+<span class="sd"> """</span>
+ <span class="n">meta_clash</span> <span class="o">=</span> <span class="p">{</span>
+ <span class="s2">"cons"</span><span class="p">:</span> <span class="p">{</span>
+ <span class="s2">"flag"</span><span class="p">:</span> <span class="mi">888</span><span class="p">,</span> <span class="s2">"msg"</span><span class="p">:</span> <span class="s2">""</span><span class="p">,</span> <span class="s2">"warn"</span><span class="p">:</span> <span class="s2">""</span><span class="p">,</span>
+ <span class="s2">"desc"</span><span class="p">:</span> <span class="s2">"high conservation"</span><span class="p">},</span>
+ <span class="s2">"cys"</span><span class="p">:</span> <span class="p">{</span>
+ <span class="s2">"flag"</span><span class="p">:</span> <span class="mi">222</span><span class="p">,</span> <span class="s2">"msg"</span><span class="p">:</span> <span class="s2">""</span><span class="p">,</span> <span class="s2">"warn"</span><span class="p">:</span> <span class="s2">""</span><span class="p">,</span>
+ <span class="s2">"desc"</span><span class="p">:</span> <span class="s2">"disulfide bonds unicity"</span><span class="p">},</span>
+ <span class="s2">"ssclash"</span><span class="p">:</span> <span class="p">{</span><span class="s2">"flag"</span><span class="p">:</span> <span class="mi">999</span><span class="p">,</span> <span class="s2">"msg"</span><span class="p">:</span> <span class="s2">""</span><span class="p">,</span> <span class="s2">"warn"</span><span class="p">:</span> <span class="s2">""</span><span class="p">,</span>
+ <span class="s2">"desc"</span><span class="p">:</span> <span class="s2">"secondary structure prediction conflict"</span><span class="p">},</span>
+ <span class="s2">"pos"</span><span class="p">:</span> <span class="p">{</span>
+ <span class="s2">"flag"</span><span class="p">:</span> <span class="s2">"physical proximity"</span><span class="p">,</span> <span class="s2">"msg"</span><span class="p">:</span> <span class="s2">""</span><span class="p">,</span> <span class="s2">"warn"</span><span class="p">:</span> <span class="s2">""</span><span class="p">,</span>
+ <span class="s2">"desc"</span><span class="p">:</span> <span class="s2">"sequence position"</span><span class="p">},</span>
+ <span class="s2">"nd"</span><span class="p">:</span> <span class="p">{</span>
+ <span class="s2">"flag"</span><span class="p">:</span> <span class="s2">"deconvol"</span><span class="p">,</span> <span class="s2">"msg"</span><span class="p">:</span> <span class="s2">""</span><span class="p">,</span> <span class="s2">"warn"</span><span class="p">:</span> <span class="s2">""</span><span class="p">,</span>
+ <span class="s2">"desc"</span><span class="p">:</span> <span class="s2">"network deconvolution"</span><span class="p">}</span>
+ <span class="p">}</span>
+ <span class="n">offset</span> <span class="o">=</span> <span class="mi">1</span> <span class="k">if</span> <span class="n">human_idx</span> <span class="k">else</span> <span class="mi">0</span>
+
+ <span class="k">for</span> <span class="n">icontact</span><span class="p">,</span> <span class="n">contact</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">contactlist</span><span class="p">):</span>
+ <span class="n">clash</span> <span class="o">=</span> <span class="s2">"0"</span>
+ <span class="n">clash_t</span> <span class="o">=</span> <span class="s2">""</span>
+ <span class="n">raw_contact</span> <span class="o">=</span> <span class="p">(</span><span class="n">contact</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">-</span> <span class="n">offset</span><span class="p">,</span> <span class="n">contact</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="o">-</span> <span class="n">offset</span><span class="p">)</span>
+ <span class="k">for</span> <span class="n">clash_t</span> <span class="ow">in</span> <span class="nb">sorted</span><span class="p">(</span><span class="n">clash_dict</span><span class="o">.</span><span class="n">keys</span><span class="p">()):</span>
+ <span class="k">if</span> <span class="n">clash_dict</span><span class="p">[</span><span class="n">clash_t</span><span class="p">]</span> <span class="ow">and</span> <span class="n">raw_contact</span> <span class="ow">in</span> <span class="n">clash_dict</span><span class="p">[</span><span class="n">clash_t</span><span class="p">]:</span>
+ <span class="n">clash</span> <span class="o">=</span> <span class="n">meta_clash</span><span class="p">[</span><span class="n">clash_t</span><span class="p">][</span><span class="s2">"flag"</span><span class="p">]</span>
+ <span class="n">meta_clash</span><span class="p">[</span><span class="n">clash_t</span><span class="p">][</span><span class="s2">"msg"</span><span class="p">]</span> <span class="o">+=</span> <span class="s2">"""</span>
+<span class="si">{clash_type}</span><span class="s2"> flag at pair </span><span class="si">{pair_nb}</span><span class="s2"> : res </span><span class="si">{res1}</span><span class="s2"> and res </span><span class="si">{res2}</span><span class="s2"> </span><span class="si">{clash_desc}</span><span class="se">\</span>
+<span class="s2">"""</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">clash_type</span><span class="o">=</span><span class="n">clash</span><span class="p">,</span> <span class="n">pair_nb</span><span class="o">=</span><span class="n">icontact</span> <span class="o">+</span> <span class="mi">1</span><span class="p">,</span>
+ <span class="n">clash_desc</span><span class="o">=</span><span class="n">desc_dict</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">raw_contact</span><span class="p">,</span> <span class="s1">''</span><span class="p">),</span>
+ <span class="n">res1</span><span class="o">=</span><span class="n">contact</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">res2</span><span class="o">=</span><span class="n">contact</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span>
+ <span class="k">break</span>
+ <span class="k">if</span> <span class="n">clashlist</span> <span class="ow">and</span> <span class="nb">str</span><span class="p">(</span><span class="n">clash</span><span class="p">)</span> <span class="o">!=</span> <span class="nb">str</span><span class="p">(</span><span class="n">clashlist</span><span class="p">[</span><span class="n">icontact</span><span class="p">]):</span>
+ <span class="k">if</span> <span class="n">clash</span> <span class="o">==</span> <span class="s2">"0"</span><span class="p">:</span>
+ <span class="n">op</span> <span class="o">=</span> <span class="s2">"removed"</span>
+ <span class="n">ctype</span> <span class="o">=</span> <span class="nb">str</span><span class="p">(</span><span class="n">clashlist</span><span class="p">[</span><span class="n">icontact</span><span class="p">])</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="n">op</span> <span class="o">=</span> <span class="s2">"added"</span>
+ <span class="n">ctype</span> <span class="o">=</span> <span class="n">clash</span>
+ <span class="n">meta_clash</span><span class="p">[</span><span class="n">clash_t</span><span class="p">][</span><span class="s2">"warn"</span><span class="p">]</span> <span class="o">+=</span> <span class="s2">"</span><span class="se">\n</span><span class="s2">/!\ Clash: </span><span class="si">{clash_desc}</span><span class="s2"> </span><span class="si">{clash}</span><span class="s2"> flag for contact "</span> \
+ <span class="s2">"</span><span class="si">{res_pos}</span><span class="s2"> (</span><span class="si">{res1}</span><span class="s2">, </span><span class="si">{res2}</span><span class="s2">)"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
+ <span class="n">clash_desc</span><span class="o">=</span><span class="n">op</span><span class="p">,</span> <span class="n">clash</span><span class="o">=</span><span class="n">ctype</span><span class="p">,</span> <span class="n">res_pos</span><span class="o">=</span><span class="n">icontact</span> <span class="o">+</span> <span class="mi">1</span><span class="p">,</span>
+ <span class="n">res1</span><span class="o">=</span><span class="n">contact</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">res2</span><span class="o">=</span><span class="n">contact</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span>
+
+ <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="s2">"</span><span class="si">%s</span><span class="s2">/</span><span class="si">%s</span><span class="s2">.filter.out"</span> <span class="o">%</span> <span class="p">(</span><span class="n">outdir</span><span class="p">,</span> <span class="n">outprefix</span><span class="p">),</span> <span class="s1">'w'</span><span class="p">)</span> <span class="k">as</span> <span class="n">out</span><span class="p">:</span>
+ <span class="n">titleprint</span><span class="p">(</span><span class="n">out</span><span class="p">,</span> <span class="n">progname</span><span class="o">=</span><span class="vm">__doc__</span><span class="p">,</span> <span class="n">desc</span><span class="o">=</span><span class="s1">'Contacts filter'</span><span class="p">)</span>
+ <span class="k">for</span> <span class="n">flt</span> <span class="ow">in</span> <span class="p">(</span><span class="s2">"nd"</span><span class="p">,</span> <span class="s2">"pos"</span><span class="p">,</span> <span class="s2">"cons"</span><span class="p">,</span> <span class="s2">"ssclash"</span><span class="p">,</span> <span class="s2">"cys"</span><span class="p">):</span>
+ <span class="n">out</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s1">'''</span>
+
+<span class="si">{filter_desc}</span><span class="s1"></span>
+<span class="si">{hd}</span><span class="s1"></span>
+<span class="s1">'''</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">filter_desc</span><span class="o">=</span><span class="n">meta_clash</span><span class="p">[</span><span class="n">flt</span><span class="p">][</span><span class="s2">"desc"</span><span class="p">]</span><span class="o">.</span><span class="n">capitalize</span><span class="p">(),</span>
+ <span class="n">hd</span><span class="o">=</span><span class="s2">"="</span> <span class="o">*</span> <span class="nb">len</span><span class="p">(</span><span class="n">meta_clash</span><span class="p">[</span><span class="n">flt</span><span class="p">][</span><span class="s2">"desc"</span><span class="p">])))</span>
+
+ <span class="k">if</span> <span class="n">meta_clash</span><span class="p">[</span><span class="n">flt</span><span class="p">]</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"warn"</span><span class="p">):</span>
+ <span class="n">out</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">meta_clash</span><span class="p">[</span><span class="n">flt</span><span class="p">][</span><span class="s2">"warn"</span><span class="p">])</span>
+ <span class="n">out</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">meta_clash</span><span class="p">[</span><span class="n">flt</span><span class="p">][</span><span class="s2">"msg"</span><span class="p">])</span></div></div>
+</pre></div>
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diff --git a/examples-dev/olds/_build/html/_modules/ariaec/reader.html b/examples-dev/olds/_build/html/_modules/ariaec/reader.html
new file mode 100644
index 0000000000000000000000000000000000000000..9e4a218501e8778b40f3d6f54a53c87278d8f23b
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@@ -0,0 +1,1141 @@
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+
+ <h1>Source code for ariaec.reader</h1><div class="highlight"><pre>
+<span></span><span class="c1"># coding=utf-8</span>
+<span class="sd">"""</span>
+<span class="sd"> Reader objects</span>
+<span class="sd">"""</span>
+<span class="kn">from</span> <span class="nn">__future__</span> <span class="k">import</span> <span class="n">absolute_import</span><span class="p">,</span> <span class="n">division</span><span class="p">,</span> <span class="n">print_function</span>
+
+<span class="kn">import</span> <span class="nn">os</span>
+<span class="kn">import</span> <span class="nn">re</span>
+<span class="kn">import</span> <span class="nn">logging</span>
+<span class="kn">import</span> <span class="nn">os.path</span>
+<span class="kn">import</span> <span class="nn">numpy</span> <span class="k">as</span> <span class="nn">np</span>
+<span class="kn">import</span> <span class="nn">collections</span>
+<span class="kn">import</span> <span class="nn">pkg_resources</span> <span class="k">as</span> <span class="nn">pkgr</span>
+<span class="kn">import</span> <span class="nn">scipy.spatial.distance</span> <span class="k">as</span> <span class="nn">distance</span>
+<span class="kn">from</span> <span class="nn">Bio</span> <span class="k">import</span> <span class="n">pairwise2</span>
+<span class="kn">from</span> <span class="nn">.common</span> <span class="k">import</span> <span class="n">sort_2dict</span>
+<span class="kn">from</span> <span class="nn">.protmap</span> <span class="k">import</span> <span class="p">(</span><span class="n">ResMap</span><span class="p">,</span> <span class="n">ResAtmMap</span><span class="p">)</span>
+
+<span class="n">LOG</span> <span class="o">=</span> <span class="n">logging</span><span class="o">.</span><span class="n">getLogger</span><span class="p">(</span><span class="vm">__name__</span><span class="p">)</span>
+<span class="c1"># TODO: check if Atom is still used ...</span>
+<span class="c1"># TODO: Should use conkit in the future</span>
+<span class="n">Atom</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">namedtuple</span><span class="p">(</span><span class="s2">"Atom"</span><span class="p">,</span> <span class="p">[</span><span class="s2">"name"</span><span class="p">,</span> <span class="s2">"coords"</span><span class="p">])</span>
+
+
+<div class="viewcode-block" id="RegexFile"><a class="viewcode-back" href="../../ariaec.html#ariaec.reader.RegexFile">[docs]</a><span class="k">class</span> <span class="nc">RegexFile</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span>
+ <span class="sd">"""File which can be parsed with a regex"""</span>
+
+ <span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">filepath</span><span class="p">,</span> <span class="n">filetype</span><span class="o">=</span><span class="s1">''</span><span class="p">,</span> <span class="n">regex</span><span class="o">=</span><span class="s1">''</span><span class="p">,</span> <span class="n">sort</span><span class="o">=</span><span class="s1">''</span><span class="p">,</span> <span class="n">default</span><span class="o">=</span><span class="s1">''</span><span class="p">):</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">regex</span> <span class="o">=</span> <span class="n">regex</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">sort</span> <span class="o">=</span> <span class="n">sort</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">lines</span> <span class="o">=</span> <span class="p">{}</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">filetype</span> <span class="o">=</span> <span class="n">filetype</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_filename</span> <span class="o">=</span> <span class="kc">None</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_filepath</span> <span class="o">=</span> <span class="n">filepath</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_defaultpath</span> <span class="o">=</span> <span class="n">default</span> <span class="k">if</span> <span class="n">pkgr</span><span class="o">.</span><span class="n">resource_exists</span><span class="p">(</span><span class="vm">__name__</span><span class="p">,</span> <span class="n">default</span><span class="p">)</span> \
+ <span class="k">else</span> <span class="kc">None</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_pkgfile</span> <span class="o">=</span> <span class="kc">False</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_checkpath</span><span class="p">()</span>
+
+ <span class="k">def</span> <span class="nf">_checkpath</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="sd">"""Check if filepath exists or is in package ressources"""</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="s2">"Checking if </span><span class="si">%s</span><span class="s2"> file exists"</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">filetype</span><span class="p">)</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">_filepath</span> <span class="ow">and</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_filepath</span><span class="p">):</span>
+ <span class="c1"># File actually exists outside of the package</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="s2">"File exists."</span><span class="p">)</span>
+ <span class="k">elif</span> <span class="bp">self</span><span class="o">.</span><span class="n">_filepath</span> <span class="ow">and</span> <span class="n">pkgr</span><span class="o">.</span><span class="n">resource_exists</span><span class="p">(</span><span class="vm">__name__</span><span class="p">,</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_filepath</span><span class="p">):</span>
+ <span class="c1"># File is in pkgr</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="s2">"Use </span><span class="si">%s</span><span class="s2"> file from package ressources"</span><span class="p">,</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">filetype</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_pkgfile</span> <span class="o">=</span> <span class="kc">True</span>
+ <span class="k">elif</span> <span class="bp">self</span><span class="o">.</span><span class="n">_defaultpath</span><span class="p">:</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="s2">"Use default </span><span class="si">%s</span><span class="s2"> file"</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">filetype</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_filepath</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_defaultpath</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_pkgfile</span> <span class="o">=</span> <span class="kc">True</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">warning</span><span class="p">(</span><span class="s2">"File </span><span class="si">%s</span><span class="s2"> does not exists"</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">filetype</span><span class="p">)</span>
+
+ <span class="nd">@property</span>
+ <span class="k">def</span> <span class="nf">filename</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="sd">"""Get basename of filepath"""</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">_filepath</span> <span class="ow">and</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">_filename</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_filename</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">basename</span><span class="p">(</span>
+ <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">splitext</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_filepath</span><span class="p">)[</span><span class="mi">0</span><span class="p">])</span>
+ <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_filename</span>
+
+ <span class="nd">@property</span>
+ <span class="k">def</span> <span class="nf">filepath</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="sd">"""File path"""</span>
+ <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_filepath</span>
+
+<div class="viewcode-block" id="RegexFile.load"><a class="viewcode-back" href="../../ariaec.html#ariaec.reader.RegexFile.load">[docs]</a> <span class="k">def</span> <span class="nf">load</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Fill lines with dictionary. Each key is a line number in the given file</span>
+<span class="sd"> :return: None</span>
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+<span class="sd"> </span>
+<span class="sd"> """</span>
+ <span class="n">lines_dict</span> <span class="o">=</span> <span class="p">{}</span>
+
+ <span class="k">if</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">regex</span><span class="p">:</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">error</span><span class="p">(</span><span class="s2">"Can't parse file </span><span class="si">%s</span><span class="s2"> without defined regex"</span><span class="p">,</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">filepath</span><span class="p">)</span>
+ <span class="k">return</span> <span class="kc">None</span>
+
+ <span class="k">with</span> <span class="n">pkgr</span><span class="o">.</span><span class="n">resource_stream</span><span class="p">(</span><span class="vm">__name__</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">filepath</span><span class="p">)</span> <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">_pkgfile</span> \
+ <span class="k">else</span> <span class="nb">open</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">filepath</span><span class="p">)</span> <span class="k">as</span> <span class="n">infile</span><span class="p">:</span>
+
+ <span class="k">for</span> <span class="n">index</span><span class="p">,</span> <span class="n">line</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">infile</span><span class="p">):</span>
+ <span class="n">match</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">regex</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="n">line</span><span class="p">)</span>
+ <span class="k">if</span> <span class="n">match</span><span class="p">:</span>
+ <span class="n">lines_dict</span><span class="p">[</span><span class="n">index</span><span class="p">]</span> <span class="o">=</span> <span class="n">match</span><span class="o">.</span><span class="n">groupdict</span><span class="p">()</span>
+
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">sort</span><span class="p">:</span>
+ <span class="n">lines_dict</span> <span class="o">=</span> <span class="n">sort_2dict</span><span class="p">(</span><span class="n">lines_dict</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">sort</span><span class="p">)</span>
+
+ <span class="bp">self</span><span class="o">.</span><span class="n">lines</span> <span class="o">=</span> <span class="n">lines_dict</span></div></div>
+
+
+<div class="viewcode-block" id="CulledPdbFile"><a class="viewcode-back" href="../../ariaec.html#ariaec.reader.CulledPdbFile">[docs]</a><span class="k">class</span> <span class="nc">CulledPdbFile</span><span class="p">(</span><span class="n">RegexFile</span><span class="p">):</span>
+ <span class="sd">"""Reader class for culled pdb list"""</span>
+ <span class="n">regex</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span>
+ <span class="sa">r</span><span class="s2">"^(?P<pdb_id>\w</span><span class="si">{4}</span><span class="s2">)"</span>
+ <span class="sa">r</span><span class="s2">"(?P<chain_id>\w)\s+"</span>
+ <span class="sa">r</span><span class="s2">"(?P<length>\d+)\s+"</span>
+ <span class="sa">r</span><span class="s2">"(?P<exp>\w+)\s+"</span>
+ <span class="sa">r</span><span class="s2">"(?P<resolution>-?\d+\.\d+)\s+"</span>
+ <span class="sa">r</span><span class="s2">"(?P<r_factor>-?\d+\.\d+)\s+"</span>
+ <span class="sa">r</span><span class="s2">"(?P<free_rvalue>-?\d+\.\d+)\s*$"</span><span class="p">)</span>
+ <span class="n">filetype</span> <span class="o">=</span> <span class="s1">'cullpdb'</span>
+ <span class="n">default</span> <span class="o">=</span> <span class="s1">'data/cullpdb/160427/cullpdb_pc25_res1.6_R0.25_d160427_chains3743'</span>
+
+ <span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+ <span class="n">kwargs</span><span class="p">[</span><span class="s1">'regex'</span><span class="p">]</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">regex</span>
+ <span class="n">kwargs</span><span class="p">[</span><span class="s1">'filetype'</span><span class="p">]</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">filetype</span>
+ <span class="n">kwargs</span><span class="p">[</span><span class="s1">'default'</span><span class="p">]</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">default</span>
+ <span class="nb">super</span><span class="p">(</span><span class="n">CulledPdbFile</span><span class="p">,</span> <span class="bp">self</span><span class="p">)</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">)</span></div>
+
+
+<div class="viewcode-block" id="TblDistFile"><a class="viewcode-back" href="../../ariaec.html#ariaec.reader.TblDistFile">[docs]</a><span class="k">class</span> <span class="nc">TblDistFile</span><span class="p">(</span><span class="n">RegexFile</span><span class="p">):</span>
+ <span class="sd">"""Reader class for TBL Distance restraint file"""</span>
+ <span class="n">regex</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span>
+ <span class="sa">r</span><span class="s2">"^\s*(?P<restflag>or|assign)\s+\(segid\s+</span><span class="se">\"</span><span class="s2">(?P<segid1>[\s\w]+)"</span>
+ <span class="sa">r</span><span class="s2">"</span><span class="se">\"</span><span class="s2">\s+and\s+resid\s+(?P<resid1>\d+)\s+and\s+name\s+(?P<atm1>\w+)"</span>
+ <span class="sa">r</span><span class="s2">"\)\s+\(segid\s+</span><span class="se">\"</span><span class="s2">(?P<segid2>[\s\w]+)</span><span class="se">\"</span><span class="s2">\s+and\s+resid\s+"</span>
+ <span class="sa">r</span><span class="s2">"(?P<resid2>\d+)\s+and\s+name\s+(?P<atm2>\w+)\)\s*"</span>
+ <span class="sa">r</span><span class="s2">"(?P<dtarget>\d+\.\d+)?\s*(?P<dminus>\d+\.\d+)?\s*(?P<dplus>\d+\.\d+)"</span>
+ <span class="sa">r</span><span class="s2">"?\s*(weight)?\s*(?P<weight>\d+\.\d+)?\s*!?\s*(spec=)?"</span>
+ <span class="sa">r</span><span class="s2">"(?P<listname>\w+)?(,\s*no=)?(?P<restno>\d+)?(,\s*id=)?"</span>
+ <span class="sa">r</span><span class="s2">"(?P<restid>\d+)?(,\s*vol=)?(?P<vol>[\w.\-+]+)?$"</span><span class="p">)</span>
+ <span class="n">filetype</span> <span class="o">=</span> <span class="s1">'tbldist'</span>
+
+ <span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+ <span class="n">kwargs</span><span class="p">[</span><span class="s1">'regex'</span><span class="p">]</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">regex</span>
+ <span class="n">kwargs</span><span class="p">[</span><span class="s1">'filetype'</span><span class="p">]</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">filetype</span>
+ <span class="nb">super</span><span class="p">(</span><span class="n">TblDistFile</span><span class="p">,</span> <span class="bp">self</span><span class="p">)</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">)</span></div>
+
+
+<div class="viewcode-block" id="MapFile"><a class="viewcode-back" href="../../ariaec.html#ariaec.reader.MapFile">[docs]</a><span class="k">class</span> <span class="nc">MapFile</span><span class="p">(</span><span class="n">RegexFile</span><span class="p">):</span>
+ <span class="sd">"""Abstract class related to all kind of protein maps"""</span>
+ <span class="c1"># List of 3tuples ("regex_file", "filetype", "sort_field")</span>
+ <span class="c1"># sort_field allow sorting lines with values into this field</span>
+ <span class="c1"># TODO: wrong regex for native_full ?</span>
+ <span class="c1"># TODO: smarter dict ...</span>
+ <span class="n">types</span> <span class="o">=</span> <span class="p">{</span>
+ <span class="s2">"plmdca"</span><span class="p">:</span> <span class="p">{</span>
+ <span class="s2">"regex"</span><span class="p">:</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span><span class="sa">r</span><span class="s2">"^(?P<res1_nb>\d+)\s+(?P<res1_name>\w)\s+"</span>
+ <span class="sa">r</span><span class="s2">"(?P<res2_nb>\d+)\s+(?P<res2_name>\w)\s+"</span>
+ <span class="sa">r</span><span class="s2">"(?P<mi_score>\d)\s+"</span>
+ <span class="sa">r</span><span class="s2">"(?P<plm_score>-?\d+\.\d+)\s*$"</span><span class="p">),</span>
+ <span class="s2">"score_field"</span><span class="p">:</span> <span class="s2">"plm_score"</span>
+ <span class="p">},</span>
+ <span class="s2">"plm"</span><span class="p">:</span> <span class="p">{</span>
+ <span class="s2">"regex"</span><span class="p">:</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span><span class="sa">r</span><span class="s2">"^(?P<res1_nb>\d+)\s+(?P<res1_name>\w)\s+"</span>
+ <span class="sa">r</span><span class="s2">"(?P<res2_nb>\d+)\s+(?P<res2_name>\w)\s+"</span>
+ <span class="sa">r</span><span class="s2">"(?P<mi_score>\d)\s+"</span>
+ <span class="sa">r</span><span class="s2">"(?P<plm_score>-?\d+\.\d+)\s*$"</span><span class="p">),</span>
+ <span class="s2">"score_field"</span><span class="p">:</span> <span class="s2">"plm_score"</span>
+ <span class="p">},</span>
+ <span class="s2">"plmev"</span><span class="p">:</span> <span class="p">{</span>
+ <span class="s2">"regex"</span><span class="p">:</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span><span class="sa">r</span><span class="s2">"^(?P<res1_nb>\d+)\s+(?P<res1_name>\w)\s+"</span>
+ <span class="sa">r</span><span class="s2">"(?P<res2_nb>\d+)\s+(?P<res2_name>\w)\s+"</span>
+ <span class="sa">r</span><span class="s2">"(?P<mi_score>\d)\s+"</span>
+ <span class="sa">r</span><span class="s2">"(?P<plm_score>-?\d+\.\d+)\s*$"</span><span class="p">),</span>
+ <span class="s2">"score_field"</span><span class="p">:</span> <span class="s2">"plm_score"</span>
+ <span class="p">},</span>
+ <span class="s2">"plmc"</span><span class="p">:</span> <span class="p">{</span>
+ <span class="s2">"regex"</span><span class="p">:</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span><span class="sa">r</span><span class="s2">"^(?P<res1_nb>\d+)\s+(?P<res1_name>\w)\s+"</span>
+ <span class="sa">r</span><span class="s2">"(?P<res2_nb>\d+)\s+(?P<res2_name>\w)\s+"</span>
+ <span class="sa">r</span><span class="s2">"(?P<mi_score>\d)\s+"</span>
+ <span class="sa">r</span><span class="s2">"(?P<plm_score>-?\d+\.\d+)\s*$"</span><span class="p">),</span>
+ <span class="s2">"score_field"</span><span class="p">:</span> <span class="s2">"plm_score"</span>
+ <span class="p">},</span>
+ <span class="s2">"evfold"</span><span class="p">:</span> <span class="p">{</span>
+ <span class="s2">"regex"</span><span class="p">:</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span>
+ <span class="sa">r</span><span class="s1">'^(?P<res1_nb>\d+),(?P<res2_nb>\d+),'</span>
+ <span class="sa">r</span><span class="s1">'(?P<ec_score>-?\d+\.\d+e?-?\d*),'</span>
+ <span class="sa">r</span><span class="s1">'(?P<placeholder>\d),(?P<res1_cons>\d+),'</span>
+ <span class="sa">r</span><span class="s1">'(?P<res2_cons>\d+),(?P<ss_filter>\d|\d</span><span class="si">{3}</span><span class="s1">),'</span>
+ <span class="sa">r</span><span class="s1">'(?P<high_cons_filter>\d|\d</span><span class="si">{3}</span><span class="s1">),'</span>
+ <span class="sa">r</span><span class="s1">'(?P<cc_filter>\d|\d</span><span class="si">{3}</span><span class="s1">),(?P<res1_name>\w),'</span>
+ <span class="sa">r</span><span class="s1">'(?P<res2_name>\w)$'</span><span class="p">),</span>
+ <span class="s2">"score_field"</span><span class="p">:</span> <span class="s2">"ec_score"</span>
+ <span class="p">},</span>
+ <span class="s2">"pconsc"</span><span class="p">:</span> <span class="p">{</span>
+ <span class="s2">"regex"</span><span class="p">:</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span>
+ <span class="sa">r</span><span class="s1">'^(?P<res1_nb>\d+) (?P<res2_nb>\d+) '</span>
+ <span class="sa">r</span><span class="s1">'(?P<ec_score>-?\d+\.\d+e?-?\d*)$'</span><span class="p">),</span>
+ <span class="s2">"score_field"</span><span class="p">:</span> <span class="s2">"ec_score"</span>
+ <span class="p">},</span>
+ <span class="s2">"pconsc1"</span><span class="p">:</span> <span class="p">{</span>
+ <span class="s2">"regex"</span><span class="p">:</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span>
+ <span class="sa">r</span><span class="s1">'^(?P<res1_nb>\d+) (?P<res2_nb>\d+) '</span>
+ <span class="sa">r</span><span class="s1">'(?P<ec_score>-?\d+\.\d+e?-?\d*)$'</span><span class="p">),</span>
+ <span class="s2">"score_field"</span><span class="p">:</span> <span class="s2">"ec_score"</span>
+ <span class="p">},</span>
+ <span class="s2">"pconsc2"</span><span class="p">:</span> <span class="p">{</span>
+ <span class="s2">"regex"</span><span class="p">:</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span>
+ <span class="sa">r</span><span class="s1">'^(?P<res1_nb>\d+) (?P<res2_nb>\d+) '</span>
+ <span class="sa">r</span><span class="s1">'(?P<ec_score>-?\d+\.\d+e?-?\d*)$'</span><span class="p">),</span>
+ <span class="s2">"score_field"</span><span class="p">:</span> <span class="s2">"ec_score"</span>
+ <span class="p">},</span>
+ <span class="s2">"metapsicov_stg1"</span><span class="p">:</span> <span class="p">{</span>
+ <span class="s2">"regex"</span><span class="p">:</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span>
+ <span class="sa">r</span><span class="s1">'^(?P<res1_nb>\d+) (?P<res2_nb>\d+) \d (?P<res_dist>-?\d+.?\d*) '</span>
+ <span class="sa">r</span><span class="s1">'(?P<ec_score>-?\d+.\d+e?-?\d*)$'</span><span class="p">),</span>
+ <span class="s2">"score_field"</span><span class="p">:</span> <span class="s2">"ec_score"</span>
+ <span class="p">},</span>
+ <span class="s2">"metapsicov_stg2"</span><span class="p">:</span> <span class="p">{</span>
+ <span class="s2">"regex"</span><span class="p">:</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span>
+ <span class="sa">r</span><span class="s1">'^(?P<res1_nb>\d+) (?P<res2_nb>\d+) \d (?P<res_dist>-?\d+.?\d*) '</span>
+ <span class="sa">r</span><span class="s1">'(?P<ec_score>-?\d+.\d+e?-?\d*)$'</span><span class="p">),</span>
+ <span class="s2">"score_field"</span><span class="p">:</span> <span class="s2">"ec_score"</span>
+ <span class="p">},</span>
+ <span class="s2">"psicov"</span><span class="p">:</span> <span class="p">{</span>
+ <span class="s2">"regex"</span><span class="p">:</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span>
+ <span class="sa">r</span><span class="s1">'^(?P<res1_nb>\d+) (?P<res2_nb>\d+) \d (?P<res_dist>-?\d+.?\d*) '</span>
+ <span class="sa">r</span><span class="s1">'(?P<ec_score>-?\d+.\d+e?-?\d*)$'</span><span class="p">),</span>
+ <span class="s2">"score_field"</span><span class="p">:</span> <span class="s2">"ec_score"</span>
+ <span class="p">},</span>
+ <span class="s2">"gremlin"</span><span class="p">:</span> <span class="p">{</span>
+ <span class="s2">"regex"</span><span class="p">:</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span>
+ <span class="sa">r</span><span class="s1">'^(?P<res1_nb>\d+)\t(?P<res2_nb>\d+)\t'</span>
+ <span class="sa">r</span><span class="s1">'(?P<res1_id>\d+_[AC-IK-NP-TVWYZ])\t'</span>
+ <span class="sa">r</span><span class="s1">'(?P<res2_id>\d+_[AC-IK-NP-TVWYZ])\t'</span>
+ <span class="sa">r</span><span class="s1">'(?P<raw_score>-?\d+\.\d+e?-?\d*)\t'</span>
+ <span class="sa">r</span><span class="s1">'(?P<scale_score>-?\d+\.\d+e?-?\d*)\t'</span>
+ <span class="sa">r</span><span class="s1">'(?P<prob>-?\d+\.\d+e?-?\d*)'</span><span class="p">),</span>
+ <span class="s2">"score_field"</span><span class="p">:</span> <span class="s2">"scale_score"</span>
+ <span class="p">},</span>
+ <span class="s2">"native"</span><span class="p">:</span> <span class="p">{</span>
+ <span class="s2">"regex"</span><span class="p">:</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span>
+ <span class="sa">r</span><span class="s1">'^\s*(?P<res1_nb>\d+)\s+(?P<res2_nb>\d+)\s+('</span>
+ <span class="sa">r</span><span class="s1">'?P<ca_ca>\d+\.\d+)\s+(?P<cb_cb>\d+\.\d+)\s+'</span>
+ <span class="sa">r</span><span class="s1">'(?P<sc_sc>\d+\.\d+)\s+(?P<valid>\w+)'</span><span class="p">),</span>
+ <span class="s2">"score_field"</span><span class="p">:</span> <span class="kc">None</span>
+ <span class="p">},</span>
+ <span class="s2">"native_full"</span><span class="p">:</span> <span class="p">{</span>
+ <span class="s2">"regex"</span><span class="p">:</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span>
+ <span class="sa">r</span><span class="s1">'^\s*(?P<res1_nb>\d+)\s+(?P<res2_nb>\d+)\s+('</span>
+ <span class="sa">r</span><span class="s1">'?P<ca_ca>\d+\.\d+)\s+(?P<cb_cb>\d+\.\d+)\s+'</span>
+ <span class="sa">r</span><span class="s1">'(?P<sc_sc>\d+\.\d+)\s+(?P<valid>\w+)'</span><span class="p">),</span>
+ <span class="s2">"score_field"</span><span class="p">:</span> <span class="kc">None</span>
+ <span class="p">},</span>
+ <span class="s2">"bbcontacts"</span><span class="p">:</span> <span class="p">{</span>
+ <span class="s2">"regex"</span><span class="p">:</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span>
+ <span class="sa">r</span><span class="s1">'\s*(?P<identifier>\w+)\s+(?P<diversity>-?\d+\.?\d*)'</span>
+ <span class="sa">r</span><span class="s1">'\s+(?P<direction>Parallel|Antiparallel)'</span>
+ <span class="sa">r</span><span class="s1">'\s+(?P<viterbiscore>-?\d+\.?\d*)'</span>
+ <span class="sa">r</span><span class="s1">'\s+(?P<indexpred>\d+)'</span>
+ <span class="sa">r</span><span class="s1">'\s+(?P<state>first|internal|last)'</span>
+ <span class="sa">r</span><span class="s1">'\s+(?P<res1_nb>\d+)\s+(?P<res2_nb>\d+)'</span><span class="p">),</span>
+ <span class="s2">"score_field"</span><span class="p">:</span> <span class="kc">None</span>
+ <span class="p">},</span>
+ <span class="s2">"contactlist"</span><span class="p">:</span> <span class="p">{</span>
+ <span class="s2">"regex"</span><span class="p">:</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span>
+ <span class="sa">r</span><span class="s1">'^\s*(?P<res1_nb>\d+)[\s,;]+(?P<res2_nb>\d+)[\s,'</span>
+ <span class="sa">r</span><span class="s1">';]*(?P<con_flag>\w*)'</span><span class="p">),</span>
+ <span class="s2">"score_field"</span><span class="p">:</span> <span class="kc">None</span>
+ <span class="p">},</span>
+ <span class="s2">"metapsicovhb"</span><span class="p">:</span> <span class="p">{</span>
+ <span class="s2">"regex"</span><span class="p">:</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span>
+ <span class="sa">r</span><span class="s1">'^\s*(?P<res_donor>\d+)[\s,;]+'</span>
+ <span class="sa">r</span><span class="s1">'(?P<res_acceptor>\d+)[\s,;]+\d[\s,;]+'</span>
+ <span class="sa">r</span><span class="s1">'(?P<res_dist>-?\d+.?\d*)[\s,;]+'</span>
+ <span class="sa">r</span><span class="s1">'(?P<hbscore>-?\d+\.?\d*)'</span><span class="p">),</span>
+ <span class="s2">"score_field"</span><span class="p">:</span> <span class="s2">"hbscore"</span>
+ <span class="p">},</span>
+ <span class="s2">"default_1"</span><span class="p">:</span> <span class="p">{</span>
+ <span class="s2">"regex"</span><span class="p">:</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span>
+ <span class="sa">r</span><span class="s1">'^\s*(?P<res1_nb>\d+)\s+(?P<res2_nb>\d+)\s+'</span>
+ <span class="sa">r</span><span class="s1">'(?P<resn1>\w+)\s+'</span>
+ <span class="sa">r</span><span class="s1">'(?P<resn2>\w+)\s+'</span>
+ <span class="sa">r</span><span class="s1">'(?P<score>[\w\d.+\-]+)'</span><span class="p">),</span>
+ <span class="s2">"score_field"</span><span class="p">:</span> <span class="s2">"score"</span>
+ <span class="p">},</span>
+ <span class="s2">"default_2"</span><span class="p">:</span> <span class="p">{</span>
+ <span class="s2">"regex"</span><span class="p">:</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span>
+ <span class="sa">r</span><span class="s1">'^\s*(?P<res1_nb>\d+)\s+(?P<res2_nb>\d+)\s+'</span>
+ <span class="sa">r</span><span class="s1">'(?P<score>[\w\d.+\-]+)'</span><span class="p">),</span>
+ <span class="s2">"score_field"</span><span class="p">:</span> <span class="s2">"score"</span>
+ <span class="p">},</span>
+ <span class="s2">"default_3"</span><span class="p">:</span> <span class="p">{</span>
+ <span class="s2">"regex"</span><span class="p">:</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span>
+ <span class="sa">r</span><span class="s1">'^\s*(?P<res1_nb>\d+)\s+(?P<res2_nb>\d+)\s+'</span>
+ <span class="sa">r</span><span class="s1">'(?P<resn1>\w+)\s+'</span>
+ <span class="sa">r</span><span class="s1">'(?P<resn2>\w+)\s+'</span><span class="p">),</span>
+ <span class="s2">"score_field"</span><span class="p">:</span> <span class="kc">None</span>
+ <span class="p">},</span>
+ <span class="s2">"default_4"</span><span class="p">:</span> <span class="p">{</span>
+ <span class="s2">"regex"</span><span class="p">:</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span>
+ <span class="sa">r</span><span class="s1">'^\s*(?P<res1_nb>\d+)\s+(?P<res2_nb>\d+)\s+'</span><span class="p">),</span>
+ <span class="s2">"score_field"</span><span class="p">:</span> <span class="kc">None</span>
+ <span class="p">},</span>
+ <span class="s2">"empty"</span><span class="p">:</span> <span class="p">{</span>
+ <span class="s2">"regex"</span><span class="p">:</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span><span class="sa">r</span><span class="s1">'^\s*$'</span><span class="p">),</span>
+ <span class="s2">"score_field"</span><span class="p">:</span> <span class="kc">None</span>
+ <span class="p">}</span>
+ <span class="p">}</span>
+ <span class="n">check_type</span> <span class="o">=</span> <span class="kc">True</span>
+
+ <span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+ <span class="sd">"""</span>
+
+<span class="sd"> :param args:</span>
+<span class="sd"> :param kwargs:</span>
+<span class="sd"> :return:</span>
+<span class="sd"> """</span>
+ <span class="nb">super</span><span class="p">(</span><span class="n">MapFile</span><span class="p">,</span> <span class="bp">self</span><span class="p">)</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">check_type</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">regex</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">filetype</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">sort</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">check_maptype</span><span class="p">()</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">mapdict</span> <span class="o">=</span> <span class="p">{</span><span class="s2">"alldistmap"</span><span class="p">:</span> <span class="kc">None</span><span class="p">,</span>
+ <span class="s2">"allcontactmap"</span><span class="p">:</span> <span class="kc">None</span><span class="p">,</span>
+ <span class="s2">"distmap"</span><span class="p">:</span> <span class="kc">None</span><span class="p">,</span>
+ <span class="s2">"maplot"</span><span class="p">:</span> <span class="kc">None</span><span class="p">,</span>
+ <span class="s2">"scoremap"</span><span class="p">:</span> <span class="kc">None</span><span class="p">}</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">clashlist</span> <span class="o">=</span> <span class="p">[]</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">distlist</span> <span class="o">=</span> <span class="p">[]</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">contactlist</span> <span class="o">=</span> <span class="p">[]</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">flaglist</span> <span class="o">=</span> <span class="p">{}</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">scorelist</span> <span class="o">=</span> <span class="p">[]</span>
+ <span class="c1"># self.maplot = None</span>
+ <span class="c1"># self.distmap = None</span>
+
+<div class="viewcode-block" id="MapFile.create_map"><a class="viewcode-back" href="../../ariaec.html#ariaec.reader.MapFile.create_map">[docs]</a> <span class="k">def</span> <span class="nf">create_map</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">protein</span><span class="p">,</span> <span class="n">contactdef</span><span class="p">,</span> <span class="n">flaglist</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">offset</span><span class="o">=</span><span class="mi">0</span><span class="p">,</span> <span class="n">sym</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span>
+ <span class="n">path</span><span class="o">=</span><span class="s2">""</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> </span>
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> path :</span>
+<span class="sd"> param protein: (Default value = "")</span>
+<span class="sd"> contactdef :</span>
+<span class="sd"> param flaglist:</span>
+<span class="sd"> offset :</span>
+<span class="sd"> param sym: (Default value = 0)</span>
+<span class="sd"> kwargs :</span>
+<span class="sd"> return:</span>
+<span class="sd"> protein :</span>
+<span class="sd"> </span>
+<span class="sd"> flaglist :</span>
+<span class="sd"> (Default value = None)</span>
+<span class="sd"> sym :</span>
+<span class="sd"> (Default value = True)</span>
+<span class="sd"> **kwargs :</span>
+<span class="sd"> </span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+<span class="sd"> </span>
+<span class="sd"> """</span>
+ <span class="k">raise</span> <span class="ne">NotImplementedError</span><span class="p">(</span><span class="s2">"Class </span><span class="si">%s</span><span class="s2"> doesn't implement create_map"</span> <span class="o">%</span>
+ <span class="bp">self</span><span class="o">.</span><span class="vm">__class__</span><span class="o">.</span><span class="vm">__name__</span><span class="p">)</span></div>
+
+<div class="viewcode-block" id="MapFile.update_map"><a class="viewcode-back" href="../../ariaec.html#ariaec.reader.MapFile.update_map">[docs]</a> <span class="k">def</span> <span class="nf">update_map</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">resmap</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> </span>
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> resmap :</span>
+<span class="sd"> return:</span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+<span class="sd"> </span>
+<span class="sd"> """</span>
+ <span class="k">raise</span> <span class="ne">NotImplementedError</span><span class="p">(</span><span class="s2">"Class </span><span class="si">%s</span><span class="s2"> doesn't implement update_map"</span> <span class="o">%</span>
+ <span class="bp">self</span><span class="o">.</span><span class="vm">__class__</span><span class="o">.</span><span class="vm">__name__</span><span class="p">)</span></div>
+
+<div class="viewcode-block" id="MapFile.check_maptype"><a class="viewcode-back" href="../../ariaec.html#ariaec.reader.MapFile.check_maptype">[docs]</a> <span class="k">def</span> <span class="nf">check_maptype</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="sd">""":return:"""</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s2">"Checking if file </span><span class="si">%s</span><span class="s2"> correspond to </span><span class="si">%s</span><span class="s2"> format"</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">filepath</span><span class="p">,</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">filetype</span><span class="p">)</span>
+ <span class="c1"># Check if given type is supported</span>
+ <span class="c1"># TODO: report this check into commands section</span>
+ <span class="n">defaults</span> <span class="o">=</span> <span class="p">(</span><span class="s2">"default_1"</span><span class="p">,</span> <span class="s2">"default_2"</span><span class="p">,</span> <span class="s2">"default_3"</span><span class="p">,</span> <span class="s2">"default_4"</span><span class="p">,</span> <span class="s2">"empty"</span><span class="p">)</span>
+ <span class="k">if</span> <span class="n">os</span><span class="o">.</span><span class="n">stat</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">filepath</span><span class="p">)</span><span class="o">.</span><span class="n">st_size</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">warning</span><span class="p">(</span><span class="s2">"File </span><span class="si">%s</span><span class="s2"> is empty !"</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">filepath</span><span class="p">)</span>
+ <span class="k">return</span> <span class="p">[</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">types</span><span class="p">[</span><span class="s2">"empty"</span><span class="p">]</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"regex"</span><span class="p">),</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">filetype</span><span class="p">,</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">types</span><span class="p">[</span><span class="s2">"empty"</span><span class="p">]</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"score_field"</span><span class="p">)</span>
+ <span class="p">]</span>
+ <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">filepath</span><span class="p">)</span> <span class="k">as</span> <span class="n">infile</span><span class="p">:</span>
+ <span class="c1"># Check first and second line of file</span>
+ <span class="k">for</span> <span class="n">index</span><span class="p">,</span> <span class="n">line</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">infile</span><span class="p">):</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">filetype</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">types</span><span class="p">:</span>
+ <span class="n">match</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">types</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">filetype</span><span class="p">]</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"regex"</span><span class="p">)</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="n">line</span><span class="p">)</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">error</span><span class="p">(</span><span class="s2">"Format </span><span class="si">%s</span><span class="s2"> not supported !"</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">filetype</span><span class="p">)</span>
+ <span class="n">match</span> <span class="o">=</span> <span class="kc">None</span>
+ <span class="k">if</span> <span class="n">match</span><span class="p">:</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s2">"Format type correct"</span><span class="p">)</span>
+ <span class="k">return</span> <span class="p">[</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">types</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">filetype</span><span class="p">]</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"regex"</span><span class="p">),</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">filetype</span><span class="p">,</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">types</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">filetype</span><span class="p">]</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"score_field"</span><span class="p">)</span>
+ <span class="p">]</span>
+ <span class="k">if</span> <span class="n">index</span> <span class="o">></span> <span class="mi">2</span><span class="p">:</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">warning</span><span class="p">(</span><span class="s2">"Given type do not correspond, checking default"</span>
+ <span class="s2">" format for contactlist or empty file..."</span><span class="p">)</span>
+ <span class="k">for</span> <span class="n">subformat</span> <span class="ow">in</span> <span class="n">defaults</span><span class="p">:</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">types</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">subformat</span><span class="p">)[</span><span class="s2">"regex"</span><span class="p">]</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="n">line</span><span class="p">):</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="s2">"Format type correct </span><span class="si">%s</span><span class="s2">"</span><span class="p">,</span> <span class="n">subformat</span><span class="p">)</span>
+ <span class="k">return</span> <span class="p">[</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">types</span><span class="p">[</span><span class="n">subformat</span><span class="p">]</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"regex"</span><span class="p">),</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">filetype</span><span class="p">,</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">types</span><span class="p">[</span><span class="n">subformat</span><span class="p">]</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"score_field"</span><span class="p">)</span>
+ <span class="p">]</span>
+ <span class="c1"># Stop checking after second line</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">error</span><span class="p">(</span><span class="s2">"Can't read </span><span class="si">%s</span><span class="s2"> file."</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">filetype</span><span class="p">)</span>
+ <span class="k">break</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">error</span><span class="p">(</span><span class="s2">"Wrong format type given ..."</span><span class="p">)</span>
+ <span class="k">return</span> <span class="p">[</span><span class="kc">None</span><span class="p">]</span> <span class="o">*</span> <span class="mi">3</span></div>
+
+<div class="viewcode-block" id="MapFile.read"><a class="viewcode-back" href="../../ariaec.html#ariaec.reader.MapFile.read">[docs]</a> <span class="k">def</span> <span class="nf">read</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">protein</span><span class="p">,</span> <span class="n">contactdef</span><span class="o">=</span><span class="mf">5.0</span><span class="p">,</span> <span class="n">groupby_method</span><span class="o">=</span><span class="s2">"min"</span><span class="p">,</span>
+ <span class="n">scsc</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> </span>
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> protein :</span>
+<span class="sd"> param contactdef: (Default value = None)</span>
+<span class="sd"> groupby_method :</span>
+<span class="sd"> param scsc: (Default value = "min")</span>
+<span class="sd"> contactdef :</span>
+<span class="sd"> (Default value = 5.0)</span>
+<span class="sd"> scsc :</span>
+<span class="sd"> (Default value = None)</span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+<span class="sd"> </span>
+<span class="sd"> """</span>
+ <span class="c1"># res1_1l_code</span>
+ <span class="n">aaseq</span> <span class="o">=</span> <span class="p">{}</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">filetype</span><span class="p">:</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s2">"Reading </span><span class="si">%s</span><span class="s2"> file"</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">filepath</span><span class="p">)</span>
+ <span class="c1"># Read file with regex related to filetype</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">load</span><span class="p">()</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">lines</span><span class="p">)</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">error</span><span class="p">(</span><span class="s2">"Unrecognized file type"</span><span class="p">)</span>
+ <span class="k">return</span> <span class="kc">None</span>
+
+ <span class="n">LOG</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s2">"Loading contact file"</span><span class="p">)</span>
+ <span class="n">sym</span> <span class="o">=</span> <span class="kc">False</span> <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">filetype</span> <span class="o">==</span> <span class="s2">"metapsicovhb"</span> <span class="k">else</span> <span class="kc">True</span>
+ <span class="n">confields</span> <span class="o">=</span> <span class="p">(</span><span class="s2">"res_donor"</span><span class="p">,</span> <span class="s2">"res_acceptor"</span><span class="p">)</span> <span class="k">if</span> \
+ <span class="bp">self</span><span class="o">.</span><span class="n">filetype</span> <span class="o">==</span> <span class="s2">"metapsicovhb"</span> <span class="k">else</span> <span class="p">(</span><span class="s1">'res1_nb'</span><span class="p">,</span> <span class="s1">'res2_nb'</span><span class="p">)</span>
+ <span class="k">for</span> <span class="n">contact</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">lines</span><span class="p">:</span>
+
+ <span class="c1"># If contact defined</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">lines</span><span class="p">[</span><span class="n">contact</span><span class="p">]</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">confields</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span> <span class="ow">and</span> \
+ <span class="bp">self</span><span class="o">.</span><span class="n">lines</span><span class="p">[</span><span class="n">contact</span><span class="p">]</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">confields</span><span class="p">[</span><span class="mi">1</span><span class="p">]):</span>
+ <span class="n">conkeys</span> <span class="o">=</span> <span class="nb">tuple</span><span class="p">(</span><span class="nb">sorted</span><span class="p">([</span>
+ <span class="nb">int</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">lines</span><span class="p">[</span><span class="n">contact</span><span class="p">]</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">confields</span><span class="p">[</span><span class="mi">0</span><span class="p">])),</span>
+ <span class="nb">int</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">lines</span><span class="p">[</span><span class="n">contact</span><span class="p">]</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">confields</span><span class="p">[</span><span class="mi">1</span><span class="p">]))]))</span>
+
+ <span class="bp">self</span><span class="o">.</span><span class="n">contactlist</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">conkeys</span><span class="p">)</span>
+
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">sort</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">scorelist</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="nb">float</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">lines</span><span class="p">[</span><span class="n">contact</span><span class="p">]</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">sort</span><span class="p">)))</span>
+
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">filetype</span> <span class="o">==</span> <span class="s2">"contactlist"</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">flaglist</span><span class="p">[</span><span class="n">conkeys</span><span class="p">]</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">lines</span><span class="p">[</span><span class="n">contact</span><span class="p">]</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"con_flag"</span><span class="p">)</span>
+
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">filetype</span> <span class="o">==</span> <span class="s2">"metapsicovhb"</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">distlist</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">lines</span><span class="p">[</span><span class="n">contact</span><span class="p">]</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"res_dist"</span><span class="p">))</span>
+
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">filetype</span> <span class="ow">in</span> <span class="p">(</span><span class="s2">"evfold"</span><span class="p">,</span> <span class="s2">"plmdca"</span><span class="p">,</span> <span class="s2">"plm"</span><span class="p">,</span> <span class="s2">"plmev"</span><span class="p">):</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">clashlist</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="nb">next</span><span class="p">(</span>
+ <span class="p">(</span><span class="n">el</span> <span class="k">for</span> <span class="n">el</span> <span class="ow">in</span> <span class="p">(</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">lines</span><span class="p">[</span><span class="n">contact</span><span class="p">]</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"ss_filter"</span><span class="p">),</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">lines</span><span class="p">[</span><span class="n">contact</span><span class="p">]</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"high_cons_filter"</span><span class="p">),</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">lines</span><span class="p">[</span><span class="n">contact</span><span class="p">]</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"cc_filter"</span><span class="p">))</span> <span class="k">if</span> <span class="n">el</span> <span class="o">!=</span> <span class="s2">"0"</span><span class="p">),</span>
+ <span class="s2">"0"</span><span class="p">))</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">lines</span><span class="p">[</span><span class="n">contact</span><span class="p">]</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"res1_name"</span><span class="p">)</span> <span class="ow">and</span> \
+ <span class="bp">self</span><span class="o">.</span><span class="n">lines</span><span class="p">[</span><span class="n">contact</span><span class="p">]</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"res2_name"</span><span class="p">):</span>
+ <span class="n">aaseq</span><span class="p">[</span><span class="nb">int</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">lines</span><span class="p">[</span><span class="n">contact</span><span class="p">]</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"res1_nb"</span><span class="p">))]</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">lines</span><span class="p">[</span>
+ <span class="n">contact</span><span class="p">]</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"res1_name"</span><span class="p">)</span>
+ <span class="n">aaseq</span><span class="p">[</span><span class="nb">int</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">lines</span><span class="p">[</span><span class="n">contact</span><span class="p">]</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"res2_nb"</span><span class="p">))]</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">lines</span><span class="p">[</span>
+ <span class="n">contact</span><span class="p">]</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"res2_name"</span><span class="p">)</span>
+
+ <span class="k">if</span> <span class="n">aaseq</span><span class="p">:</span>
+ <span class="c1"># Align evfold amino acid sequence with sequence obtained from seq</span>
+ <span class="c1"># file</span>
+ <span class="nb">print</span><span class="p">(</span><span class="n">aaseq</span><span class="p">)</span>
+ <span class="n">seq</span> <span class="o">=</span> <span class="s1">''</span><span class="o">.</span><span class="n">join</span><span class="p">([</span>
+ <span class="n">aaseq</span><span class="p">[</span><span class="n">key</span><span class="p">]</span> <span class="k">if</span> <span class="n">key</span> <span class="ow">in</span> <span class="n">aaseq</span> <span class="k">else</span> <span class="s1">'*'</span>
+ <span class="k">for</span> <span class="n">key</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="nb">max</span><span class="p">(</span><span class="n">aaseq</span><span class="p">)</span> <span class="o">+</span> <span class="mi">1</span><span class="p">)])</span>
+ <span class="c1"># With gap penalty set to -1, we should only have an alignment without</span>
+ <span class="c1"># gap since mismatch is the preferred way (with score set to 0)</span>
+ <span class="n">alignment</span> <span class="o">=</span> <span class="n">pairwise2</span><span class="o">.</span><span class="n">align</span><span class="o">.</span><span class="n">localxs</span><span class="p">(</span>
+ <span class="n">seq</span><span class="p">,</span> <span class="n">protein</span><span class="o">.</span><span class="n">aa_sequence</span><span class="o">.</span><span class="n">sequence</span><span class="p">,</span> <span class="o">-</span><span class="mi">1</span><span class="p">,</span> <span class="o">-</span><span class="mi">1</span><span class="p">,</span>
+ <span class="n">one_alignment_only</span><span class="o">=</span><span class="kc">True</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s1">'Alignment of amino acid sequence with contact file</span><span class="se">\n</span><span class="s1">'</span>
+ <span class="s1">'</span><span class="si">%s</span><span class="s1">'</span> <span class="o">%</span> <span class="n">pairwise2</span><span class="o">.</span><span class="n">format_alignment</span><span class="p">(</span><span class="o">*</span><span class="n">alignment</span><span class="p">))</span>
+ <span class="n">shift</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="sa">r</span><span class="s1">'^-*'</span><span class="p">,</span> <span class="n">alignment</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span>
+ <span class="n">shift</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">shift</span><span class="o">.</span><span class="n">group</span><span class="p">(</span><span class="mi">0</span><span class="p">))</span> <span class="k">if</span> <span class="n">shift</span> <span class="k">else</span> <span class="mi">0</span>
+ <span class="k">if</span> <span class="n">shift</span><span class="p">:</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">warning</span><span class="p">(</span><span class="s2">"Found a shift of </span><span class="si">%d</span><span class="s2"> residues in positions given"</span>
+ <span class="s2">" within contact list"</span><span class="p">,</span> <span class="n">shift</span><span class="p">)</span>
+
+ <span class="n">LOG</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s2">"Update index in contact list and remove unassigned "</span>
+ <span class="s2">"contacts"</span><span class="p">)</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="s2">"Old contact list</span><span class="se">\n</span><span class="si">%s</span><span class="s2">"</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">contactlist</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">contactlist</span> <span class="o">=</span> <span class="p">[</span>
+ <span class="p">(</span><span class="n">contact</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">-</span> <span class="n">shift</span><span class="p">,</span> <span class="n">contact</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="o">-</span> <span class="n">shift</span><span class="p">)</span>
+ <span class="k">for</span> <span class="n">contact</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">contactlist</span>
+ <span class="p">]</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="s2">"New contact list</span><span class="se">\n</span><span class="si">%s</span><span class="s2">"</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">contactlist</span><span class="p">)</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s2">"Remove contacts outside sequence bonds"</span><span class="p">)</span>
+
+ <span class="c1"># Checking for unassigned contacts</span>
+ <span class="n">validx</span> <span class="o">=</span> <span class="nb">range</span><span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="nb">len</span><span class="p">(</span><span class="n">protein</span><span class="o">.</span><span class="n">aa_sequence</span><span class="o">.</span><span class="n">sequence</span><span class="p">)</span> <span class="o">+</span> <span class="mi">1</span><span class="p">)</span>
+ <span class="n">unascon</span> <span class="o">=</span> <span class="p">[</span><span class="n">contactidx</span>
+ <span class="k">for</span> <span class="n">contactidx</span><span class="p">,</span> <span class="n">contact</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">contactlist</span><span class="p">)</span>
+ <span class="k">if</span> <span class="n">contact</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">validx</span> <span class="ow">or</span> <span class="n">contact</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">validx</span><span class="p">]</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="s2">"Old contact list (</span><span class="si">%d</span><span class="s2"> contacts)</span><span class="se">\n</span><span class="si">%s</span><span class="s2">"</span><span class="p">,</span>
+ <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">contactlist</span><span class="p">),</span> <span class="bp">self</span><span class="o">.</span><span class="n">contactlist</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">contactlist</span> <span class="o">=</span> <span class="p">[</span><span class="n">contact</span>
+ <span class="k">for</span> <span class="n">idx</span><span class="p">,</span> <span class="n">contact</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">contactlist</span><span class="p">)</span>
+ <span class="k">if</span> <span class="n">idx</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">unascon</span><span class="p">]</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="s2">"New contact list (</span><span class="si">%d</span><span class="s2"> contacts)</span><span class="se">\n</span><span class="si">%s</span><span class="s2">"</span><span class="p">,</span>
+ <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">contactlist</span><span class="p">),</span> <span class="bp">self</span><span class="o">.</span><span class="n">contactlist</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">clashlist</span> <span class="o">=</span> <span class="p">[</span><span class="n">clash</span> <span class="k">for</span> <span class="n">idx</span><span class="p">,</span> <span class="n">clash</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">clashlist</span><span class="p">)</span>
+ <span class="k">if</span> <span class="n">idx</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">unascon</span><span class="p">]</span> <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">clashlist</span> <span class="k">else</span> <span class="p">[]</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">distlist</span> <span class="o">=</span> <span class="p">[</span><span class="n">dist</span> <span class="k">for</span> <span class="n">idx</span><span class="p">,</span> <span class="n">dist</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">distlist</span><span class="p">)</span>
+ <span class="k">if</span> <span class="n">idx</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">unascon</span><span class="p">]</span> <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">distlist</span> <span class="k">else</span> <span class="p">[]</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">scorelist</span> <span class="o">=</span> <span class="p">[</span><span class="n">score</span> <span class="k">for</span> <span class="n">idx</span><span class="p">,</span> <span class="n">score</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">scorelist</span><span class="p">)</span>
+ <span class="k">if</span> <span class="n">idx</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">unascon</span><span class="p">]</span> <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">scorelist</span> <span class="k">else</span> <span class="p">[]</span>
+
+ <span class="bp">self</span><span class="o">.</span><span class="n">create_map</span><span class="p">(</span><span class="n">protein</span><span class="p">,</span> <span class="n">contactdef</span><span class="p">,</span>
+ <span class="n">groupby_method</span><span class="o">=</span><span class="n">groupby_method</span><span class="p">,</span> <span class="n">scsc</span><span class="o">=</span><span class="n">scsc</span><span class="p">,</span>
+ <span class="n">flaglist</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">flaglist</span><span class="p">,</span> <span class="n">sym</span><span class="o">=</span><span class="n">sym</span><span class="p">,</span> <span class="n">path</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">filepath</span><span class="p">)</span></div></div>
+
+
+<div class="viewcode-block" id="ContactMapFile"><a class="viewcode-back" href="../../ariaec.html#ariaec.reader.ContactMapFile">[docs]</a><span class="k">class</span> <span class="nc">ContactMapFile</span><span class="p">(</span><span class="n">MapFile</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Contact map file</span>
+<span class="sd"> """</span>
+
+ <span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">filepath</span><span class="p">,</span> <span class="n">filetype</span><span class="p">):</span>
+ <span class="sd">"""</span>
+
+<span class="sd"> :param filepath:</span>
+<span class="sd"> :param filetype:</span>
+<span class="sd"> :return:</span>
+<span class="sd"> """</span>
+ <span class="nb">super</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="vm">__class__</span><span class="p">,</span> <span class="bp">self</span><span class="p">)</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="n">filepath</span><span class="p">,</span> <span class="n">filetype</span><span class="p">)</span>
+
+<div class="viewcode-block" id="ContactMapFile.update_map"><a class="viewcode-back" href="../../ariaec.html#ariaec.reader.ContactMapFile.update_map">[docs]</a> <span class="k">def</span> <span class="nf">update_map</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">resmap</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> </span>
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> resmap :</span>
+<span class="sd"> return:</span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+<span class="sd"> </span>
+<span class="sd"> """</span>
+ <span class="c1"># TODO: swap dataframe factory here</span>
+ <span class="k">raise</span> <span class="ne">NotImplementedError</span></div>
+
+<div class="viewcode-block" id="ContactMapFile.create_map"><a class="viewcode-back" href="../../ariaec.html#ariaec.reader.ContactMapFile.create_map">[docs]</a> <span class="k">def</span> <span class="nf">create_map</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">protein</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Initialize and fill Res - Res maps based on contactlist</span>
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> protein :</span>
+<span class="sd"> </span>
+<span class="sd"> args :</span>
+<span class="sd"> </span>
+<span class="sd"> kwargs :</span>
+<span class="sd"> </span>
+<span class="sd"> *args :</span>
+<span class="sd"> </span>
+<span class="sd"> **kwargs :</span>
+<span class="sd"> </span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+<span class="sd"> </span>
+<span class="sd"> """</span>
+ <span class="n">offset</span> <span class="o">=</span> <span class="nb">min</span><span class="p">(</span><span class="n">protein</span><span class="o">.</span><span class="n">index</span><span class="p">)</span> <span class="c1"># Should be 1 or upper (human_idx)</span>
+ <span class="n">idxnames</span> <span class="o">=</span> <span class="s2">"residuex"</span> <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">filetype</span> <span class="o">!=</span> <span class="s2">"metapsicovhb"</span> <span class="k">else</span> <span class="s2">"donor"</span>
+ <span class="n">colnames</span> <span class="o">=</span> <span class="s2">"residuey"</span> <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">filetype</span> <span class="o">!=</span> <span class="s2">"metapsicovhb"</span> <span class="k">else</span> <span class="s2">"acceptor"</span>
+ <span class="n">contactmap</span> <span class="o">=</span> <span class="n">ResMap</span><span class="p">(</span><span class="n">protein</span><span class="o">.</span><span class="n">aa_sequence</span><span class="o">.</span><span class="n">sequence</span><span class="p">,</span> <span class="n">mtype</span><span class="o">=</span><span class="s1">'contact'</span><span class="p">,</span>
+ <span class="n">flaglist</span><span class="o">=</span><span class="n">kwargs</span><span class="p">[</span><span class="s1">'flaglist'</span><span class="p">],</span>
+ <span class="n">seqidx</span><span class="o">=</span><span class="n">protein</span><span class="o">.</span><span class="n">index</span><span class="p">,</span> <span class="n">idxnames</span><span class="o">=</span><span class="n">idxnames</span><span class="p">,</span>
+ <span class="n">colnames</span><span class="o">=</span><span class="n">colnames</span><span class="p">,</span> <span class="n">sym</span><span class="o">=</span><span class="n">kwargs</span><span class="p">[</span><span class="s1">'sym'</span><span class="p">],</span>
+ <span class="n">desc</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">filetype</span><span class="p">,</span> <span class="n">path</span><span class="o">=</span><span class="n">kwargs</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"path"</span><span class="p">))</span>
+ <span class="c1"># DataFrame containing ec scores</span>
+ <span class="n">scoremap</span> <span class="o">=</span> <span class="n">ResMap</span><span class="p">(</span><span class="n">protein</span><span class="o">.</span><span class="n">aa_sequence</span><span class="o">.</span><span class="n">sequence</span><span class="p">,</span> <span class="n">mtype</span><span class="o">=</span><span class="s1">'score'</span><span class="p">,</span>
+ <span class="n">seqidx</span><span class="o">=</span><span class="n">protein</span><span class="o">.</span><span class="n">index</span><span class="p">,</span> <span class="n">idxnames</span><span class="o">=</span><span class="n">idxnames</span><span class="p">,</span>
+ <span class="n">colnames</span><span class="o">=</span><span class="n">colnames</span><span class="p">,</span> <span class="n">sym</span><span class="o">=</span><span class="n">kwargs</span><span class="p">[</span><span class="s1">'sym'</span><span class="p">],</span>
+ <span class="n">path</span><span class="o">=</span><span class="n">kwargs</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"path"</span><span class="p">),</span>
+ <span class="n">desc</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">filetype</span><span class="p">)</span> <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">sort</span> <span class="k">else</span> <span class="kc">None</span>
+ <span class="n">distmap</span> <span class="o">=</span> <span class="n">ResMap</span><span class="p">(</span><span class="n">protein</span><span class="o">.</span><span class="n">aa_sequence</span><span class="o">.</span><span class="n">sequence</span><span class="p">,</span> <span class="n">mtype</span><span class="o">=</span><span class="s1">'distance'</span><span class="p">,</span>
+ <span class="n">seqidx</span><span class="o">=</span><span class="n">protein</span><span class="o">.</span><span class="n">index</span><span class="p">,</span> <span class="n">idxnames</span><span class="o">=</span><span class="n">idxnames</span><span class="p">,</span> <span class="n">path</span><span class="o">=</span><span class="n">kwargs</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"path"</span><span class="p">),</span>
+ <span class="n">colnames</span><span class="o">=</span><span class="n">colnames</span><span class="p">,</span> <span class="n">sym</span><span class="o">=</span><span class="n">kwargs</span><span class="p">[</span><span class="s1">'sym'</span><span class="p">],</span>
+ <span class="n">desc</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">filetype</span><span class="p">)</span> <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">filetype</span> <span class="o">==</span> <span class="s2">"metapsicovhb"</span> <span class="k">else</span> <span class="kc">None</span>
+
+ <span class="k">for</span> <span class="n">idx</span><span class="p">,</span> <span class="n">contact</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">contactlist</span><span class="p">):</span>
+ <span class="n">contact_id</span> <span class="o">=</span> <span class="n">idx</span> <span class="o">+</span> <span class="mi">1</span>
+ <span class="n">resid1</span><span class="p">,</span> <span class="n">resid2</span> <span class="o">=</span> <span class="n">contact</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">contact</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
+ <span class="n">dist</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">distlist</span><span class="p">[</span><span class="n">idx</span><span class="p">]</span> <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">distlist</span> <span class="k">else</span> <span class="kc">None</span>
+
+ <span class="c1"># Res id start from 0 in res-res map</span>
+ <span class="n">residx1</span> <span class="o">=</span> <span class="n">contactmap</span><span class="o">.</span><span class="n">index</span><span class="p">[</span><span class="n">resid1</span> <span class="o">-</span> <span class="n">offset</span><span class="p">]</span>
+ <span class="n">residx2</span> <span class="o">=</span> <span class="n">contactmap</span><span class="o">.</span><span class="n">index</span><span class="p">[</span><span class="n">resid2</span> <span class="o">-</span> <span class="n">offset</span><span class="p">]</span>
+
+ <span class="k">if</span> <span class="p">(</span><span class="nb">int</span><span class="p">(</span><span class="n">residx1</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s2">"-"</span><span class="p">)[</span><span class="mi">0</span><span class="p">])</span> <span class="o">!=</span> <span class="n">resid1</span><span class="p">)</span> <span class="ow">or</span> \
+ <span class="p">(</span><span class="n">resid2</span> <span class="o">!=</span> <span class="nb">int</span><span class="p">(</span><span class="n">residx2</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s2">"-"</span><span class="p">)[</span><span class="mi">0</span><span class="p">])):</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">error</span><span class="p">(</span><span class="s2">"Wrong resid humanidx (</span><span class="si">%d</span><span class="s2">, </span><span class="si">%d</span><span class="s2">) in contact (</span><span class="si">%d</span><span class="s2">) is "</span>
+ <span class="s2">"not the same in resmap (</span><span class="si">%s</span><span class="s2">, </span><span class="si">%s</span><span class="s2">)"</span><span class="p">,</span>
+ <span class="n">resid1</span><span class="p">,</span> <span class="n">resid2</span><span class="p">,</span> <span class="n">contact_id</span><span class="p">,</span>
+ <span class="n">residx1</span><span class="p">,</span> <span class="n">residx2</span><span class="p">)</span>
+
+ <span class="n">contactmap</span><span class="o">.</span><span class="n">set_value</span><span class="p">(</span><span class="n">residx1</span><span class="p">,</span> <span class="n">residx2</span><span class="p">,</span> <span class="kc">True</span><span class="p">)</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">sort</span><span class="p">:</span>
+ <span class="n">scoremap</span><span class="o">.</span><span class="n">sort_list</span><span class="o">.</span><span class="n">append</span><span class="p">((</span><span class="n">resid1</span> <span class="o">-</span> <span class="n">offset</span><span class="p">,</span> <span class="n">resid2</span> <span class="o">-</span> <span class="n">offset</span><span class="p">))</span>
+ <span class="n">scoremap</span><span class="o">.</span><span class="n">set_value</span><span class="p">(</span><span class="n">residx1</span><span class="p">,</span> <span class="n">residx2</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">scorelist</span><span class="p">[</span><span class="n">idx</span><span class="p">])</span>
+ <span class="k">if</span> <span class="n">distmap</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+ <span class="n">distmap</span><span class="o">.</span><span class="n">set_value</span><span class="p">(</span><span class="n">residx1</span><span class="p">,</span> <span class="n">residx2</span><span class="p">,</span> <span class="n">dist</span><span class="p">)</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="s2">"</span><span class="si">%s</span><span class="s2"> contact map:</span><span class="se">\n</span><span class="si">%s</span><span class="s2">"</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">filetype</span><span class="p">,</span> <span class="n">contactmap</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">mapdict</span><span class="p">[</span><span class="s2">"maplot"</span><span class="p">]</span> <span class="o">=</span> <span class="n">contactmap</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="s2">"</span><span class="si">%s</span><span class="s2"> score map:</span><span class="se">\n</span><span class="si">%s</span><span class="s2">"</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">filetype</span><span class="p">,</span> <span class="n">scoremap</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">mapdict</span><span class="p">[</span><span class="s2">"scoremap"</span><span class="p">]</span> <span class="o">=</span> <span class="n">scoremap</span>
+ <span class="k">if</span> <span class="n">distmap</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">mapdict</span><span class="p">[</span><span class="s2">"distmap"</span><span class="p">]</span> <span class="o">=</span> <span class="n">distmap</span></div></div>
+
+
+<div class="viewcode-block" id="PDBFile"><a class="viewcode-back" href="../../ariaec.html#ariaec.reader.PDBFile">[docs]</a><span class="k">class</span> <span class="nc">PDBFile</span><span class="p">(</span><span class="n">MapFile</span><span class="p">):</span>
+ <span class="sd">"""PDB file"""</span>
+ <span class="n">pdbreg</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span><span class="sa">r</span><span class="s1">'^(?P<record>ATOM |HETATM)(?P<serial>[\s\w]</span><span class="si">{5}</span><span class="s1">)'</span>
+ <span class="sa">r</span><span class="s1">'\s(?P<name>[\s\w]</span><span class="si">{4}</span><span class="s1">)'</span>
+ <span class="sa">r</span><span class="s1">'(?P<altLoc>[\s\w])'</span>
+ <span class="sa">r</span><span class="s1">'(?P<resName>\w</span><span class="si">{3}</span><span class="s1">)\s(?P<chainID>\w)'</span>
+ <span class="sa">r</span><span class="s1">'(?P<resSeq>[\s\w]</span><span class="si">{4}</span><span class="s1">)(?P<iCode>[\s\w])'</span>
+ <span class="sa">r</span><span class="s1">'\s</span><span class="si">{3}</span><span class="s1">(?P<x>[\s\d-]</span><span class="si">{4}</span><span class="s1">\.\d</span><span class="si">{3}</span><span class="s1">)(?P<y>[\s\d-]</span><span class="si">{4}</span><span class="s1">\.\d</span><span class="si">{3}</span><span class="s1">)'</span>
+ <span class="sa">r</span><span class="s1">'(?P<z>[\s\d-]</span><span class="si">{4}</span><span class="s1">\.\d</span><span class="si">{3}</span><span class="s1">)'</span>
+ <span class="sa">r</span><span class="s1">'(?P<occupancy>[\s\d-]</span><span class="si">{3}</span><span class="s1">\.\d</span><span class="si">{2}</span><span class="s1">)'</span>
+ <span class="sa">r</span><span class="s1">'(?P<tempFactor>[\s\d-]</span><span class="si">{3}</span><span class="s1">\.\d</span><span class="si">{2}</span><span class="s1">)'</span>
+ <span class="sa">r</span><span class="s1">'\s</span><span class="si">{10}</span><span class="s1">(?P<element>[\s\w]</span><span class="si">{2}</span><span class="s1">)'</span>
+ <span class="sa">r</span><span class="s1">'(?P<charge>[\s\w]</span><span class="si">{2}</span><span class="s1">)'</span><span class="p">)</span>
+
+ <span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+ <span class="c1"># TODO: use PDB object in aria</span>
+ <span class="c1"># TODO: write dataframe in a separated file</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">check_type</span> <span class="o">=</span> <span class="kc">False</span>
+ <span class="nb">super</span><span class="p">(</span><span class="n">PDBFile</span><span class="p">,</span> <span class="bp">self</span><span class="p">)</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="n">regex</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">pdbreg</span><span class="p">,</span> <span class="n">filetype</span><span class="o">=</span><span class="s2">"pdb"</span><span class="p">,</span>
+ <span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
+
+<div class="viewcode-block" id="PDBFile.create_map"><a class="viewcode-back" href="../../ariaec.html#ariaec.reader.PDBFile.create_map">[docs]</a> <span class="k">def</span> <span class="nf">create_map</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">protein</span><span class="p">,</span> <span class="n">contactdef</span><span class="p">,</span> <span class="n">groupby_method</span><span class="o">=</span><span class="s2">"min"</span><span class="p">,</span> <span class="n">scsc</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
+ <span class="n">flaglist</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">sym</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">path</span><span class="o">=</span><span class="s2">""</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> </span>
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> protein :</span>
+<span class="sd"> contactdef:</span>
+<span class="sd"> groupby_method :</span>
+<span class="sd"> (Default value = "min")</span>
+<span class="sd"> scsc: </span>
+<span class="sd"> (Default value = None)</span>
+<span class="sd"> flaglist :</span>
+<span class="sd"> (Default value = None)</span>
+<span class="sd"> sym: </span>
+<span class="sd"> (Default value = True)</span>
+<span class="sd"> path :</span>
+<span class="sd"> (Default value = "")</span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+<span class="sd"> </span>
+<span class="sd"> """</span>
+ <span class="n">resmap</span> <span class="o">=</span> <span class="n">ResAtmMap</span><span class="p">(</span><span class="n">protein</span><span class="o">.</span><span class="n">aa_sequence</span><span class="o">.</span><span class="n">sequence</span><span class="p">,</span> <span class="n">mtype</span><span class="o">=</span><span class="s1">'distance'</span><span class="p">,</span>
+ <span class="n">flaglist</span><span class="o">=</span><span class="n">flaglist</span><span class="p">,</span> <span class="n">path</span><span class="o">=</span><span class="n">path</span><span class="p">,</span>
+ <span class="n">seqidx</span><span class="o">=</span><span class="n">protein</span><span class="o">.</span><span class="n">index</span><span class="p">,</span> <span class="n">desc</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">filetype</span><span class="p">)</span>
+ <span class="c1"># noinspection PyTypeChecker</span>
+ <span class="n">resmap</span><span class="p">[:]</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">update_map</span><span class="p">(</span><span class="n">resmap</span><span class="p">,</span> <span class="n">sym</span><span class="o">=</span><span class="n">sym</span><span class="p">)</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="s2">"pdb distance map:</span><span class="se">\n</span><span class="si">%s</span><span class="s2">"</span><span class="p">,</span> <span class="n">resmap</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">mapdict</span><span class="p">[</span><span class="s2">"alldistmap"</span><span class="p">]</span> <span class="o">=</span> <span class="n">resmap</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">mapdict</span><span class="p">[</span><span class="s2">"distmap"</span><span class="p">]</span> <span class="o">=</span> <span class="n">resmap</span><span class="o">.</span><span class="n">reduce</span><span class="p">(</span><span class="n">groupby</span><span class="o">=</span><span class="n">groupby_method</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">mapdict</span><span class="p">[</span><span class="s2">"allcontactmap"</span><span class="p">]</span> <span class="o">=</span> <span class="n">resmap</span><span class="o">.</span><span class="n">contact_map</span><span class="p">(</span>
+ <span class="n">contactdef</span><span class="o">=</span><span class="n">contactdef</span><span class="p">,</span> <span class="n">scsc_min</span><span class="o">=</span><span class="n">scsc</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">mapdict</span><span class="p">[</span><span class="s2">"maplot"</span><span class="p">]</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">mapdict</span><span class="p">[</span><span class="s2">"allcontactmap"</span><span class="p">]</span><span class="o">.</span><span class="n">reduce</span><span class="p">()</span></div>
+
+<div class="viewcode-block" id="PDBFile.update_map"><a class="viewcode-back" href="../../ariaec.html#ariaec.reader.PDBFile.update_map">[docs]</a> <span class="k">def</span> <span class="nf">update_map</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">resmap</span><span class="p">,</span> <span class="n">sym</span><span class="o">=</span><span class="kc">True</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> </span>
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> resmap :</span>
+<span class="sd"> param sym:</span>
+<span class="sd"> sym :</span>
+<span class="sd"> (Default value = True)</span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+<span class="sd"> </span>
+<span class="sd"> """</span>
+ <span class="c1"># Map only on heavy atoms</span>
+ <span class="c1"># TODO: check if same sequence in pdb file</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s2">"Updating distance map with pdb file"</span><span class="p">)</span>
+ <span class="n">newmap</span> <span class="o">=</span> <span class="n">resmap</span><span class="o">.</span><span class="n">copy</span><span class="p">()</span>
+ <span class="n">heavylist</span> <span class="o">=</span> <span class="p">[]</span>
+ <span class="n">error_list</span> <span class="o">=</span> <span class="nb">set</span><span class="p">()</span>
+ <span class="k">for</span> <span class="n">atom</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">lines</span><span class="p">:</span>
+ <span class="k">if</span> <span class="n">resmap</span><span class="o">.</span><span class="n">heavy_reg</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">lines</span><span class="p">[</span><span class="n">atom</span><span class="p">][</span><span class="s1">'name'</span><span class="p">]</span><span class="o">.</span><span class="n">strip</span><span class="p">()):</span>
+ <span class="n">heavylist</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">atom</span><span class="p">)</span>
+
+ <span class="c1"># For each heavy atom</span>
+ <span class="k">for</span> <span class="n">x</span><span class="p">,</span> <span class="n">atomx</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">heavylist</span><span class="p">):</span>
+ <span class="k">for</span> <span class="n">atomy</span> <span class="ow">in</span> <span class="n">heavylist</span><span class="p">[</span><span class="n">x</span><span class="p">:]:</span>
+ <span class="c1"># TODO: Check first residue number in pdb file</span>
+ <span class="n">indx</span> <span class="o">=</span> <span class="s2">"</span><span class="si">%03d</span><span class="s2">-</span><span class="si">%s</span><span class="s2">"</span> <span class="o">%</span> <span class="p">(</span><span class="nb">int</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">lines</span><span class="p">[</span><span class="n">atomx</span><span class="p">][</span><span class="s1">'resSeq'</span><span class="p">]),</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">lines</span><span class="p">[</span><span class="n">atomx</span><span class="p">][</span><span class="s1">'resName'</span><span class="p">]</span><span class="o">.</span><span class="n">strip</span><span class="p">()),</span> \
+ <span class="bp">self</span><span class="o">.</span><span class="n">lines</span><span class="p">[</span><span class="n">atomx</span><span class="p">][</span><span class="s1">'name'</span><span class="p">]</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span>
+ <span class="n">indy</span> <span class="o">=</span> <span class="s2">"</span><span class="si">%03d</span><span class="s2">-</span><span class="si">%s</span><span class="s2">"</span> <span class="o">%</span> <span class="p">(</span><span class="nb">int</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">lines</span><span class="p">[</span><span class="n">atomy</span><span class="p">][</span><span class="s1">'resSeq'</span><span class="p">]),</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">lines</span><span class="p">[</span><span class="n">atomy</span><span class="p">][</span><span class="s1">'resName'</span><span class="p">]</span><span class="o">.</span><span class="n">strip</span><span class="p">()),</span> \
+ <span class="bp">self</span><span class="o">.</span><span class="n">lines</span><span class="p">[</span><span class="n">atomy</span><span class="p">][</span><span class="s1">'name'</span><span class="p">]</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span>
+ <span class="n">coordx</span> <span class="o">=</span> <span class="p">(</span><span class="nb">float</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">lines</span><span class="p">[</span><span class="n">atomx</span><span class="p">][</span><span class="s1">'x'</span><span class="p">]),</span>
+ <span class="nb">float</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">lines</span><span class="p">[</span><span class="n">atomx</span><span class="p">][</span><span class="s1">'y'</span><span class="p">]),</span>
+ <span class="nb">float</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">lines</span><span class="p">[</span><span class="n">atomx</span><span class="p">][</span><span class="s1">'z'</span><span class="p">]))</span>
+ <span class="n">coordy</span> <span class="o">=</span> <span class="p">(</span><span class="nb">float</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">lines</span><span class="p">[</span><span class="n">atomy</span><span class="p">][</span><span class="s1">'x'</span><span class="p">]),</span>
+ <span class="nb">float</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">lines</span><span class="p">[</span><span class="n">atomy</span><span class="p">][</span><span class="s1">'y'</span><span class="p">]),</span>
+ <span class="nb">float</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">lines</span><span class="p">[</span><span class="n">atomy</span><span class="p">][</span><span class="s1">'z'</span><span class="p">]))</span>
+
+ <span class="n">dist</span> <span class="o">=</span> <span class="n">distance</span><span class="o">.</span><span class="n">euclidean</span><span class="p">(</span><span class="n">coordx</span><span class="p">,</span> <span class="n">coordy</span><span class="p">)</span>
+ <span class="k">if</span> <span class="n">indx</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="ow">in</span> <span class="nb">list</span><span class="p">(</span><span class="n">resmap</span><span class="o">.</span><span class="n">index</span><span class="o">.</span><span class="n">get_level_values</span><span class="p">(</span><span class="s2">"residuex"</span><span class="p">))</span>\
+ <span class="ow">and</span> <span class="n">indy</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="ow">in</span> <span class="nb">list</span><span class="p">(</span><span class="n">resmap</span><span class="o">.</span><span class="n">index</span><span class="o">.</span><span class="n">get_level_values</span><span class="p">(</span><span class="s2">"residuex"</span><span class="p">)):</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="s2">"Update distance value (</span><span class="si">%s</span><span class="s2">, </span><span class="si">%s</span><span class="s2">)"</span><span class="p">,</span> <span class="n">indx</span><span class="p">,</span> <span class="n">indy</span><span class="p">)</span>
+ <span class="n">newmap</span><span class="o">.</span><span class="n">at</span><span class="p">[</span><span class="n">indx</span><span class="p">,</span> <span class="n">indy</span><span class="p">]</span> <span class="o">=</span> <span class="n">dist</span>
+ <span class="k">if</span> <span class="n">sym</span><span class="p">:</span>
+ <span class="c1"># If symmetric matrix</span>
+ <span class="n">newmap</span><span class="o">.</span><span class="n">at</span><span class="p">[</span><span class="n">indy</span><span class="p">,</span> <span class="n">indx</span><span class="p">]</span> <span class="o">=</span> <span class="n">dist</span>
+ <span class="k">elif</span> <span class="n">indx</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="ow">not</span> <span class="ow">in</span> <span class="nb">list</span><span class="p">(</span><span class="n">resmap</span><span class="o">.</span><span class="n">index</span><span class="o">.</span><span class="n">get_level_values</span><span class="p">(</span><span class="s2">"residuex"</span><span class="p">)):</span>
+ <span class="n">error_list</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">indx</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span>
+ <span class="k">elif</span> <span class="n">indy</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="ow">not</span> <span class="ow">in</span> <span class="nb">list</span><span class="p">(</span><span class="n">resmap</span><span class="o">.</span><span class="n">index</span><span class="o">.</span><span class="n">get_level_values</span><span class="p">(</span><span class="s2">"residuex"</span><span class="p">)):</span>
+ <span class="n">error_list</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">indy</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span>
+ <span class="k">if</span> <span class="n">error_list</span><span class="p">:</span>
+ <span class="c1"># Listing related humanidx in the initial df</span>
+ <span class="n">idxlist</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="n">resmap</span><span class="o">.</span><span class="n">index</span><span class="o">.</span><span class="n">get_level_values</span><span class="p">(</span><span class="s2">"residuex"</span><span class="p">))</span>
+ <span class="n">erridx</span> <span class="o">=</span> <span class="p">[</span><span class="n">idx</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s2">"-"</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span> <span class="k">for</span> <span class="n">idx</span> <span class="ow">in</span> <span class="nb">list</span><span class="p">(</span><span class="n">error_list</span><span class="p">)]</span>
+ <span class="n">missidx</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="nb">set</span><span class="p">([</span><span class="n">idx</span> <span class="k">for</span> <span class="n">idx</span> <span class="ow">in</span> <span class="n">idxlist</span>
+ <span class="k">if</span> <span class="n">idx</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s2">"-"</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span> <span class="ow">in</span> <span class="n">erridx</span><span class="p">]))</span>
+ <span class="k">for</span> <span class="n">idx</span> <span class="ow">in</span> <span class="n">missidx</span><span class="p">:</span>
+ <span class="n">newmap</span><span class="o">.</span><span class="n">loc</span><span class="p">[</span><span class="n">idx</span><span class="p">]</span> <span class="o">=</span> <span class="kc">None</span>
+ <span class="k">if</span> <span class="n">sym</span><span class="p">:</span>
+ <span class="n">newmap</span><span class="o">.</span><span class="n">loc</span><span class="p">[:][</span><span class="n">idx</span><span class="p">]</span> <span class="o">=</span> <span class="kc">None</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">error</span><span class="p">(</span><span class="s2">"Can't update pdb distance map for pos in pdb file "</span>
+ <span class="s2">"</span><span class="si">%s</span><span class="s2"> with </span><span class="si">%s</span><span class="s2">"</span><span class="p">,</span> <span class="nb">list</span><span class="p">(</span><span class="n">error_list</span><span class="p">),</span> <span class="n">missidx</span><span class="p">)</span>
+ <span class="k">return</span> <span class="n">newmap</span></div></div>
+
+
+<div class="viewcode-block" id="DistanceMapFile"><a class="viewcode-back" href="../../ariaec.html#ariaec.reader.DistanceMapFile">[docs]</a><span class="k">class</span> <span class="nc">DistanceMapFile</span><span class="p">(</span><span class="n">MapFile</span><span class="p">):</span>
+ <span class="sd">"""Distance matrix file"""</span>
+ <span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">filepath</span><span class="p">,</span> <span class="n">filetype</span><span class="p">):</span>
+ <span class="nb">super</span><span class="p">(</span><span class="n">MapFile</span><span class="p">)</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="n">filepath</span><span class="p">,</span> <span class="n">filetype</span><span class="p">)</span>
+ <span class="k">raise</span> <span class="ne">NotImplementedError</span>
+
+<div class="viewcode-block" id="DistanceMapFile.create_map"><a class="viewcode-back" href="../../ariaec.html#ariaec.reader.DistanceMapFile.create_map">[docs]</a> <span class="k">def</span> <span class="nf">create_map</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">aa_seq</span><span class="p">,</span> <span class="n">contactdef</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> </span>
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> aa_seq :</span>
+<span class="sd"> param contactdef:</span>
+<span class="sd"> kwargs :</span>
+<span class="sd"> return:</span>
+<span class="sd"> contactdef :</span>
+<span class="sd"> </span>
+<span class="sd"> **kwargs :</span>
+<span class="sd"> </span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+<span class="sd"> </span>
+<span class="sd"> """</span>
+ <span class="k">pass</span></div>
+
+ <span class="c1"># Native dist</span>
+<div class="viewcode-block" id="DistanceMapFile.update_map"><a class="viewcode-back" href="../../ariaec.html#ariaec.reader.DistanceMapFile.update_map">[docs]</a> <span class="k">def</span> <span class="nf">update_map</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">resmap</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> </span>
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> resmap :</span>
+<span class="sd"> return:</span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+<span class="sd"> </span>
+<span class="sd"> """</span>
+ <span class="k">pass</span></div></div>
+ <span class="c1"># Construit map avec la liste de residus + infos de distance du fichier</span>
+ <span class="c1"># return DistanceMap</span>
+
+
+<div class="viewcode-block" id="MapFileListReader"><a class="viewcode-back" href="../../ariaec.html#ariaec.reader.MapFileListReader">[docs]</a><span class="k">class</span> <span class="nc">MapFileListReader</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span>
+ <span class="sd">"""Reader class for Map files"""</span>
+
+ <span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">cont_def</span><span class="o">=</span><span class="mf">5.0</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> cont_def: float, optional</span>
+<span class="sd"> Contact threshold used to filter native contacts (if reference</span>
+<span class="sd"> structure given)</span>
+<span class="sd"> """</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">maps</span> <span class="o">=</span> <span class="p">[]</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">contactdef</span> <span class="o">=</span> <span class="n">cont_def</span>
+
+<div class="viewcode-block" id="MapFileListReader.clear"><a class="viewcode-back" href="../../ariaec.html#ariaec.reader.MapFileListReader.clear">[docs]</a> <span class="k">def</span> <span class="nf">clear</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="sd">"""Initiatize object from scratch object"""</span>
+ <span class="c1"># TODO: Init supprime bien les fichiers du cache ?</span>
+ <span class="bp">self</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">contactdef</span><span class="p">)</span></div>
+
+ <span class="k">def</span> <span class="nf">_add_maps</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">maps</span><span class="p">,</span> <span class="n">maptypes</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Add Map file to the mapfile reader</span>
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> maps : :obj: `list` of :obj: `str`</span>
+<span class="sd"> List of Map file paths</span>
+<span class="sd"> maptypes : :obj: `list` of :obj: `str`, optional</span>
+<span class="sd"> (Default value = None)</span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+<span class="sd"> </span>
+<span class="sd"> """</span>
+ <span class="n">maps</span> <span class="o">=</span> <span class="p">[</span><span class="n">maps</span><span class="p">]</span> <span class="k">if</span> <span class="nb">type</span><span class="p">(</span><span class="n">maps</span><span class="p">)</span> <span class="o">!=</span> <span class="nb">list</span> <span class="k">else</span> <span class="n">maps</span>
+ <span class="n">maptypes</span> <span class="o">=</span> <span class="p">[</span><span class="n">maptypes</span><span class="p">]</span> <span class="k">if</span> <span class="nb">type</span><span class="p">(</span>
+ <span class="n">maptypes</span><span class="p">)</span> <span class="o">!=</span> <span class="nb">list</span> <span class="k">else</span> <span class="n">maptypes</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="n">maptypes</span> <span class="ow">or</span> <span class="nb">len</span><span class="p">(</span><span class="n">maps</span><span class="p">)</span> <span class="o">!=</span> <span class="nb">len</span><span class="p">(</span><span class="n">maptypes</span><span class="p">):</span>
+ <span class="n">maptypes</span> <span class="o">=</span> <span class="p">[</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">splitext</span><span class="p">(</span><span class="n">_</span><span class="p">)[</span><span class="mi">1</span><span class="p">][</span><span class="mi">1</span><span class="p">:]</span> <span class="k">for</span> <span class="n">_</span> <span class="ow">in</span> <span class="n">maps</span><span class="p">]</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s2">"Reader focused on file(s) </span><span class="si">%s</span><span class="s2"> </span><span class="si">%s</span><span class="s2">"</span><span class="p">,</span> <span class="n">maps</span><span class="p">,</span>
+ <span class="n">maptypes</span><span class="p">)</span>
+ <span class="k">for</span> <span class="n">i</span><span class="p">,</span> <span class="n">filepath</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">maps</span><span class="p">):</span>
+ <span class="k">if</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">(</span><span class="n">filepath</span><span class="p">):</span>
+ <span class="c1"># TODO: check_type functionstr</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="s2">"Adding </span><span class="si">%s</span><span class="s2"> file to watchlist"</span><span class="p">,</span> <span class="n">maptypes</span><span class="p">[</span><span class="n">i</span><span class="p">])</span>
+ <span class="k">if</span> <span class="p">(</span><span class="n">maptypes</span><span class="p">[</span><span class="n">i</span><span class="p">]</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span> <span class="o">==</span> <span class="s2">"pdb"</span> <span class="ow">and</span>
+ <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">splitext</span><span class="p">(</span><span class="n">filepath</span><span class="p">)[</span><span class="mi">1</span><span class="p">][</span><span class="mi">1</span><span class="p">:]</span> <span class="o">==</span> <span class="s2">"pdb"</span><span class="p">)</span> <span class="ow">or</span> <span class="p">(</span>
+ <span class="n">maptypes</span><span class="p">[</span><span class="n">i</span><span class="p">]</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span> <span class="o">==</span> <span class="s2">"distfile"</span> <span class="ow">and</span>
+ <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">splitext</span><span class="p">(</span><span class="n">filepath</span><span class="p">)[</span><span class="mi">1</span><span class="p">][</span><span class="mi">1</span><span class="p">:]</span> <span class="o">==</span> <span class="s2">"pdb"</span><span class="p">):</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">maps</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">PDBFile</span><span class="p">(</span><span class="n">filepath</span><span class="p">))</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">maps</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">ContactMapFile</span><span class="p">(</span><span class="n">filepath</span><span class="p">,</span>
+ <span class="n">maptypes</span><span class="p">[</span><span class="n">i</span><span class="p">]))</span>
+ <span class="c1"># else:</span>
+ <span class="c1"># self.maps.append(DistanceMapFile(filepath,</span>
+ <span class="c1"># maptypes[i]))</span>
+ <span class="c1"># TODO: DistanceMapFile condition</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">maps</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">regex</span><span class="p">:</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">warning</span><span class="p">(</span><span class="s2">"Can't read </span><span class="si">%s</span><span class="s2">"</span><span class="p">,</span> <span class="n">filepath</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">maps</span><span class="o">.</span><span class="n">pop</span><span class="p">()</span>
+
+<div class="viewcode-block" id="MapFileListReader.read"><a class="viewcode-back" href="../../ariaec.html#ariaec.reader.MapFileListReader.read">[docs]</a> <span class="k">def</span> <span class="nf">read</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">maps</span><span class="p">,</span> <span class="n">maptypes</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">protein</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">scsc</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Read contact map files. The generated maps will be accessible in</span>
+<span class="sd"> `self.maps`</span>
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> maps : :obj: `list` of :obj: `str`</span>
+<span class="sd"> List of Map file paths</span>
+<span class="sd"> maptypes : :obj: `list` of :obj: `str`, optional</span>
+<span class="sd"> List of Map file types (Default value = None)</span>
+<span class="sd"> protein : ariaec.protein.Protein object or None, optional</span>
+<span class="sd"> (Default value = None)</span>
+<span class="sd"> scsc : dict, optional</span>
+<span class="sd"> Optional dictionary used for Atom Map reduction by selecting only</span>
+<span class="sd"> one atom in the side chain. (Default value = None)</span>
+<span class="sd"> kwargs :</span>
+<span class="sd"> Optional arguments used for MapFile readers</span>
+<span class="sd"> **kwargs :</span>
+<span class="sd"> </span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+<span class="sd"> </span>
+<span class="sd"> """</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">clear</span><span class="p">()</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_add_maps</span><span class="p">(</span><span class="n">maps</span><span class="p">,</span> <span class="n">maptypes</span><span class="o">=</span><span class="n">maptypes</span><span class="p">)</span>
+ <span class="k">for</span> <span class="n">fo</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">maps</span><span class="p">:</span>
+ <span class="n">fo</span><span class="o">.</span><span class="n">read</span><span class="p">(</span><span class="n">protein</span><span class="o">=</span><span class="n">protein</span><span class="p">,</span> <span class="n">contactdef</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">contactdef</span><span class="p">,</span>
+ <span class="n">scsc</span><span class="o">=</span><span class="n">scsc</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">)</span></div></div>
+</pre></div>
+
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diff --git a/examples-dev/olds/_build/html/_modules/ariaec/settings.html b/examples-dev/olds/_build/html/_modules/ariaec/settings.html
new file mode 100644
index 0000000000000000000000000000000000000000..6091331161d386c74be008a6d7bf4127b27cc912
--- /dev/null
+++ b/examples-dev/olds/_build/html/_modules/ariaec/settings.html
@@ -0,0 +1,543 @@
+
+
+<!DOCTYPE html>
+<!--[if IE 8]><html class="no-js lt-ie9" lang="en" > <![endif]-->
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+
+ <h1>Source code for ariaec.settings</h1><div class="highlight"><pre>
+<span></span><span class="c1"># coding=utf-8</span>
+<span class="sd">"""</span>
+<span class="sd"> Settings section</span>
+<span class="sd">"""</span>
+<span class="kn">from</span> <span class="nn">__future__</span> <span class="k">import</span> <span class="n">absolute_import</span><span class="p">,</span> <span class="n">division</span><span class="p">,</span> <span class="n">print_function</span>
+
+<span class="kn">import</span> <span class="nn">os</span>
+<span class="kn">import</span> <span class="nn">logging</span>
+<span class="kn">import</span> <span class="nn">pickle</span>
+<span class="kn">import</span> <span class="nn">collections</span>
+<span class="c1"># noinspection PyCompatibility</span>
+<span class="kn">from</span> <span class="nn">ConfigParser</span> <span class="k">import</span> <span class="n">ConfigParser</span>
+<span class="kn">import</span> <span class="nn">pkg_resources</span> <span class="k">as</span> <span class="nn">pkgr</span>
+
+<span class="kn">from</span> <span class="nn">.common</span> <span class="k">import</span> <span class="n">format_dict</span>
+
+<span class="n">LOG</span> <span class="o">=</span> <span class="n">logging</span><span class="o">.</span><span class="n">getLogger</span><span class="p">(</span><span class="vm">__name__</span><span class="p">)</span>
+
+
+<div class="viewcode-block" id="Setting"><a class="viewcode-back" href="../../ariaec.html#ariaec.settings.Setting">[docs]</a><span class="k">class</span> <span class="nc">Setting</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span>
+ <span class="sd">"""Main setting object with args and config section"""</span>
+
+ <span class="c1"># TODO: merge config and args</span>
+ <span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">config</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">defaultdict</span><span class="p">()</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">args</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">defaultdict</span><span class="p">()</span>
+
+ <span class="k">def</span> <span class="nf">__getitem__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">item</span><span class="p">):</span>
+ <span class="k">if</span> <span class="n">item</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">args</span><span class="p">:</span>
+ <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">args</span><span class="p">[</span><span class="n">item</span><span class="p">]</span>
+ <span class="k">elif</span> <span class="n">item</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">config</span><span class="p">:</span>
+ <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">config</span><span class="p">[</span><span class="n">item</span><span class="p">]</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">raise</span> <span class="ne">KeyError</span><span class="p">(</span><span class="n">item</span><span class="p">)</span>
+
+ <span class="k">def</span> <span class="nf">__repr__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="k">return</span> <span class="s2">"Setting object</span><span class="se">\n</span><span class="s2"> config: </span><span class="si">%s</span><span class="se">\n</span><span class="s2"> args : </span><span class="si">%s</span><span class="s2">"</span> <span class="o">%</span> <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">config</span><span class="p">,</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">args</span><span class="p">)</span></div>
+
+
+<div class="viewcode-block" id="Settings"><a class="viewcode-back" href="../../ariaec.html#ariaec.settings.Settings">[docs]</a><span class="k">class</span> <span class="nc">Settings</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span>
+ <span class="sd">"""Group settings with each section corresponding to a Setting object"""</span>
+
+ <span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">sections</span><span class="p">):</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_sections</span> <span class="o">=</span> <span class="nb">set</span><span class="p">(</span><span class="n">sections</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">configfile</span> <span class="o">=</span> <span class="s1">''</span>
+ <span class="k">for</span> <span class="n">section</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">_sections</span><span class="p">:</span>
+ <span class="nb">setattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">section</span><span class="p">,</span> <span class="n">Setting</span><span class="p">())</span>
+
+<div class="viewcode-block" id="Settings.load_config"><a class="viewcode-back" href="../../ariaec.html#ariaec.settings.Settings.load_config">[docs]</a> <span class="k">def</span> <span class="nf">load_config</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">configpath</span><span class="p">,</span> <span class="n">pkg</span><span class="o">=</span><span class="kc">False</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Use ConfigParser module to load config sections</span>
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> pkg :</span>
+<span class="sd"> file is inside the package (Default value = False)</span>
+<span class="sd"> configpath :</span>
+<span class="sd"> return:</span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+<span class="sd"> </span>
+<span class="sd"> """</span>
+ <span class="k">if</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">(</span><span class="n">configpath</span><span class="p">):</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">configfile</span> <span class="o">=</span> <span class="n">configpath</span>
+ <span class="k">elif</span> <span class="ow">not</span> <span class="n">pkg</span><span class="p">:</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">error</span><span class="p">(</span><span class="s2">"Configuration file not found (</span><span class="si">%s</span><span class="s2">)"</span><span class="p">,</span> <span class="n">configpath</span><span class="p">)</span>
+ <span class="k">return</span> <span class="kc">None</span>
+ <span class="c1"># config = SafeConfigParser(allow_no_value=True)</span>
+ <span class="n">config</span> <span class="o">=</span> <span class="n">ConfigParser</span><span class="p">(</span><span class="n">allow_no_value</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
+ <span class="k">if</span> <span class="n">pkg</span><span class="p">:</span>
+ <span class="k">with</span> <span class="n">pkgr</span><span class="o">.</span><span class="n">resource_stream</span><span class="p">(</span><span class="vm">__name__</span><span class="p">,</span> <span class="n">configpath</span><span class="p">)</span> <span class="k">as</span> <span class="n">conf</span><span class="p">:</span>
+ <span class="n">config</span><span class="o">.</span><span class="n">readfp</span><span class="p">(</span><span class="n">conf</span><span class="p">)</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="n">config</span><span class="o">.</span><span class="n">read</span><span class="p">(</span><span class="n">configpath</span><span class="p">)</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="n">config</span><span class="p">)</span>
+ <span class="k">for</span> <span class="n">section</span> <span class="ow">in</span> <span class="n">config</span><span class="o">.</span><span class="n">sections</span><span class="p">():</span>
+ <span class="k">if</span> <span class="nb">hasattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">section</span><span class="p">):</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="s2">"Formatting items of </span><span class="si">%s</span><span class="s2"> section"</span><span class="p">,</span> <span class="n">section</span><span class="p">)</span>
+ <span class="n">tmp</span> <span class="o">=</span> <span class="n">format_dict</span><span class="p">(</span><span class="nb">dict</span><span class="p">(</span><span class="n">config</span><span class="o">.</span><span class="n">items</span><span class="p">(</span><span class="n">section</span><span class="p">)))</span>
+ <span class="nb">getattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">section</span><span class="p">)</span><span class="o">.</span><span class="n">config</span><span class="o">.</span><span class="n">update</span><span class="p">(</span><span class="n">tmp</span><span class="p">)</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="s2">"</span><span class="si">%s</span><span class="s2"> config updated"</span><span class="p">,</span> <span class="n">section</span><span class="p">)</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="s2">"</span><span class="si">%s</span><span class="s2">.</span><span class="si">%s</span><span class="s2"> : </span><span class="si">%s</span><span class="s2">"</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="vm">__class__</span><span class="o">.</span><span class="vm">__name__</span><span class="p">,</span> <span class="n">section</span><span class="p">,</span>
+ <span class="nb">getattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">section</span><span class="p">))</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">warning</span><span class="p">(</span><span class="s2">"Unknow config section </span><span class="si">%s</span><span class="s2">"</span><span class="p">,</span> <span class="n">section</span><span class="p">)</span></div>
+
+<div class="viewcode-block" id="Settings.write_config"><a class="viewcode-back" href="../../ariaec.html#ariaec.settings.Settings.write_config">[docs]</a> <span class="k">def</span> <span class="nf">write_config</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">filename</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Write config of all sections into another file</span>
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> filename :</span>
+<span class="sd"> </span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+<span class="sd"> </span>
+<span class="sd"> """</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s2">"Writing .ini file (</span><span class="si">%s</span><span class="s2">)"</span><span class="p">,</span> <span class="n">filename</span><span class="p">)</span>
+ <span class="n">config</span> <span class="o">=</span> <span class="n">ConfigParser</span><span class="p">(</span><span class="n">allow_no_value</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
+ <span class="n">iniout</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="n">filename</span><span class="p">,</span> <span class="n">mode</span><span class="o">=</span><span class="s2">"w"</span><span class="p">)</span>
+ <span class="k">for</span> <span class="n">section</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">_sections</span><span class="p">:</span>
+ <span class="n">config</span><span class="o">.</span><span class="n">add_section</span><span class="p">(</span><span class="n">section</span><span class="p">)</span>
+ <span class="k">if</span> <span class="nb">hasattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">section</span><span class="p">):</span>
+ <span class="k">for</span> <span class="n">opt</span> <span class="ow">in</span> <span class="nb">getattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">section</span><span class="p">)</span><span class="o">.</span><span class="n">config</span><span class="p">:</span>
+ <span class="n">config</span><span class="o">.</span><span class="n">set</span><span class="p">(</span><span class="n">section</span><span class="p">,</span> <span class="nb">str</span><span class="p">(</span><span class="n">opt</span><span class="p">),</span>
+ <span class="nb">str</span><span class="p">(</span><span class="nb">getattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">section</span><span class="p">)</span><span class="o">.</span><span class="n">config</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">opt</span><span class="p">)))</span>
+ <span class="n">config</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">iniout</span><span class="p">)</span></div>
+
+ <span class="k">def</span> <span class="nf">__repr__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="k">return</span> <span class="s2">"<Settings object></span><span class="se">\n</span><span class="s2"> sections: </span><span class="si">%s</span><span class="s2">"</span> <span class="o">%</span> <span class="bp">self</span><span class="o">.</span><span class="n">_sections</span></div>
+
+
+<span class="c1"># TODO: AriaEcSettings should probably be an astract class.</span>
+<div class="viewcode-block" id="AriaEcSettings"><a class="viewcode-back" href="../../ariaec.html#ariaec.settings.AriaEcSettings">[docs]</a><span class="k">class</span> <span class="nc">AriaEcSettings</span><span class="p">(</span><span class="n">Settings</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Settings object for ariaec</span>
+<span class="sd"> @DynamicAttrs</span>
+<span class="sd"> """</span>
+ <span class="c1"># ss_dist = os.path.join(os.path.dirname(os.path.realpath(__file__)),</span>
+ <span class="c1"># 'conf/ss_dist.txt')</span>
+ <span class="c1"># TODO: move these constant variable in objects which can read these file !!</span>
+ <span class="c1"># TODO: Baseclass inspired from this class and ariabase class. All</span>
+ <span class="c1"># objects in this package should extend the base object</span>
+ <span class="n">ARIAPROJ_TEMPLATE</span> <span class="o">=</span> <span class="s1">'templates/aria_project_v2.3.0.xml'</span>
+ <span class="n">SS_DIST</span> <span class="o">=</span> <span class="s1">'data/ss_dist.txt'</span>
+ <span class="n">SCSC_MIN</span> <span class="o">=</span> <span class="s1">'data/scsc_min.p'</span>
+ <span class="n">INTERLOWERBOUNDS</span> <span class="o">=</span> <span class="s1">'data/pdbdists/lowerbounds.inter.p'</span>
+ <span class="n">INTERTARGET</span> <span class="o">=</span> <span class="s1">'data/pdbdists/targetdists.inter.p'</span>
+ <span class="n">INTERUPPERBOUNDS</span> <span class="o">=</span> <span class="s1">'data/pdbdists/upperbounds.inter.p'</span>
+ <span class="n">INTRALOWERBOUNDS</span> <span class="o">=</span> <span class="s1">'data/pdbdists/lowerbounds.intra.p'</span>
+ <span class="n">INTRATARGET</span> <span class="o">=</span> <span class="s1">'data/pdbdists/targetdists.intra.p'</span>
+ <span class="n">INTRAUPPERBOUNDS</span> <span class="o">=</span> <span class="s1">'data/pdbdists/upperbounds.intra.p'</span>
+ <span class="c1"># TODO: If aria installed in site-packages, use topallhdg file from aria !</span>
+ <span class="n">TOPO</span> <span class="o">=</span> <span class="s1">'data/topallhdg5.3.pro'</span>
+ <span class="c1"># TODO: Should define sections in one object, actually we have to define</span>
+ <span class="c1"># sections in settings and also command objects ...</span>
+ <span class="n">SECTIONS</span> <span class="o">=</span> <span class="p">(</span><span class="s2">"main"</span><span class="p">,</span> <span class="s2">"setup"</span><span class="p">,</span> <span class="s2">"maplot"</span><span class="p">,</span> <span class="s2">"bbconv"</span><span class="p">,</span> <span class="s2">"contactdef"</span><span class="p">,</span>
+ <span class="s2">"pdbqual"</span><span class="p">,</span> <span class="s2">"pdbdist"</span><span class="p">,</span> <span class="s2">"analysis"</span><span class="p">,</span> <span class="s2">"tbl2xml"</span><span class="p">,</span> <span class="s2">"pdbstat"</span><span class="p">)</span>
+ <span class="c1"># TODO: options in main section should be accessible from all sections ! DO</span>
+ <span class="c1"># not use this a other section as it is done actually</span>
+
+ <span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">name</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Initiate settings with name related to a command</span>
+<span class="sd"> :param name:</span>
+<span class="sd"> """</span>
+ <span class="nb">super</span><span class="p">(</span><span class="n">AriaEcSettings</span><span class="p">,</span> <span class="bp">self</span><span class="p">)</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">SECTIONS</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_infra</span> <span class="o">=</span> <span class="p">{}</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_scsc_min</span> <span class="o">=</span> <span class="kc">None</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_ssdist</span> <span class="o">=</span> <span class="kc">None</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_template</span> <span class="o">=</span> <span class="kc">None</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">outdir</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">getcwd</span><span class="p">()</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">name</span> <span class="o">=</span> <span class="n">name</span>
+
+ <span class="k">def</span> <span class="nf">_up_infra</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="sd">""" """</span>
+ <span class="k">for</span> <span class="n">dirpath</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">infra</span><span class="p">:</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="s2">"set </span><span class="si">%s</span><span class="s2"> dir: </span><span class="si">%s</span><span class="s2">"</span><span class="p">,</span> <span class="n">dirpath</span><span class="p">,</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">outdir</span><span class="p">,</span>
+ <span class="n">dirpath</span><span class="p">))</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_infra</span><span class="p">[</span><span class="n">dirpath</span><span class="p">]</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">outdir</span><span class="p">,</span> <span class="n">dirpath</span><span class="p">)</span>
+
+ <span class="nd">@property</span>
+ <span class="k">def</span> <span class="nf">infra</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Infrastructure for a specific command</span>
+<span class="sd"> :return:</span>
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+<span class="sd"> </span>
+<span class="sd"> """</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">name</span> <span class="o">==</span> <span class="s2">"setup"</span> <span class="ow">and</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">_infra</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_infra</span> <span class="o">=</span> <span class="p">{</span><span class="s2">"xml"</span><span class="p">:</span> <span class="s2">""</span><span class="p">,</span> <span class="s2">"tbl"</span><span class="p">:</span> <span class="s2">""</span><span class="p">,</span> <span class="s2">"etc"</span><span class="p">:</span> <span class="s2">""</span><span class="p">}</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_up_infra</span><span class="p">()</span>
+ <span class="k">elif</span> <span class="bp">self</span><span class="o">.</span><span class="n">name</span> <span class="o">==</span> <span class="s2">"maplot"</span> <span class="ow">and</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">_infra</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_infra</span> <span class="o">=</span> <span class="p">{</span><span class="s2">"graphics"</span><span class="p">:</span> <span class="s2">""</span><span class="p">}</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_up_infra</span><span class="p">()</span>
+ <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_infra</span>
+
+ <span class="nd">@infra</span><span class="o">.</span><span class="n">setter</span>
+ <span class="k">def</span> <span class="nf">infra</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">root</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Change infra root</span>
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> root :</span>
+<span class="sd"> return:</span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+<span class="sd"> </span>
+<span class="sd"> """</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">outdir</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">abspath</span><span class="p">(</span><span class="n">root</span><span class="p">)</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">infra</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_up_infra</span><span class="p">()</span>
+
+ <span class="nd">@property</span>
+ <span class="k">def</span> <span class="nf">ssdist</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Get distance file for secondary structures in the package or in config</span>
+<span class="sd"> file</span>
+<span class="sd"> :return:</span>
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+<span class="sd"> </span>
+<span class="sd"> """</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">_ssdist</span><span class="p">:</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="p">[</span><span class="s2">"ss_dist_file"</span><span class="p">]</span> <span class="ow">and</span> \
+ <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">(</span><span class="bp">self</span><span class="p">[</span><span class="s2">"ss_dist_file"</span><span class="p">]):</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_ssdist</span> <span class="o">=</span> <span class="bp">self</span><span class="p">[</span><span class="s2">"ss_dist_file"</span><span class="p">]</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_ssdist</span> <span class="o">=</span> <span class="n">pkgr</span><span class="o">.</span><span class="n">resource_filename</span><span class="p">(</span><span class="vm">__name__</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">SS_DIST</span><span class="p">)</span>
+ <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_ssdist</span>
+
+ <span class="nd">@property</span>
+ <span class="k">def</span> <span class="nf">template</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Get template files in config file or in the package</span>
+<span class="sd"> :return:</span>
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+<span class="sd"> </span>
+<span class="sd"> """</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">_template</span><span class="p">:</span>
+ <span class="n">templatepath</span> <span class="o">=</span> <span class="s2">"templates/aria_project_v</span><span class="si">%s</span><span class="s2">.xml"</span> <span class="o">%</span> \
+ <span class="nb">str</span><span class="p">(</span><span class="bp">self</span><span class="p">[</span><span class="s2">"ariaproject_template"</span><span class="p">])</span>
+ <span class="k">if</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">(</span><span class="n">pkgr</span><span class="o">.</span><span class="n">resource_filename</span><span class="p">(</span><span class="vm">__name__</span><span class="p">,</span> <span class="n">templatepath</span><span class="p">)):</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_template</span> <span class="o">=</span> <span class="n">pkgr</span><span class="o">.</span><span class="n">resource_filename</span><span class="p">(</span><span class="vm">__name__</span><span class="p">,</span> <span class="n">templatepath</span><span class="p">)</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">error</span><span class="p">(</span><span class="s2">"Template version for aria project (</span><span class="si">%s</span><span class="s2">) is not "</span>
+ <span class="s2">"supported"</span><span class="p">,</span> <span class="bp">self</span><span class="p">[</span><span class="s2">"ariaproject_template"</span><span class="p">])</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_template</span> <span class="o">=</span> <span class="n">pkgr</span><span class="o">.</span><span class="n">resource_filename</span><span class="p">(</span><span class="vm">__name__</span><span class="p">,</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">ARIAPROJ_TEMPLATE</span><span class="p">)</span>
+ <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_template</span>
+
+ <span class="nd">@property</span>
+ <span class="k">def</span> <span class="nf">scsc_min</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Get contact index for side chains in package or config file</span>
+<span class="sd"> :return:</span>
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+<span class="sd"> </span>
+<span class="sd"> """</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">_scsc_min</span><span class="p">:</span>
+ <span class="k">try</span><span class="p">:</span>
+ <span class="c1"># Read scsc_min_file given in config.ini</span>
+ <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="bp">self</span><span class="p">[</span><span class="s2">"scsc_min_file"</span><span class="p">])</span> <span class="k">as</span> <span class="n">scsc</span><span class="p">:</span>
+ <span class="n">scsc_min</span> <span class="o">=</span> <span class="n">pickle</span><span class="o">.</span><span class="n">load</span><span class="p">(</span><span class="n">scsc</span><span class="p">)</span>
+ <span class="k">except</span> <span class="p">(</span><span class="ne">IOError</span><span class="p">,</span> <span class="ne">KeyError</span><span class="p">,</span> <span class="ne">TypeError</span><span class="p">):</span>
+ <span class="c1"># If file can't be open or given key is invalid, load default</span>
+ <span class="c1"># package file</span>
+ <span class="k">with</span> <span class="n">pkgr</span><span class="o">.</span><span class="n">resource_stream</span><span class="p">(</span><span class="vm">__name__</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">SCSC_MIN</span><span class="p">)</span> <span class="k">as</span> <span class="n">scsc</span><span class="p">:</span>
+ <span class="n">scsc_min</span> <span class="o">=</span> <span class="n">pickle</span><span class="o">.</span><span class="n">load</span><span class="p">(</span><span class="n">scsc</span><span class="p">)</span>
+ <span class="n">scsc_min</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">(</span>
+ <span class="p">(</span><span class="n">aa1</span><span class="p">,</span> <span class="nb">dict</span><span class="p">((</span><span class="n">aa2</span><span class="p">,</span> <span class="nb">tuple</span><span class="p">(</span><span class="n">atm_pair</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">', '</span><span class="p">)))</span>
+ <span class="k">for</span> <span class="n">aa2</span><span class="p">,</span> <span class="n">atm_pair</span> <span class="ow">in</span> <span class="n">atm_pairs</span><span class="o">.</span><span class="n">items</span><span class="p">()))</span>
+ <span class="k">for</span> <span class="n">aa1</span><span class="p">,</span> <span class="n">atm_pairs</span> <span class="ow">in</span> <span class="n">scsc_min</span><span class="o">.</span><span class="n">items</span><span class="p">())</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_scsc_min</span> <span class="o">=</span> <span class="n">scsc_min</span>
+ <span class="k">return</span> <span class="n">scsc_min</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_scsc_min</span>
+
+<div class="viewcode-block" id="AriaEcSettings.make_infra"><a class="viewcode-back" href="../../ariaec.html#ariaec.settings.AriaEcSettings.make_infra">[docs]</a> <span class="k">def</span> <span class="nf">make_infra</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="sd">"""Generate infrastructure"""</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s2">"Making output directories"</span><span class="p">)</span>
+ <span class="k">for</span> <span class="n">direct</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">infra</span><span class="p">:</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="s2">"Create </span><span class="si">%s</span><span class="s2"> directory"</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">infra</span><span class="p">[</span><span class="n">direct</span><span class="p">])</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">infra</span><span class="p">[</span><span class="n">direct</span><span class="p">]):</span>
+ <span class="n">os</span><span class="o">.</span><span class="n">makedirs</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">abspath</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">infra</span><span class="p">[</span><span class="n">direct</span><span class="p">]))</span></div>
+
+<div class="viewcode-block" id="AriaEcSettings.load_config"><a class="viewcode-back" href="../../ariaec.html#ariaec.settings.AriaEcSettings.load_config">[docs]</a> <span class="k">def</span> <span class="nf">load_config</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">configpath</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> </span>
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> configpath :</span>
+<span class="sd"> param kwargs:</span>
+<span class="sd"> **kwargs :</span>
+<span class="sd"> </span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+<span class="sd"> </span>
+<span class="sd"> """</span>
+ <span class="nb">super</span><span class="p">(</span><span class="n">AriaEcSettings</span><span class="p">,</span> <span class="bp">self</span><span class="p">)</span><span class="o">.</span><span class="n">load_config</span><span class="p">(</span><span class="n">configpath</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">)</span></div>
+
+ <span class="k">def</span> <span class="nf">__getitem__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">item</span><span class="p">):</span>
+ <span class="k">for</span> <span class="n">section</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">_sections</span><span class="p">:</span>
+ <span class="k">if</span> <span class="n">item</span> <span class="ow">in</span> <span class="nb">getattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">section</span><span class="p">)</span><span class="o">.</span><span class="n">args</span><span class="p">:</span>
+ <span class="k">return</span> <span class="nb">getattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">section</span><span class="p">)</span><span class="o">.</span><span class="n">args</span><span class="p">[</span><span class="n">item</span><span class="p">]</span>
+ <span class="k">elif</span> <span class="n">item</span> <span class="ow">in</span> <span class="nb">getattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">section</span><span class="p">)</span><span class="o">.</span><span class="n">config</span><span class="p">:</span>
+ <span class="k">return</span> <span class="nb">getattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">section</span><span class="p">)</span><span class="o">.</span><span class="n">config</span><span class="p">[</span><span class="n">item</span><span class="p">]</span></div>
+</pre></div>
+
+ </div>
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diff --git a/examples-dev/olds/_build/html/_modules/ariaec/setup.html b/examples-dev/olds/_build/html/_modules/ariaec/setup.html
new file mode 100644
index 0000000000000000000000000000000000000000..31b0401a0aebb9a0d2f74ba49a640982c1152516
--- /dev/null
+++ b/examples-dev/olds/_build/html/_modules/ariaec/setup.html
@@ -0,0 +1,541 @@
+
+
+<!DOCTYPE html>
+<!--[if IE 8]><html class="no-js lt-ie9" lang="en" > <![endif]-->
+<!--[if gt IE 8]><!--> <html class="no-js" lang="en" > <!--<![endif]-->
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+ <div itemprop="articleBody">
+
+ <h1>Source code for ariaec.setup</h1><div class="highlight"><pre>
+<span></span><span class="c1"># coding=utf-8</span>
+<span class="sd">"""</span>
+<span class="sd"> Input/Output aria_ec scripts</span>
+<span class="sd">"""</span>
+<span class="kn">from</span> <span class="nn">__future__</span> <span class="k">import</span> <span class="n">absolute_import</span><span class="p">,</span> <span class="n">division</span><span class="p">,</span> <span class="n">print_function</span>
+
+<span class="kn">import</span> <span class="nn">os</span>
+<span class="kn">import</span> <span class="nn">json</span>
+<span class="kn">import</span> <span class="nn">logging</span>
+
+<span class="kn">from</span> <span class="nn">.protein</span> <span class="k">import</span> <span class="n">Protein</span>
+<span class="kn">from</span> <span class="nn">.reader</span> <span class="k">import</span> <span class="n">MapFileListReader</span>
+<span class="kn">from</span> <span class="nn">.common</span> <span class="k">import</span> <span class="n">get_filename</span>
+<span class="kn">from</span> <span class="nn">.protmap</span> <span class="k">import</span> <span class="n">MapFilter</span>
+<span class="kn">from</span> <span class="nn">.converter</span> <span class="k">import</span> <span class="n">AriaEcXMLConverter</span>
+
+<span class="c1"># TODO: S'inspirer de pandas/__init__.py pour les dependances</span>
+
+<span class="n">LOG</span> <span class="o">=</span> <span class="n">logging</span><span class="o">.</span><span class="n">getLogger</span><span class="p">(</span><span class="vm">__name__</span><span class="p">)</span>
+
+
+<div class="viewcode-block" id="AriaEcSetup"><a class="viewcode-back" href="../../ariaec.html#ariaec.setup.AriaEcSetup">[docs]</a><span class="k">class</span> <span class="nc">AriaEcSetup</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span>
+ <span class="sd">"""Aria Ec Setup protocol"""</span>
+
+ <span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">settings</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> :param settings:</span>
+<span class="sd"> :return:</span>
+<span class="sd"> """</span>
+ <span class="c1"># TODO: check_type settings (AriaEcSettings)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">settings</span> <span class="o">=</span> <span class="n">settings</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">protein</span> <span class="o">=</span> <span class="n">Protein</span><span class="p">(</span><span class="n">settings</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">outprefix</span> <span class="o">=</span> <span class="s1">''</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">reader</span> <span class="o">=</span> <span class="n">MapFileListReader</span><span class="p">(</span><span class="n">cont_def</span><span class="o">=</span><span class="n">settings</span><span class="o">.</span><span class="n">contactdef</span><span class="o">.</span><span class="n">config</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">allresmap</span> <span class="o">=</span> <span class="p">{}</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">targetmaps</span> <span class="o">=</span> <span class="kc">None</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">refmaps</span> <span class="o">=</span> <span class="kc">None</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">hbmaps</span> <span class="o">=</span> <span class="kc">None</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">filter</span> <span class="o">=</span> <span class="n">MapFilter</span><span class="p">(</span>
+ <span class="n">settings</span><span class="o">.</span><span class="n">setup</span><span class="o">.</span><span class="n">config</span><span class="p">,</span>
+ <span class="n">nofilter</span><span class="o">=</span><span class="n">settings</span><span class="o">.</span><span class="n">setup</span><span class="o">.</span><span class="n">args</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"no_filter"</span><span class="p">))</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">converter</span> <span class="o">=</span> <span class="n">AriaEcXMLConverter</span><span class="p">(</span><span class="n">settings</span><span class="p">)</span>
+
+<div class="viewcode-block" id="AriaEcSetup.run"><a class="viewcode-back" href="../../ariaec.html#ariaec.setup.AriaEcSetup.run">[docs]</a> <span class="k">def</span> <span class="nf">run</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> main method</span>
+<span class="sd"> :return:</span>
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+<span class="sd"> </span>
+<span class="sd"> """</span>
+ <span class="c1"># Check input</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="s2">"Settings:</span><span class="se">\n</span><span class="s2">"</span> <span class="o">+</span> <span class="n">json</span><span class="o">.</span><span class="n">dumps</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">setup</span><span class="o">.</span><span class="n">config</span><span class="p">,</span>
+ <span class="n">indent</span><span class="o">=</span><span class="mi">4</span><span class="p">))</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="s2">"Args:</span><span class="se">\n</span><span class="s2">"</span> <span class="o">+</span> <span class="n">json</span><span class="o">.</span><span class="n">dumps</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">setup</span><span class="o">.</span><span class="n">args</span><span class="p">,</span>
+ <span class="n">indent</span><span class="o">=</span><span class="mi">4</span><span class="p">))</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">make_infra</span><span class="p">()</span>
+ <span class="c1"># -------------------------------------------------------------------- #</span>
+ <span class="c1"># ----------------------------- Input -------------------------------- #</span>
+ <span class="c1"># -------------------------------------------------------------------- #</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">outprefix</span> <span class="o">=</span> <span class="n">get_filename</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">setup</span><span class="o">.</span><span class="n">args</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"seq"</span><span class="p">,</span> <span class="s2">""</span><span class="p">))</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">converter</span><span class="o">.</span><span class="n">outprefix</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">outprefix</span>
+ <span class="c1"># ------------------------- Load sequence ---------------------------- #</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">protein</span><span class="o">.</span><span class="n">set_aa_sequence</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">setup</span><span class="o">.</span><span class="n">args</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"seq"</span><span class="p">,</span> <span class="kc">None</span><span class="p">))</span>
+ <span class="c1"># -------------- Load secondary structure prediction ----------------- #</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">setup</span><span class="o">.</span><span class="n">args</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"sspred"</span><span class="p">,</span> <span class="kc">None</span><span class="p">):</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">protein</span><span class="o">.</span><span class="n">set_sec_struct</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">setup</span><span class="o">.</span><span class="n">args</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"sspred"</span><span class="p">,</span>
+ <span class="kc">None</span><span class="p">),</span>
+ <span class="n">ssdist_filename</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">ssdist</span><span class="p">,</span>
+ <span class="n">ssidx</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">setup</span><span class="o">.</span><span class="n">args</span><span class="o">.</span><span class="n">get</span><span class="p">(</span>
+ <span class="s2">"ssidx"</span><span class="p">,</span> <span class="kc">False</span><span class="p">))</span>
+ <span class="c1"># -------------------------------------------------------------------- #</span>
+ <span class="c1"># ---------------------------- Processing ---------------------------- #</span>
+ <span class="c1"># -------------------------------------------------------------------- #</span>
+ <span class="c1"># TODO: write submatrix in a file</span>
+ <span class="c1"># TODO: change read method in reader to __call__</span>
+ <span class="c1"># -------------------------- contact maps ---------------------------- #</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">reader</span><span class="o">.</span><span class="n">read</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">setup</span><span class="o">.</span><span class="n">args</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"infiles"</span><span class="p">),</span>
+ <span class="n">maptypes</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">setup</span><span class="o">.</span><span class="n">args</span><span class="o">.</span><span class="n">get</span><span class="p">(</span>
+ <span class="s2">"contact_types"</span><span class="p">),</span>
+ <span class="n">protein</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">protein</span><span class="p">,</span>
+ <span class="n">groupby_method</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">setup</span><span class="o">.</span><span class="n">config</span><span class="p">[</span>
+ <span class="s1">'groupby_method'</span><span class="p">],</span>
+ <span class="n">scsc</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">scsc_min</span><span class="p">)</span>
+ <span class="k">for</span> <span class="n">mapfile</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">reader</span><span class="o">.</span><span class="n">maps</span><span class="p">:</span>
+ <span class="c1"># fo need a maplot in order to wite XML dist restraints</span>
+ <span class="c1"># TODO: filter pour toutes les map de mapdict !! (fonction remove</span>
+ <span class="c1"># s'applique sur l'humanidx contenant les residus)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">filter</span><span class="p">(</span><span class="n">mapfile</span><span class="o">.</span><span class="n">mapdict</span><span class="p">,</span> <span class="n">mapfile</span><span class="o">.</span><span class="n">filetype</span><span class="p">,</span> <span class="n">mapfile</span><span class="o">.</span><span class="n">contactlist</span><span class="p">,</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">protein</span><span class="p">,</span> <span class="n">clashlist</span><span class="o">=</span><span class="n">mapfile</span><span class="o">.</span><span class="n">clashlist</span><span class="p">,</span>
+ <span class="n">outprefix</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">outprefix</span><span class="p">,</span>
+ <span class="n">outdir</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">infra</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"etc"</span><span class="p">,</span> <span class="s1">''</span><span class="p">))</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">allresmap</span><span class="p">[</span><span class="n">mapfile</span><span class="o">.</span><span class="n">filetype</span><span class="p">]</span> <span class="o">=</span> <span class="n">mapfile</span><span class="o">.</span><span class="n">mapdict</span>
+
+ <span class="k">if</span> <span class="n">mapfile</span><span class="o">.</span><span class="n">filetype</span> <span class="o">!=</span> <span class="s2">"pdb"</span> <span class="ow">and</span> <span class="s2">"pdb"</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">allresmap</span><span class="p">:</span>
+ <span class="n">mapfile</span><span class="o">.</span><span class="n">maplot</span><span class="o">.</span><span class="n">compareplot</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">allresmap</span><span class="p">[</span><span class="s2">"pdb"</span><span class="p">])</span>
+
+ <span class="c1"># ---------------------------- target map ---------------------------- #</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">setup</span><span class="o">.</span><span class="n">args</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"distfile"</span><span class="p">)</span> <span class="ow">and</span> \
+ <span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">setup</span><span class="o">.</span><span class="n">config</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"distance_type"</span><span class="p">)</span> <span class="o">==</span> <span class="s2">"distfile"</span><span class="p">:</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s2">"Loading target distance file"</span><span class="p">)</span>
+ <span class="c1"># Read distance file</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">reader</span><span class="o">.</span><span class="n">read</span><span class="p">(</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">setup</span><span class="o">.</span><span class="n">args</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"distfile"</span><span class="p">),</span>
+ <span class="n">maptypes</span><span class="o">=</span><span class="s2">"distfile"</span><span class="p">,</span>
+ <span class="n">protein</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">protein</span><span class="p">,</span>
+ <span class="n">groupby_method</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">setup</span><span class="o">.</span><span class="n">config</span><span class="p">[</span><span class="s1">'groupby_method'</span><span class="p">],</span>
+ <span class="n">scsc</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">scsc_min</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">targetmaps</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">converter</span><span class="o">.</span><span class="n">targetdistmaps</span><span class="p">(</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">protein</span><span class="o">.</span><span class="n">aa_sequence</span><span class="o">.</span><span class="n">sequence</span><span class="p">,</span> <span class="n">distfile</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">reader</span><span class="o">.</span><span class="n">maps</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="c1"># Default targetmaps using config parameters</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">targetmaps</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">converter</span><span class="o">.</span><span class="n">targetdistmaps</span><span class="p">(</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">protein</span><span class="o">.</span><span class="n">aa_sequence</span><span class="o">.</span><span class="n">sequence</span><span class="p">)</span>
+
+ <span class="c1"># ---------------------------- ref map ----------------------------- #</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">setup</span><span class="o">.</span><span class="n">args</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"ref"</span><span class="p">):</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">reader</span><span class="o">.</span><span class="n">read</span><span class="p">(</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">setup</span><span class="o">.</span><span class="n">args</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"ref"</span><span class="p">),</span>
+ <span class="n">maptypes</span><span class="o">=</span><span class="s2">"pdb"</span><span class="p">,</span>
+ <span class="n">protein</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">protein</span><span class="p">,</span>
+ <span class="n">groupby_method</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">setup</span><span class="o">.</span><span class="n">config</span><span class="p">[</span><span class="s1">'groupby_method'</span><span class="p">],</span>
+ <span class="n">scsc</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">scsc_min</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">refmaps</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">reader</span><span class="o">.</span><span class="n">maps</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">mapdict</span>
+
+ <span class="c1"># ---------------------------- hbond map ----------------------------- #</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">setup</span><span class="o">.</span><span class="n">args</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"hb"</span><span class="p">)</span> <span class="ow">and</span> \
+ <span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">setup</span><span class="o">.</span><span class="n">config</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"longrange_hb"</span><span class="p">,</span> <span class="kc">False</span><span class="p">):</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">reader</span><span class="o">.</span><span class="n">read</span><span class="p">(</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">setup</span><span class="o">.</span><span class="n">args</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"hb"</span><span class="p">),</span>
+ <span class="n">maptypes</span><span class="o">=</span><span class="s2">"metapsicovhb"</span><span class="p">,</span>
+ <span class="n">protein</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">protein</span><span class="p">,</span>
+ <span class="n">groupby_method</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">setup</span><span class="o">.</span><span class="n">config</span><span class="p">[</span><span class="s1">'groupby_method'</span><span class="p">],</span>
+ <span class="n">scsc</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">scsc_min</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">hbmaps</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">reader</span><span class="o">.</span><span class="n">maps</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">mapdict</span>
+ <span class="k">elif</span> <span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">setup</span><span class="o">.</span><span class="n">config</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"longrange_hb"</span><span class="p">,</span> <span class="kc">False</span><span class="p">):</span>
+ <span class="c1"># Create HBMAP with naive metapsicov method</span>
+ <span class="c1"># Consider as hbond ec predicted between beta strand</span>
+ <span class="k">raise</span> <span class="ne">NotImplementedError</span>
+
+ <span class="c1"># -------------------------------------------------------------------- #</span>
+ <span class="c1"># ------------------------------ Output ------------------------------ #</span>
+
+ <span class="c1"># ----------------------------- SEQ file ----------------------------- #</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">protein</span><span class="o">.</span><span class="n">write_seq</span><span class="p">(</span>
+ <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">infra</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"etc"</span><span class="p">,</span> <span class="s1">''</span><span class="p">),</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">outprefix</span> <span class="o">+</span> <span class="s2">".seq"</span><span class="p">))</span>
+ <span class="c1"># Load aria molecule object from seq file and convert it into xml format</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s2">"Load molecule file and convert it into xml format"</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">converter</span><span class="o">.</span><span class="n">read_seq</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">protein</span><span class="o">.</span><span class="n">seqfile_path</span><span class="p">)</span>
+ <span class="c1"># --------------------------- TBL restraints ------------------------- #</span>
+ <span class="c1"># Setting contact number limit for hbmap</span>
+ <span class="n">n_hb</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">protein</span><span class="o">.</span><span class="n">aa_sequence</span><span class="o">.</span><span class="n">sequence</span><span class="p">)</span> <span class="o">*</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">setup</span><span class="o">.</span><span class="n">config</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"nf_longrange_hb"</span><span class="p">))</span>
+ <span class="n">LOG</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s2">"Writing tbl files ..."</span><span class="p">)</span>
+ <span class="n">tbl_files</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">converter</span><span class="o">.</span><span class="n">write_tbl_restraints</span><span class="p">(</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">protein</span><span class="p">,</span> <span class="n">hbmap</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">hbmaps</span><span class="p">,</span> <span class="n">n_hb</span><span class="o">=</span><span class="n">n_hb</span><span class="p">)</span>
+
+ <span class="c1"># --------------------------- XML restraints ------------------------- #</span>
+ <span class="c1"># Setting contact number limit for map restraints (native, ec, ...)</span>
+
+ <span class="n">dist_files</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">converter</span><span class="o">.</span><span class="n">write_maplist_restraints</span><span class="p">(</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">allresmap</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">targetmaps</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">protein</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span>
+
+ <span class="c1"># --------------------------- XML SEQ file --------------------------- #</span>
+ <span class="n">xmlseq_file</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">converter</span><span class="o">.</span><span class="n">write_xmlseq</span><span class="p">()</span>
+
+ <span class="c1"># ---------------------- ARIA XML project file ----------------------- #</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">converter</span><span class="o">.</span><span class="n">write_ariaproject</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">template</span><span class="p">,</span>
+ <span class="n">xmlseq_file</span><span class="p">,</span> <span class="n">dist_files</span><span class="p">,</span> <span class="n">tbl_files</span><span class="p">,</span>
+ <span class="n">desclist</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">allresmap</span><span class="o">.</span><span class="n">keys</span><span class="p">())</span>
+ <span class="c1"># -------------------------------- etc ------------------------------- #</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">write_optional_files</span><span class="p">()</span></div>
+
+<div class="viewcode-block" id="AriaEcSetup.write_optional_files"><a class="viewcode-back" href="../../ariaec.html#ariaec.setup.AriaEcSetup.write_optional_files">[docs]</a> <span class="k">def</span> <span class="nf">write_optional_files</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Write filtered contacts & distance maps (.csv)</span>
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+<span class="sd"> </span>
+<span class="sd"> """</span>
+ <span class="c1"># Indextableplus file (submatrix)</span>
+ <span class="c1"># Contacts_refined.out</span>
+ <span class="k">for</span> <span class="n">maptype</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">allresmap</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">allresmap</span><span class="p">[</span><span class="n">maptype</span><span class="p">]</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"maplot"</span><span class="p">)</span><span class="o">.</span><span class="n">write_contacts</span><span class="p">(</span>
+ <span class="s2">"_"</span><span class="o">.</span><span class="n">join</span><span class="p">((</span><span class="bp">self</span><span class="o">.</span><span class="n">outprefix</span><span class="p">,</span> <span class="n">maptype</span><span class="p">,</span> <span class="s2">"filtered"</span><span class="p">)),</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">infra</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"etc"</span><span class="p">),</span> <span class="n">scoremap</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">allresmap</span><span class="p">[</span>
+ <span class="n">maptype</span><span class="p">]</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"scoremap"</span><span class="p">))</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">allresmap</span><span class="p">[</span><span class="n">maptype</span><span class="p">][</span><span class="s2">"alldistmap"</span><span class="p">]</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">allresmap</span><span class="p">[</span><span class="n">maptype</span><span class="p">][</span><span class="s2">"alldistmap"</span><span class="p">]</span><span class="o">.</span><span class="n">to_csv</span><span class="p">(</span>
+ <span class="s2">"</span><span class="si">%s</span><span class="s2">/</span><span class="si">%s</span><span class="s2">.distmap.csv"</span> <span class="o">%</span> <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">infra</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"etc"</span><span class="p">),</span>
+ <span class="n">maptype</span><span class="p">))</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">refmaps</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_write_contacts</span><span class="p">(</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">allresmap</span><span class="p">[</span><span class="n">maptype</span><span class="p">]</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"filteredlist"</span><span class="p">,</span> <span class="kc">None</span><span class="p">),</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">protein</span><span class="o">.</span><span class="n">aa_sequence</span><span class="o">.</span><span class="n">sequence</span><span class="p">,</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">infra</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"etc"</span><span class="p">,</span> <span class="s1">''</span><span class="p">),</span>
+ <span class="s2">"_"</span><span class="o">.</span><span class="n">join</span><span class="p">((</span><span class="bp">self</span><span class="o">.</span><span class="n">outprefix</span><span class="p">,</span> <span class="n">maptype</span><span class="p">,</span> <span class="s2">"filtered"</span><span class="p">)),</span>
+ <span class="n">ref</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">refmaps</span><span class="p">[</span><span class="s2">"maplot"</span><span class="p">],</span>
+ <span class="n">distmap</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">refmaps</span><span class="p">[</span><span class="s2">"distmap"</span><span class="p">])</span>
+ <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">refmaps</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">refmaps</span><span class="p">[</span><span class="s2">"alldistmap"</span><span class="p">]</span><span class="o">.</span><span class="n">to_csv</span><span class="p">(</span>
+ <span class="s2">"</span><span class="si">%s</span><span class="s2">/</span><span class="si">%s</span><span class="s2">_</span><span class="si">%s</span><span class="s2">.distmap.csv"</span> <span class="o">%</span> <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">infra</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"etc"</span><span class="p">),</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">outprefix</span><span class="p">,</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">refmaps</span><span class="o">.</span><span class="n">filetype</span><span class="p">))</span></div>
+
+ <span class="k">def</span> <span class="nf">_write_contacts</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">contacts_list</span><span class="p">,</span> <span class="n">seq</span><span class="p">,</span> <span class="n">out</span><span class="p">,</span> <span class="n">prefix</span><span class="p">,</span> <span class="n">nc</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
+ <span class="n">append</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span> <span class="n">ref</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">distmap</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
+ <span class="sd">"""</span>
+<span class="sd"> Write contacts from contact_list (sorted !)</span>
+
+<span class="sd"> Parameters</span>
+<span class="sd"> ----------</span>
+<span class="sd"> contacts_list :</span>
+<span class="sd"> param seq:</span>
+<span class="sd"> out :</span>
+<span class="sd"> param prefix:</span>
+<span class="sd"> nc :</span>
+<span class="sd"> param append: (Default value = None)</span>
+<span class="sd"> ref :</span>
+<span class="sd"> return: (Default value = None)</span>
+<span class="sd"> seq :</span>
+<span class="sd"> </span>
+<span class="sd"> prefix :</span>
+<span class="sd"> </span>
+<span class="sd"> append :</span>
+<span class="sd"> (Default value = False)</span>
+<span class="sd"> distmap :</span>
+<span class="sd"> (Default value = None)</span>
+
+<span class="sd"> Returns</span>
+<span class="sd"> -------</span>
+
+<span class="sd"> </span>
+<span class="sd"> """</span>
+ <span class="n">mapy</span> <span class="o">=</span> <span class="p">[]</span>
+ <span class="n">tp_count</span> <span class="o">=</span> <span class="mi">0</span>
+ <span class="n">filemode</span> <span class="o">=</span> <span class="s1">'a'</span> <span class="k">if</span> <span class="n">append</span> <span class="k">else</span> <span class="s1">'w'</span>
+ <span class="n">dist_desc</span> <span class="o">=</span> <span class="s1">'</span><span class="se">\t</span><span class="s1">TP/FP</span><span class="se">\t</span><span class="s1">dist</span><span class="si">%s</span><span class="s1">(ref)'</span> <span class="o">%</span> <span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">setup</span><span class="o">.</span><span class="n">config</span><span class="p">[</span>
+ <span class="s2">"groupby_method"</span><span class="p">]</span> <span class="k">if</span> \
+ <span class="n">distmap</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span> \
+ <span class="k">else</span> <span class="s1">''</span>
+ <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="s2">"</span><span class="si">%s</span><span class="s2">/</span><span class="si">%s</span><span class="s2">.contacts.txt"</span> <span class="o">%</span> <span class="p">(</span><span class="n">out</span><span class="p">,</span> <span class="n">prefix</span><span class="p">),</span> <span class="n">filemode</span><span class="p">)</span> <span class="k">as</span> <span class="n">outfile</span><span class="p">:</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="n">append</span><span class="p">:</span>
+ <span class="n">outfile</span><span class="o">.</span><span class="n">write</span><span class="p">(</span>
+ <span class="sd">'''# resid1\tresid2\tres1\tres2%s\n'''</span> <span class="o">%</span> <span class="n">dist_desc</span><span class="p">)</span>
+
+ <span class="k">if</span> <span class="nb">hasattr</span><span class="p">(</span><span class="n">contacts_list</span><span class="p">,</span> <span class="s1">'keys'</span><span class="p">):</span>
+ <span class="n">contacts</span> <span class="o">=</span> <span class="n">contacts_list</span><span class="o">.</span><span class="n">keys</span><span class="p">()</span> <span class="k">if</span> <span class="ow">not</span> <span class="n">nc</span> <span class="k">else</span> \
+ <span class="n">contacts_list</span><span class="o">.</span><span class="n">keys</span><span class="p">()[:</span><span class="n">nc</span><span class="p">]</span>
+ <span class="n">d_type</span> <span class="o">=</span> <span class="kc">True</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="c1"># Check if contacts is 2-tuple</span>
+ <span class="k">if</span> <span class="kc">False</span> <span class="ow">in</span> <span class="p">[</span><span class="nb">len</span><span class="p">(</span><span class="n">item</span><span class="p">)</span> <span class="o">==</span> <span class="mi">2</span> <span class="k">for</span> <span class="n">item</span> <span class="ow">in</span> <span class="n">contacts_list</span><span class="p">]:</span>
+ <span class="k">raise</span> <span class="ne">TypeError</span><span class="p">(</span><span class="s1">'Contact list must be 2-tuple !'</span><span class="p">)</span>
+ <span class="n">contacts</span> <span class="o">=</span> <span class="n">contacts_list</span> <span class="k">if</span> <span class="ow">not</span> <span class="n">nc</span> <span class="k">else</span> <span class="n">contacts_list</span><span class="p">[:</span><span class="n">nc</span><span class="p">]</span>
+ <span class="n">d_type</span> <span class="o">=</span> <span class="kc">False</span>
+
+ <span class="n">LOG</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="s2">"Contact list </span><span class="si">%s</span><span class="s2">"</span><span class="p">,</span> <span class="n">contacts</span><span class="p">)</span>
+ <span class="k">for</span> <span class="n">contact</span> <span class="ow">in</span> <span class="n">contacts</span><span class="p">:</span>
+
+ <span class="k">if</span> <span class="n">d_type</span><span class="p">:</span>
+ <span class="c1"># If dictionary</span>
+ <span class="n">resid1</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">contacts_list</span><span class="p">[</span><span class="n">contact</span><span class="p">]</span><span class="o">.</span><span class="n">setdefault</span><span class="p">(</span><span class="s1">'res1_nb'</span><span class="p">))</span>
+ <span class="n">resid2</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">contacts_list</span><span class="p">[</span><span class="n">contact</span><span class="p">]</span><span class="o">.</span><span class="n">setdefault</span><span class="p">(</span><span class="s1">'res2_nb'</span><span class="p">))</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="n">resid1</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">contact</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span>
+ <span class="n">resid2</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">contact</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span>
+
+ <span class="n">LOG</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="s2">"Contact </span><span class="si">%s</span><span class="s2">"</span><span class="p">,</span> <span class="nb">str</span><span class="p">(</span><span class="n">contact</span><span class="p">))</span>
+ <span class="k">if</span> <span class="n">distmap</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+ <span class="n">dist</span> <span class="o">=</span> <span class="n">distmap</span><span class="o">.</span><span class="n">ix</span><span class="p">[(</span><span class="n">resid1</span><span class="p">,</span> <span class="n">resid2</span><span class="p">)]</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="n">dist</span> <span class="o">=</span> <span class="p">{</span><span class="s1">'dist'</span><span class="p">:</span> <span class="s1">''</span><span class="p">,</span> <span class="s1">'atoms'</span><span class="p">:</span> <span class="s1">''</span><span class="p">}</span>
+
+ <span class="k">if</span> <span class="p">(</span><span class="n">resid1</span><span class="p">,</span> <span class="n">resid2</span><span class="p">)</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">mapy</span><span class="p">:</span>
+ <span class="n">mapy</span><span class="o">.</span><span class="n">append</span><span class="p">((</span><span class="n">resid1</span><span class="p">,</span> <span class="n">resid2</span><span class="p">))</span>
+ <span class="k">if</span> <span class="n">ref</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+ <span class="k">if</span> <span class="n">ref</span><span class="o">.</span><span class="n">ix</span><span class="p">[(</span><span class="n">resid1</span><span class="p">,</span> <span class="n">resid2</span><span class="p">)]:</span>
+ <span class="n">asses</span> <span class="o">=</span> <span class="s1">'TP'</span>
+ <span class="n">tp_count</span> <span class="o">+=</span> <span class="mi">1</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="n">asses</span> <span class="o">=</span> <span class="s1">'FP'</span>
+ <span class="n">outfile</span><span class="o">.</span><span class="n">write</span><span class="p">(</span>
+ <span class="s2">"</span><span class="si">%s</span><span class="se">\t</span><span class="si">%s</span><span class="se">\t</span><span class="si">%s</span><span class="se">\t</span><span class="si">%s</span><span class="se">\t</span><span class="si">%s</span><span class="se">\t</span><span class="si">%s</span><span class="se">\n</span><span class="s2">"</span> <span class="o">%</span> <span class="p">(</span><span class="n">resid1</span> <span class="o">+</span> <span class="mi">1</span><span class="p">,</span>
+ <span class="n">resid2</span> <span class="o">+</span> <span class="mi">1</span><span class="p">,</span>
+ <span class="n">seq</span><span class="p">[</span><span class="n">resid1</span><span class="p">],</span>
+ <span class="n">seq</span><span class="p">[</span><span class="n">resid2</span><span class="p">],</span> <span class="n">asses</span><span class="p">,</span>
+ <span class="n">dist</span><span class="p">))</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="n">outfile</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">"</span><span class="si">%s</span><span class="se">\t</span><span class="si">%s</span><span class="se">\t</span><span class="si">%s</span><span class="se">\t</span><span class="si">%s</span><span class="se">\n</span><span class="s2">"</span> <span class="o">%</span> <span class="p">(</span><span class="n">resid1</span> <span class="o">+</span> <span class="mi">1</span><span class="p">,</span>
+ <span class="n">resid2</span> <span class="o">+</span> <span class="mi">1</span><span class="p">,</span>
+ <span class="n">seq</span><span class="p">[</span><span class="n">resid1</span><span class="p">],</span>
+ <span class="n">seq</span><span class="p">[</span><span class="n">resid2</span><span class="p">]))</span>
+
+ <span class="n">ptp</span> <span class="o">=</span> <span class="p">(</span><span class="n">tp_count</span> <span class="o">/</span> <span class="nb">float</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">contacts</span><span class="p">)))</span> <span class="o">*</span> <span class="mf">100.0</span> <span class="k">if</span> <span class="n">ref</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span> <span class="k">else</span> \
+ <span class="kc">None</span>
+ <span class="n">outfile</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s1">'''</span>
+<span class="s1"># TP number : </span><span class="si">{tp}</span><span class="s1"> (</span><span class="si">{ptp:.2f}</span><span class="s1"> %)</span>
+<span class="s1"># Number of contacts : </span><span class="si">{nc}</span><span class="s1"></span>
+<span class="s1">'''</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">tp</span><span class="o">=</span><span class="n">tp_count</span><span class="p">,</span> <span class="n">ptp</span><span class="o">=</span><span class="n">ptp</span><span class="p">,</span> <span class="n">nc</span><span class="o">=</span><span class="nb">len</span><span class="p">(</span><span class="n">contacts</span><span class="p">)))</span></div>
+
+
+<span class="k">if</span> <span class="vm">__name__</span> <span class="o">==</span> <span class="s2">"__main__"</span><span class="p">:</span>
+ <span class="c1"># Test AriaEcCommand object</span>
+ <span class="kn">from</span> <span class="nn">.settings</span> <span class="k">import</span> <span class="n">AriaEcSettings</span>
+
+ <span class="n">logging</span><span class="o">.</span><span class="n">basicConfig</span><span class="p">(</span><span class="n">level</span><span class="o">=</span><span class="n">logging</span><span class="o">.</span><span class="n">DEBUG</span><span class="p">)</span>
+ <span class="n">LOG</span> <span class="o">=</span> <span class="n">logging</span><span class="o">.</span><span class="n">getLogger</span><span class="p">(</span><span class="s2">"Setup"</span><span class="p">)</span>
+ <span class="n">AriaEcSettings</span><span class="p">(</span><span class="s1">'setup'</span><span class="p">)</span><span class="o">.</span><span class="n">load_config</span><span class="p">(</span><span class="s1">'config.ini'</span><span class="p">)</span>
+</pre></div>
+
+ </div>
+ <div class="articleComments">
+
+ </div>
+ </div>
+ <footer>
+
+
+ <hr/>
+
+ <div role="contentinfo">
+ <p>
+ © Copyright 2017, Fabrice Allain.
+
+ </p>
+ </div>
+ Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>.
+
+</footer>
+
+ </div>
+ </div>
+
+ </section>
+
+ </div>
+
+
+
+
+
+ <script type="text/javascript">
+ var DOCUMENTATION_OPTIONS = {
+ URL_ROOT:'../../',
+ VERSION:'0.2',
+ COLLAPSE_INDEX:false,
+ FILE_SUFFIX:'.html',
+ HAS_SOURCE: true,
+ SOURCELINK_SUFFIX: '.txt'
+ };
+ </script>
+ <script type="text/javascript" src="../../_static/jquery.js"></script>
+ <script type="text/javascript" src="../../_static/underscore.js"></script>
+ <script type="text/javascript" src="../../_static/doctools.js"></script>
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+
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+
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+ SphinxRtdTheme.StickyNav.enable();
+ });
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\ No newline at end of file
diff --git a/docs/_build/html/genindex.html b/examples-dev/olds/_build/html/_modules/index.html
similarity index 60%
rename from docs/_build/html/genindex.html
rename to examples-dev/olds/_build/html/_modules/index.html
index 127f52a8d4abf25e627e1db945919f44d75cfa76..2fa5593f52a52bbb0fa414d3e868d9f0c7e25db7 100644
--- a/docs/_build/html/genindex.html
+++ b/examples-dev/olds/_build/html/_modules/index.html
@@ -1,6 +1,5 @@
-
<!DOCTYPE html>
<!--[if IE 8]><html class="no-js lt-ie9" lang="en" > <![endif]-->
<!--[if gt IE 8]><!--> <html class="no-js" lang="en" > <!--<![endif]-->
@@ -9,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>Index — ARIA 4 documentation</title>
+ <title>Overview: module code — Aria-EC 0.3 documentation</title>
@@ -27,20 +26,19 @@
- <link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
+ <link rel="stylesheet" href="../_static/css/theme.css" type="text/css" />
<link rel="index" title="Index"
- href="#"/>
- <link rel="search" title="Search" href="search.html"/>
- <link rel="copyright" title="Copyright" href="copyright.html"/>
- <link rel="top" title="ARIA 4 documentation" href="index.html"/>
+ href="../genindex.html"/>
+ <link rel="search" title="Search" href="../search.html"/>
+ <link rel="top" title="Aria-EC 0.3 documentation" href="../index.html"/>
- <script src="_static/js/modernizr.min.js"></script>
+ <script src="../_static/js/modernizr.min.js"></script>
</head>
@@ -56,7 +54,7 @@
- <a href="index.html" class="icon icon-home"> ARIA
+ <a href="../index.html" class="icon icon-home"> Aria-EC
@@ -66,14 +64,14 @@
<div class="version">
- 2
+ 0.3
</div>
<div role="search">
- <form id="rtd-search-form" class="wy-form" action="search.html" method="get">
+ <form id="rtd-search-form" class="wy-form" action="../search.html" method="get">
<input type="text" name="q" placeholder="Search docs" />
<input type="hidden" name="check_keywords" value="yes" />
<input type="hidden" name="area" value="default" />
@@ -104,7 +102,7 @@
<nav class="wy-nav-top" role="navigation" aria-label="top navigation">
<i data-toggle="wy-nav-top" class="fa fa-bars"></i>
- <a href="index.html">ARIA</a>
+ <a href="../index.html">Aria-EC</a>
</nav>
@@ -132,9 +130,9 @@
<ul class="wy-breadcrumbs">
- <li><a href="index.html">Docs</a> »</li>
+ <li><a href="../index.html">Docs</a> »</li>
- <li>Index</li>
+ <li>Overview: module code</li>
<li class="wy-breadcrumbs-aside">
@@ -151,13 +149,20 @@
<div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
<div itemprop="articleBody">
-
-<h1 id="index">Index</h1>
-
-<div class="genindex-jumpbox">
-
-</div>
-
+ <h1>All modules for which code is available</h1>
+<ul><li><a href="aria/conbox/analysis.html">aria.conbox.analysis</a></li>
+<li><a href="aria/conbox/commands.html">aria.conbox.commands</a></li>
+<li><a href="aria/conbox/converter.html">aria.conbox.converter</a></li>
+<li><a href="aria/conbox/maplot.html">aria.conbox.maplot</a></li>
+<li><a href="aria/conbox/ndconv.html">aria.conbox.ndconv</a></li>
+<li><a href="aria/conbox/pdbdist.html">aria.conbox.pdbdist</a></li>
+<li><a href="aria/conbox/pdbqual.html">aria.conbox.pdbqual</a></li>
+<li><a href="aria/conbox/protein.html">aria.conbox.protein</a></li>
+<li><a href="aria/conbox/protmap.html">aria.conbox.protmap</a></li>
+<li><a href="aria/conbox/reader.html">aria.conbox.reader</a></li>
+<li><a href="aria/conbox/settings.html">aria.conbox.settings</a></li>
+<li><a href="aria/conbox/setup.html">aria.conbox.setup</a></li>
+</ul>
</div>
<div class="articleComments">
@@ -171,7 +176,7 @@
<div role="contentinfo">
<p>
- © <a href="copyright.html">Copyright</a> 2017, Benjamin Bardiaux, Michael Habeck, Therese Malliavin, Wolfgang Rieping, and Michael Nilges.
+ © Copyright 2017, Fabrice Allain, Benjamin Bardiaux, Michael Habeck, Therese Malliavin, Wolfgang Rieping, and Michael Nilges.
</p>
</div>
@@ -192,24 +197,24 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
- URL_ROOT:'./',
- VERSION:'4',
+ URL_ROOT:'../',
+ VERSION:'0.3',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
HAS_SOURCE: true,
SOURCELINK_SUFFIX: '.txt'
};
</script>
- <script type="text/javascript" src="_static/jquery.js"></script>
- <script type="text/javascript" src="_static/underscore.js"></script>
- <script type="text/javascript" src="_static/doctools.js"></script>
+ <script type="text/javascript" src="../_static/jquery.js"></script>
+ <script type="text/javascript" src="../_static/underscore.js"></script>
+ <script type="text/javascript" src="../_static/doctools.js"></script>
<script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.1/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
- <script type="text/javascript" src="_static/js/theme.js"></script>
+ <script type="text/javascript" src="../_static/js/theme.js"></script>
diff --git a/examples-dev/olds/_build/html/_sources/ariaec.rst.txt b/examples-dev/olds/_build/html/_sources/ariaec.rst.txt
new file mode 100644
index 0000000000000000000000000000000000000000..20f786da216a97258bdcca94acc1a648a5ca7a0d
--- /dev/null
+++ b/examples-dev/olds/_build/html/_sources/ariaec.rst.txt
@@ -0,0 +1,123 @@
+aria.conbox package
+===================
+
+Subpackages
+-----------
+
+.. toctree::
+
+Submodules
+----------
+
+aria.conbox.analysis module
+---------------------------
+
+.. automodule:: aria.conbox.analysis
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+aria.conbox.base module
+-----------------------
+
+.. automodule:: aria.conbox.base
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+aria.conbox.commands module
+---------------------------
+
+.. automodule:: aria.conbox.commands
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+aria.conbox.converter module
+----------------------------
+
+.. automodule:: aria.conbox.converter
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+aria.conbox.maplot module
+-------------------------
+
+.. automodule:: aria.conbox.maplot
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+aria.conbox.ndconv module
+-------------------------
+
+.. automodule:: aria.conbox.ndconv
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+aria.conbox.pdbdist module
+--------------------------
+
+.. automodule:: aria.conbox.pdbdist
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+aria.conbox.pdbqual module
+--------------------------
+
+.. automodule:: aria.conbox.pdbqual
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+aria.conbox.protein module
+--------------------------
+
+.. automodule:: aria.conbox.protein
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+aria.conbox.protmap module
+--------------------------
+
+.. automodule:: aria.conbox.protmap
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+aria.conbox.reader module
+-------------------------
+
+.. automodule:: aria.conbox.reader
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+aria.conbox.settings module
+---------------------------
+
+.. automodule:: aria.conbox.settings
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+aria.conbox.setup module
+------------------------
+
+.. automodule:: aria.conbox.setup
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+
+Module contents
+---------------
+
+.. automodule:: aria.conbox
+ :members:
+ :undoc-members:
+ :show-inheritance:
diff --git a/examples-dev/olds/_build/html/_sources/ariaec.test.rst.txt b/examples-dev/olds/_build/html/_sources/ariaec.test.rst.txt
new file mode 100644
index 0000000000000000000000000000000000000000..8813337fd0c5d4145318936b602a55b20912fba0
--- /dev/null
+++ b/examples-dev/olds/_build/html/_sources/ariaec.test.rst.txt
@@ -0,0 +1,10 @@
+ariaec.test package
+===================
+
+Module contents
+---------------
+
+.. automodule:: ariaec.test
+ :members:
+ :undoc-members:
+ :show-inheritance:
diff --git a/docs/_build/html/_sources/index.rst.txt b/examples-dev/olds/_build/html/_sources/index.rst.txt
similarity index 61%
rename from docs/_build/html/_sources/index.rst.txt
rename to examples-dev/olds/_build/html/_sources/index.rst.txt
index b737aaf93725db144448ea732bc66f79e326e29a..c213df6f85ef924e67d93b9ad7c0bb1d687239bf 100644
--- a/docs/_build/html/_sources/index.rst.txt
+++ b/examples-dev/olds/_build/html/_sources/index.rst.txt
@@ -1,10 +1,10 @@
-.. ARIAEC documentation master file, created by
- sphinx-quickstart on Mon Oct 23 16:10:18 2017.
+.. AriaEc documentation master file, created by
+ sphinx-quickstart on Fri Apr 21 16:27:42 2017.
You can adapt this file completely to your liking, but it should at least
contain the root `toctree` directive.
-Welcome to ARIAEC's documentation!
-==================================
+Welcome to Aria-EC's documentation!
+===================================
.. toctree::
:maxdepth: 2
diff --git a/docs/_build/html/_sources/modules.rst.txt b/examples-dev/olds/_build/html/_sources/modules.rst.txt
similarity index 100%
rename from docs/_build/html/_sources/modules.rst.txt
rename to examples-dev/olds/_build/html/_sources/modules.rst.txt
diff --git a/docs/_build/html/_static/ajax-loader.gif b/examples-dev/olds/_build/html/_static/ajax-loader.gif
similarity index 100%
rename from docs/_build/html/_static/ajax-loader.gif
rename to examples-dev/olds/_build/html/_static/ajax-loader.gif
diff --git a/docs/_build/html/_static/basic.css b/examples-dev/olds/_build/html/_static/basic.css
similarity index 98%
rename from docs/_build/html/_static/basic.css
rename to examples-dev/olds/_build/html/_static/basic.css
index 6f408303f8353eac5731eef280694f62a5a4f479..6df76b0a6c56968b5e521311839cf4139adba1cc 100644
--- a/docs/_build/html/_static/basic.css
+++ b/examples-dev/olds/_build/html/_static/basic.css
@@ -4,7 +4,7 @@
*
* Sphinx stylesheet -- basic theme.
*
- * :copyright: Copyright 2007-2018 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2017 by the Sphinx team, see AUTHORS.
* :license: BSD, see LICENSE for details.
*
*/
@@ -445,14 +445,10 @@ dd {
margin-left: 30px;
}
-dt:target, span.highlighted {
+dt:target, .highlighted {
background-color: #fbe54e;
}
-rect.highlighted {
- fill: #fbe54e;
-}
-
dl.glossary dt {
font-weight: bold;
font-size: 1.1em;
diff --git a/docs/_build/html/_static/comment-bright.png b/examples-dev/olds/_build/html/_static/comment-bright.png
similarity index 100%
rename from docs/_build/html/_static/comment-bright.png
rename to examples-dev/olds/_build/html/_static/comment-bright.png
diff --git a/docs/_build/html/_static/comment-close.png b/examples-dev/olds/_build/html/_static/comment-close.png
similarity index 100%
rename from docs/_build/html/_static/comment-close.png
rename to examples-dev/olds/_build/html/_static/comment-close.png
diff --git a/docs/_build/html/_static/comment.png b/examples-dev/olds/_build/html/_static/comment.png
similarity index 100%
rename from docs/_build/html/_static/comment.png
rename to examples-dev/olds/_build/html/_static/comment.png
diff --git a/docs/_build/html/_static/css/badge_only.css b/examples-dev/olds/_build/html/_static/css/badge_only.css
similarity index 100%
rename from docs/_build/html/_static/css/badge_only.css
rename to examples-dev/olds/_build/html/_static/css/badge_only.css
diff --git a/docs/_build/html/_static/css/theme.css b/examples-dev/olds/_build/html/_static/css/theme.css
similarity index 100%
rename from docs/_build/html/_static/css/theme.css
rename to examples-dev/olds/_build/html/_static/css/theme.css
diff --git a/docs/_build/html/_static/doctools.js b/examples-dev/olds/_build/html/_static/doctools.js
similarity index 82%
rename from docs/_build/html/_static/doctools.js
rename to examples-dev/olds/_build/html/_static/doctools.js
index 0c15c0099b5df57d89479a679ae7b060d514e8e2..56549772348502981be27d8a3196baf789b40794 100644
--- a/docs/_build/html/_static/doctools.js
+++ b/examples-dev/olds/_build/html/_static/doctools.js
@@ -4,7 +4,7 @@
*
* Sphinx JavaScript utilities for all documentation.
*
- * :copyright: Copyright 2007-2018 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2017 by the Sphinx team, see AUTHORS.
* :license: BSD, see LICENSE for details.
*
*/
@@ -45,7 +45,7 @@ jQuery.urlencode = encodeURIComponent;
* it will always return arrays of strings for the value parts.
*/
jQuery.getQueryParameters = function(s) {
- if (typeof s === 'undefined')
+ if (typeof s == 'undefined')
s = document.location.search;
var parts = s.substr(s.indexOf('?') + 1).split('&');
var result = {};
@@ -66,53 +66,29 @@ jQuery.getQueryParameters = function(s) {
* span elements with the given class name.
*/
jQuery.fn.highlightText = function(text, className) {
- function highlight(node, addItems) {
- if (node.nodeType === 3) {
+ function highlight(node) {
+ if (node.nodeType == 3) {
var val = node.nodeValue;
var pos = val.toLowerCase().indexOf(text);
if (pos >= 0 && !jQuery(node.parentNode).hasClass(className)) {
- var span;
- var isInSVG = jQuery(node).closest("body, svg, foreignObject").is("svg");
- if (isInSVG) {
- span = document.createElementNS("http://www.w3.org/2000/svg", "tspan");
- } else {
- span = document.createElement("span");
- span.className = className;
- }
+ var span = document.createElement("span");
+ span.className = className;
span.appendChild(document.createTextNode(val.substr(pos, text.length)));
node.parentNode.insertBefore(span, node.parentNode.insertBefore(
document.createTextNode(val.substr(pos + text.length)),
node.nextSibling));
node.nodeValue = val.substr(0, pos);
- if (isInSVG) {
- var bbox = span.getBBox();
- var rect = document.createElementNS("http://www.w3.org/2000/svg", "rect");
- rect.x.baseVal.value = bbox.x;
- rect.y.baseVal.value = bbox.y;
- rect.width.baseVal.value = bbox.width;
- rect.height.baseVal.value = bbox.height;
- rect.setAttribute('class', className);
- var parentOfText = node.parentNode.parentNode;
- addItems.push({
- "parent": node.parentNode,
- "target": rect});
- }
}
}
else if (!jQuery(node).is("button, select, textarea")) {
jQuery.each(node.childNodes, function() {
- highlight(this, addItems);
+ highlight(this);
});
}
}
- var addItems = [];
- var result = this.each(function() {
- highlight(this, addItems);
+ return this.each(function() {
+ highlight(this);
});
- for (var i = 0; i < addItems.length; ++i) {
- jQuery(addItems[i].parent).before(addItems[i].target);
- }
- return result;
};
/*
@@ -155,21 +131,21 @@ var Documentation = {
* i18n support
*/
TRANSLATIONS : {},
- PLURAL_EXPR : function(n) { return n === 1 ? 0 : 1; },
+ PLURAL_EXPR : function(n) { return n == 1 ? 0 : 1; },
LOCALE : 'unknown',
// gettext and ngettext don't access this so that the functions
// can safely bound to a different name (_ = Documentation.gettext)
gettext : function(string) {
var translated = Documentation.TRANSLATIONS[string];
- if (typeof translated === 'undefined')
+ if (typeof translated == 'undefined')
return string;
- return (typeof translated === 'string') ? translated : translated[0];
+ return (typeof translated == 'string') ? translated : translated[0];
},
ngettext : function(singular, plural, n) {
var translated = Documentation.TRANSLATIONS[singular];
- if (typeof translated === 'undefined')
+ if (typeof translated == 'undefined')
return (n == 1) ? singular : plural;
return translated[Documentation.PLURALEXPR(n)];
},
@@ -204,7 +180,7 @@ var Documentation = {
* see: https://bugzilla.mozilla.org/show_bug.cgi?id=645075
*/
fixFirefoxAnchorBug : function() {
- if (document.location.hash && $.browser.mozilla)
+ if (document.location.hash)
window.setTimeout(function() {
document.location.href += '';
}, 10);
@@ -240,7 +216,7 @@ var Documentation = {
var src = $(this).attr('src');
var idnum = $(this).attr('id').substr(7);
$('tr.cg-' + idnum).toggle();
- if (src.substr(-9) === 'minus.png')
+ if (src.substr(-9) == 'minus.png')
$(this).attr('src', src.substr(0, src.length-9) + 'plus.png');
else
$(this).attr('src', src.substr(0, src.length-8) + 'minus.png');
@@ -272,7 +248,7 @@ var Documentation = {
var path = document.location.pathname;
var parts = path.split(/\//);
$.each(DOCUMENTATION_OPTIONS.URL_ROOT.split(/\//), function() {
- if (this === '..')
+ if (this == '..')
parts.pop();
});
var url = parts.join('/');
diff --git a/docs/_build/html/_static/down-pressed.png b/examples-dev/olds/_build/html/_static/down-pressed.png
similarity index 100%
rename from docs/_build/html/_static/down-pressed.png
rename to examples-dev/olds/_build/html/_static/down-pressed.png
diff --git a/docs/_build/html/_static/down.png b/examples-dev/olds/_build/html/_static/down.png
similarity index 100%
rename from docs/_build/html/_static/down.png
rename to examples-dev/olds/_build/html/_static/down.png
diff --git a/docs/_build/html/_static/file.png b/examples-dev/olds/_build/html/_static/file.png
similarity index 100%
rename from docs/_build/html/_static/file.png
rename to examples-dev/olds/_build/html/_static/file.png
diff --git a/docs/_build/html/_static/fonts/Inconsolata-Bold.ttf b/examples-dev/olds/_build/html/_static/fonts/Inconsolata-Bold.ttf
similarity index 100%
rename from docs/_build/html/_static/fonts/Inconsolata-Bold.ttf
rename to examples-dev/olds/_build/html/_static/fonts/Inconsolata-Bold.ttf
diff --git a/docs/_build/html/_static/fonts/Inconsolata-Regular.ttf b/examples-dev/olds/_build/html/_static/fonts/Inconsolata-Regular.ttf
similarity index 100%
rename from docs/_build/html/_static/fonts/Inconsolata-Regular.ttf
rename to examples-dev/olds/_build/html/_static/fonts/Inconsolata-Regular.ttf
diff --git a/docs/_build/html/_static/fonts/Lato-Bold.ttf b/examples-dev/olds/_build/html/_static/fonts/Lato-Bold.ttf
similarity index 100%
rename from docs/_build/html/_static/fonts/Lato-Bold.ttf
rename to examples-dev/olds/_build/html/_static/fonts/Lato-Bold.ttf
diff --git a/docs/_build/html/_static/fonts/Lato-Regular.ttf b/examples-dev/olds/_build/html/_static/fonts/Lato-Regular.ttf
similarity index 100%
rename from docs/_build/html/_static/fonts/Lato-Regular.ttf
rename to examples-dev/olds/_build/html/_static/fonts/Lato-Regular.ttf
diff --git a/docs/_build/html/_static/fonts/RobotoSlab-Bold.ttf b/examples-dev/olds/_build/html/_static/fonts/RobotoSlab-Bold.ttf
similarity index 100%
rename from docs/_build/html/_static/fonts/RobotoSlab-Bold.ttf
rename to examples-dev/olds/_build/html/_static/fonts/RobotoSlab-Bold.ttf
diff --git a/docs/_build/html/_static/fonts/RobotoSlab-Regular.ttf b/examples-dev/olds/_build/html/_static/fonts/RobotoSlab-Regular.ttf
similarity index 100%
rename from docs/_build/html/_static/fonts/RobotoSlab-Regular.ttf
rename to examples-dev/olds/_build/html/_static/fonts/RobotoSlab-Regular.ttf
diff --git a/docs/_build/html/_static/fonts/fontawesome-webfont.eot b/examples-dev/olds/_build/html/_static/fonts/fontawesome-webfont.eot
similarity index 100%
rename from docs/_build/html/_static/fonts/fontawesome-webfont.eot
rename to examples-dev/olds/_build/html/_static/fonts/fontawesome-webfont.eot
diff --git a/docs/_build/html/_static/fonts/fontawesome-webfont.svg b/examples-dev/olds/_build/html/_static/fonts/fontawesome-webfont.svg
similarity index 100%
rename from docs/_build/html/_static/fonts/fontawesome-webfont.svg
rename to examples-dev/olds/_build/html/_static/fonts/fontawesome-webfont.svg
diff --git a/docs/_build/html/_static/fonts/fontawesome-webfont.ttf b/examples-dev/olds/_build/html/_static/fonts/fontawesome-webfont.ttf
similarity index 100%
rename from docs/_build/html/_static/fonts/fontawesome-webfont.ttf
rename to examples-dev/olds/_build/html/_static/fonts/fontawesome-webfont.ttf
diff --git a/docs/_build/html/_static/fonts/fontawesome-webfont.woff b/examples-dev/olds/_build/html/_static/fonts/fontawesome-webfont.woff
similarity index 100%
rename from docs/_build/html/_static/fonts/fontawesome-webfont.woff
rename to examples-dev/olds/_build/html/_static/fonts/fontawesome-webfont.woff
diff --git a/docs/_build/html/_static/jquery-3.1.0.js b/examples-dev/olds/_build/html/_static/jquery-3.1.0.js
similarity index 100%
rename from docs/_build/html/_static/jquery-3.1.0.js
rename to examples-dev/olds/_build/html/_static/jquery-3.1.0.js
diff --git a/docs/_build/html/_static/jquery.js b/examples-dev/olds/_build/html/_static/jquery.js
similarity index 100%
rename from docs/_build/html/_static/jquery.js
rename to examples-dev/olds/_build/html/_static/jquery.js
diff --git a/docs/_build/html/_static/js/modernizr.min.js b/examples-dev/olds/_build/html/_static/js/modernizr.min.js
similarity index 100%
rename from docs/_build/html/_static/js/modernizr.min.js
rename to examples-dev/olds/_build/html/_static/js/modernizr.min.js
diff --git a/docs/_build/html/_static/js/theme.js b/examples-dev/olds/_build/html/_static/js/theme.js
similarity index 100%
rename from docs/_build/html/_static/js/theme.js
rename to examples-dev/olds/_build/html/_static/js/theme.js
diff --git a/docs/_build/html/_static/minus.png b/examples-dev/olds/_build/html/_static/minus.png
similarity index 100%
rename from docs/_build/html/_static/minus.png
rename to examples-dev/olds/_build/html/_static/minus.png
diff --git a/docs/_build/html/_static/plus.png b/examples-dev/olds/_build/html/_static/plus.png
similarity index 100%
rename from docs/_build/html/_static/plus.png
rename to examples-dev/olds/_build/html/_static/plus.png
diff --git a/docs/_build/html/_static/pygments.css b/examples-dev/olds/_build/html/_static/pygments.css
similarity index 100%
rename from docs/_build/html/_static/pygments.css
rename to examples-dev/olds/_build/html/_static/pygments.css
diff --git a/docs/_build/html/_static/searchtools.js b/examples-dev/olds/_build/html/_static/searchtools.js
similarity index 99%
rename from docs/_build/html/_static/searchtools.js
rename to examples-dev/olds/_build/html/_static/searchtools.js
index 41b8336776442fbc64332ffbd3d2c1ddd8b3b9c2..c82157380b008f641a14e50619a23cc5c0b4b04d 100644
--- a/docs/_build/html/_static/searchtools.js
+++ b/examples-dev/olds/_build/html/_static/searchtools.js
@@ -4,7 +4,7 @@
*
* Sphinx JavaScript utilities for the full-text search.
*
- * :copyright: Copyright 2007-2018 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2017 by the Sphinx team, see AUTHORS.
* :license: BSD, see LICENSE for details.
*
*/
@@ -540,9 +540,6 @@ var Search = {
});
} else if (DOCUMENTATION_OPTIONS.HAS_SOURCE) {
var suffix = DOCUMENTATION_OPTIONS.SOURCELINK_SUFFIX;
- if (suffix === undefined) {
- suffix = '.txt';
- }
$.ajax({url: DOCUMENTATION_OPTIONS.URL_ROOT + '_sources/' + item[5] + (item[5].slice(-suffix.length) === suffix ? '' : suffix),
dataType: "text",
complete: function(jqxhr, textstatus) {
diff --git a/docs/_build/html/_static/underscore-1.3.1.js b/examples-dev/olds/_build/html/_static/underscore-1.3.1.js
similarity index 100%
rename from docs/_build/html/_static/underscore-1.3.1.js
rename to examples-dev/olds/_build/html/_static/underscore-1.3.1.js
diff --git a/docs/_build/html/_static/underscore.js b/examples-dev/olds/_build/html/_static/underscore.js
similarity index 100%
rename from docs/_build/html/_static/underscore.js
rename to examples-dev/olds/_build/html/_static/underscore.js
diff --git a/docs/_build/html/_static/up-pressed.png b/examples-dev/olds/_build/html/_static/up-pressed.png
similarity index 100%
rename from docs/_build/html/_static/up-pressed.png
rename to examples-dev/olds/_build/html/_static/up-pressed.png
diff --git a/docs/_build/html/_static/up.png b/examples-dev/olds/_build/html/_static/up.png
similarity index 100%
rename from docs/_build/html/_static/up.png
rename to examples-dev/olds/_build/html/_static/up.png
diff --git a/docs/_build/html/_static/websupport.js b/examples-dev/olds/_build/html/_static/websupport.js
similarity index 99%
rename from docs/_build/html/_static/websupport.js
rename to examples-dev/olds/_build/html/_static/websupport.js
index 79b18e3898556c26eeebd259cb91868b8b6200c8..53f6a4525cd3db79b5076e557b0d4c89d810fcae 100644
--- a/docs/_build/html/_static/websupport.js
+++ b/examples-dev/olds/_build/html/_static/websupport.js
@@ -4,7 +4,7 @@
*
* sphinx.websupport utilities for all documentation.
*
- * :copyright: Copyright 2007-2018 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2017 by the Sphinx team, see AUTHORS.
* :license: BSD, see LICENSE for details.
*
*/
diff --git a/examples-dev/olds/_build/html/ariaec.html b/examples-dev/olds/_build/html/ariaec.html
new file mode 100644
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+<li><a class="reference internal" href="#">aria.conbox package</a><ul>
+<li><a class="reference internal" href="#subpackages">Subpackages</a></li>
+<li><a class="reference internal" href="#submodules">Submodules</a></li>
+<li><a class="reference internal" href="#module-aria.conbox.analysis">aria.conbox.analysis module</a></li>
+<li><a class="reference internal" href="#aria-conbox-base-module">aria.conbox.base module</a></li>
+<li><a class="reference internal" href="#module-aria.conbox.commands">aria.conbox.commands module</a></li>
+<li><a class="reference internal" href="#module-aria.conbox.converter">aria.conbox.converter module</a></li>
+<li><a class="reference internal" href="#module-aria.conbox.maplot">aria.conbox.maplot module</a></li>
+<li><a class="reference internal" href="#module-aria.conbox.ndconv">aria.conbox.ndconv module</a></li>
+<li><a class="reference internal" href="#module-aria.conbox.pdbdist">aria.conbox.pdbdist module</a></li>
+<li><a class="reference internal" href="#module-aria.conbox.pdbqual">aria.conbox.pdbqual module</a></li>
+<li><a class="reference internal" href="#module-aria.conbox.protein">aria.conbox.protein module</a></li>
+<li><a class="reference internal" href="#module-aria.conbox.protmap">aria.conbox.protmap module</a></li>
+<li><a class="reference internal" href="#module-aria.conbox.reader">aria.conbox.reader module</a></li>
+<li><a class="reference internal" href="#module-aria.conbox.settings">aria.conbox.settings module</a></li>
+<li><a class="reference internal" href="#module-aria.conbox.setup">aria.conbox.setup module</a></li>
+<li><a class="reference internal" href="#module-aria.conbox">Module contents</a></li>
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+ <div class="section" id="aria-conbox-package">
+<h1>aria.conbox package<a class="headerlink" href="#aria-conbox-package" title="Permalink to this headline">¶</a></h1>
+<div class="section" id="subpackages">
+<h2>Subpackages<a class="headerlink" href="#subpackages" title="Permalink to this headline">¶</a></h2>
+<div class="toctree-wrapper compound">
+</div>
+</div>
+<div class="section" id="submodules">
+<h2>Submodules<a class="headerlink" href="#submodules" title="Permalink to this headline">¶</a></h2>
+</div>
+<div class="section" id="module-aria.conbox.analysis">
+<span id="aria-conbox-analysis-module"></span><h2>aria.conbox.analysis module<a class="headerlink" href="#module-aria.conbox.analysis" title="Permalink to this headline">¶</a></h2>
+<p>Created on 4/7/17</p>
+<p>@author: fallain</p>
+<dl class="class">
+<dt id="aria.conbox.analysis.EnsembleAnalysis">
+<em class="property">class </em><code class="descclassname">aria.conbox.analysis.</code><code class="descname">EnsembleAnalysis</code><span class="sig-paren">(</span><em>settings</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/analysis.html#EnsembleAnalysis"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.analysis.EnsembleAnalysis" title="Permalink to this definition">¶</a></dt>
+<dd><p>Bases: <code class="xref py py-class docutils literal"><span class="pre">object</span></code></p>
+<p>ARIA extended ensemble analysis</p>
+<dl class="staticmethod">
+<dt id="aria.conbox.analysis.EnsembleAnalysis.pca_projection">
+<em class="property">static </em><code class="descname">pca_projection</code><span class="sig-paren">(</span><em>ensemble</em>, <em>molecule</em>, <em>infos</em>, <em>atmask='CA'</em>, <em>title='3D PCA projection on backbone coordinates'</em>, <em>outfile=None</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/analysis.html#EnsembleAnalysis.pca_projection"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.analysis.EnsembleAnalysis.pca_projection" title="Permalink to this definition">¶</a></dt>
+<dd><p>PCA projection of ensemble coordinates</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>ensemble</strong> – </li>
+<li><strong>molecule</strong> – </li>
+<li><strong>infos</strong> – </li>
+<li><strong>atmask</strong> – (Default value = “CAâ€)</li>
+<li><strong>title</strong> – </li>
+<li><strong>outfile</strong> – </li>
+</ul>
+</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
+<dt id="aria.conbox.analysis.EnsembleAnalysis.run">
+<code class="descname">run</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/analysis.html#EnsembleAnalysis.run"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.analysis.EnsembleAnalysis.run" title="Permalink to this definition">¶</a></dt>
+<dd><p>Execute Ensemble analysis</p>
+</dd></dl>
+
+<dl class="staticmethod">
+<dt id="aria.conbox.analysis.EnsembleAnalysis.violation_analysis">
+<em class="property">static </em><code class="descname">violation_analysis</code><span class="sig-paren">(</span><em>project</em>, <em>iteration_id</em>, <em>restraints</em>, <em>ensemble</em>, <em>out_file</em>, <em>dists_ref=None</em>, <em>headerflag=True</em>, <em>clusteridx=0</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/analysis.html#EnsembleAnalysis.violation_analysis"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.analysis.EnsembleAnalysis.violation_analysis" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>clusteridx</strong> – </li>
+<li><strong>project</strong> (<em>aria.Project.Project object</em>) – </li>
+<li><strong>iteration_id</strong> – </li>
+<li><strong>restraints</strong> – </li>
+<li><strong>ensemble</strong> – </li>
+<li><strong>out_file</strong> – </li>
+<li><strong>dists_ref</strong> – Reference distances (Default value = None)</li>
+<li><strong>headerflag</strong> – (Default value = True)</li>
+</ul>
+</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+</dd></dl>
+
+<dl class="function">
+<dt id="aria.conbox.analysis.colscatter">
+<code class="descclassname">aria.conbox.analysis.</code><code class="descname">colscatter</code><span class="sig-paren">(</span><em>X</em>, <em>axe</em>, <em>colors</em>, <em>ndim=2</em>, <em>axtitle=''</em>, <em>xlabel='x'</em>, <em>ylabel='y'</em>, <em>zlabel='z'</em>, <em>legend_prefix=''</em>, <em>others=False</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/analysis.html#colscatter"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.analysis.colscatter" title="Permalink to this definition">¶</a></dt>
+<dd><p>Scatter plot with palette colors</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>X</strong> – </li>
+<li><strong>axe</strong> – </li>
+<li><strong>colors</strong> – </li>
+<li><strong>ndim</strong> – (Default value = 2)</li>
+<li><strong>axtitle</strong> – (Default value = “â€)</li>
+<li><strong>xlabel</strong> – (Default value = “xâ€)</li>
+<li><strong>ylabel</strong> – (Default value = “yâ€)</li>
+<li><strong>zlabel</strong> – (Default value = “zâ€)</li>
+<li><strong>legend_prefix</strong> – (Default value = “â€)</li>
+<li><strong>others</strong> – (Default value = False)</li>
+</ul>
+</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+</div>
+<div class="section" id="aria-conbox-base-module">
+<h2>aria.conbox.base module<a class="headerlink" href="#aria-conbox-base-module" title="Permalink to this headline">¶</a></h2>
+</div>
+<div class="section" id="module-aria.conbox.commands">
+<span id="aria-conbox-commands-module"></span><h2>aria.conbox.commands module<a class="headerlink" href="#module-aria.conbox.commands" title="Permalink to this headline">¶</a></h2>
+<p>ARIA Evolutive Contact toolbox</p>
+<dl class="class">
+<dt id="aria.conbox.commands.AriaEcCommands">
+<em class="property">class </em><code class="descclassname">aria.conbox.commands.</code><code class="descname">AriaEcCommands</code><span class="sig-paren">(</span><em>custom_logging=None</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/commands.html#AriaEcCommands"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.commands.AriaEcCommands" title="Permalink to this definition">¶</a></dt>
+<dd><p>Bases: <code class="xref py py-class docutils literal"><span class="pre">object</span></code></p>
+<p>Argparse interface for aria_ec</p>
+<dl class="method">
+<dt id="aria.conbox.commands.AriaEcCommands.analysis">
+<code class="descname">analysis</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/commands.html#AriaEcCommands.analysis"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.commands.AriaEcCommands.analysis" title="Permalink to this definition">¶</a></dt>
+<dd><p>Extended ensemble analysis of distance restraints</p>
+</dd></dl>
+
+<dl class="method">
+<dt id="aria.conbox.commands.AriaEcCommands.bbconv">
+<code class="descname">bbconv</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/commands.html#AriaEcCommands.bbconv"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.commands.AriaEcCommands.bbconv" title="Permalink to this definition">¶</a></dt>
+<dd><p>bbcontacts converter call</p>
+</dd></dl>
+
+<dl class="attribute">
+<dt id="aria.conbox.commands.AriaEcCommands.command_list">
+<code class="descname">command_list</code><em class="property"> = ('setup', 'bbconv', 'maplot', 'pdbqual', 'analysis', 'tbl2xml', 'pdbdist', 'pdbstat')</em><a class="headerlink" href="#aria.conbox.commands.AriaEcCommands.command_list" title="Permalink to this definition">¶</a></dt>
+<dd></dd></dl>
+
+<dl class="attribute">
+<dt id="aria.conbox.commands.AriaEcCommands.contact_types">
+<code class="descname">contact_types</code><em class="property"> = ('evfold', 'plmev', 'plm', 'plmdca', 'plmc', 'bbcontacts', 'pconsc', 'pconsc1', 'pconsc2', 'psicov', 'metapsicovhb', 'metapsicov_stg1', 'metapsicov_stg2', 'gremlin', 'pdb', 'native', 'native_full', 'contactlist')</em><a class="headerlink" href="#aria.conbox.commands.AriaEcCommands.contact_types" title="Permalink to this definition">¶</a></dt>
+<dd></dd></dl>
+
+<dl class="method">
+<dt id="aria.conbox.commands.AriaEcCommands.create_settings">
+<code class="descname">create_settings</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/commands.html#AriaEcCommands.create_settings"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.commands.AriaEcCommands.create_settings" title="Permalink to this definition">¶</a></dt>
+<dd><p>Create settings relative to args.command</p>
+</dd></dl>
+
+<dl class="attribute">
+<dt id="aria.conbox.commands.AriaEcCommands.default_confile">
+<code class="descname">default_confile</code><em class="property"> = 'conf/config.ini'</em><a class="headerlink" href="#aria.conbox.commands.AriaEcCommands.default_confile" title="Permalink to this definition">¶</a></dt>
+<dd></dd></dl>
+
+<dl class="attribute">
+<dt id="aria.conbox.commands.AriaEcCommands.desc_list">
+<code class="descname">desc_list</code><em class="property"> = (u'Setup ARIA infrastructure with contact maps translated into ARIA restraints', u'Convert a contact map in bbcontact format', u'Contactmap visualization tool', u'Quality tool for pdb file(s)', u'Extended ARIA ensemble analysis on a specific iteration ', u'XML converter for tbl distance restraint', u'Extract distance distribution from culled list of pdb files', u'Analyze distance distribution with GMM, ...')</em><a class="headerlink" href="#aria.conbox.commands.AriaEcCommands.desc_list" title="Permalink to this definition">¶</a></dt>
+<dd></dd></dl>
+
+<dl class="method">
+<dt id="aria.conbox.commands.AriaEcCommands.maplot">
+<code class="descname">maplot</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/commands.html#AriaEcCommands.maplot"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.commands.AriaEcCommands.maplot" title="Permalink to this definition">¶</a></dt>
+<dd><p>instantiate AriaEcContactmap with AriaSettings</p>
+</dd></dl>
+
+<dl class="method">
+<dt id="aria.conbox.commands.AriaEcCommands.pdbdist">
+<code class="descname">pdbdist</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/commands.html#AriaEcCommands.pdbdist"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.commands.AriaEcCommands.pdbdist" title="Permalink to this definition">¶</a></dt>
+<dd><p>Extract pdb distance distributions</p>
+</dd></dl>
+
+<dl class="method">
+<dt id="aria.conbox.commands.AriaEcCommands.pdbqual">
+<code class="descname">pdbqual</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/commands.html#AriaEcCommands.pdbqual"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.commands.AriaEcCommands.pdbqual" title="Permalink to this definition">¶</a></dt>
+<dd><p>Quality run subcommand</p>
+</dd></dl>
+
+<dl class="method">
+<dt id="aria.conbox.commands.AriaEcCommands.pdbstat">
+<code class="descname">pdbstat</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/commands.html#AriaEcCommands.pdbstat"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.commands.AriaEcCommands.pdbstat" title="Permalink to this definition">¶</a></dt>
+<dd><p>Analyse pdb distance distribution</p>
+</dd></dl>
+
+<dl class="method">
+<dt id="aria.conbox.commands.AriaEcCommands.run">
+<code class="descname">run</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/commands.html#AriaEcCommands.run"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.commands.AriaEcCommands.run" title="Permalink to this definition">¶</a></dt>
+<dd><p>call method relative to args.command</p>
+</dd></dl>
+
+<dl class="method">
+<dt id="aria.conbox.commands.AriaEcCommands.setup">
+<code class="descname">setup</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/commands.html#AriaEcCommands.setup"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.commands.AriaEcCommands.setup" title="Permalink to this definition">¶</a></dt>
+<dd><p>Setup call</p>
+</dd></dl>
+
+<dl class="method">
+<dt id="aria.conbox.commands.AriaEcCommands.tbl2xml">
+<code class="descname">tbl2xml</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/commands.html#AriaEcCommands.tbl2xml"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.commands.AriaEcCommands.tbl2xml" title="Permalink to this definition">¶</a></dt>
+<dd><p>tbl2xml command</p>
+</dd></dl>
+
+</dd></dl>
+
+<dl class="class">
+<dt id="aria.conbox.commands.ReadableFile">
+<em class="property">class </em><code class="descclassname">aria.conbox.commands.</code><code class="descname">ReadableFile</code><span class="sig-paren">(</span><em>*args</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/commands.html#ReadableFile"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.commands.ReadableFile" title="Permalink to this definition">¶</a></dt>
+<dd><p>Bases: <code class="xref py py-class docutils literal"><span class="pre">argparse.Action</span></code></p>
+<p>Class used with argparse action to check if a file is readable</p>
+</dd></dl>
+
+<dl class="function">
+<dt id="aria.conbox.commands.check_file">
+<code class="descclassname">aria.conbox.commands.</code><code class="descname">check_file</code><span class="sig-paren">(</span><em>prospective_file</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/commands.html#check_file"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.commands.check_file" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>prospective_file</strong> – </td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="function">
+<dt id="aria.conbox.commands.main">
+<code class="descclassname">aria.conbox.commands.</code><code class="descname">main</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/commands.html#main"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.commands.main" title="Permalink to this definition">¶</a></dt>
+<dd><p>Launch ariaec command interface</p>
+</dd></dl>
+
+</div>
+<div class="section" id="module-aria.conbox.converter">
+<span id="aria-conbox-converter-module"></span><h2>aria.conbox.converter module<a class="headerlink" href="#module-aria.conbox.converter" title="Permalink to this headline">¶</a></h2>
+<p>Input/Output aria_ec scripts</p>
+<dl class="class">
+<dt id="aria.conbox.converter.AriaEcBbConverter">
+<em class="property">class </em><code class="descclassname">aria.conbox.converter.</code><code class="descname">AriaEcBbConverter</code><span class="sig-paren">(</span><em>settings</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/converter.html#AriaEcBbConverter"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.converter.AriaEcBbConverter" title="Permalink to this definition">¶</a></dt>
+<dd><p>Bases: <code class="xref py py-class docutils literal"><span class="pre">object</span></code></p>
+<p>Bbcontacts convert main class</p>
+<dl class="staticmethod">
+<dt id="aria.conbox.converter.AriaEcBbConverter.compute_diversityvalue">
+<em class="property">static </em><code class="descname">compute_diversityvalue</code><span class="sig-paren">(</span><em>msa</em>, <em>seqlen</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/converter.html#AriaEcBbConverter.compute_diversityvalue"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.converter.AriaEcBbConverter.compute_diversityvalue" title="Permalink to this definition">¶</a></dt>
+<dd><blockquote>
+<div><p>Compute bbcontacts diversity value</p>
+<dl class="docutils">
+<dt>msa <span class="classifier-delimiter">:</span> <span class="classifier"><cite>str</cite></span></dt>
+<dd>multiple sequence alignment file path</dd>
+<dt>seqlen <span class="classifier-delimiter">:</span> <span class="classifier"><cite>int</cite></span></dt>
+<dd>protein sequence length</dd>
+</dl>
+<p>diversity_score : <cite>float</cite></p>
+<blockquote>
+<div><p>Diversity score correspond to the square root of the multiple
+sequence alignment length (<span class="math">\(m\)</span>) over the length of the protein
+sequence (<span class="math">\(l\)</span>)</p>
+<div class="math">
+\[Divscore =\]</div>
+</div></blockquote>
+</div></blockquote>
+<p>rac{sqrt{m}}{l}</p>
+</dd></dl>
+
+<dl class="method">
+<dt id="aria.conbox.converter.AriaEcBbConverter.run">
+<code class="descname">run</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/converter.html#AriaEcBbConverter.run"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.converter.AriaEcBbConverter.run" title="Permalink to this definition">¶</a></dt>
+<dd><p>BBConverter command</p>
+</dd></dl>
+
+</dd></dl>
+
+<dl class="class">
+<dt id="aria.conbox.converter.AriaEcXMLConverter">
+<em class="property">class </em><code class="descclassname">aria.conbox.converter.</code><code class="descname">AriaEcXMLConverter</code><span class="sig-paren">(</span><em>*args</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/converter.html#AriaEcXMLConverter"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.converter.AriaEcXMLConverter" title="Permalink to this definition">¶</a></dt>
+<dd><p>Bases: <a class="reference internal" href="#aria.conbox.converter.AriaXMLConverter" title="aria.conbox.converter.AriaXMLConverter"><code class="xref py py-class docutils literal"><span class="pre">aria.conbox.converter.AriaXMLConverter</span></code></a></p>
+<p>XML converter ariaec to aria</p>
+<dl class="method">
+<dt id="aria.conbox.converter.AriaEcXMLConverter.atm_list">
+<code class="descname">atm_list</code><span class="sig-paren">(</span><em>idx1</em>, <em>res1</em>, <em>idx2</em>, <em>res2</em>, <em>list_type='min'</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/converter.html#AriaEcXMLConverter.atm_list"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.converter.AriaEcXMLConverter.atm_list" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>idx1</strong> – </li>
+<li><strong>res1</strong> – </li>
+<li><strong>idx2</strong> – </li>
+<li><strong>res2</strong> – </li>
+<li><strong>list_type</strong> – </li>
+</ul>
+</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
+<dt id="aria.conbox.converter.AriaEcXMLConverter.atm_product">
+<code class="descname">atm_product</code><span class="sig-paren">(</span><em>idx1</em>, <em>res1</em>, <em>idx2</em>, <em>res2</em>, <em>list_type='min'</em>, <em>adr_flag=False</em>, <em>product_type='allvsall'</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/converter.html#AriaEcXMLConverter.atm_product"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.converter.AriaEcXMLConverter.atm_product" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>product_type</strong> – </li>
+<li><strong>adr_flag</strong> – </li>
+<li><strong>idx1</strong> – </li>
+<li><strong>res1</strong> – </li>
+<li><strong>idx2</strong> – </li>
+<li><strong>res2</strong> – </li>
+<li><strong>list_type</strong> – type of atoms in the product (Default value = “minâ€)</li>
+<li><strong>res1</strong> – </li>
+<li><strong>res2</strong> – </li>
+</ul>
+</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
+<dt id="aria.conbox.converter.AriaEcXMLConverter.get_dist">
+<code class="descname">get_dist</code><span class="sig-paren">(</span><em>distmap</em>, <em>contribs</em>, <em>defaultdist</em>, <em>protein</em>, <em>groupby=None</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/converter.html#AriaEcXMLConverter.get_dist"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.converter.AriaEcXMLConverter.get_dist" title="Permalink to this definition">¶</a></dt>
+<dd><p>Get target distance from distance map</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>distmap</strong> – </li>
+<li><strong>contribs</strong> – </li>
+<li><strong>defaultdist</strong> – </li>
+<li><strong>protein</strong> – </li>
+<li><strong>groupby</strong> – </li>
+</ul>
+</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="staticmethod">
+<dt id="aria.conbox.converter.AriaEcXMLConverter.neighcontact">
+<em class="property">static </em><code class="descname">neighcontact</code><span class="sig-paren">(</span><em>contact</em>, <em>maxidx</em>, <em>offset=0</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/converter.html#AriaEcXMLConverter.neighcontact"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.converter.AriaEcXMLConverter.neighcontact" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>contact</strong> (<em>tuple object</em>) – </li>
+<li><strong>maxidx</strong> (<em>int</em>) – </li>
+<li><strong>offset</strong> (<em>int</em>) – </li>
+</ul>
+</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="staticmethod">
+<dt id="aria.conbox.converter.AriaEcXMLConverter.neighcontacts">
+<em class="property">static </em><code class="descname">neighcontacts</code><span class="sig-paren">(</span><em>contacts</em>, <em>maxidx</em>, <em>offset=0</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/converter.html#AriaEcXMLConverter.neighcontacts"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.converter.AriaEcXMLConverter.neighcontacts" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>contacts</strong> (<em>list of tuple</em>) – </li>
+<li><strong>maxidx</strong> (<em>int</em>) – Maximum index value in pairs</li>
+<li><strong>offset</strong> (<em>int</em>) – If indexes in pairs start by 0 or 0 + offset</li>
+</ul>
+</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
+<dt id="aria.conbox.converter.AriaEcXMLConverter.run_tbl2xml">
+<code class="descname">run_tbl2xml</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/converter.html#AriaEcXMLConverter.run_tbl2xml"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.converter.AriaEcXMLConverter.run_tbl2xml" title="Permalink to this definition">¶</a></dt>
+<dd><p>Main command to convert tbl file(s) in ARIA XML Format</p>
+</dd></dl>
+
+<dl class="method">
+<dt id="aria.conbox.converter.AriaEcXMLConverter.targetdistmaps">
+<code class="descname">targetdistmaps</code><span class="sig-paren">(</span><em>sequence</em>, <em>distfile=None</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/converter.html#AriaEcXMLConverter.targetdistmaps"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.converter.AriaEcXMLConverter.targetdistmaps" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>distfile</strong> – param groupby: (Default value = None)</li>
+<li><strong>sequence</strong> – </li>
+</ul>
+</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="staticmethod">
+<dt id="aria.conbox.converter.AriaEcXMLConverter.tbl2xml">
+<em class="property">static </em><code class="descname">tbl2xml</code><span class="sig-paren">(</span><em>outdir_path</em>, <em>molecule_path</em>, <em>tbl_paths</em>, <em>list_name</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/converter.html#AriaEcXMLConverter.tbl2xml"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.converter.AriaEcXMLConverter.tbl2xml" title="Permalink to this definition">¶</a></dt>
+<dd><p>Read cns distance restraints in TBL format and convert them into ARIA
+XML format</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>outdir_path</strong> (<em>str</em>) – Path where ARIA XML files are saved</li>
+<li><strong>molecule_path</strong> (<em>str</em>) – Path of molecule file in ARIA XML format</li>
+<li><strong>tbl_paths</strong> (<em>list of str</em>) – List of distance restraints paths</li>
+<li><strong>list_name</strong> (<em>str</em>) – Name of spec in tbl file which will be converted into XML format</li>
+</ul>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first"><strong>xml_paths</strong> – List of distance restraints in ARIA XML format</p>
+</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last">str</p>
+</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
+<dt id="aria.conbox.converter.AriaEcXMLConverter.write_ariaproject">
+<code class="descname">write_ariaproject</code><span class="sig-paren">(</span><em>aria_template</em>, <em>seqfile</em>, <em>dist_files</em>, <em>tbl_files</em>, <em>desclist=None</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/converter.html#AriaEcXMLConverter.write_ariaproject"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.converter.AriaEcXMLConverter.write_ariaproject" title="Permalink to this definition">¶</a></dt>
+<dd><p>Generate ariaproject.xml file</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>aria_template</strong> (<em>str</em>) – ariaproject.xml template path</li>
+<li><strong>seqfile</strong> (<em>str</em>) – path of molecule sequence in SEQ format</li>
+<li><strong>dist_files</strong> (<em>list of str</em>) – List of distance restraint files in ARIA XML format</li>
+<li><strong>tbl_files</strong> (<em>dict</em>) – Distance restraint files in CNS TBL format</li>
+<li><strong>desclist</strong> (<em>list of str</em>) – List of data descriptor for the actual run (Default value = None).</li>
+</ul>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first"></p>
+</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last">None</p>
+</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
+<dt id="aria.conbox.converter.AriaEcXMLConverter.write_map_restraint">
+<code class="descname">write_map_restraint</code><span class="sig-paren">(</span><em>protein</em>, <em>contactmap</em>, <em>nb_c</em>, <em>targetdists</em>, <em>scoremap=None</em>, <em>listname=''</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/converter.html#AriaEcXMLConverter.write_map_restraint"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.converter.AriaEcXMLConverter.write_map_restraint" title="Permalink to this definition">¶</a></dt>
+<dd><p>Translate maplot in ARIA XML restraint</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>protein</strong> – </li>
+<li><strong>listname</strong> – param contactmap: ResAtmMap for a protein (Default value = “â€)</li>
+<li><strong>nb_c</strong> – Number of restraints selected</li>
+<li><strong>targetdists</strong> (<em>dict</em>) – ResAtmMap for each atom for each amino acid</li>
+<li><strong>scoremap</strong> – sorted list of contacts (Default value = None)</li>
+<li><strong>contactmap</strong> – </li>
+</ul>
+</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
+<dt id="aria.conbox.converter.AriaEcXMLConverter.write_maplist_restraints">
+<code class="descname">write_maplist_restraints</code><span class="sig-paren">(</span><em>maplist</em>, <em>targetmaps</em>, <em>protein</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/converter.html#AriaEcXMLConverter.write_maplist_restraints"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.converter.AriaEcXMLConverter.write_maplist_restraints" title="Permalink to this definition">¶</a></dt>
+<dd><p>Generate ARIA XML restraints from maplist</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>maplist</strong> (<em>list of ResAtmMap</em><em> or </em><em>ResMap object</em>) – </li>
+<li><strong>targetmaps</strong> (<em>dict</em>) – </li>
+<li><strong>protein</strong> – </li>
+</ul>
+</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
+<dt id="aria.conbox.converter.AriaEcXMLConverter.write_tbl_restraints">
+<code class="descname">write_tbl_restraints</code><span class="sig-paren">(</span><em>protein</em>, <em>hbmap=None</em>, <em>n_hb=None</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/converter.html#AriaEcXMLConverter.write_tbl_restraints"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.converter.AriaEcXMLConverter.write_tbl_restraints" title="Permalink to this definition">¶</a></dt>
+<dd><p>Write tbl restraints</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>protein</strong> – </li>
+<li><strong>hbmap</strong> – Extra hbond map (eg: metapsicov hbonds) (Default value = None)</li>
+<li><strong>n_hb</strong> – </li>
+</ul>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">{‘hbond’: hb_file, ‘dihed’: dihed_file, ‘ssdist’: ssdist_file}</p>
+</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last">dict</p>
+</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+</dd></dl>
+
+<dl class="class">
+<dt id="aria.conbox.converter.AriaXMLConverter">
+<em class="property">class </em><code class="descclassname">aria.conbox.converter.</code><code class="descname">AriaXMLConverter</code><span class="sig-paren">(</span><em>settings</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/converter.html#AriaXMLConverter"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.converter.AriaXMLConverter" title="Permalink to this definition">¶</a></dt>
+<dd><p>Bases: <code class="xref py py-class docutils literal"><span class="pre">aria.core.conversion.Converter</span></code>, <code class="xref py py-class docutils literal"><span class="pre">object</span></code></p>
+<p>XML converter for aria files</p>
+<dl class="staticmethod">
+<dt id="aria.conbox.converter.AriaXMLConverter.deff">
+<em class="property">static </em><code class="descname">deff</code><span class="sig-paren">(</span><em>atm_dists</em>, <em>dpow=6</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/converter.html#AriaXMLConverter.deff"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.converter.AriaXMLConverter.deff" title="Permalink to this definition">¶</a></dt>
+<dd><p>Compute aria effective distance from input distances</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>atm_dists</strong> (<em>list</em>) – list of atm-atm distances</li>
+<li><strong>dpow</strong> (<em>int</em>) – effective distance exponant (Default value = 6)</li>
+</ul>
+</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="attribute">
+<dt id="aria.conbox.converter.AriaXMLConverter.molecule">
+<code class="descname">molecule</code><a class="headerlink" href="#aria.conbox.converter.AriaXMLConverter.molecule" title="Permalink to this definition">¶</a></dt>
+<dd><p>aria.Molecule.Molecule object or None. If a structure has been loaded,
+use it to update the molecule</p>
+</dd></dl>
+
+<dl class="method">
+<dt id="aria.conbox.converter.AriaXMLConverter.read_pdb">
+<code class="descname">read_pdb</code><span class="sig-paren">(</span><em>pdbpath</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/converter.html#AriaXMLConverter.read_pdb"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.converter.AriaXMLConverter.read_pdb" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>pdbpath</strong> – </td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
+<dt id="aria.conbox.converter.AriaXMLConverter.read_seq">
+<code class="descname">read_seq</code><span class="sig-paren">(</span><em>seqpath</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/converter.html#AriaXMLConverter.read_seq"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.converter.AriaXMLConverter.read_seq" title="Permalink to this definition">¶</a></dt>
+<dd><p>Load aria Molecule object from seq file</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>seqpath</strong> – </td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="staticmethod">
+<dt id="aria.conbox.converter.AriaXMLConverter.upd_mol">
+<em class="property">static </em><code class="descname">upd_mol</code><span class="sig-paren">(</span><em>molecule</em>, <em>structure</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/converter.html#AriaXMLConverter.upd_mol"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.converter.AriaXMLConverter.upd_mol" title="Permalink to this definition">¶</a></dt>
+<dd><p>Update molecule object according to pdb structure</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>molecule</strong> – </li>
+<li><strong>structure</strong> – </li>
+</ul>
+</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="staticmethod">
+<dt id="aria.conbox.converter.AriaXMLConverter.write_dihedral_tbl">
+<em class="property">static </em><code class="descname">write_dihedral_tbl</code><span class="sig-paren">(</span><em>secstructs</em>, <em>outfile</em>, <em>knrj=0.5</em>, <em>exp=2</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/converter.html#AriaXMLConverter.write_dihedral_tbl"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.converter.AriaXMLConverter.write_dihedral_tbl" title="Permalink to this definition">¶</a></dt>
+<dd><p>Build dihedral angle restraints (phi, psi) in tbl format</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>secstructs</strong> – </li>
+<li><strong>outfile</strong> – </li>
+<li><strong>knrj</strong> – (Default value = 0.5)</li>
+<li><strong>exp</strong> – (Default value = 2)</li>
+</ul>
+</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="staticmethod">
+<dt id="aria.conbox.converter.AriaXMLConverter.write_dist_xml">
+<em class="property">static </em><code class="descname">write_dist_xml</code><span class="sig-paren">(</span><em>dist_restraints</em>, <em>outfile</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/converter.html#AriaXMLConverter.write_dist_xml"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.converter.AriaXMLConverter.write_dist_xml" title="Permalink to this definition">¶</a></dt>
+<dd><p>Write aria distance restraint xml file</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>dist_restraints</strong> – </li>
+<li><strong>outfile</strong> – </li>
+</ul>
+</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
+<dt id="aria.conbox.converter.AriaXMLConverter.write_hb_tbl">
+<code class="descname">write_hb_tbl</code><span class="sig-paren">(</span><em>protein</em>, <em>outfile</em>, <em>hbmap=None</em>, <em>dminus=0.0</em>, <em>dplus=0.5</em>, <em>n_hb=None</em>, <em>lr_type='main'</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/converter.html#AriaXMLConverter.write_hb_tbl"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.converter.AriaXMLConverter.write_hb_tbl" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>protein</strong> – param outfile:</li>
+<li><strong>hbmap</strong> – param dminus: (Default value = None)</li>
+<li><strong>dplus</strong> – param n_hb: (Default value = 0.5)</li>
+<li><strong>lr_type</strong> – return: (Default value = ‘main’)</li>
+<li><strong>outfile</strong> – </li>
+<li><strong>dminus</strong> – (Default value = 0.0)</li>
+<li><strong>n_hb</strong> – (Default value = None)</li>
+</ul>
+</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="staticmethod">
+<dt id="aria.conbox.converter.AriaXMLConverter.write_ssdist_tbl">
+<em class="property">static </em><code class="descname">write_ssdist_tbl</code><span class="sig-paren">(</span><em>sec_struct</em>, <em>ss_dist</em>, <em>outfile</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/converter.html#AriaXMLConverter.write_ssdist_tbl"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.converter.AriaXMLConverter.write_ssdist_tbl" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>sec_struct</strong> – </li>
+<li><strong>ss_dist</strong> – </li>
+<li><strong>outfile</strong> – </li>
+</ul>
+</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
+<dt id="aria.conbox.converter.AriaXMLConverter.write_xmlseq">
+<code class="descname">write_xmlseq</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/converter.html#AriaXMLConverter.write_xmlseq"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.converter.AriaXMLConverter.write_xmlseq" title="Permalink to this definition">¶</a></dt>
+<dd><p>Use aria xml pickler to generate xml molecule file</p>
+</dd></dl>
+
+</dd></dl>
+
+</div>
+<div class="section" id="module-aria.conbox.maplot">
+<span id="aria-conbox-maplot-module"></span><h2>aria.conbox.maplot module<a class="headerlink" href="#module-aria.conbox.maplot" title="Permalink to this headline">¶</a></h2>
+<p>Input/Output aria_ec scripts</p>
+<dl class="class">
+<dt id="aria.conbox.maplot.AriaEcContactMap">
+<em class="property">class </em><code class="descclassname">aria.conbox.maplot.</code><code class="descname">AriaEcContactMap</code><span class="sig-paren">(</span><em>settings</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/maplot.html#AriaEcContactMap"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.maplot.AriaEcContactMap" title="Permalink to this definition">¶</a></dt>
+<dd><p>Bases: <code class="xref py py-class docutils literal"><span class="pre">object</span></code></p>
+<p>Contact maplot class</p>
+<dl class="method">
+<dt id="aria.conbox.maplot.AriaEcContactMap.run">
+<code class="descname">run</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/maplot.html#AriaEcContactMap.run"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.maplot.AriaEcContactMap.run" title="Permalink to this definition">¶</a></dt>
+<dd><p>Contact map analysis command</p>
+</dd></dl>
+
+</dd></dl>
+
+</div>
+<div class="section" id="module-aria.conbox.ndconv">
+<span id="aria-conbox-ndconv-module"></span><h2>aria.conbox.ndconv module<a class="headerlink" href="#module-aria.conbox.ndconv" title="Permalink to this headline">¶</a></h2>
+<p>Network deconvolution tool</p>
+<dl class="function">
+<dt id="aria.conbox.ndconv.net_deconv">
+<code class="descclassname">aria.conbox.ndconv.</code><code class="descname">net_deconv</code><span class="sig-paren">(</span><em>npmat</em>, <em>beta=0.99</em>, <em>alpha=1</em>, <em>control=0</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/ndconv.html#net_deconv"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.ndconv.net_deconv" title="Permalink to this definition">¶</a></dt>
+<dd><p>This is a python implementation/translation of network deconvolution by
+MIT-KELLIS LAB</p>
+<blockquote>
+<div><p>LICENSE: MIT-KELLIS LAB</p>
+<dl class="docutils">
+<dt>AUTHORS:</dt>
+<dd>Algorithm was programmed by Soheil Feizi.
+Paper authors are S. Feizi, D. Marbach, M. Medard and M. Kellis</dd>
+</dl>
+</div></blockquote>
+<p>Python implementation: Gideon Rosenthal</p>
+<p class="rubric">References</p>
+<dl class="docutils">
+<dt>For more details, see the following paper:</dt>
+<dd>Network Deconvolution as a General Method to Distinguish
+Direct Dependencies over Networks
+By: Soheil Feizi, Daniel Marbach, Muriel Medard and Manolis Kellis
+Nature Biotechnology</dd>
+</dl>
+<blockquote>
+<div>ND.m: network deconvolution</div></blockquote>
+<p>DESCRIPTION:</p>
+<blockquote>
+<div><dl class="docutils">
+<dt>USAGE:</dt>
+<dd>mat_nd = ND(npmat)
+mat_nd = ND(npmat,beta)
+mat_nd = ND(npmat,beta,alpha,control)</dd>
+</dl>
+</div></blockquote>
+<p>INPUT ARGUMENTS:</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>npmat</strong> – Input matrix, if it is a square matrix, the program assumes
+it is a relevance matrix where npmat(i,j) represents the
+similarity content between nodes i and j. Elements of
+matrix should be non-negative.
+optional parameters:</li>
+<li><strong>beta</strong> – Scaling parameter, the program maps the largest absolute
+eigenvalue of the direct dependency matrix to beta. It
+should be between 0 and 1. (Default value = 0.99)</li>
+<li><strong>alpha</strong> – fraction of edges of the observed dependency matrix to be
+kept in deconvolution process. (Default value = 1)</li>
+<li><strong>control</strong> – if 0, displaying direct weights for observed
+interactions, if 1, displaying direct weights for both
+observed and
+non-observed interactions.
+OUTPUT ARGUMENTS:
+mat_nd Output deconvolved matrix (direct dependency matrix). Its
+components
+represent direct edge weights of observed interactions.
+Choosing top direct interactions (a cut-off) depends on
+the application and
+is not implemented in this code.
+To apply ND on regulatory networks, follow steps explained in
+Supplementary notes
+1.4.1 and 2.1 and 2.3 of the paper.
+In this implementation, input matrices are made symmetric.
+<strong>**********************************************************************</strong>
+loading scaling and thresholding parameters (Default value = 0)</li>
+</ul>
+</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+</div>
+<div class="section" id="module-aria.conbox.pdbdist">
+<span id="aria-conbox-pdbdist-module"></span><h2>aria.conbox.pdbdist module<a class="headerlink" href="#module-aria.conbox.pdbdist" title="Permalink to this headline">¶</a></h2>
+<p>PDB distance distribution generation</p>
+<dl class="class">
+<dt id="aria.conbox.pdbdist.PDBDist">
+<em class="property">class </em><code class="descclassname">aria.conbox.pdbdist.</code><code class="descname">PDBDist</code><span class="sig-paren">(</span><em>settings</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/pdbdist.html#PDBDist"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.pdbdist.PDBDist" title="Permalink to this definition">¶</a></dt>
+<dd><p>Bases: <code class="xref py py-class docutils literal"><span class="pre">object</span></code></p>
+<p>Extract pdb distance distribution from culled list of pdb files provided by
+PICSES server [G. Wang and R. L. Dunbrack, Jr. PISCES: a protein sequence
+culling server. Bioinformatics, 19:1589-1591, 2003.] with Bio.PDB tools
+[Hamelryck, T., Manderick, B. (2003) PDB pdbparser and structure class
+implemented in Python. Bioinformatics 19: 2308–2310]</p>
+<dl class="staticmethod">
+<dt id="aria.conbox.pdbdist.PDBDist.get_proteinblocks">
+<em class="property">static </em><code class="descname">get_proteinblocks</code><span class="sig-paren">(</span><em>pdb</em>, <em>chain</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/pdbdist.html#PDBDist.get_proteinblocks"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.pdbdist.PDBDist.get_proteinblocks" title="Permalink to this definition">¶</a></dt>
+<dd><p>Get Protein Block assignment index for chain with pbxplore</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>pdb</strong> (<em>pdb file path</em>) – </li>
+<li><strong>chain</strong> (<em>str</em>) – </li>
+</ul>
+</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="staticmethod">
+<dt id="aria.conbox.pdbdist.PDBDist.get_secstructs">
+<em class="property">static </em><code class="descname">get_secstructs</code><span class="sig-paren">(</span><em>backbone</em>, <em>dssp_dict</em>, <em>chain</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/pdbdist.html#PDBDist.get_secstructs"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.pdbdist.PDBDist.get_secstructs" title="Permalink to this definition">¶</a></dt>
+<dd><p>Return related secondary structure dictionary for each backbone residue</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>backbone</strong> – List of bacbkone residues</li>
+<li><strong>dssp_dict</strong> – </li>
+<li><strong>chain</strong> – </li>
+</ul>
+</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
+<dt id="aria.conbox.pdbdist.PDBDist.pdbdists">
+<code class="descname">pdbdists</code><span class="sig-paren">(</span><em>pdb</em>, <em>pdbid</em>, <em>chain</em>, <em>pair_list='all'</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/pdbdist.html#PDBDist.pdbdists"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.pdbdist.PDBDist.pdbdists" title="Permalink to this definition">¶</a></dt>
+<dd><p>Get distance matrix from pdb file and write distances into output file</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>pdb</strong> (<em>str</em>) – Path of pdb file</li>
+<li><strong>pdbid</strong> (<em>str</em>) – PDB id</li>
+<li><strong>chain</strong> (<em>str</em>) – Chain id</li>
+<li><strong>pair_list</strong> (<em>{'all'</em><em>, </em><em>'min'</em><em>, </em><em>'heavy'}</em>) – Defining if we generate a distance distribution for a minimal set
+of atom pairs, heavy pairs or all atom pairs (Default value = “allâ€)</li>
+</ul>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first"><strong>dists</strong></p>
+</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">obj:</th><td class="field-body"><cite>list</cite> of :obj: <cite>OrderedDict</cite></td>
+</tr>
+</tbody>
+</table>
+</p>
+</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
+<dt id="aria.conbox.pdbdist.PDBDist.run">
+<code class="descname">run</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/pdbdist.html#PDBDist.run"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.pdbdist.PDBDist.run" title="Permalink to this definition">¶</a></dt>
+<dd><p>main method</p>
+</dd></dl>
+
+</dd></dl>
+
+</div>
+<div class="section" id="module-aria.conbox.pdbqual">
+<span id="aria-conbox-pdbqual-module"></span><h2>aria.conbox.pdbqual module<a class="headerlink" href="#module-aria.conbox.pdbqual" title="Permalink to this headline">¶</a></h2>
+<p>Created on 9/5/16
+@author: fallain</p>
+<p>Derived from qual.py script by Dr. Benjamin Bardiaux</p>
+<dl class="class">
+<dt id="aria.conbox.pdbqual.AriaEcPdbqual">
+<em class="property">class </em><code class="descclassname">aria.conbox.pdbqual.</code><code class="descname">AriaEcPdbqual</code><span class="sig-paren">(</span><em>*args</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/pdbqual.html#AriaEcPdbqual"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.pdbqual.AriaEcPdbqual" title="Permalink to this definition">¶</a></dt>
+<dd><p>Bases: <code class="xref py py-class docutils literal"><span class="pre">aria.conbox.common.CommandProtocol</span></code></p>
+<p>Quality pdb tool</p>
+<dl class="method">
+<dt id="aria.conbox.pdbqual.AriaEcPdbqual.run">
+<code class="descname">run</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/pdbqual.html#AriaEcPdbqual.run"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.pdbqual.AriaEcPdbqual.run" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"></td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+</dd></dl>
+
+</div>
+<div class="section" id="module-aria.conbox.protein">
+<span id="aria-conbox-protein-module"></span><h2>aria.conbox.protein module<a class="headerlink" href="#module-aria.conbox.protein" title="Permalink to this headline">¶</a></h2>
+<p>Secondary structure list</p>
+<dl class="class">
+<dt id="aria.conbox.protein.AminoAcidSequence">
+<em class="property">class </em><code class="descclassname">aria.conbox.protein.</code><code class="descname">AminoAcidSequence</code><span class="sig-paren">(</span><em>topologyfile</em>, <em>*args</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/protein.html#AminoAcidSequence"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.protein.AminoAcidSequence" title="Permalink to this definition">¶</a></dt>
+<dd><p>Bases: <code class="xref py py-class docutils literal"><span class="pre">aria.core.legacy.SequenceList.SequenceList</span></code>, <code class="xref py py-class docutils literal"><span class="pre">object</span></code></p>
+<p>Amino acid sequence</p>
+<dl class="attribute">
+<dt id="aria.conbox.protein.AminoAcidSequence.end_reg">
+<code class="descname">end_reg</code><em class="property"> = <_sre.SRE_Pattern object></em><a class="headerlink" href="#aria.conbox.protein.AminoAcidSequence.end_reg" title="Permalink to this definition">¶</a></dt>
+<dd></dd></dl>
+
+<dl class="attribute">
+<dt id="aria.conbox.protein.AminoAcidSequence.humanidx">
+<code class="descname">humanidx</code><a class="headerlink" href="#aria.conbox.protein.AminoAcidSequence.humanidx" title="Permalink to this definition">¶</a></dt>
+<dd><p><em>return</em></p>
+</dd></dl>
+
+<dl class="method">
+<dt id="aria.conbox.protein.AminoAcidSequence.read">
+<code class="descname">read</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/protein.html#AminoAcidSequence.read"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.protein.AminoAcidSequence.read" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>filename</strong> – return:</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
+<dt id="aria.conbox.protein.AminoAcidSequence.readtopo">
+<code class="descname">readtopo</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/protein.html#AminoAcidSequence.readtopo"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.protein.AminoAcidSequence.readtopo" title="Permalink to this definition">¶</a></dt>
+<dd><p>Parse topology file for amino acids
+:return:</p>
+</dd></dl>
+
+<dl class="attribute">
+<dt id="aria.conbox.protein.AminoAcidSequence.restatement_reg">
+<code class="descname">restatement_reg</code><em class="property"> = {u'dihedral': <_sre.SRE_Pattern object at 0x4ced770>, u'acce': <_sre.SRE_Pattern object>, u'improper': <_sre.SRE_Pattern object at 0x4c62630>, u'atom': <_sre.SRE_Pattern object at 0x4d63060>, u'dono': <_sre.SRE_Pattern object>, u'bond': <_sre.SRE_Pattern object>}</em><a class="headerlink" href="#aria.conbox.protein.AminoAcidSequence.restatement_reg" title="Permalink to this definition">¶</a></dt>
+<dd></dd></dl>
+
+<dl class="attribute">
+<dt id="aria.conbox.protein.AminoAcidSequence.startres_reg">
+<code class="descname">startres_reg</code><em class="property"> = <_sre.SRE_Pattern object></em><a class="headerlink" href="#aria.conbox.protein.AminoAcidSequence.startres_reg" title="Permalink to this definition">¶</a></dt>
+<dd></dd></dl>
+
+<dl class="attribute">
+<dt id="aria.conbox.protein.AminoAcidSequence.topology">
+<code class="descname">topology</code><a class="headerlink" href="#aria.conbox.protein.AminoAcidSequence.topology" title="Permalink to this definition">¶</a></dt>
+<dd><p>Topology dict with 3l code as dict key
+:return:</p>
+</dd></dl>
+
+</dd></dl>
+
+<dl class="class">
+<dt id="aria.conbox.protein.Protein">
+<em class="property">class </em><code class="descclassname">aria.conbox.protein.</code><code class="descname">Protein</code><span class="sig-paren">(</span><em>sett</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/protein.html#Protein"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.protein.Protein" title="Permalink to this definition">¶</a></dt>
+<dd><p>Bases: <code class="xref py py-class docutils literal"><span class="pre">object</span></code></p>
+<p>Protein class</p>
+<dl class="method">
+<dt id="aria.conbox.protein.Protein.set_aa_sequence">
+<code class="descname">set_aa_sequence</code><span class="sig-paren">(</span><em>filename</em>, <em>ssidx=False</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/protein.html#Protein.set_aa_sequence"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.protein.Protein.set_aa_sequence" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>filename</strong> – param ssidx:</li>
+<li><strong>ssidx</strong> – (Default value = False)</li>
+</ul>
+</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
+<dt id="aria.conbox.protein.Protein.set_sec_struct">
+<code class="descname">set_sec_struct</code><span class="sig-paren">(</span><em>filename</em>, <em>ssdist_filename=u''</em>, <em>ssidx=False</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/protein.html#Protein.set_sec_struct"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.protein.Protein.set_sec_struct" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>filename</strong> – param ssdist_filename:</li>
+<li><strong>ssidx</strong> – return: (Default value = False)</li>
+<li><strong>ssdist_filename</strong> – (Default value = ‘’)</li>
+</ul>
+</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="staticmethod">
+<dt id="aria.conbox.protein.Protein.sync_index">
+<em class="property">static </em><code class="descname">sync_index</code><span class="sig-paren">(</span><em>index1</em>, <em>index2</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/protein.html#Protein.sync_index"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.protein.Protein.sync_index" title="Permalink to this definition">¶</a></dt>
+<dd><p>Return humanidx with upper min from existing humanidx</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>index1</strong> – param index2:</li>
+<li><strong>index2</strong> – </li>
+</ul>
+</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="attribute">
+<dt id="aria.conbox.protein.Protein.topology">
+<code class="descname">topology</code><a class="headerlink" href="#aria.conbox.protein.Protein.topology" title="Permalink to this definition">¶</a></dt>
+<dd><p><em>return</em></p>
+</dd></dl>
+
+<dl class="method">
+<dt id="aria.conbox.protein.Protein.write_seq">
+<code class="descname">write_seq</code><span class="sig-paren">(</span><em>outfile</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/protein.html#Protein.write_seq"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.protein.Protein.write_seq" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>outfile</strong> – return:</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+</dd></dl>
+
+<dl class="class">
+<dt id="aria.conbox.protein.SsList">
+<em class="property">class </em><code class="descclassname">aria.conbox.protein.</code><code class="descname">SsList</code><span class="sig-paren">(</span><em>sett</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/protein.html#SsList"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.protein.SsList" title="Permalink to this definition">¶</a></dt>
+<dd><p>Bases: <code class="xref py py-class docutils literal"><span class="pre">object</span></code></p>
+<p>Reader for secondary prediction structure files</p>
+<dl class="method">
+<dt id="aria.conbox.protein.SsList.check_filetype">
+<code class="descname">check_filetype</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/protein.html#SsList.check_filetype"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.protein.SsList.check_filetype" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>filename</strong> – return:</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="attribute">
+<dt id="aria.conbox.protein.SsList.index">
+<code class="descname">index</code><a class="headerlink" href="#aria.conbox.protein.SsList.index" title="Permalink to this definition">¶</a></dt>
+<dd><p><em>return</em></p>
+</dd></dl>
+
+<dl class="attribute">
+<dt id="aria.conbox.protein.SsList.indxplus_reg">
+<code class="descname">indxplus_reg</code><em class="property"> = <_sre.SRE_Pattern object at 0x4d527b0></em><a class="headerlink" href="#aria.conbox.protein.SsList.indxplus_reg" title="Permalink to this definition">¶</a></dt>
+<dd></dd></dl>
+
+<dl class="attribute">
+<dt id="aria.conbox.protein.SsList.psipred2_reg">
+<code class="descname">psipred2_reg</code><em class="property"> = <_sre.SRE_Pattern object></em><a class="headerlink" href="#aria.conbox.protein.SsList.psipred2_reg" title="Permalink to this definition">¶</a></dt>
+<dd></dd></dl>
+
+<dl class="attribute">
+<dt id="aria.conbox.protein.SsList.psipred3_reg">
+<code class="descname">psipred3_reg</code><em class="property"> = <_sre.SRE_Pattern object at 0x4d52fd0></em><a class="headerlink" href="#aria.conbox.protein.SsList.psipred3_reg" title="Permalink to this definition">¶</a></dt>
+<dd></dd></dl>
+
+<dl class="attribute">
+<dt id="aria.conbox.protein.SsList.psipred_reg">
+<code class="descname">psipred_reg</code><em class="property"> = <_sre.SRE_Pattern object></em><a class="headerlink" href="#aria.conbox.protein.SsList.psipred_reg" title="Permalink to this definition">¶</a></dt>
+<dd></dd></dl>
+
+<dl class="method">
+<dt id="aria.conbox.protein.SsList.read">
+<code class="descname">read</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/protein.html#SsList.read"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.protein.SsList.read" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>filename</strong> – return:</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
+<dt id="aria.conbox.protein.SsList.read_indextableplus">
+<code class="descname">read_indextableplus</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/protein.html#SsList.read_indextableplus"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.protein.SsList.read_indextableplus" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>filename</strong> – return:</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
+<dt id="aria.conbox.protein.SsList.read_psipred">
+<code class="descname">read_psipred</code><span class="sig-paren">(</span><em>filename</em>, <em>ss2=False</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/protein.html#SsList.read_psipred"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.protein.SsList.read_psipred" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>filename</strong> – </td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
+<dt id="aria.conbox.protein.SsList.read_ssdist">
+<code class="descname">read_ssdist</code><span class="sig-paren">(</span><em>ssdistpath=None</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/protein.html#SsList.read_ssdist"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.protein.SsList.read_ssdist" title="Permalink to this definition">¶</a></dt>
+<dd><p>Read average dist file generated using PDB</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>ssdistpath</strong> – return: (Default value = None)</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
+<dt id="aria.conbox.protein.SsList.seq_sublist">
+<code class="descname">seq_sublist</code><span class="sig-paren">(</span><em>sequence</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/protein.html#SsList.seq_sublist"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.protein.SsList.seq_sublist" title="Permalink to this definition">¶</a></dt>
+<dd><p>Check and adjust sslist with given sequence</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>sequence</strong> – input amino acid sequence (one letter format)</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="attribute">
+<dt id="aria.conbox.protein.SsList.sequence">
+<code class="descname">sequence</code><a class="headerlink" href="#aria.conbox.protein.SsList.sequence" title="Permalink to this definition">¶</a></dt>
+<dd></dd></dl>
+
+<dl class="attribute">
+<dt id="aria.conbox.protein.SsList.ss_dist_reg">
+<code class="descname">ss_dist_reg</code><em class="property"> = <_sre.SRE_Pattern object></em><a class="headerlink" href="#aria.conbox.protein.SsList.ss_dist_reg" title="Permalink to this definition">¶</a></dt>
+<dd></dd></dl>
+
+<dl class="method">
+<dt id="aria.conbox.protein.SsList.write_ssfasta">
+<code class="descname">write_ssfasta</code><span class="sig-paren">(</span><em>filename</em>, <em>desc=u'pdbid'</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/protein.html#SsList.write_ssfasta"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.protein.SsList.write_ssfasta" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>filename</strong> – param desc:</li>
+<li><strong>desc</strong> – (Default value = “pdbidâ€)</li>
+</ul>
+</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+</dd></dl>
+
+</div>
+<div class="section" id="module-aria.conbox.protmap">
+<span id="aria-conbox-protmap-module"></span><h2>aria.conbox.protmap module<a class="headerlink" href="#module-aria.conbox.protmap" title="Permalink to this headline">¶</a></h2>
+<p>ARIA Evolutionary Constraints Tools</p>
+<dl class="class">
+<dt id="aria.conbox.protmap.AaAtmMap">
+<em class="property">class </em><code class="descclassname">aria.conbox.protmap.</code><code class="descname">AaAtmMap</code><span class="sig-paren">(</span><em>*args</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/protmap.html#AaAtmMap"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.protmap.AaAtmMap" title="Permalink to this definition">¶</a></dt>
+<dd><p>Bases: <a class="reference internal" href="#aria.conbox.protmap.AaMap" title="aria.conbox.protmap.AaMap"><code class="xref py py-class docutils literal"><span class="pre">aria.conbox.protmap.AaMap</span></code></a></p>
+<p>Amino acid map with atom levels</p>
+<dl class="method">
+<dt id="aria.conbox.protmap.AaAtmMap.contact_map">
+<code class="descname">contact_map</code><span class="sig-paren">(</span><em>contactdef</em>, <em>scsc_min=None</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/protmap.html#AaAtmMap.contact_map"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.protmap.AaAtmMap.contact_map" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>contactdef</strong> – </li>
+<li><strong>scsc_min</strong> – </li>
+</ul>
+</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
+<dt id="aria.conbox.protmap.AaAtmMap.copy">
+<code class="descname">copy</code><span class="sig-paren">(</span><em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/protmap.html#AaAtmMap.copy"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.protmap.AaAtmMap.copy" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>kwargs</strong> – </li>
+<li><strong>**kwargs</strong> – </li>
+</ul>
+</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
+<dt id="aria.conbox.protmap.AaAtmMap.create_heatmap">
+<code class="descname">create_heatmap</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/protmap.html#AaAtmMap.create_heatmap"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.protmap.AaAtmMap.create_heatmap" title="Permalink to this definition">¶</a></dt>
+<dd></dd></dl>
+
+<dl class="method">
+<dt id="aria.conbox.protmap.AaAtmMap.create_index">
+<code class="descname">create_index</code><span class="sig-paren">(</span><em>sequence</em>, <em>atom_types='min'</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/protmap.html#AaAtmMap.create_index"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.protmap.AaAtmMap.create_index" title="Permalink to this definition">¶</a></dt>
+<dd><p>Update Aa index with atoms</p>
+</dd></dl>
+
+</dd></dl>
+
+<dl class="class">
+<dt id="aria.conbox.protmap.AaMap">
+<em class="property">class </em><code class="descclassname">aria.conbox.protmap.</code><code class="descname">AaMap</code><span class="sig-paren">(</span><em>*args</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/protmap.html#AaMap"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.protmap.AaMap" title="Permalink to this definition">¶</a></dt>
+<dd><p>Bases: <a class="reference internal" href="#aria.conbox.protmap.ProteinMap" title="aria.conbox.protmap.ProteinMap"><code class="xref py py-class docutils literal"><span class="pre">aria.conbox.protmap.ProteinMap</span></code></a></p>
+<p>Amino Acid Distance Matrix</p>
+<dl class="method">
+<dt id="aria.conbox.protmap.AaMap.contact_map">
+<code class="descname">contact_map</code><span class="sig-paren">(</span><em>contactdef</em>, <em>scsc_min=None</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/protmap.html#AaMap.contact_map"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.protmap.AaMap.contact_map" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>contactdef</strong> – </li>
+<li><strong>scsc_min</strong> – </li>
+</ul>
+</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
+<dt id="aria.conbox.protmap.AaMap.copy">
+<code class="descname">copy</code><span class="sig-paren">(</span><em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/protmap.html#AaMap.copy"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.protmap.AaMap.copy" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>kwargs</strong> – </li>
+<li><strong>**kwargs</strong> – </li>
+</ul>
+</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
+<dt id="aria.conbox.protmap.AaMap.create_heatmap">
+<code class="descname">create_heatmap</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/protmap.html#AaMap.create_heatmap"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.protmap.AaMap.create_heatmap" title="Permalink to this definition">¶</a></dt>
+<dd></dd></dl>
+
+<dl class="method">
+<dt id="aria.conbox.protmap.AaMap.create_index">
+<code class="descname">create_index</code><span class="sig-paren">(</span><em>sequence</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/protmap.html#AaMap.create_index"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.protmap.AaMap.create_index" title="Permalink to this definition">¶</a></dt>
+<dd></dd></dl>
+
+<dl class="method">
+<dt id="aria.conbox.protmap.AaMap.reduce">
+<code class="descname">reduce</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/protmap.html#AaMap.reduce"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.protmap.AaMap.reduce" title="Permalink to this definition">¶</a></dt>
+<dd><p>Reduce level of the contactmap</p>
+</dd></dl>
+
+<dl class="attribute">
+<dt id="aria.conbox.protmap.AaMap.sequence">
+<code class="descname">sequence</code><a class="headerlink" href="#aria.conbox.protmap.AaMap.sequence" title="Permalink to this definition">¶</a></dt>
+<dd><p>returns: String containing all amino acid 1L code
+:rtype: str</p>
+</dd></dl>
+
+</dd></dl>
+
+<dl class="class">
+<dt id="aria.conbox.protmap.AtmMap">
+<em class="property">class </em><code class="descclassname">aria.conbox.protmap.</code><code class="descname">AtmMap</code><span class="sig-paren">(</span><em>*args</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/protmap.html#AtmMap"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.protmap.AtmMap" title="Permalink to this definition">¶</a></dt>
+<dd><p>Bases: <a class="reference internal" href="#aria.conbox.protmap.Map" title="aria.conbox.protmap.Map"><code class="xref py py-class docutils literal"><span class="pre">aria.conbox.protmap.Map</span></code></a></p>
+<p>Atom Distance Matrix</p>
+<dl class="method">
+<dt id="aria.conbox.protmap.AtmMap.copy">
+<code class="descname">copy</code><span class="sig-paren">(</span><em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/protmap.html#AtmMap.copy"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.protmap.AtmMap.copy" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>kwargs</strong> – </li>
+<li><strong>**kwargs</strong> – </li>
+</ul>
+</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
+<dt id="aria.conbox.protmap.AtmMap.create_index">
+<code class="descname">create_index</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/protmap.html#AtmMap.create_index"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.protmap.AtmMap.create_index" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"></td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
+<dt id="aria.conbox.protmap.AtmMap.reduce">
+<code class="descname">reduce</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/protmap.html#AtmMap.reduce"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.protmap.AtmMap.reduce" title="Permalink to this definition">¶</a></dt>
+<dd><p>Reduce level of the contactmap</p>
+</dd></dl>
+
+</dd></dl>
+
+<dl class="class">
+<dt id="aria.conbox.protmap.Map">
+<em class="property">class </em><code class="descclassname">aria.conbox.protmap.</code><code class="descname">Map</code><span class="sig-paren">(</span><em>index=None</em>, <em>columns=None</em>, <em>mtype='distance'</em>, <em>duplicate_levels=False</em>, <em>data=None</em>, <em>dtype=None</em>, <em>sym=True</em>, <em>desc=''</em>, <em>path=''</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/protmap.html#Map"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.protmap.Map" title="Permalink to this definition">¶</a></dt>
+<dd><p>Bases: <code class="xref py py-class docutils literal"><span class="pre">pandas.core.frame.DataFrame</span></code></p>
+<p>Distance/contact matrix</p>
+<dl class="method">
+<dt id="aria.conbox.protmap.Map.check_type">
+<code class="descname">check_type</code><span class="sig-paren">(</span><em>mtype</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/protmap.html#Map.check_type"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.protmap.Map.check_type" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>mtype</strong> – return:</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
+<dt id="aria.conbox.protmap.Map.copy">
+<code class="descname">copy</code><span class="sig-paren">(</span><em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/protmap.html#Map.copy"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.protmap.Map.copy" title="Permalink to this definition">¶</a></dt>
+<dd><p>Copy the current map</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>**kwargs</strong> – </td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="attribute">
+<dt id="aria.conbox.protmap.Map.mtype_choices">
+<code class="descname">mtype_choices</code><em class="property"> = {'distance': <type 'float'>, 'contact': <type 'bool'>, 'score': <type 'float'>}</em><a class="headerlink" href="#aria.conbox.protmap.Map.mtype_choices" title="Permalink to this definition">¶</a></dt>
+<dd></dd></dl>
+
+<dl class="method">
+<dt id="aria.conbox.protmap.Map.reduce">
+<code class="descname">reduce</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/protmap.html#Map.reduce"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.protmap.Map.reduce" title="Permalink to this definition">¶</a></dt>
+<dd><p>Low complexcity dataframe</p>
+</dd></dl>
+
+<dl class="method">
+<dt id="aria.conbox.protmap.Map.remove">
+<code class="descname">remove</code><span class="sig-paren">(</span><em>rm_list</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/protmap.html#Map.remove"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.protmap.Map.remove" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>rm_list</strong> – </td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
+<dt id="aria.conbox.protmap.Map.set_value">
+<code class="descname">set_value</code><span class="sig-paren">(</span><em>index</em>, <em>col</em>, <em>value</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/protmap.html#Map.set_value"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.protmap.Map.set_value" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>index</strong> – param col:</li>
+<li><strong>value</strong> – param kwargs:</li>
+<li><strong>col</strong> – </li>
+<li><strong>**kwargs</strong> – </li>
+</ul>
+</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
+<dt id="aria.conbox.protmap.Map.sortedset">
+<code class="descname">sortedset</code><span class="sig-paren">(</span><em>human_idx=False</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/protmap.html#Map.sortedset"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.protmap.Map.sortedset" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>human_idx</strong> – (Default value = False)</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
+<dt id="aria.conbox.protmap.Map.subfill">
+<code class="descname">subfill</code><span class="sig-paren">(</span><em>pairdict</em>, <em>level=0</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/protmap.html#Map.subfill"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.protmap.Map.subfill" title="Permalink to this definition">¶</a></dt>
+<dd><p>Fill map with dict giving</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>pairdict</strong> – param level:</li>
+<li><strong>level</strong> – (Default value = 0)</li>
+</ul>
+</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
+<dt id="aria.conbox.protmap.Map.to_series">
+<code class="descname">to_series</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/protmap.html#Map.to_series"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.protmap.Map.to_series" title="Permalink to this definition">¶</a></dt>
+<dd><p>Return panda series related to lower triangle values</p>
+</dd></dl>
+
+<dl class="method">
+<dt id="aria.conbox.protmap.Map.topmap">
+<code class="descname">topmap</code><span class="sig-paren">(</span><em>scoremap</em>, <em>nb_topcontact</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/protmap.html#Map.topmap"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.protmap.Map.topmap" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>scoremap</strong> – param nb_topcontact:</li>
+<li><strong>nb_topcontact</strong> – </li>
+</ul>
+</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
+<dt id="aria.conbox.protmap.Map.update">
+<code class="descname">update</code><span class="sig-paren">(</span><em>*args</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/protmap.html#Map.update"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.protmap.Map.update" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>args</strong> – param kwargs:</li>
+<li><strong>*args</strong> – </li>
+<li><strong>**kwargs</strong> – </li>
+</ul>
+</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+</dd></dl>
+
+<dl class="class">
+<dt id="aria.conbox.protmap.MapFilter">
+<em class="property">class </em><code class="descclassname">aria.conbox.protmap.</code><code class="descname">MapFilter</code><span class="sig-paren">(</span><em>settings</em>, <em>nofilter=False</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/protmap.html#MapFilter"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.protmap.MapFilter" title="Permalink to this definition">¶</a></dt>
+<dd><p>Bases: <code class="xref py py-class docutils literal"><span class="pre">object</span></code></p>
+<dl class="docutils">
+<dt>Filter maplot/distancemap</dt>
+<dd>nd : Network deconvolution
+pos : remove close contacts
+cons : remove contacts with highly conservated residues
+cys-cys : unicity of ss contacts
+ssclash : secondary structure conflict</dd>
+</dl>
+<dl class="attribute">
+<dt id="aria.conbox.protmap.MapFilter.clash_dict">
+<code class="descname">clash_dict</code><em class="property"> = {'cys': {'clash': '222', 'desc': 'disulfide bond unicity'}, 'cons': {'clash': '888', 'desc': 'high conservation'}, 'pos': {'clash': 'physical proximity', 'desc': 'sequence position'}, 'ssclash': {'clash': '999', 'desc': 'secondary structure prediction conflict'}}</em><a class="headerlink" href="#aria.conbox.protmap.MapFilter.clash_dict" title="Permalink to this definition">¶</a></dt>
+<dd></dd></dl>
+
+<dl class="method">
+<dt id="aria.conbox.protmap.MapFilter.cons_filter">
+<code class="descname">cons_filter</code><span class="sig-paren">(</span><em>mapdict</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/protmap.html#MapFilter.cons_filter"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.protmap.MapFilter.cons_filter" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>mapdict</strong> – </li>
+<li><strong>**kwargs</strong> – </li>
+</ul>
+</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="staticmethod">
+<dt id="aria.conbox.protmap.MapFilter.cys_filter">
+<em class="property">static </em><code class="descname">cys_filter</code><span class="sig-paren">(</span><em>mapdict</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/protmap.html#MapFilter.cys_filter"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.protmap.MapFilter.cys_filter" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>mapdict</strong> – </li>
+<li><strong>**kwargs</strong> – </li>
+</ul>
+</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="attribute">
+<dt id="aria.conbox.protmap.MapFilter.filter_types">
+<code class="descname">filter_types</code><em class="property"> = ('pos', 'cons', 'ssclash', 'cys')</em><a class="headerlink" href="#aria.conbox.protmap.MapFilter.filter_types" title="Permalink to this definition">¶</a></dt>
+<dd></dd></dl>
+
+<dl class="method">
+<dt id="aria.conbox.protmap.MapFilter.nd_filter">
+<code class="descname">nd_filter</code><span class="sig-paren">(</span><em>mapdict</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/protmap.html#MapFilter.nd_filter"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.protmap.MapFilter.nd_filter" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>mapdict</strong> – </td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
+<dt id="aria.conbox.protmap.MapFilter.pos_filter">
+<code class="descname">pos_filter</code><span class="sig-paren">(</span><em>mapdict</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/protmap.html#MapFilter.pos_filter"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.protmap.MapFilter.pos_filter" title="Permalink to this definition">¶</a></dt>
+<dd><p>Position filter on maplot</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>kwargs</strong> – param mapdict: dict with maplot key</li>
+<li><strong>mapdict</strong> – </li>
+<li><strong>**kwargs</strong> – </li>
+</ul>
+</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="staticmethod">
+<dt id="aria.conbox.protmap.MapFilter.ssclash_filter">
+<em class="property">static </em><code class="descname">ssclash_filter</code><span class="sig-paren">(</span><em>mapdict</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/protmap.html#MapFilter.ssclash_filter"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.protmap.MapFilter.ssclash_filter" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>mapdict</strong> – param kwargs:</li>
+<li><strong>**kwargs</strong> – </li>
+</ul>
+</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="staticmethod">
+<dt id="aria.conbox.protmap.MapFilter.write_filtout">
+<em class="property">static </em><code class="descname">write_filtout</code><span class="sig-paren">(</span><em>clash_dict</em>, <em>desc_dict</em>, <em>contactlist</em>, <em>outdir=''</em>, <em>outprefix='protein'</em>, <em>clashlist=None</em>, <em>human_idx=True</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/protmap.html#MapFilter.write_filtout"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.protmap.MapFilter.write_filtout" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>clash_dict</strong> – </li>
+<li><strong>desc_dict</strong> – </li>
+<li><strong>contactlist</strong> – </li>
+<li><strong>outdir</strong> – (Default value = “â€)</li>
+<li><strong>outprefix</strong> – (Default value = “proteinâ€)</li>
+<li><strong>clashlist</strong> – (Default value = None)</li>
+<li><strong>human_idx</strong> – (Default value = True)</li>
+</ul>
+</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+</dd></dl>
+
+<dl class="class">
+<dt id="aria.conbox.protmap.ProtMapCollection">
+<em class="property">class </em><code class="descclassname">aria.conbox.protmap.</code><code class="descname">ProtMapCollection</code><span class="sig-paren">(</span><em>settings</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/protmap.html#ProtMapCollection"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.protmap.ProtMapCollection" title="Permalink to this definition">¶</a></dt>
+<dd><p>Bases: <code class="xref py py-class docutils literal"><span class="pre">object</span></code></p>
+<p>Group all protein maps</p>
+<dl class="attribute">
+<dt id="aria.conbox.protmap.ProtMapCollection.allcontactmap">
+<code class="descname">allcontactmap</code><a class="headerlink" href="#aria.conbox.protmap.ProtMapCollection.allcontactmap" title="Permalink to this definition">¶</a></dt>
+<dd><p>Atom level contact map. If alldistmap exists, return the maplot
+form
+:return:</p>
+</dd></dl>
+
+<dl class="attribute">
+<dt id="aria.conbox.protmap.ProtMapCollection.alldistmap">
+<code class="descname">alldistmap</code><a class="headerlink" href="#aria.conbox.protmap.ProtMapCollection.alldistmap" title="Permalink to this definition">¶</a></dt>
+<dd><p>Atom level distance map.
+:return:</p>
+</dd></dl>
+
+<dl class="attribute">
+<dt id="aria.conbox.protmap.ProtMapCollection.allscoremap">
+<code class="descname">allscoremap</code><a class="headerlink" href="#aria.conbox.protmap.ProtMapCollection.allscoremap" title="Permalink to this definition">¶</a></dt>
+<dd><p>Atom level score map
+:return:</p>
+</dd></dl>
+
+<dl class="attribute">
+<dt id="aria.conbox.protmap.ProtMapCollection.distmap">
+<code class="descname">distmap</code><a class="headerlink" href="#aria.conbox.protmap.ProtMapCollection.distmap" title="Permalink to this definition">¶</a></dt>
+<dd><p><em>return</em></p>
+</dd></dl>
+
+</dd></dl>
+
+<dl class="class">
+<dt id="aria.conbox.protmap.ProteinMap">
+<em class="property">class </em><code class="descclassname">aria.conbox.protmap.</code><code class="descname">ProteinMap</code><span class="sig-paren">(</span><em>sequence</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/protmap.html#ProteinMap"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.protmap.ProteinMap" title="Permalink to this definition">¶</a></dt>
+<dd><p>Bases: <a class="reference internal" href="#aria.conbox.protmap.Map" title="aria.conbox.protmap.Map"><code class="xref py py-class docutils literal"><span class="pre">aria.conbox.protmap.Map</span></code></a></p>
+<p>Abstract class for protein contact map objects</p>
+<dl class="attribute">
+<dt id="aria.conbox.protmap.ProteinMap.all_reg">
+<code class="descname">all_reg</code><em class="property"> = <_sre.SRE_Pattern object></em><a class="headerlink" href="#aria.conbox.protmap.ProteinMap.all_reg" title="Permalink to this definition">¶</a></dt>
+<dd></dd></dl>
+
+<dl class="staticmethod">
+<dt id="aria.conbox.protmap.ProteinMap.classification_metrics">
+<em class="property">static </em><code class="descname">classification_metrics</code><span class="sig-paren">(</span><em>y_true</em>, <em>y_pred</em>, <em>y_scores=None</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/protmap.html#ProteinMap.classification_metrics"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.protmap.ProteinMap.classification_metrics" title="Permalink to this definition">¶</a></dt>
+<dd><p>Compute classification metrics</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>y_true</strong> (<em>numpy array of true values</em>) – </li>
+<li><strong>y_pred</strong> (<em>numpy array of predicted values</em>) – </li>
+<li><strong>y_scores</strong> (<em>numpy array of prediction scores</em>) – (Default value = None)</li>
+</ul>
+</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
+<dt id="aria.conbox.protmap.ProteinMap.compare_contactmap">
+<code class="descname">compare_contactmap</code><span class="sig-paren">(</span><em>cmpmap</em>, <em>contactlist</em>, <em>outprefix</em>, <em>outdir=''</em>, <em>distmap=None</em>, <em>human_idx=True</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/protmap.html#ProteinMap.compare_contactmap"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.protmap.ProteinMap.compare_contactmap" title="Permalink to this definition">¶</a></dt>
+<dd><p>Compare 2 contact map and plot differences</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>cmpmap</strong> – param contactlist:</li>
+<li><strong>outprefix</strong> – param outdir:</li>
+<li><strong>distmap</strong> – param human_idx: (Default value = None)</li>
+<li><strong>contactlist</strong> – </li>
+<li><strong>outdir</strong> – (Default value = “â€)</li>
+<li><strong>human_idx</strong> – (Default value = True)</li>
+</ul>
+</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
+<dt id="aria.conbox.protmap.ProteinMap.compareplot">
+<code class="descname">compareplot</code><span class="sig-paren">(</span><em>protmap</em>, <em>save_fig=True</em>, <em>alpha=None</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/protmap.html#ProteinMap.compareplot"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.protmap.ProteinMap.compareplot" title="Permalink to this definition">¶</a></dt>
+<dd><p>Compare 2 contact map and plot differences</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>protmap</strong> – param save_fig:</li>
+<li><strong>alpha</strong> – param kwargs: (Default value = None)</li>
+<li><strong>save_fig</strong> – (Default value = True)</li>
+<li><strong>**kwargs</strong> – </li>
+</ul>
+</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
+<dt id="aria.conbox.protmap.ProteinMap.contact_list">
+<code class="descname">contact_list</code><span class="sig-paren">(</span><em>human_idx=False</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/protmap.html#ProteinMap.contact_list"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.protmap.ProteinMap.contact_list" title="Permalink to this definition">¶</a></dt>
+<dd><p>Return contact list</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>human_idx</strong> – return: (Default value = False)</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"></td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body">list</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
+<dt id="aria.conbox.protmap.ProteinMap.contact_map">
+<code class="descname">contact_map</code><span class="sig-paren">(</span><em>contactdef</em>, <em>scsc_min=None</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/protmap.html#ProteinMap.contact_map"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.protmap.ProteinMap.contact_map" title="Permalink to this definition">¶</a></dt>
+<dd><p>Generate contact map</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>contactdef</strong> – param scsc_min:</li>
+<li><strong>scsc_min</strong> – (Default value = None)</li>
+</ul>
+</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
+<dt id="aria.conbox.protmap.ProteinMap.contactset">
+<code class="descname">contactset</code><span class="sig-paren">(</span><em>human_idx=False</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/protmap.html#ProteinMap.contactset"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.protmap.ProteinMap.contactset" title="Permalink to this definition">¶</a></dt>
+<dd><p>Remove duplicate in contact_list</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>human_idx</strong> – return: (Default value = False)</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"></td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body">list</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
+<dt id="aria.conbox.protmap.ProteinMap.copy">
+<code class="descname">copy</code><span class="sig-paren">(</span><em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/protmap.html#ProteinMap.copy"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.protmap.ProteinMap.copy" title="Permalink to this definition">¶</a></dt>
+<dd><p>Copy dataframe and related attributes of the map</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>**kwargs</strong> – </td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
+<dt id="aria.conbox.protmap.ProteinMap.create_heatmap">
+<code class="descname">create_heatmap</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/protmap.html#ProteinMap.create_heatmap"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.protmap.ProteinMap.create_heatmap" title="Permalink to this definition">¶</a></dt>
+<dd><p>Generate heatmap</p>
+</dd></dl>
+
+<dl class="method">
+<dt id="aria.conbox.protmap.ProteinMap.create_index">
+<code class="descname">create_index</code><span class="sig-paren">(</span><em>sequence</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/protmap.html#ProteinMap.create_index"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.protmap.ProteinMap.create_index" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>sequence</strong> – </li>
+<li><strong>kwargs</strong> – </li>
+</ul>
+</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="attribute">
+<dt id="aria.conbox.protmap.ProteinMap.distance_method">
+<code class="descname">distance_method</code><em class="property"> = 'euclidean'</em><a class="headerlink" href="#aria.conbox.protmap.ProteinMap.distance_method" title="Permalink to this definition">¶</a></dt>
+<dd></dd></dl>
+
+<dl class="attribute">
+<dt id="aria.conbox.protmap.ProteinMap.heavy_reg">
+<code class="descname">heavy_reg</code><em class="property"> = <_sre.SRE_Pattern object></em><a class="headerlink" href="#aria.conbox.protmap.ProteinMap.heavy_reg" title="Permalink to this definition">¶</a></dt>
+<dd></dd></dl>
+
+<dl class="attribute">
+<dt id="aria.conbox.protmap.ProteinMap.maplot">
+<code class="descname">maplot</code><a class="headerlink" href="#aria.conbox.protmap.ProteinMap.maplot" title="Permalink to this definition">¶</a></dt>
+<dd><p>Contact map plot
+:return:</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>linewidths</strong> – (Default value = 0.0)</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
+<dt id="aria.conbox.protmap.ProteinMap.plotflush">
+<code class="descname">plotflush</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/protmap.html#ProteinMap.plotflush"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.protmap.ProteinMap.plotflush" title="Permalink to this definition">¶</a></dt>
+<dd><p>Flush contact map plot</p>
+</dd></dl>
+
+<dl class="method">
+<dt id="aria.conbox.protmap.ProteinMap.reduce">
+<code class="descname">reduce</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/protmap.html#ProteinMap.reduce"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.protmap.ProteinMap.reduce" title="Permalink to this definition">¶</a></dt>
+<dd><p>Lower index level if multi index</p>
+</dd></dl>
+
+<dl class="method">
+<dt id="aria.conbox.protmap.ProteinMap.report">
+<code class="descname">report</code><span class="sig-paren">(</span><em>cmpmap</em>, <em>scoremap=None</em>, <em>outprefix=''</em>, <em>outdir=''</em>, <em>plotdir=''</em>, <em>plot_ext='pdf'</em>, <em>plotag=True</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/protmap.html#ProteinMap.report"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.protmap.ProteinMap.report" title="Permalink to this definition">¶</a></dt>
+<dd><p>Generate contact map report file</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>cmpmap</strong> – </li>
+<li><strong>scoremap</strong> – (Default value = None)</li>
+<li><strong>outprefix</strong> – (Default value = “â€)</li>
+<li><strong>outdir</strong> – (Default value = “â€)</li>
+<li><strong>plotdir</strong> – (Default value = “â€)</li>
+<li><strong>plot_ext</strong> – (Default value = “pdfâ€)</li>
+<li><strong>plotag</strong> – (Default value = True)</li>
+</ul>
+</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
+<dt id="aria.conbox.protmap.ProteinMap.saveplot">
+<code class="descname">saveplot</code><span class="sig-paren">(</span><em>outdir=''</em>, <em>outprefix='protein'</em>, <em>size_fig=10</em>, <em>plot_ext='pdf'</em>, <em>plot_dpi=200</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/protmap.html#ProteinMap.saveplot"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.protmap.ProteinMap.saveplot" title="Permalink to this definition">¶</a></dt>
+<dd><p>Save plot</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>outdir</strong> – param outprefix: (Default value = ‘’)</li>
+<li><strong>size_fig</strong> – param plot_ext: (Default value = 10)</li>
+<li><strong>plot_dpi</strong> – (Default value = 200)</li>
+<li><strong>outprefix</strong> – (Default value = “proteinâ€)</li>
+<li><strong>plot_ext</strong> – (Default value = “pdfâ€)</li>
+</ul>
+</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="attribute">
+<dt id="aria.conbox.protmap.ProteinMap.sequence">
+<code class="descname">sequence</code><a class="headerlink" href="#aria.conbox.protmap.ProteinMap.sequence" title="Permalink to this definition">¶</a></dt>
+<dd><p>Specific sequence related to the map in a string
+:returns:
+:rtype: str</p>
+</dd></dl>
+
+<dl class="method">
+<dt id="aria.conbox.protmap.ProteinMap.write_contacts">
+<code class="descname">write_contacts</code><span class="sig-paren">(</span><em>filename</em>, <em>outdir=''</em>, <em>prefix=''</em>, <em>human_idx=True</em>, <em>scoremap=None</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/protmap.html#ProteinMap.write_contacts"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.protmap.ProteinMap.write_contacts" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>prefix</strong> – </li>
+<li><strong>filename</strong> – param outdir:</li>
+<li><strong>human_idx</strong> – param scoremap: (Default value = True)</li>
+<li><strong>outdir</strong> – (Default value = “â€)</li>
+<li><strong>scoremap</strong> – (Default value = None)</li>
+</ul>
+</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+</dd></dl>
+
+<dl class="class">
+<dt id="aria.conbox.protmap.ResAtmMap">
+<em class="property">class </em><code class="descclassname">aria.conbox.protmap.</code><code class="descname">ResAtmMap</code><span class="sig-paren">(</span><em>sequence</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/protmap.html#ResAtmMap"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.protmap.ResAtmMap" title="Permalink to this definition">¶</a></dt>
+<dd><p>Bases: <a class="reference internal" href="#aria.conbox.protmap.ProteinMap" title="aria.conbox.protmap.ProteinMap"><code class="xref py py-class docutils literal"><span class="pre">aria.conbox.protmap.ProteinMap</span></code></a></p>
+<p>Protein distance/contact matrix for all atom pairs. If no sequence given,
+protein distance/contact matrix for all amino acids
+Ex:
+residue PHE1 atom CD1 CD2 CB CA CG CZ
+residue atom
+PHE1 CD1 0.000000 2.394145 2.455440 3.269219 1.391024 2.421148</p>
+<blockquote>
+<div>CD2 2.394145 0.000000 2.509243 3.407996 1.379875 2.401098
+CB 2.455440 2.509243 0.000000 1.507025 1.478053 4.267602
+CA 3.269219 3.407996 1.507025 0.000000 2.505414 5.085997
+CG 1.391024 1.379875 1.478053 2.505414 0.000000 2.790403</div></blockquote>
+<dl class="method">
+<dt id="aria.conbox.protmap.ResAtmMap.contact_map">
+<code class="descname">contact_map</code><span class="sig-paren">(</span><em>contactdef</em>, <em>scsc_min=None</em>, <em>def_cut=5.0</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/protmap.html#ResAtmMap.contact_map"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.protmap.ResAtmMap.contact_map" title="Permalink to this definition">¶</a></dt>
+<dd><p>Contact map generator from all atoms distance map. There’s a contact
+with 2 residues iff dist between 2 atoms are below the given treshold</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>def_cut</strong> – (Default value = 5.0)</li>
+<li><strong>contactdef</strong> – for all atom pair</li>
+<li><strong>scsc_min</strong> – (Default value = None)</li>
+</ul>
+</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
+<dt id="aria.conbox.protmap.ResAtmMap.copy">
+<code class="descname">copy</code><span class="sig-paren">(</span><em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/protmap.html#ResAtmMap.copy"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.protmap.ResAtmMap.copy" title="Permalink to this definition">¶</a></dt>
+<dd><p>Copy dataframe and related attributes of the map</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>**kwargs</strong> – </td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
+<dt id="aria.conbox.protmap.ResAtmMap.create_heatmap">
+<code class="descname">create_heatmap</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/protmap.html#ResAtmMap.create_heatmap"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.protmap.ResAtmMap.create_heatmap" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"></td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
+<dt id="aria.conbox.protmap.ResAtmMap.create_index">
+<code class="descname">create_index</code><span class="sig-paren">(</span><em>sequence</em>, <em>seq_pos=True</em>, <em>seqidx=None</em>, <em>idxnames=None</em>, <em>colnames=None</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/protmap.html#ResAtmMap.create_index"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.protmap.ResAtmMap.create_index" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>sequence</strong> – </li>
+<li><strong>seq_pos</strong> – </li>
+<li><strong>seqidx</strong> (<em>pandas.MultiIndex</em><em>, </em><em>optional</em>) – </li>
+<li><strong>idxnames</strong> – </li>
+<li><strong>colnames</strong> – </li>
+</ul>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first"></p>
+</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last">tuple of pandas.MultiIndex objects</p>
+</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
+<dt id="aria.conbox.protmap.ResAtmMap.reduce">
+<code class="descname">reduce</code><span class="sig-paren">(</span><em>groupby='min'</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/protmap.html#ResAtmMap.reduce"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.protmap.ResAtmMap.reduce" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>groupby</strong> – return: (Default value = “minâ€)</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="attribute">
+<dt id="aria.conbox.protmap.ResAtmMap.sequence">
+<code class="descname">sequence</code><a class="headerlink" href="#aria.conbox.protmap.ResAtmMap.sequence" title="Permalink to this definition">¶</a></dt>
+<dd><p>Amino Acid sequence string in humanidx</p>
+</dd></dl>
+
+</dd></dl>
+
+<dl class="class">
+<dt id="aria.conbox.protmap.ResMap">
+<em class="property">class </em><code class="descclassname">aria.conbox.protmap.</code><code class="descname">ResMap</code><span class="sig-paren">(</span><em>sequence</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/protmap.html#ResMap"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.protmap.ResMap" title="Permalink to this definition">¶</a></dt>
+<dd><p>Bases: <a class="reference internal" href="#aria.conbox.protmap.ResAtmMap" title="aria.conbox.protmap.ResAtmMap"><code class="xref py py-class docutils literal"><span class="pre">aria.conbox.protmap.ResAtmMap</span></code></a></p>
+<p>Res - res distance/contact matrix</p>
+<dl class="method">
+<dt id="aria.conbox.protmap.ResMap.contact_map">
+<code class="descname">contact_map</code><span class="sig-paren">(</span><em>contactdef</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/protmap.html#ResMap.contact_map"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.protmap.ResMap.contact_map" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>contactdef</strong> – param kwargs:</li>
+<li><strong>**kwargs</strong> – </li>
+</ul>
+</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
+<dt id="aria.conbox.protmap.ResMap.copy">
+<code class="descname">copy</code><span class="sig-paren">(</span><em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/protmap.html#ResMap.copy"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.protmap.ResMap.copy" title="Permalink to this definition">¶</a></dt>
+<dd><p>Copy dataframe and related attributes of the map</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>**kwargs</strong> – </td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
+<dt id="aria.conbox.protmap.ResMap.create_heatmap">
+<code class="descname">create_heatmap</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/protmap.html#ResMap.create_heatmap"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.protmap.ResMap.create_heatmap" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"></td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
+<dt id="aria.conbox.protmap.ResMap.create_index">
+<code class="descname">create_index</code><span class="sig-paren">(</span><em>sequence</em>, <em>seqidx=None</em>, <em>idxnames=None</em>, <em>colnames=None</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/protmap.html#ResMap.create_index"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.protmap.ResMap.create_index" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>sequence</strong> – </li>
+<li><strong>seqidx</strong> (<em>pandas.Index</em>) – </li>
+<li><strong>idxnames</strong> – </li>
+<li><strong>colnames</strong> – </li>
+<li><strong>kwargs</strong> – </li>
+</ul>
+</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="attribute">
+<dt id="aria.conbox.protmap.ResMap.sequence">
+<code class="descname">sequence</code><a class="headerlink" href="#aria.conbox.protmap.ResMap.sequence" title="Permalink to this definition">¶</a></dt>
+<dd><p>Amino Acid sequence string in humanidx</p>
+</dd></dl>
+
+</dd></dl>
+
+<dl class="class">
+<dt id="aria.conbox.protmap.SsAaAtmMap">
+<em class="property">class </em><code class="descclassname">aria.conbox.protmap.</code><code class="descname">SsAaAtmMap</code><span class="sig-paren">(</span><em>*args</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/protmap.html#SsAaAtmMap"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.protmap.SsAaAtmMap" title="Permalink to this definition">¶</a></dt>
+<dd><p>Bases: <a class="reference internal" href="#aria.conbox.protmap.AaAtmMap" title="aria.conbox.protmap.AaAtmMap"><code class="xref py py-class docutils literal"><span class="pre">aria.conbox.protmap.AaAtmMap</span></code></a></p>
+<p>Amino acid map with atom and secondary structure levels</p>
+<dl class="method">
+<dt id="aria.conbox.protmap.SsAaAtmMap.contact_map">
+<code class="descname">contact_map</code><span class="sig-paren">(</span><em>contactdef</em>, <em>scsc_min=None</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/protmap.html#SsAaAtmMap.contact_map"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.protmap.SsAaAtmMap.contact_map" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>contactdef</strong> – </li>
+<li><strong>scsc_min</strong> – </li>
+</ul>
+</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
+<dt id="aria.conbox.protmap.SsAaAtmMap.copy">
+<code class="descname">copy</code><span class="sig-paren">(</span><em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/protmap.html#SsAaAtmMap.copy"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.protmap.SsAaAtmMap.copy" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>kwargs</strong> – </li>
+<li><strong>**kwargs</strong> – </li>
+</ul>
+</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
+<dt id="aria.conbox.protmap.SsAaAtmMap.create_heatmap">
+<code class="descname">create_heatmap</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/protmap.html#SsAaAtmMap.create_heatmap"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.protmap.SsAaAtmMap.create_heatmap" title="Permalink to this definition">¶</a></dt>
+<dd></dd></dl>
+
+<dl class="method">
+<dt id="aria.conbox.protmap.SsAaAtmMap.create_index">
+<code class="descname">create_index</code><span class="sig-paren">(</span><em>sequence</em>, <em>atom_types='min'</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/protmap.html#SsAaAtmMap.create_index"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.protmap.SsAaAtmMap.create_index" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>atom_types</strong> – </li>
+<li><strong>sequence</strong> – </li>
+<li><strong>kwargs</strong> – </li>
+</ul>
+</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
+<dt id="aria.conbox.protmap.SsAaAtmMap.reduce">
+<code class="descname">reduce</code><span class="sig-paren">(</span><em>groupby='min'</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/protmap.html#SsAaAtmMap.reduce"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.protmap.SsAaAtmMap.reduce" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>groupby</strong> – return: (Default value = “minâ€)</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="attribute">
+<dt id="aria.conbox.protmap.SsAaAtmMap.ss_types">
+<code class="descname">ss_types</code><em class="property"> = ('H', 'E', 'X')</em><a class="headerlink" href="#aria.conbox.protmap.SsAaAtmMap.ss_types" title="Permalink to this definition">¶</a></dt>
+<dd></dd></dl>
+
+</dd></dl>
+
+</div>
+<div class="section" id="module-aria.conbox.reader">
+<span id="aria-conbox-reader-module"></span><h2>aria.conbox.reader module<a class="headerlink" href="#module-aria.conbox.reader" title="Permalink to this headline">¶</a></h2>
+<p>Reader objects</p>
+<dl class="class">
+<dt id="aria.conbox.reader.Atom">
+<em class="property">class </em><code class="descclassname">aria.conbox.reader.</code><code class="descname">Atom</code><span class="sig-paren">(</span><em>name</em>, <em>coords</em><span class="sig-paren">)</span><a class="headerlink" href="#aria.conbox.reader.Atom" title="Permalink to this definition">¶</a></dt>
+<dd><p>Bases: <code class="xref py py-class docutils literal"><span class="pre">tuple</span></code></p>
+<dl class="attribute">
+<dt id="aria.conbox.reader.Atom.coords">
+<code class="descname">coords</code><a class="headerlink" href="#aria.conbox.reader.Atom.coords" title="Permalink to this definition">¶</a></dt>
+<dd><p>Alias for field number 1</p>
+</dd></dl>
+
+<dl class="attribute">
+<dt id="aria.conbox.reader.Atom.name">
+<code class="descname">name</code><a class="headerlink" href="#aria.conbox.reader.Atom.name" title="Permalink to this definition">¶</a></dt>
+<dd><p>Alias for field number 0</p>
+</dd></dl>
+
+</dd></dl>
+
+<dl class="class">
+<dt id="aria.conbox.reader.ContactMapFile">
+<em class="property">class </em><code class="descclassname">aria.conbox.reader.</code><code class="descname">ContactMapFile</code><span class="sig-paren">(</span><em>filepath</em>, <em>filetype</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/reader.html#ContactMapFile"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.reader.ContactMapFile" title="Permalink to this definition">¶</a></dt>
+<dd><p>Bases: <a class="reference internal" href="#aria.conbox.reader.MapFile" title="aria.conbox.reader.MapFile"><code class="xref py py-class docutils literal"><span class="pre">aria.conbox.reader.MapFile</span></code></a></p>
+<p>Contact map file</p>
+<dl class="method">
+<dt id="aria.conbox.reader.ContactMapFile.create_map">
+<code class="descname">create_map</code><span class="sig-paren">(</span><em>protein</em>, <em>*args</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/reader.html#ContactMapFile.create_map"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.reader.ContactMapFile.create_map" title="Permalink to this definition">¶</a></dt>
+<dd><p>Initialize and fill Res - Res maps based on contactlist</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>protein</strong> – </li>
+<li><strong>args</strong> – </li>
+<li><strong>kwargs</strong> – </li>
+<li><strong>*args</strong> – </li>
+<li><strong>**kwargs</strong> – </li>
+</ul>
+</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
+<dt id="aria.conbox.reader.ContactMapFile.update_map">
+<code class="descname">update_map</code><span class="sig-paren">(</span><em>resmap</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/reader.html#ContactMapFile.update_map"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.reader.ContactMapFile.update_map" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>resmap</strong> – return:</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+</dd></dl>
+
+<dl class="class">
+<dt id="aria.conbox.reader.CulledPdbFile">
+<em class="property">class </em><code class="descclassname">aria.conbox.reader.</code><code class="descname">CulledPdbFile</code><span class="sig-paren">(</span><em>*args</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/reader.html#CulledPdbFile"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.reader.CulledPdbFile" title="Permalink to this definition">¶</a></dt>
+<dd><p>Bases: <a class="reference internal" href="#aria.conbox.reader.RegexFile" title="aria.conbox.reader.RegexFile"><code class="xref py py-class docutils literal"><span class="pre">aria.conbox.reader.RegexFile</span></code></a></p>
+<p>Reader class for culled pdb list</p>
+<dl class="attribute">
+<dt id="aria.conbox.reader.CulledPdbFile.default">
+<code class="descname">default</code><em class="property"> = 'data/cullpdb/160427/cullpdb_pc25_res1.6_R0.25_d160427_chains3743'</em><a class="headerlink" href="#aria.conbox.reader.CulledPdbFile.default" title="Permalink to this definition">¶</a></dt>
+<dd></dd></dl>
+
+<dl class="attribute">
+<dt id="aria.conbox.reader.CulledPdbFile.filetype">
+<code class="descname">filetype</code><em class="property"> = 'cullpdb'</em><a class="headerlink" href="#aria.conbox.reader.CulledPdbFile.filetype" title="Permalink to this definition">¶</a></dt>
+<dd></dd></dl>
+
+<dl class="attribute">
+<dt id="aria.conbox.reader.CulledPdbFile.regex">
+<code class="descname">regex</code><em class="property"> = <_sre.SRE_Pattern object at 0x4d7b8a0></em><a class="headerlink" href="#aria.conbox.reader.CulledPdbFile.regex" title="Permalink to this definition">¶</a></dt>
+<dd></dd></dl>
+
+</dd></dl>
+
+<dl class="class">
+<dt id="aria.conbox.reader.DistanceMapFile">
+<em class="property">class </em><code class="descclassname">aria.conbox.reader.</code><code class="descname">DistanceMapFile</code><span class="sig-paren">(</span><em>filepath</em>, <em>filetype</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/reader.html#DistanceMapFile"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.reader.DistanceMapFile" title="Permalink to this definition">¶</a></dt>
+<dd><p>Bases: <a class="reference internal" href="#aria.conbox.reader.MapFile" title="aria.conbox.reader.MapFile"><code class="xref py py-class docutils literal"><span class="pre">aria.conbox.reader.MapFile</span></code></a></p>
+<p>Distance matrix file</p>
+<dl class="method">
+<dt id="aria.conbox.reader.DistanceMapFile.create_map">
+<code class="descname">create_map</code><span class="sig-paren">(</span><em>aa_seq</em>, <em>contactdef</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/reader.html#DistanceMapFile.create_map"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.reader.DistanceMapFile.create_map" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>aa_seq</strong> – param contactdef:</li>
+<li><strong>kwargs</strong> – return:</li>
+<li><strong>contactdef</strong> – </li>
+<li><strong>**kwargs</strong> – </li>
+</ul>
+</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
+<dt id="aria.conbox.reader.DistanceMapFile.update_map">
+<code class="descname">update_map</code><span class="sig-paren">(</span><em>resmap</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/reader.html#DistanceMapFile.update_map"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.reader.DistanceMapFile.update_map" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>resmap</strong> – return:</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+</dd></dl>
+
+<dl class="class">
+<dt id="aria.conbox.reader.MapFile">
+<em class="property">class </em><code class="descclassname">aria.conbox.reader.</code><code class="descname">MapFile</code><span class="sig-paren">(</span><em>*args</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/reader.html#MapFile"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.reader.MapFile" title="Permalink to this definition">¶</a></dt>
+<dd><p>Bases: <a class="reference internal" href="#aria.conbox.reader.RegexFile" title="aria.conbox.reader.RegexFile"><code class="xref py py-class docutils literal"><span class="pre">aria.conbox.reader.RegexFile</span></code></a></p>
+<p>Abstract class related to all kind of protein maps</p>
+<dl class="method">
+<dt id="aria.conbox.reader.MapFile.check_maptype">
+<code class="descname">check_maptype</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/reader.html#MapFile.check_maptype"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.reader.MapFile.check_maptype" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"></td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="attribute">
+<dt id="aria.conbox.reader.MapFile.check_type">
+<code class="descname">check_type</code><em class="property"> = True</em><a class="headerlink" href="#aria.conbox.reader.MapFile.check_type" title="Permalink to this definition">¶</a></dt>
+<dd></dd></dl>
+
+<dl class="method">
+<dt id="aria.conbox.reader.MapFile.create_map">
+<code class="descname">create_map</code><span class="sig-paren">(</span><em>protein</em>, <em>contactdef</em>, <em>flaglist=None</em>, <em>offset=0</em>, <em>sym=True</em>, <em>path=''</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/reader.html#MapFile.create_map"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.reader.MapFile.create_map" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>path</strong> – param protein: (Default value = “â€)</li>
+<li><strong>contactdef</strong> – param flaglist:</li>
+<li><strong>offset</strong> – param sym: (Default value = 0)</li>
+<li><strong>kwargs</strong> – return:</li>
+<li><strong>protein</strong> – </li>
+<li><strong>flaglist</strong> – (Default value = None)</li>
+<li><strong>sym</strong> – (Default value = True)</li>
+<li><strong>**kwargs</strong> – </li>
+</ul>
+</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
+<dt id="aria.conbox.reader.MapFile.read">
+<code class="descname">read</code><span class="sig-paren">(</span><em>protein</em>, <em>contactdef=5.0</em>, <em>groupby_method='min'</em>, <em>scsc=None</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/reader.html#MapFile.read"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.reader.MapFile.read" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>protein</strong> – param contactdef: (Default value = None)</li>
+<li><strong>groupby_method</strong> – param scsc: (Default value = “minâ€)</li>
+<li><strong>contactdef</strong> – (Default value = 5.0)</li>
+<li><strong>scsc</strong> – (Default value = None)</li>
+</ul>
+</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="attribute">
+<dt id="aria.conbox.reader.MapFile.types">
+<code class="descname">types</code><em class="property"> = {'pconsc1': {'regex': <_sre.SRE_Pattern object>, 'score_field': 'ec_score'}, 'pconsc2': {'regex': <_sre.SRE_Pattern object>, 'score_field': 'ec_score'}, 'plmc': {'regex': <_sre.SRE_Pattern object at 0x4d72420>, 'score_field': 'plm_score'}, 'metapsicovhb': {'regex': <_sre.SRE_Pattern object at 0x4d7ec70>, 'score_field': 'hbscore'}, 'evfold': {'regex': <_sre.SRE_Pattern object at 0x4d74780>, 'score_field': 'ec_score'}, 'native': {'regex': <_sre.SRE_Pattern object at 0x4d7d8d0>, 'score_field': None}, 'psicov': {'regex': <_sre.SRE_Pattern object at 0x4d75410>, 'score_field': 'ec_score'}, 'metapsicov_stg1': {'regex': <_sre.SRE_Pattern object at 0x4d75410>, 'score_field': 'ec_score'}, 'metapsicov_stg2': {'regex': <_sre.SRE_Pattern object at 0x4d75410>, 'score_field': 'ec_score'}, 'empty': {'regex': <_sre.SRE_Pattern object>, 'score_field': None}, 'gremlin': {'regex': <_sre.SRE_Pattern object at 0x4d7de60>, 'score_field': 'scale_score'}, 'bbcontacts': {'regex': <_sre.SRE_Pattern object at 0x4d7f140>, 'score_field': None}, 'default_4': {'regex': <_sre.SRE_Pattern object>, 'score_field': None}, 'default_3': {'regex': <_sre.SRE_Pattern object at 0x4d76640>, 'score_field': None}, 'default_2': {'regex': <_sre.SRE_Pattern object>, 'score_field': 'score'}, 'default_1': {'regex': <_sre.SRE_Pattern object at 0x4d74500>, 'score_field': 'score'}, 'plm': {'regex': <_sre.SRE_Pattern object at 0x4d72420>, 'score_field': 'plm_score'}, 'pconsc': {'regex': <_sre.SRE_Pattern object>, 'score_field': 'ec_score'}, 'plmdca': {'regex': <_sre.SRE_Pattern object at 0x4d72420>, 'score_field': 'plm_score'}, 'native_full': {'regex': <_sre.SRE_Pattern object at 0x4d7d8d0>, 'score_field': None}, 'contactlist': {'regex': <_sre.SRE_Pattern object>, 'score_field': None}, 'plmev': {'regex': <_sre.SRE_Pattern object at 0x4d72420>, 'score_field': 'plm_score'}}</em><a class="headerlink" href="#aria.conbox.reader.MapFile.types" title="Permalink to this definition">¶</a></dt>
+<dd></dd></dl>
+
+<dl class="method">
+<dt id="aria.conbox.reader.MapFile.update_map">
+<code class="descname">update_map</code><span class="sig-paren">(</span><em>resmap</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/reader.html#MapFile.update_map"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.reader.MapFile.update_map" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>resmap</strong> – return:</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+</dd></dl>
+
+<dl class="class">
+<dt id="aria.conbox.reader.MapFileListReader">
+<em class="property">class </em><code class="descclassname">aria.conbox.reader.</code><code class="descname">MapFileListReader</code><span class="sig-paren">(</span><em>cont_def=5.0</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/reader.html#MapFileListReader"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.reader.MapFileListReader" title="Permalink to this definition">¶</a></dt>
+<dd><p>Bases: <code class="xref py py-class docutils literal"><span class="pre">object</span></code></p>
+<p>Reader class for Map files</p>
+<dl class="method">
+<dt id="aria.conbox.reader.MapFileListReader.clear">
+<code class="descname">clear</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/reader.html#MapFileListReader.clear"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.reader.MapFileListReader.clear" title="Permalink to this definition">¶</a></dt>
+<dd><p>Initiatize object from scratch object</p>
+</dd></dl>
+
+<dl class="method">
+<dt id="aria.conbox.reader.MapFileListReader.read">
+<code class="descname">read</code><span class="sig-paren">(</span><em>maps</em>, <em>maptypes=None</em>, <em>protein=None</em>, <em>scsc=None</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/reader.html#MapFileListReader.read"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.reader.MapFileListReader.read" title="Permalink to this definition">¶</a></dt>
+<dd><p>Read contact map files. The generated maps will be accessible in
+<cite>self.maps</cite></p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>maps</strong> – List of Map file paths</li>
+<li><strong>maptypes</strong> – List of Map file types (Default value = None)</li>
+<li><strong>protein</strong> (<em>ariaec.protein.Protein object</em><em> or </em><em>None</em><em>, </em><em>optional</em>) – (Default value = None)</li>
+<li><strong>scsc</strong> (<em>dict</em><em>, </em><em>optional</em>) – Optional dictionary used for Atom Map reduction by selecting only
+one atom in the side chain. (Default value = None)</li>
+<li><strong>kwargs</strong> – Optional arguments used for MapFile readers</li>
+<li><strong>**kwargs</strong> – </li>
+</ul>
+</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+</dd></dl>
+
+<dl class="class">
+<dt id="aria.conbox.reader.PDBFile">
+<em class="property">class </em><code class="descclassname">aria.conbox.reader.</code><code class="descname">PDBFile</code><span class="sig-paren">(</span><em>*args</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/reader.html#PDBFile"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.reader.PDBFile" title="Permalink to this definition">¶</a></dt>
+<dd><p>Bases: <a class="reference internal" href="#aria.conbox.reader.MapFile" title="aria.conbox.reader.MapFile"><code class="xref py py-class docutils literal"><span class="pre">aria.conbox.reader.MapFile</span></code></a></p>
+<p>PDB file</p>
+<dl class="method">
+<dt id="aria.conbox.reader.PDBFile.create_map">
+<code class="descname">create_map</code><span class="sig-paren">(</span><em>protein</em>, <em>contactdef</em>, <em>groupby_method='min'</em>, <em>scsc=None</em>, <em>flaglist=None</em>, <em>sym=True</em>, <em>path=''</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/reader.html#PDBFile.create_map"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.reader.PDBFile.create_map" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>protein</strong> – </li>
+<li><strong>contactdef</strong> – </li>
+<li><strong>groupby_method</strong> – (Default value = “minâ€)</li>
+<li><strong>scsc</strong> – (Default value = None)</li>
+<li><strong>flaglist</strong> – (Default value = None)</li>
+<li><strong>sym</strong> – (Default value = True)</li>
+<li><strong>path</strong> – (Default value = “â€)</li>
+</ul>
+</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="attribute">
+<dt id="aria.conbox.reader.PDBFile.pdbreg">
+<code class="descname">pdbreg</code><em class="property"> = <_sre.SRE_Pattern object at 0x4d817b0></em><a class="headerlink" href="#aria.conbox.reader.PDBFile.pdbreg" title="Permalink to this definition">¶</a></dt>
+<dd></dd></dl>
+
+<dl class="method">
+<dt id="aria.conbox.reader.PDBFile.update_map">
+<code class="descname">update_map</code><span class="sig-paren">(</span><em>resmap</em>, <em>sym=True</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/reader.html#PDBFile.update_map"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.reader.PDBFile.update_map" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>resmap</strong> – param sym:</li>
+<li><strong>sym</strong> – (Default value = True)</li>
+</ul>
+</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+</dd></dl>
+
+<dl class="class">
+<dt id="aria.conbox.reader.RegexFile">
+<em class="property">class </em><code class="descclassname">aria.conbox.reader.</code><code class="descname">RegexFile</code><span class="sig-paren">(</span><em>filepath</em>, <em>filetype=''</em>, <em>regex=''</em>, <em>sort=''</em>, <em>default=''</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/reader.html#RegexFile"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.reader.RegexFile" title="Permalink to this definition">¶</a></dt>
+<dd><p>Bases: <code class="xref py py-class docutils literal"><span class="pre">object</span></code></p>
+<p>File which can be parsed with a regex</p>
+<dl class="attribute">
+<dt id="aria.conbox.reader.RegexFile.filename">
+<code class="descname">filename</code><a class="headerlink" href="#aria.conbox.reader.RegexFile.filename" title="Permalink to this definition">¶</a></dt>
+<dd><p>Get basename of filepath</p>
+</dd></dl>
+
+<dl class="attribute">
+<dt id="aria.conbox.reader.RegexFile.filepath">
+<code class="descname">filepath</code><a class="headerlink" href="#aria.conbox.reader.RegexFile.filepath" title="Permalink to this definition">¶</a></dt>
+<dd><p>File path</p>
+</dd></dl>
+
+<dl class="method">
+<dt id="aria.conbox.reader.RegexFile.load">
+<code class="descname">load</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/reader.html#RegexFile.load"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.reader.RegexFile.load" title="Permalink to this definition">¶</a></dt>
+<dd><p>Fill lines with dictionary. Each key is a line number in the given file
+:return: None</p>
+</dd></dl>
+
+</dd></dl>
+
+<dl class="class">
+<dt id="aria.conbox.reader.TblDistFile">
+<em class="property">class </em><code class="descclassname">aria.conbox.reader.</code><code class="descname">TblDistFile</code><span class="sig-paren">(</span><em>*args</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/reader.html#TblDistFile"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.reader.TblDistFile" title="Permalink to this definition">¶</a></dt>
+<dd><p>Bases: <a class="reference internal" href="#aria.conbox.reader.RegexFile" title="aria.conbox.reader.RegexFile"><code class="xref py py-class docutils literal"><span class="pre">aria.conbox.reader.RegexFile</span></code></a></p>
+<p>Reader class for TBL Distance restraint file</p>
+<dl class="attribute">
+<dt id="aria.conbox.reader.TblDistFile.filetype">
+<code class="descname">filetype</code><em class="property"> = 'tbldist'</em><a class="headerlink" href="#aria.conbox.reader.TblDistFile.filetype" title="Permalink to this definition">¶</a></dt>
+<dd></dd></dl>
+
+<dl class="attribute">
+<dt id="aria.conbox.reader.TblDistFile.regex">
+<code class="descname">regex</code><em class="property"> = <_sre.SRE_Pattern object at 0x4d7c8b0></em><a class="headerlink" href="#aria.conbox.reader.TblDistFile.regex" title="Permalink to this definition">¶</a></dt>
+<dd></dd></dl>
+
+</dd></dl>
+
+</div>
+<div class="section" id="module-aria.conbox.settings">
+<span id="aria-conbox-settings-module"></span><h2>aria.conbox.settings module<a class="headerlink" href="#module-aria.conbox.settings" title="Permalink to this headline">¶</a></h2>
+<p>Settings section</p>
+<dl class="class">
+<dt id="aria.conbox.settings.AriaEcSettings">
+<em class="property">class </em><code class="descclassname">aria.conbox.settings.</code><code class="descname">AriaEcSettings</code><span class="sig-paren">(</span><em>name</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/settings.html#AriaEcSettings"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.settings.AriaEcSettings" title="Permalink to this definition">¶</a></dt>
+<dd><p>Bases: <a class="reference internal" href="#aria.conbox.settings.Settings" title="aria.conbox.settings.Settings"><code class="xref py py-class docutils literal"><span class="pre">aria.conbox.settings.Settings</span></code></a></p>
+<p>Settings object for ariaec
+@DynamicAttrs</p>
+<dl class="attribute">
+<dt id="aria.conbox.settings.AriaEcSettings.ARIAPROJ_TEMPLATE">
+<code class="descname">ARIAPROJ_TEMPLATE</code><em class="property"> = 'templates/aria_project_v2.3.0.xml'</em><a class="headerlink" href="#aria.conbox.settings.AriaEcSettings.ARIAPROJ_TEMPLATE" title="Permalink to this definition">¶</a></dt>
+<dd></dd></dl>
+
+<dl class="attribute">
+<dt id="aria.conbox.settings.AriaEcSettings.INTERLOWERBOUNDS">
+<code class="descname">INTERLOWERBOUNDS</code><em class="property"> = 'data/pdbdists/lowerbounds.inter.p'</em><a class="headerlink" href="#aria.conbox.settings.AriaEcSettings.INTERLOWERBOUNDS" title="Permalink to this definition">¶</a></dt>
+<dd></dd></dl>
+
+<dl class="attribute">
+<dt id="aria.conbox.settings.AriaEcSettings.INTERTARGET">
+<code class="descname">INTERTARGET</code><em class="property"> = 'data/pdbdists/targetdists.inter.p'</em><a class="headerlink" href="#aria.conbox.settings.AriaEcSettings.INTERTARGET" title="Permalink to this definition">¶</a></dt>
+<dd></dd></dl>
+
+<dl class="attribute">
+<dt id="aria.conbox.settings.AriaEcSettings.INTERUPPERBOUNDS">
+<code class="descname">INTERUPPERBOUNDS</code><em class="property"> = 'data/pdbdists/upperbounds.inter.p'</em><a class="headerlink" href="#aria.conbox.settings.AriaEcSettings.INTERUPPERBOUNDS" title="Permalink to this definition">¶</a></dt>
+<dd></dd></dl>
+
+<dl class="attribute">
+<dt id="aria.conbox.settings.AriaEcSettings.INTRALOWERBOUNDS">
+<code class="descname">INTRALOWERBOUNDS</code><em class="property"> = 'data/pdbdists/lowerbounds.intra.p'</em><a class="headerlink" href="#aria.conbox.settings.AriaEcSettings.INTRALOWERBOUNDS" title="Permalink to this definition">¶</a></dt>
+<dd></dd></dl>
+
+<dl class="attribute">
+<dt id="aria.conbox.settings.AriaEcSettings.INTRATARGET">
+<code class="descname">INTRATARGET</code><em class="property"> = 'data/pdbdists/targetdists.intra.p'</em><a class="headerlink" href="#aria.conbox.settings.AriaEcSettings.INTRATARGET" title="Permalink to this definition">¶</a></dt>
+<dd></dd></dl>
+
+<dl class="attribute">
+<dt id="aria.conbox.settings.AriaEcSettings.INTRAUPPERBOUNDS">
+<code class="descname">INTRAUPPERBOUNDS</code><em class="property"> = 'data/pdbdists/upperbounds.intra.p'</em><a class="headerlink" href="#aria.conbox.settings.AriaEcSettings.INTRAUPPERBOUNDS" title="Permalink to this definition">¶</a></dt>
+<dd></dd></dl>
+
+<dl class="attribute">
+<dt id="aria.conbox.settings.AriaEcSettings.SCSC_MIN">
+<code class="descname">SCSC_MIN</code><em class="property"> = 'data/scsc_min.p'</em><a class="headerlink" href="#aria.conbox.settings.AriaEcSettings.SCSC_MIN" title="Permalink to this definition">¶</a></dt>
+<dd></dd></dl>
+
+<dl class="attribute">
+<dt id="aria.conbox.settings.AriaEcSettings.SECTIONS">
+<code class="descname">SECTIONS</code><em class="property"> = ('main', 'setup', 'maplot', 'bbconv', 'contactdef', 'pdbqual', 'pdbdist', 'analysis', 'tbl2xml', 'pdbstat')</em><a class="headerlink" href="#aria.conbox.settings.AriaEcSettings.SECTIONS" title="Permalink to this definition">¶</a></dt>
+<dd></dd></dl>
+
+<dl class="attribute">
+<dt id="aria.conbox.settings.AriaEcSettings.SS_DIST">
+<code class="descname">SS_DIST</code><em class="property"> = 'data/ss_dist.txt'</em><a class="headerlink" href="#aria.conbox.settings.AriaEcSettings.SS_DIST" title="Permalink to this definition">¶</a></dt>
+<dd></dd></dl>
+
+<dl class="attribute">
+<dt id="aria.conbox.settings.AriaEcSettings.TOPO">
+<code class="descname">TOPO</code><em class="property"> = 'data/topallhdg5.3.pro'</em><a class="headerlink" href="#aria.conbox.settings.AriaEcSettings.TOPO" title="Permalink to this definition">¶</a></dt>
+<dd></dd></dl>
+
+<dl class="attribute">
+<dt id="aria.conbox.settings.AriaEcSettings.infra">
+<code class="descname">infra</code><a class="headerlink" href="#aria.conbox.settings.AriaEcSettings.infra" title="Permalink to this definition">¶</a></dt>
+<dd><p>Infrastructure for a specific command
+:return:</p>
+</dd></dl>
+
+<dl class="method">
+<dt id="aria.conbox.settings.AriaEcSettings.load_config">
+<code class="descname">load_config</code><span class="sig-paren">(</span><em>configpath</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/settings.html#AriaEcSettings.load_config"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.settings.AriaEcSettings.load_config" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>configpath</strong> – param kwargs:</li>
+<li><strong>**kwargs</strong> – </li>
+</ul>
+</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
+<dt id="aria.conbox.settings.AriaEcSettings.make_infra">
+<code class="descname">make_infra</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/settings.html#AriaEcSettings.make_infra"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.settings.AriaEcSettings.make_infra" title="Permalink to this definition">¶</a></dt>
+<dd><p>Generate infrastructure</p>
+</dd></dl>
+
+<dl class="attribute">
+<dt id="aria.conbox.settings.AriaEcSettings.scsc_min">
+<code class="descname">scsc_min</code><a class="headerlink" href="#aria.conbox.settings.AriaEcSettings.scsc_min" title="Permalink to this definition">¶</a></dt>
+<dd><p>Get contact index for side chains in package or config file
+:return:</p>
+</dd></dl>
+
+<dl class="attribute">
+<dt id="aria.conbox.settings.AriaEcSettings.ssdist">
+<code class="descname">ssdist</code><a class="headerlink" href="#aria.conbox.settings.AriaEcSettings.ssdist" title="Permalink to this definition">¶</a></dt>
+<dd><p>Get distance file for secondary structures in the package or in config
+file
+:return:</p>
+</dd></dl>
+
+<dl class="attribute">
+<dt id="aria.conbox.settings.AriaEcSettings.template">
+<code class="descname">template</code><a class="headerlink" href="#aria.conbox.settings.AriaEcSettings.template" title="Permalink to this definition">¶</a></dt>
+<dd><p>Get template files in config file or in the package
+:return:</p>
+</dd></dl>
+
+</dd></dl>
+
+<dl class="class">
+<dt id="aria.conbox.settings.Setting">
+<em class="property">class </em><code class="descclassname">aria.conbox.settings.</code><code class="descname">Setting</code><a class="reference internal" href="_modules/aria/conbox/settings.html#Setting"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.settings.Setting" title="Permalink to this definition">¶</a></dt>
+<dd><p>Bases: <code class="xref py py-class docutils literal"><span class="pre">object</span></code></p>
+<p>Main setting object with args and config section</p>
+</dd></dl>
+
+<dl class="class">
+<dt id="aria.conbox.settings.Settings">
+<em class="property">class </em><code class="descclassname">aria.conbox.settings.</code><code class="descname">Settings</code><span class="sig-paren">(</span><em>sections</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/settings.html#Settings"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.settings.Settings" title="Permalink to this definition">¶</a></dt>
+<dd><p>Bases: <code class="xref py py-class docutils literal"><span class="pre">object</span></code></p>
+<p>Group settings with each section corresponding to a Setting object</p>
+<dl class="method">
+<dt id="aria.conbox.settings.Settings.load_config">
+<code class="descname">load_config</code><span class="sig-paren">(</span><em>configpath</em>, <em>pkg=False</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/settings.html#Settings.load_config"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.settings.Settings.load_config" title="Permalink to this definition">¶</a></dt>
+<dd><p>Use ConfigParser module to load config sections</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>pkg</strong> – file is inside the package (Default value = False)</li>
+<li><strong>configpath</strong> – return:</li>
+</ul>
+</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
+<dt id="aria.conbox.settings.Settings.write_config">
+<code class="descname">write_config</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/settings.html#Settings.write_config"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.settings.Settings.write_config" title="Permalink to this definition">¶</a></dt>
+<dd><p>Write config of all sections into another file</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>filename</strong> – </td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+</dd></dl>
+
+</div>
+<div class="section" id="module-aria.conbox.setup">
+<span id="aria-conbox-setup-module"></span><h2>aria.conbox.setup module<a class="headerlink" href="#module-aria.conbox.setup" title="Permalink to this headline">¶</a></h2>
+<p>Input/Output aria_ec scripts</p>
+<dl class="class">
+<dt id="aria.conbox.setup.AriaEcSetup">
+<em class="property">class </em><code class="descclassname">aria.conbox.setup.</code><code class="descname">AriaEcSetup</code><span class="sig-paren">(</span><em>settings</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/setup.html#AriaEcSetup"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.setup.AriaEcSetup" title="Permalink to this definition">¶</a></dt>
+<dd><p>Bases: <code class="xref py py-class docutils literal"><span class="pre">object</span></code></p>
+<p>Aria Ec Setup protocol</p>
+<dl class="method">
+<dt id="aria.conbox.setup.AriaEcSetup.run">
+<code class="descname">run</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/setup.html#AriaEcSetup.run"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.setup.AriaEcSetup.run" title="Permalink to this definition">¶</a></dt>
+<dd><p>main method
+:return:</p>
+</dd></dl>
+
+<dl class="method">
+<dt id="aria.conbox.setup.AriaEcSetup.write_optional_files">
+<code class="descname">write_optional_files</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/aria/conbox/setup.html#AriaEcSetup.write_optional_files"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#aria.conbox.setup.AriaEcSetup.write_optional_files" title="Permalink to this definition">¶</a></dt>
+<dd><p>Write filtered contacts & distance maps (.csv)</p>
+</dd></dl>
+
+</dd></dl>
+
+</div>
+<div class="section" id="module-aria.conbox">
+<span id="module-contents"></span><h2>Module contents<a class="headerlink" href="#module-aria.conbox" title="Permalink to this headline">¶</a></h2>
+<p>ARIA Evolutive Contact toolbox</p>
+</div>
+</div>
+
+
+ </div>
+ <div class="articleComments">
+
+ </div>
+ </div>
+ <footer>
+
+
+ <hr/>
+
+ <div role="contentinfo">
+ <p>
+ © Copyright 2017, Fabrice Allain, Benjamin Bardiaux, Michael Habeck, Therese Malliavin, Wolfgang Rieping, and Michael Nilges.
+
+ </p>
+ </div>
+ Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>.
+
+</footer>
+
+ </div>
+ </div>
+
+ </section>
+
+ </div>
+
+
+
+
+
+ <script type="text/javascript">
+ var DOCUMENTATION_OPTIONS = {
+ URL_ROOT:'./',
+ VERSION:'0.3',
+ COLLAPSE_INDEX:false,
+ FILE_SUFFIX:'.html',
+ HAS_SOURCE: true,
+ SOURCELINK_SUFFIX: '.txt'
+ };
+ </script>
+ <script type="text/javascript" src="_static/jquery.js"></script>
+ <script type="text/javascript" src="_static/underscore.js"></script>
+ <script type="text/javascript" src="_static/doctools.js"></script>
+ <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.1/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
+
+
+
+
+ <script type="text/javascript" src="_static/js/theme.js"></script>
+
+
+
+
+ <script type="text/javascript">
+ jQuery(function () {
+ SphinxRtdTheme.StickyNav.enable();
+ });
+ </script>
+
+
+</body>
+</html>
\ No newline at end of file
diff --git a/docs/_build/html/glossary.html b/examples-dev/olds/_build/html/ariaec.test.html
similarity index 77%
rename from docs/_build/html/glossary.html
rename to examples-dev/olds/_build/html/ariaec.test.html
index fc38f6ce6c277baa907f8c1ce46bdcb39cbab545..b22619c7d87596311e9224e9dab1f4311195ffea 100644
--- a/docs/_build/html/glossary.html
+++ b/examples-dev/olds/_build/html/ariaec.test.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title><no title> — ARIA 4 documentation</title>
+ <title>ariaec.test package — Aria-EC 0.3 documentation</title>
@@ -35,8 +35,7 @@
<link rel="index" title="Index"
href="genindex.html"/>
<link rel="search" title="Search" href="search.html"/>
- <link rel="copyright" title="Copyright" href="copyright.html"/>
- <link rel="top" title="ARIA 4 documentation" href="index.html"/>
+ <link rel="top" title="Aria-EC 0.3 documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script>
@@ -55,7 +54,7 @@
- <a href="index.html" class="icon icon-home"> ARIA
+ <a href="index.html" class="icon icon-home"> Aria-EC
@@ -65,7 +64,7 @@
<div class="version">
- 2
+ 0.3
</div>
@@ -90,7 +89,11 @@
<!-- Local TOC -->
- <div class="local-toc"><ul class="simple">
+ <div class="local-toc"><ul>
+<li><a class="reference internal" href="#">ariaec.test package</a><ul>
+<li><a class="reference internal" href="#module-contents">Module contents</a></li>
+</ul>
+</li>
</ul>
</div>
@@ -105,7 +108,7 @@
<nav class="wy-nav-top" role="navigation" aria-label="top navigation">
<i data-toggle="wy-nav-top" class="fa fa-bars"></i>
- <a href="index.html">ARIA</a>
+ <a href="index.html">Aria-EC</a>
</nav>
@@ -135,13 +138,13 @@
<li><a href="index.html">Docs</a> »</li>
- <li><no title></li>
+ <li>ariaec.test package</li>
<li class="wy-breadcrumbs-aside">
- <a href="_sources/glossary.rst.txt" rel="nofollow"> View page source</a>
+ <a href="_sources/ariaec.test.rst.txt" rel="nofollow"> View page source</a>
</li>
@@ -154,7 +157,13 @@
<div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
<div itemprop="articleBody">
-
+ <div class="section" id="ariaec-test-package">
+<h1>ariaec.test package<a class="headerlink" href="#ariaec-test-package" title="Permalink to this headline">¶</a></h1>
+<div class="section" id="module-contents">
+<h2>Module contents<a class="headerlink" href="#module-contents" title="Permalink to this headline">¶</a></h2>
+</div>
+</div>
+
</div>
<div class="articleComments">
@@ -168,7 +177,7 @@
<div role="contentinfo">
<p>
- © <a href="copyright.html">Copyright</a> 2017, Benjamin Bardiaux, Michael Habeck, Therese Malliavin, Wolfgang Rieping, and Michael Nilges.
+ © Copyright 2017, Fabrice Allain, Benjamin Bardiaux, Michael Habeck, Therese Malliavin, Wolfgang Rieping, and Michael Nilges.
</p>
</div>
@@ -190,7 +199,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
- VERSION:'4',
+ VERSION:'0.3',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
HAS_SOURCE: true,
diff --git a/examples-dev/olds/_build/html/genindex.html b/examples-dev/olds/_build/html/genindex.html
new file mode 100644
index 0000000000000000000000000000000000000000..7dab38fecd3e6ba5ba8e34cdf503e9d1d55b0d09
--- /dev/null
+++ b/examples-dev/olds/_build/html/genindex.html
@@ -0,0 +1,905 @@
+
+
+
+<!DOCTYPE html>
+<!--[if IE 8]><html class="no-js lt-ie9" lang="en" > <![endif]-->
+<!--[if gt IE 8]><!--> <html class="no-js" lang="en" > <!--<![endif]-->
+<head>
+ <meta charset="utf-8">
+
+ <meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+ <title>Index — Aria-EC 0.3 documentation</title>
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ <link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
+
+
+
+
+
+ <link rel="index" title="Index"
+ href="#"/>
+ <link rel="search" title="Search" href="search.html"/>
+ <link rel="top" title="Aria-EC 0.3 documentation" href="index.html"/>
+
+
+ <script src="_static/js/modernizr.min.js"></script>
+
+</head>
+
+<body class="wy-body-for-nav" role="document">
+
+
+ <div class="wy-grid-for-nav">
+
+
+ <nav data-toggle="wy-nav-shift" class="wy-nav-side">
+ <div class="wy-side-scroll">
+ <div class="wy-side-nav-search">
+
+
+
+ <a href="index.html" class="icon icon-home"> Aria-EC
+
+
+
+ </a>
+
+
+
+
+ <div class="version">
+ 0.3
+ </div>
+
+
+
+
+<div role="search">
+ <form id="rtd-search-form" class="wy-form" action="search.html" method="get">
+ <input type="text" name="q" placeholder="Search docs" />
+ <input type="hidden" name="check_keywords" value="yes" />
+ <input type="hidden" name="area" value="default" />
+ </form>
+</div>
+
+
+ </div>
+
+ <div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="main navigation">
+
+
+
+
+
+
+ <!-- Local TOC -->
+ <div class="local-toc"></div>
+
+
+ </div>
+ </div>
+ </nav>
+
+ <section data-toggle="wy-nav-shift" class="wy-nav-content-wrap">
+
+
+ <nav class="wy-nav-top" role="navigation" aria-label="top navigation">
+
+ <i data-toggle="wy-nav-top" class="fa fa-bars"></i>
+ <a href="index.html">Aria-EC</a>
+
+ </nav>
+
+
+
+ <div class="wy-nav-content">
+ <div class="rst-content">
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+<div role="navigation" aria-label="breadcrumbs navigation">
+
+ <ul class="wy-breadcrumbs">
+
+ <li><a href="index.html">Docs</a> »</li>
+
+ <li>Index</li>
+
+
+ <li class="wy-breadcrumbs-aside">
+
+
+
+ </li>
+
+ </ul>
+
+
+ <hr/>
+</div>
+ <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
+ <div itemprop="articleBody">
+
+
+<h1 id="index">Index</h1>
+
+<div class="genindex-jumpbox">
+ <a href="#A"><strong>A</strong></a>
+ | <a href="#B"><strong>B</strong></a>
+ | <a href="#C"><strong>C</strong></a>
+ | <a href="#D"><strong>D</strong></a>
+ | <a href="#E"><strong>E</strong></a>
+ | <a href="#F"><strong>F</strong></a>
+ | <a href="#G"><strong>G</strong></a>
+ | <a href="#H"><strong>H</strong></a>
+ | <a href="#I"><strong>I</strong></a>
+ | <a href="#L"><strong>L</strong></a>
+ | <a href="#M"><strong>M</strong></a>
+ | <a href="#N"><strong>N</strong></a>
+ | <a href="#P"><strong>P</strong></a>
+ | <a href="#R"><strong>R</strong></a>
+ | <a href="#S"><strong>S</strong></a>
+ | <a href="#T"><strong>T</strong></a>
+ | <a href="#U"><strong>U</strong></a>
+ | <a href="#V"><strong>V</strong></a>
+ | <a href="#W"><strong>W</strong></a>
+
+</div>
+<h2 id="A">A</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+ <td style="width: 33%; vertical-align: top;"><ul>
+ <li><a href="ariaec.html#aria.conbox.protmap.AaAtmMap">AaAtmMap (class in aria.conbox.protmap)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.protmap.AaMap">AaMap (class in aria.conbox.protmap)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.protmap.ProteinMap.all_reg">all_reg (aria.conbox.protmap.ProteinMap attribute)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.protmap.ProtMapCollection.allcontactmap">allcontactmap (aria.conbox.protmap.ProtMapCollection attribute)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.protmap.ProtMapCollection.alldistmap">alldistmap (aria.conbox.protmap.ProtMapCollection attribute)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.protmap.ProtMapCollection.allscoremap">allscoremap (aria.conbox.protmap.ProtMapCollection attribute)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.protein.AminoAcidSequence">AminoAcidSequence (class in aria.conbox.protein)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.commands.AriaEcCommands.analysis">analysis() (aria.conbox.commands.AriaEcCommands method)</a>
+</li>
+ <li><a href="ariaec.html#module-aria.conbox">aria.conbox (module)</a>
+</li>
+ <li><a href="ariaec.html#module-aria.conbox.analysis">aria.conbox.analysis (module)</a>
+</li>
+ <li><a href="ariaec.html#module-aria.conbox.commands">aria.conbox.commands (module)</a>
+</li>
+ <li><a href="ariaec.html#module-aria.conbox.converter">aria.conbox.converter (module)</a>
+</li>
+ <li><a href="ariaec.html#module-aria.conbox.maplot">aria.conbox.maplot (module)</a>
+</li>
+ <li><a href="ariaec.html#module-aria.conbox.ndconv">aria.conbox.ndconv (module)</a>
+</li>
+ <li><a href="ariaec.html#module-aria.conbox.pdbdist">aria.conbox.pdbdist (module)</a>
+</li>
+ <li><a href="ariaec.html#module-aria.conbox.pdbqual">aria.conbox.pdbqual (module)</a>
+</li>
+ <li><a href="ariaec.html#module-aria.conbox.protein">aria.conbox.protein (module)</a>
+</li>
+ </ul></td>
+ <td style="width: 33%; vertical-align: top;"><ul>
+ <li><a href="ariaec.html#module-aria.conbox.protmap">aria.conbox.protmap (module)</a>
+</li>
+ <li><a href="ariaec.html#module-aria.conbox.reader">aria.conbox.reader (module)</a>
+</li>
+ <li><a href="ariaec.html#module-aria.conbox.settings">aria.conbox.settings (module)</a>
+</li>
+ <li><a href="ariaec.html#module-aria.conbox.setup">aria.conbox.setup (module)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.converter.AriaEcBbConverter">AriaEcBbConverter (class in aria.conbox.converter)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.commands.AriaEcCommands">AriaEcCommands (class in aria.conbox.commands)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.maplot.AriaEcContactMap">AriaEcContactMap (class in aria.conbox.maplot)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.pdbqual.AriaEcPdbqual">AriaEcPdbqual (class in aria.conbox.pdbqual)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.settings.AriaEcSettings">AriaEcSettings (class in aria.conbox.settings)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.setup.AriaEcSetup">AriaEcSetup (class in aria.conbox.setup)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.converter.AriaEcXMLConverter">AriaEcXMLConverter (class in aria.conbox.converter)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.settings.AriaEcSettings.ARIAPROJ_TEMPLATE">ARIAPROJ_TEMPLATE (aria.conbox.settings.AriaEcSettings attribute)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.converter.AriaXMLConverter">AriaXMLConverter (class in aria.conbox.converter)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.converter.AriaEcXMLConverter.atm_list">atm_list() (aria.conbox.converter.AriaEcXMLConverter method)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.converter.AriaEcXMLConverter.atm_product">atm_product() (aria.conbox.converter.AriaEcXMLConverter method)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.protmap.AtmMap">AtmMap (class in aria.conbox.protmap)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.reader.Atom">Atom (class in aria.conbox.reader)</a>
+</li>
+ </ul></td>
+</tr></table>
+
+<h2 id="B">B</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+ <td style="width: 33%; vertical-align: top;"><ul>
+ <li><a href="ariaec.html#aria.conbox.commands.AriaEcCommands.bbconv">bbconv() (aria.conbox.commands.AriaEcCommands method)</a>
+</li>
+ </ul></td>
+</tr></table>
+
+<h2 id="C">C</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+ <td style="width: 33%; vertical-align: top;"><ul>
+ <li><a href="ariaec.html#aria.conbox.commands.check_file">check_file() (in module aria.conbox.commands)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.protein.SsList.check_filetype">check_filetype() (aria.conbox.protein.SsList method)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.reader.MapFile.check_maptype">check_maptype() (aria.conbox.reader.MapFile method)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.reader.MapFile.check_type">check_type (aria.conbox.reader.MapFile attribute)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.protmap.Map.check_type">check_type() (aria.conbox.protmap.Map method)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.protmap.MapFilter.clash_dict">clash_dict (aria.conbox.protmap.MapFilter attribute)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.protmap.ProteinMap.classification_metrics">classification_metrics() (aria.conbox.protmap.ProteinMap static method)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.reader.MapFileListReader.clear">clear() (aria.conbox.reader.MapFileListReader method)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.analysis.colscatter">colscatter() (in module aria.conbox.analysis)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.commands.AriaEcCommands.command_list">command_list (aria.conbox.commands.AriaEcCommands attribute)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.protmap.ProteinMap.compare_contactmap">compare_contactmap() (aria.conbox.protmap.ProteinMap method)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.protmap.ProteinMap.compareplot">compareplot() (aria.conbox.protmap.ProteinMap method)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.converter.AriaEcBbConverter.compute_diversityvalue">compute_diversityvalue() (aria.conbox.converter.AriaEcBbConverter static method)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.protmap.MapFilter.cons_filter">cons_filter() (aria.conbox.protmap.MapFilter method)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.protmap.ProteinMap.contact_list">contact_list() (aria.conbox.protmap.ProteinMap method)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.protmap.AaAtmMap.contact_map">contact_map() (aria.conbox.protmap.AaAtmMap method)</a>
+
+ <ul>
+ <li><a href="ariaec.html#aria.conbox.protmap.AaMap.contact_map">(aria.conbox.protmap.AaMap method)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.protmap.ProteinMap.contact_map">(aria.conbox.protmap.ProteinMap method)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.protmap.ResAtmMap.contact_map">(aria.conbox.protmap.ResAtmMap method)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.protmap.ResMap.contact_map">(aria.conbox.protmap.ResMap method)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.protmap.SsAaAtmMap.contact_map">(aria.conbox.protmap.SsAaAtmMap method)</a>
+</li>
+ </ul></li>
+ <li><a href="ariaec.html#aria.conbox.commands.AriaEcCommands.contact_types">contact_types (aria.conbox.commands.AriaEcCommands attribute)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.reader.ContactMapFile">ContactMapFile (class in aria.conbox.reader)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.protmap.ProteinMap.contactset">contactset() (aria.conbox.protmap.ProteinMap method)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.reader.Atom.coords">coords (aria.conbox.reader.Atom attribute)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.protmap.AaAtmMap.copy">copy() (aria.conbox.protmap.AaAtmMap method)</a>
+
+ <ul>
+ <li><a href="ariaec.html#aria.conbox.protmap.AaMap.copy">(aria.conbox.protmap.AaMap method)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.protmap.AtmMap.copy">(aria.conbox.protmap.AtmMap method)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.protmap.Map.copy">(aria.conbox.protmap.Map method)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.protmap.ProteinMap.copy">(aria.conbox.protmap.ProteinMap method)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.protmap.ResAtmMap.copy">(aria.conbox.protmap.ResAtmMap method)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.protmap.ResMap.copy">(aria.conbox.protmap.ResMap method)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.protmap.SsAaAtmMap.copy">(aria.conbox.protmap.SsAaAtmMap method)</a>
+</li>
+ </ul></li>
+ </ul></td>
+ <td style="width: 33%; vertical-align: top;"><ul>
+ <li><a href="ariaec.html#aria.conbox.protmap.AaAtmMap.create_heatmap">create_heatmap() (aria.conbox.protmap.AaAtmMap method)</a>
+
+ <ul>
+ <li><a href="ariaec.html#aria.conbox.protmap.AaMap.create_heatmap">(aria.conbox.protmap.AaMap method)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.protmap.ProteinMap.create_heatmap">(aria.conbox.protmap.ProteinMap method)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.protmap.ResAtmMap.create_heatmap">(aria.conbox.protmap.ResAtmMap method)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.protmap.ResMap.create_heatmap">(aria.conbox.protmap.ResMap method)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.protmap.SsAaAtmMap.create_heatmap">(aria.conbox.protmap.SsAaAtmMap method)</a>
+</li>
+ </ul></li>
+ <li><a href="ariaec.html#aria.conbox.protmap.AaAtmMap.create_index">create_index() (aria.conbox.protmap.AaAtmMap method)</a>
+
+ <ul>
+ <li><a href="ariaec.html#aria.conbox.protmap.AaMap.create_index">(aria.conbox.protmap.AaMap method)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.protmap.AtmMap.create_index">(aria.conbox.protmap.AtmMap method)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.protmap.ProteinMap.create_index">(aria.conbox.protmap.ProteinMap method)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.protmap.ResAtmMap.create_index">(aria.conbox.protmap.ResAtmMap method)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.protmap.ResMap.create_index">(aria.conbox.protmap.ResMap method)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.protmap.SsAaAtmMap.create_index">(aria.conbox.protmap.SsAaAtmMap method)</a>
+</li>
+ </ul></li>
+ <li><a href="ariaec.html#aria.conbox.reader.ContactMapFile.create_map">create_map() (aria.conbox.reader.ContactMapFile method)</a>
+
+ <ul>
+ <li><a href="ariaec.html#aria.conbox.reader.DistanceMapFile.create_map">(aria.conbox.reader.DistanceMapFile method)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.reader.MapFile.create_map">(aria.conbox.reader.MapFile method)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.reader.PDBFile.create_map">(aria.conbox.reader.PDBFile method)</a>
+</li>
+ </ul></li>
+ <li><a href="ariaec.html#aria.conbox.commands.AriaEcCommands.create_settings">create_settings() (aria.conbox.commands.AriaEcCommands method)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.reader.CulledPdbFile">CulledPdbFile (class in aria.conbox.reader)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.protmap.MapFilter.cys_filter">cys_filter() (aria.conbox.protmap.MapFilter static method)</a>
+</li>
+ </ul></td>
+</tr></table>
+
+<h2 id="D">D</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+ <td style="width: 33%; vertical-align: top;"><ul>
+ <li><a href="ariaec.html#aria.conbox.reader.CulledPdbFile.default">default (aria.conbox.reader.CulledPdbFile attribute)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.commands.AriaEcCommands.default_confile">default_confile (aria.conbox.commands.AriaEcCommands attribute)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.converter.AriaXMLConverter.deff">deff() (aria.conbox.converter.AriaXMLConverter static method)</a>
+</li>
+ </ul></td>
+ <td style="width: 33%; vertical-align: top;"><ul>
+ <li><a href="ariaec.html#aria.conbox.commands.AriaEcCommands.desc_list">desc_list (aria.conbox.commands.AriaEcCommands attribute)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.protmap.ProteinMap.distance_method">distance_method (aria.conbox.protmap.ProteinMap attribute)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.reader.DistanceMapFile">DistanceMapFile (class in aria.conbox.reader)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.protmap.ProtMapCollection.distmap">distmap (aria.conbox.protmap.ProtMapCollection attribute)</a>
+</li>
+ </ul></td>
+</tr></table>
+
+<h2 id="E">E</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+ <td style="width: 33%; vertical-align: top;"><ul>
+ <li><a href="ariaec.html#aria.conbox.protein.AminoAcidSequence.end_reg">end_reg (aria.conbox.protein.AminoAcidSequence attribute)</a>
+</li>
+ </ul></td>
+ <td style="width: 33%; vertical-align: top;"><ul>
+ <li><a href="ariaec.html#aria.conbox.analysis.EnsembleAnalysis">EnsembleAnalysis (class in aria.conbox.analysis)</a>
+</li>
+ </ul></td>
+</tr></table>
+
+<h2 id="F">F</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+ <td style="width: 33%; vertical-align: top;"><ul>
+ <li><a href="ariaec.html#aria.conbox.reader.RegexFile.filename">filename (aria.conbox.reader.RegexFile attribute)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.reader.RegexFile.filepath">filepath (aria.conbox.reader.RegexFile attribute)</a>
+</li>
+ </ul></td>
+ <td style="width: 33%; vertical-align: top;"><ul>
+ <li><a href="ariaec.html#aria.conbox.reader.CulledPdbFile.filetype">filetype (aria.conbox.reader.CulledPdbFile attribute)</a>
+
+ <ul>
+ <li><a href="ariaec.html#aria.conbox.reader.TblDistFile.filetype">(aria.conbox.reader.TblDistFile attribute)</a>
+</li>
+ </ul></li>
+ <li><a href="ariaec.html#aria.conbox.protmap.MapFilter.filter_types">filter_types (aria.conbox.protmap.MapFilter attribute)</a>
+</li>
+ </ul></td>
+</tr></table>
+
+<h2 id="G">G</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+ <td style="width: 33%; vertical-align: top;"><ul>
+ <li><a href="ariaec.html#aria.conbox.converter.AriaEcXMLConverter.get_dist">get_dist() (aria.conbox.converter.AriaEcXMLConverter method)</a>
+</li>
+ </ul></td>
+ <td style="width: 33%; vertical-align: top;"><ul>
+ <li><a href="ariaec.html#aria.conbox.pdbdist.PDBDist.get_proteinblocks">get_proteinblocks() (aria.conbox.pdbdist.PDBDist static method)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.pdbdist.PDBDist.get_secstructs">get_secstructs() (aria.conbox.pdbdist.PDBDist static method)</a>
+</li>
+ </ul></td>
+</tr></table>
+
+<h2 id="H">H</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+ <td style="width: 33%; vertical-align: top;"><ul>
+ <li><a href="ariaec.html#aria.conbox.protmap.ProteinMap.heavy_reg">heavy_reg (aria.conbox.protmap.ProteinMap attribute)</a>
+</li>
+ </ul></td>
+ <td style="width: 33%; vertical-align: top;"><ul>
+ <li><a href="ariaec.html#aria.conbox.protein.AminoAcidSequence.humanidx">humanidx (aria.conbox.protein.AminoAcidSequence attribute)</a>
+</li>
+ </ul></td>
+</tr></table>
+
+<h2 id="I">I</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+ <td style="width: 33%; vertical-align: top;"><ul>
+ <li><a href="ariaec.html#aria.conbox.protein.SsList.index">index (aria.conbox.protein.SsList attribute)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.protein.SsList.indxplus_reg">indxplus_reg (aria.conbox.protein.SsList attribute)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.settings.AriaEcSettings.infra">infra (aria.conbox.settings.AriaEcSettings attribute)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.settings.AriaEcSettings.INTERLOWERBOUNDS">INTERLOWERBOUNDS (aria.conbox.settings.AriaEcSettings attribute)</a>
+</li>
+ </ul></td>
+ <td style="width: 33%; vertical-align: top;"><ul>
+ <li><a href="ariaec.html#aria.conbox.settings.AriaEcSettings.INTERTARGET">INTERTARGET (aria.conbox.settings.AriaEcSettings attribute)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.settings.AriaEcSettings.INTERUPPERBOUNDS">INTERUPPERBOUNDS (aria.conbox.settings.AriaEcSettings attribute)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.settings.AriaEcSettings.INTRALOWERBOUNDS">INTRALOWERBOUNDS (aria.conbox.settings.AriaEcSettings attribute)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.settings.AriaEcSettings.INTRATARGET">INTRATARGET (aria.conbox.settings.AriaEcSettings attribute)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.settings.AriaEcSettings.INTRAUPPERBOUNDS">INTRAUPPERBOUNDS (aria.conbox.settings.AriaEcSettings attribute)</a>
+</li>
+ </ul></td>
+</tr></table>
+
+<h2 id="L">L</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+ <td style="width: 33%; vertical-align: top;"><ul>
+ <li><a href="ariaec.html#aria.conbox.reader.RegexFile.load">load() (aria.conbox.reader.RegexFile method)</a>
+</li>
+ </ul></td>
+ <td style="width: 33%; vertical-align: top;"><ul>
+ <li><a href="ariaec.html#aria.conbox.settings.AriaEcSettings.load_config">load_config() (aria.conbox.settings.AriaEcSettings method)</a>
+
+ <ul>
+ <li><a href="ariaec.html#aria.conbox.settings.Settings.load_config">(aria.conbox.settings.Settings method)</a>
+</li>
+ </ul></li>
+ </ul></td>
+</tr></table>
+
+<h2 id="M">M</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+ <td style="width: 33%; vertical-align: top;"><ul>
+ <li><a href="ariaec.html#aria.conbox.commands.main">main() (in module aria.conbox.commands)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.settings.AriaEcSettings.make_infra">make_infra() (aria.conbox.settings.AriaEcSettings method)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.protmap.Map">Map (class in aria.conbox.protmap)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.reader.MapFile">MapFile (class in aria.conbox.reader)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.reader.MapFileListReader">MapFileListReader (class in aria.conbox.reader)</a>
+</li>
+ </ul></td>
+ <td style="width: 33%; vertical-align: top;"><ul>
+ <li><a href="ariaec.html#aria.conbox.protmap.MapFilter">MapFilter (class in aria.conbox.protmap)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.protmap.ProteinMap.maplot">maplot (aria.conbox.protmap.ProteinMap attribute)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.commands.AriaEcCommands.maplot">maplot() (aria.conbox.commands.AriaEcCommands method)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.converter.AriaXMLConverter.molecule">molecule (aria.conbox.converter.AriaXMLConverter attribute)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.protmap.Map.mtype_choices">mtype_choices (aria.conbox.protmap.Map attribute)</a>
+</li>
+ </ul></td>
+</tr></table>
+
+<h2 id="N">N</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+ <td style="width: 33%; vertical-align: top;"><ul>
+ <li><a href="ariaec.html#aria.conbox.reader.Atom.name">name (aria.conbox.reader.Atom attribute)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.protmap.MapFilter.nd_filter">nd_filter() (aria.conbox.protmap.MapFilter method)</a>
+</li>
+ </ul></td>
+ <td style="width: 33%; vertical-align: top;"><ul>
+ <li><a href="ariaec.html#aria.conbox.converter.AriaEcXMLConverter.neighcontact">neighcontact() (aria.conbox.converter.AriaEcXMLConverter static method)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.converter.AriaEcXMLConverter.neighcontacts">neighcontacts() (aria.conbox.converter.AriaEcXMLConverter static method)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.ndconv.net_deconv">net_deconv() (in module aria.conbox.ndconv)</a>
+</li>
+ </ul></td>
+</tr></table>
+
+<h2 id="P">P</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+ <td style="width: 33%; vertical-align: top;"><ul>
+ <li><a href="ariaec.html#aria.conbox.analysis.EnsembleAnalysis.pca_projection">pca_projection() (aria.conbox.analysis.EnsembleAnalysis static method)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.pdbdist.PDBDist">PDBDist (class in aria.conbox.pdbdist)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.commands.AriaEcCommands.pdbdist">pdbdist() (aria.conbox.commands.AriaEcCommands method)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.pdbdist.PDBDist.pdbdists">pdbdists() (aria.conbox.pdbdist.PDBDist method)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.reader.PDBFile">PDBFile (class in aria.conbox.reader)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.commands.AriaEcCommands.pdbqual">pdbqual() (aria.conbox.commands.AriaEcCommands method)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.reader.PDBFile.pdbreg">pdbreg (aria.conbox.reader.PDBFile attribute)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.commands.AriaEcCommands.pdbstat">pdbstat() (aria.conbox.commands.AriaEcCommands method)</a>
+</li>
+ </ul></td>
+ <td style="width: 33%; vertical-align: top;"><ul>
+ <li><a href="ariaec.html#aria.conbox.protmap.ProteinMap.plotflush">plotflush() (aria.conbox.protmap.ProteinMap method)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.protmap.MapFilter.pos_filter">pos_filter() (aria.conbox.protmap.MapFilter method)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.protein.Protein">Protein (class in aria.conbox.protein)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.protmap.ProteinMap">ProteinMap (class in aria.conbox.protmap)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.protmap.ProtMapCollection">ProtMapCollection (class in aria.conbox.protmap)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.protein.SsList.psipred2_reg">psipred2_reg (aria.conbox.protein.SsList attribute)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.protein.SsList.psipred3_reg">psipred3_reg (aria.conbox.protein.SsList attribute)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.protein.SsList.psipred_reg">psipred_reg (aria.conbox.protein.SsList attribute)</a>
+</li>
+ </ul></td>
+</tr></table>
+
+<h2 id="R">R</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+ <td style="width: 33%; vertical-align: top;"><ul>
+ <li><a href="ariaec.html#aria.conbox.protein.AminoAcidSequence.read">read() (aria.conbox.protein.AminoAcidSequence method)</a>
+
+ <ul>
+ <li><a href="ariaec.html#aria.conbox.protein.SsList.read">(aria.conbox.protein.SsList method)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.reader.MapFile.read">(aria.conbox.reader.MapFile method)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.reader.MapFileListReader.read">(aria.conbox.reader.MapFileListReader method)</a>
+</li>
+ </ul></li>
+ <li><a href="ariaec.html#aria.conbox.protein.SsList.read_indextableplus">read_indextableplus() (aria.conbox.protein.SsList method)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.converter.AriaXMLConverter.read_pdb">read_pdb() (aria.conbox.converter.AriaXMLConverter method)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.protein.SsList.read_psipred">read_psipred() (aria.conbox.protein.SsList method)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.converter.AriaXMLConverter.read_seq">read_seq() (aria.conbox.converter.AriaXMLConverter method)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.protein.SsList.read_ssdist">read_ssdist() (aria.conbox.protein.SsList method)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.commands.ReadableFile">ReadableFile (class in aria.conbox.commands)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.protein.AminoAcidSequence.readtopo">readtopo() (aria.conbox.protein.AminoAcidSequence method)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.protmap.AaMap.reduce">reduce() (aria.conbox.protmap.AaMap method)</a>
+
+ <ul>
+ <li><a href="ariaec.html#aria.conbox.protmap.AtmMap.reduce">(aria.conbox.protmap.AtmMap method)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.protmap.Map.reduce">(aria.conbox.protmap.Map method)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.protmap.ProteinMap.reduce">(aria.conbox.protmap.ProteinMap method)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.protmap.ResAtmMap.reduce">(aria.conbox.protmap.ResAtmMap method)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.protmap.SsAaAtmMap.reduce">(aria.conbox.protmap.SsAaAtmMap method)</a>
+</li>
+ </ul></li>
+ </ul></td>
+ <td style="width: 33%; vertical-align: top;"><ul>
+ <li><a href="ariaec.html#aria.conbox.reader.CulledPdbFile.regex">regex (aria.conbox.reader.CulledPdbFile attribute)</a>
+
+ <ul>
+ <li><a href="ariaec.html#aria.conbox.reader.TblDistFile.regex">(aria.conbox.reader.TblDistFile attribute)</a>
+</li>
+ </ul></li>
+ <li><a href="ariaec.html#aria.conbox.reader.RegexFile">RegexFile (class in aria.conbox.reader)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.protmap.Map.remove">remove() (aria.conbox.protmap.Map method)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.protmap.ProteinMap.report">report() (aria.conbox.protmap.ProteinMap method)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.protmap.ResAtmMap">ResAtmMap (class in aria.conbox.protmap)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.protmap.ResMap">ResMap (class in aria.conbox.protmap)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.protein.AminoAcidSequence.restatement_reg">restatement_reg (aria.conbox.protein.AminoAcidSequence attribute)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.analysis.EnsembleAnalysis.run">run() (aria.conbox.analysis.EnsembleAnalysis method)</a>
+
+ <ul>
+ <li><a href="ariaec.html#aria.conbox.commands.AriaEcCommands.run">(aria.conbox.commands.AriaEcCommands method)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.converter.AriaEcBbConverter.run">(aria.conbox.converter.AriaEcBbConverter method)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.maplot.AriaEcContactMap.run">(aria.conbox.maplot.AriaEcContactMap method)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.pdbdist.PDBDist.run">(aria.conbox.pdbdist.PDBDist method)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.pdbqual.AriaEcPdbqual.run">(aria.conbox.pdbqual.AriaEcPdbqual method)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.setup.AriaEcSetup.run">(aria.conbox.setup.AriaEcSetup method)</a>
+</li>
+ </ul></li>
+ <li><a href="ariaec.html#aria.conbox.converter.AriaEcXMLConverter.run_tbl2xml">run_tbl2xml() (aria.conbox.converter.AriaEcXMLConverter method)</a>
+</li>
+ </ul></td>
+</tr></table>
+
+<h2 id="S">S</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+ <td style="width: 33%; vertical-align: top;"><ul>
+ <li><a href="ariaec.html#aria.conbox.protmap.ProteinMap.saveplot">saveplot() (aria.conbox.protmap.ProteinMap method)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.settings.AriaEcSettings.SCSC_MIN">SCSC_MIN (aria.conbox.settings.AriaEcSettings attribute)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.settings.AriaEcSettings.scsc_min">scsc_min (aria.conbox.settings.AriaEcSettings attribute)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.settings.AriaEcSettings.SECTIONS">SECTIONS (aria.conbox.settings.AriaEcSettings attribute)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.protein.SsList.seq_sublist">seq_sublist() (aria.conbox.protein.SsList method)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.protein.SsList.sequence">sequence (aria.conbox.protein.SsList attribute)</a>
+
+ <ul>
+ <li><a href="ariaec.html#aria.conbox.protmap.AaMap.sequence">(aria.conbox.protmap.AaMap attribute)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.protmap.ProteinMap.sequence">(aria.conbox.protmap.ProteinMap attribute)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.protmap.ResAtmMap.sequence">(aria.conbox.protmap.ResAtmMap attribute)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.protmap.ResMap.sequence">(aria.conbox.protmap.ResMap attribute)</a>
+</li>
+ </ul></li>
+ <li><a href="ariaec.html#aria.conbox.protein.Protein.set_aa_sequence">set_aa_sequence() (aria.conbox.protein.Protein method)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.protein.Protein.set_sec_struct">set_sec_struct() (aria.conbox.protein.Protein method)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.protmap.Map.set_value">set_value() (aria.conbox.protmap.Map method)</a>
+</li>
+ </ul></td>
+ <td style="width: 33%; vertical-align: top;"><ul>
+ <li><a href="ariaec.html#aria.conbox.settings.Setting">Setting (class in aria.conbox.settings)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.settings.Settings">Settings (class in aria.conbox.settings)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.commands.AriaEcCommands.setup">setup() (aria.conbox.commands.AriaEcCommands method)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.protmap.Map.sortedset">sortedset() (aria.conbox.protmap.Map method)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.settings.AriaEcSettings.SS_DIST">SS_DIST (aria.conbox.settings.AriaEcSettings attribute)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.protein.SsList.ss_dist_reg">ss_dist_reg (aria.conbox.protein.SsList attribute)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.protmap.SsAaAtmMap.ss_types">ss_types (aria.conbox.protmap.SsAaAtmMap attribute)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.protmap.SsAaAtmMap">SsAaAtmMap (class in aria.conbox.protmap)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.protmap.MapFilter.ssclash_filter">ssclash_filter() (aria.conbox.protmap.MapFilter static method)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.settings.AriaEcSettings.ssdist">ssdist (aria.conbox.settings.AriaEcSettings attribute)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.protein.SsList">SsList (class in aria.conbox.protein)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.protein.AminoAcidSequence.startres_reg">startres_reg (aria.conbox.protein.AminoAcidSequence attribute)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.protmap.Map.subfill">subfill() (aria.conbox.protmap.Map method)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.protein.Protein.sync_index">sync_index() (aria.conbox.protein.Protein static method)</a>
+</li>
+ </ul></td>
+</tr></table>
+
+<h2 id="T">T</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+ <td style="width: 33%; vertical-align: top;"><ul>
+ <li><a href="ariaec.html#aria.conbox.converter.AriaEcXMLConverter.targetdistmaps">targetdistmaps() (aria.conbox.converter.AriaEcXMLConverter method)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.commands.AriaEcCommands.tbl2xml">tbl2xml() (aria.conbox.commands.AriaEcCommands method)</a>
+
+ <ul>
+ <li><a href="ariaec.html#aria.conbox.converter.AriaEcXMLConverter.tbl2xml">(aria.conbox.converter.AriaEcXMLConverter static method)</a>
+</li>
+ </ul></li>
+ <li><a href="ariaec.html#aria.conbox.reader.TblDistFile">TblDistFile (class in aria.conbox.reader)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.settings.AriaEcSettings.template">template (aria.conbox.settings.AriaEcSettings attribute)</a>
+</li>
+ </ul></td>
+ <td style="width: 33%; vertical-align: top;"><ul>
+ <li><a href="ariaec.html#aria.conbox.protmap.Map.to_series">to_series() (aria.conbox.protmap.Map method)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.protmap.Map.topmap">topmap() (aria.conbox.protmap.Map method)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.settings.AriaEcSettings.TOPO">TOPO (aria.conbox.settings.AriaEcSettings attribute)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.protein.AminoAcidSequence.topology">topology (aria.conbox.protein.AminoAcidSequence attribute)</a>
+
+ <ul>
+ <li><a href="ariaec.html#aria.conbox.protein.Protein.topology">(aria.conbox.protein.Protein attribute)</a>
+</li>
+ </ul></li>
+ <li><a href="ariaec.html#aria.conbox.reader.MapFile.types">types (aria.conbox.reader.MapFile attribute)</a>
+</li>
+ </ul></td>
+</tr></table>
+
+<h2 id="U">U</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+ <td style="width: 33%; vertical-align: top;"><ul>
+ <li><a href="ariaec.html#aria.conbox.converter.AriaXMLConverter.upd_mol">upd_mol() (aria.conbox.converter.AriaXMLConverter static method)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.protmap.Map.update">update() (aria.conbox.protmap.Map method)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.reader.ContactMapFile.update_map">update_map() (aria.conbox.reader.ContactMapFile method)</a>
+
+ <ul>
+ <li><a href="ariaec.html#aria.conbox.reader.DistanceMapFile.update_map">(aria.conbox.reader.DistanceMapFile method)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.reader.MapFile.update_map">(aria.conbox.reader.MapFile method)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.reader.PDBFile.update_map">(aria.conbox.reader.PDBFile method)</a>
+</li>
+ </ul></li>
+ </ul></td>
+</tr></table>
+
+<h2 id="V">V</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+ <td style="width: 33%; vertical-align: top;"><ul>
+ <li><a href="ariaec.html#aria.conbox.analysis.EnsembleAnalysis.violation_analysis">violation_analysis() (aria.conbox.analysis.EnsembleAnalysis static method)</a>
+</li>
+ </ul></td>
+</tr></table>
+
+<h2 id="W">W</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+ <td style="width: 33%; vertical-align: top;"><ul>
+ <li><a href="ariaec.html#aria.conbox.converter.AriaEcXMLConverter.write_ariaproject">write_ariaproject() (aria.conbox.converter.AriaEcXMLConverter method)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.settings.Settings.write_config">write_config() (aria.conbox.settings.Settings method)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.protmap.ProteinMap.write_contacts">write_contacts() (aria.conbox.protmap.ProteinMap method)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.converter.AriaXMLConverter.write_dihedral_tbl">write_dihedral_tbl() (aria.conbox.converter.AriaXMLConverter static method)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.converter.AriaXMLConverter.write_dist_xml">write_dist_xml() (aria.conbox.converter.AriaXMLConverter static method)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.protmap.MapFilter.write_filtout">write_filtout() (aria.conbox.protmap.MapFilter static method)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.converter.AriaXMLConverter.write_hb_tbl">write_hb_tbl() (aria.conbox.converter.AriaXMLConverter method)</a>
+</li>
+ </ul></td>
+ <td style="width: 33%; vertical-align: top;"><ul>
+ <li><a href="ariaec.html#aria.conbox.converter.AriaEcXMLConverter.write_map_restraint">write_map_restraint() (aria.conbox.converter.AriaEcXMLConverter method)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.converter.AriaEcXMLConverter.write_maplist_restraints">write_maplist_restraints() (aria.conbox.converter.AriaEcXMLConverter method)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.setup.AriaEcSetup.write_optional_files">write_optional_files() (aria.conbox.setup.AriaEcSetup method)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.protein.Protein.write_seq">write_seq() (aria.conbox.protein.Protein method)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.converter.AriaXMLConverter.write_ssdist_tbl">write_ssdist_tbl() (aria.conbox.converter.AriaXMLConverter static method)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.protein.SsList.write_ssfasta">write_ssfasta() (aria.conbox.protein.SsList method)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.converter.AriaEcXMLConverter.write_tbl_restraints">write_tbl_restraints() (aria.conbox.converter.AriaEcXMLConverter method)</a>
+</li>
+ <li><a href="ariaec.html#aria.conbox.converter.AriaXMLConverter.write_xmlseq">write_xmlseq() (aria.conbox.converter.AriaXMLConverter method)</a>
+</li>
+ </ul></td>
+</tr></table>
+
+
+
+ </div>
+ <div class="articleComments">
+
+ </div>
+ </div>
+ <footer>
+
+
+ <hr/>
+
+ <div role="contentinfo">
+ <p>
+ © Copyright 2017, Fabrice Allain, Benjamin Bardiaux, Michael Habeck, Therese Malliavin, Wolfgang Rieping, and Michael Nilges.
+
+ </p>
+ </div>
+ Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>.
+
+</footer>
+
+ </div>
+ </div>
+
+ </section>
+
+ </div>
+
+
+
+
+
+ <script type="text/javascript">
+ var DOCUMENTATION_OPTIONS = {
+ URL_ROOT:'./',
+ VERSION:'0.3',
+ COLLAPSE_INDEX:false,
+ FILE_SUFFIX:'.html',
+ HAS_SOURCE: true,
+ SOURCELINK_SUFFIX: '.txt'
+ };
+ </script>
+ <script type="text/javascript" src="_static/jquery.js"></script>
+ <script type="text/javascript" src="_static/underscore.js"></script>
+ <script type="text/javascript" src="_static/doctools.js"></script>
+ <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.1/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
+
+
+
+
+ <script type="text/javascript" src="_static/js/theme.js"></script>
+
+
+
+
+ <script type="text/javascript">
+ jQuery(function () {
+ SphinxRtdTheme.StickyNav.enable();
+ });
+ </script>
+
+
+</body>
+</html>
\ No newline at end of file
diff --git a/docs/_build/html/index.html b/examples-dev/olds/_build/html/index.html
similarity index 84%
rename from docs/_build/html/index.html
rename to examples-dev/olds/_build/html/index.html
index 4dc42399dc79f80d97593b8a10875134aaf94518..775a39dbafd7ce003a859fc623a8b8e3c7c1a8f7 100644
--- a/docs/_build/html/index.html
+++ b/examples-dev/olds/_build/html/index.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>Welcome to ARIAEC’s documentation! — ARIA 4 documentation</title>
+ <title>Welcome to Aria-EC’s documentation! — Aria-EC 0.3 documentation</title>
@@ -35,8 +35,7 @@
<link rel="index" title="Index"
href="genindex.html"/>
<link rel="search" title="Search" href="search.html"/>
- <link rel="copyright" title="Copyright" href="copyright.html"/>
- <link rel="top" title="ARIA 4 documentation" href="#"/>
+ <link rel="top" title="Aria-EC 0.3 documentation" href="#"/>
<script src="_static/js/modernizr.min.js"></script>
@@ -55,7 +54,7 @@
- <a href="#" class="icon icon-home"> ARIA
+ <a href="#" class="icon icon-home"> Aria-EC
@@ -65,7 +64,7 @@
<div class="version">
- 2
+ 0.3
</div>
@@ -91,7 +90,7 @@
<!-- Local TOC -->
<div class="local-toc"><ul>
-<li><a class="reference internal" href="#">Welcome to ARIAEC’s documentation!</a></li>
+<li><a class="reference internal" href="#">Welcome to Aria-EC’s documentation!</a></li>
<li><a class="reference internal" href="#indices-and-tables">Indices and tables</a></li>
</ul>
</div>
@@ -107,7 +106,7 @@
<nav class="wy-nav-top" role="navigation" aria-label="top navigation">
<i data-toggle="wy-nav-top" class="fa fa-bars"></i>
- <a href="#">ARIA</a>
+ <a href="#">Aria-EC</a>
</nav>
@@ -137,7 +136,7 @@
<li><a href="#">Docs</a> »</li>
- <li>Welcome to ARIAEC’s documentation!</li>
+ <li>Welcome to Aria-EC’s documentation!</li>
<li class="wy-breadcrumbs-aside">
@@ -156,8 +155,8 @@
<div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
<div itemprop="articleBody">
- <div class="section" id="welcome-to-ariaec-s-documentation">
-<h1>Welcome to ARIAEC’s documentation!<a class="headerlink" href="#welcome-to-ariaec-s-documentation" title="Permalink to this headline">¶</a></h1>
+ <div class="section" id="welcome-to-aria-ec-s-documentation">
+<h1>Welcome to Aria-EC’s documentation!<a class="headerlink" href="#welcome-to-aria-ec-s-documentation" title="Permalink to this headline">¶</a></h1>
<div class="toctree-wrapper compound">
</div>
</div>
@@ -183,7 +182,7 @@
<div role="contentinfo">
<p>
- © <a href="copyright.html">Copyright</a> 2017, Benjamin Bardiaux, Michael Habeck, Therese Malliavin, Wolfgang Rieping, and Michael Nilges.
+ © Copyright 2017, Fabrice Allain, Benjamin Bardiaux, Michael Habeck, Therese Malliavin, Wolfgang Rieping, and Michael Nilges.
</p>
</div>
@@ -205,7 +204,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
- VERSION:'4',
+ VERSION:'0.3',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
HAS_SOURCE: true,
diff --git a/docs/_build/html/modules.html b/examples-dev/olds/_build/html/modules.html
similarity index 89%
rename from docs/_build/html/modules.html
rename to examples-dev/olds/_build/html/modules.html
index 931ee32b1703cb6da45cd1e593856aa055cf6c0f..215b78d750a8a8354b038d7aa8ba5d77cd46836b 100644
--- a/docs/_build/html/modules.html
+++ b/examples-dev/olds/_build/html/modules.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>ariaec — ARIA 4 documentation</title>
+ <title>ariaec — Aria-EC 0.3 documentation</title>
@@ -35,8 +35,7 @@
<link rel="index" title="Index"
href="genindex.html"/>
<link rel="search" title="Search" href="search.html"/>
- <link rel="copyright" title="Copyright" href="copyright.html"/>
- <link rel="top" title="ARIA 4 documentation" href="index.html"/>
+ <link rel="top" title="Aria-EC 0.3 documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script>
@@ -55,7 +54,7 @@
- <a href="index.html" class="icon icon-home"> ARIA
+ <a href="index.html" class="icon icon-home"> Aria-EC
@@ -65,7 +64,7 @@
<div class="version">
- 2
+ 0.3
</div>
@@ -106,7 +105,7 @@
<nav class="wy-nav-top" role="navigation" aria-label="top navigation">
<i data-toggle="wy-nav-top" class="fa fa-bars"></i>
- <a href="index.html">ARIA</a>
+ <a href="index.html">Aria-EC</a>
</nav>
@@ -174,7 +173,7 @@
<div role="contentinfo">
<p>
- © <a href="copyright.html">Copyright</a> 2017, Benjamin Bardiaux, Michael Habeck, Therese Malliavin, Wolfgang Rieping, and Michael Nilges.
+ © Copyright 2017, Fabrice Allain, Benjamin Bardiaux, Michael Habeck, Therese Malliavin, Wolfgang Rieping, and Michael Nilges.
</p>
</div>
@@ -196,7 +195,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
- VERSION:'4',
+ VERSION:'0.3',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
HAS_SOURCE: true,
diff --git a/examples-dev/olds/_build/html/objects.inv b/examples-dev/olds/_build/html/objects.inv
new file mode 100644
index 0000000000000000000000000000000000000000..c900d64e5731d3f63b395fad172e6a70709faee8
Binary files /dev/null and b/examples-dev/olds/_build/html/objects.inv differ
diff --git a/docs/_build/html/copyright.html b/examples-dev/olds/_build/html/py-modindex.html
similarity index 50%
rename from docs/_build/html/copyright.html
rename to examples-dev/olds/_build/html/py-modindex.html
index fe1f0a9081a0365fd217d64c141e04b408ad989c..83c11458948c2ddf00c1aa9f1147e2d86e400a22 100644
--- a/docs/_build/html/copyright.html
+++ b/examples-dev/olds/_build/html/py-modindex.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>Sphinx authors — ARIA 4 documentation</title>
+ <title>Python Module Index — Aria-EC 0.3 documentation</title>
@@ -35,8 +35,10 @@
<link rel="index" title="Index"
href="genindex.html"/>
<link rel="search" title="Search" href="search.html"/>
- <link rel="copyright" title="Copyright" href="#"/>
- <link rel="top" title="ARIA 4 documentation" href="index.html"/>
+ <link rel="top" title="Aria-EC 0.3 documentation" href="index.html"/>
+
+
+
<script src="_static/js/modernizr.min.js"></script>
@@ -55,7 +57,7 @@
- <a href="index.html" class="icon icon-home"> ARIA
+ <a href="index.html" class="icon icon-home"> Aria-EC
@@ -65,7 +67,7 @@
<div class="version">
- 2
+ 0.3
</div>
@@ -90,10 +92,7 @@
<!-- Local TOC -->
- <div class="local-toc"><ul>
-<li><a class="reference internal" href="#">Sphinx authors</a></li>
-</ul>
-</div>
+ <div class="local-toc"></div>
</div>
@@ -106,7 +105,7 @@
<nav class="wy-nav-top" role="navigation" aria-label="top navigation">
<i data-toggle="wy-nav-top" class="fa fa-bars"></i>
- <a href="index.html">ARIA</a>
+ <a href="index.html">Aria-EC</a>
</nav>
@@ -136,14 +135,12 @@
<li><a href="index.html">Docs</a> »</li>
- <li>Sphinx authors</li>
+ <li>Python Module Index</li>
<li class="wy-breadcrumbs-aside">
- <a href="_sources/copyright.rst.txt" rel="nofollow"> View page source</a>
-
</li>
@@ -155,32 +152,89 @@
<div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
<div itemprop="articleBody">
- <div class="section" id="sphinx-authors">
-<span id="copyright"></span><h1>Sphinx authors<a class="headerlink" href="#sphinx-authors" title="Permalink to this headline">¶</a></h1>
-<dl class="docutils">
-<dt>“â€â€œ</dt>
-<dd><p class="first">ARIA – Ambiguous Restraints for Iterative Assignment</p>
-<blockquote class="last">
-<div><p>A software for automated NOE assignment</p>
-<blockquote>
-<div>Version 2.3</div></blockquote>
-</div></blockquote>
-</dd>
-<dt>Copyright (C) Benjamin Bardiaux, Michael Habeck, Therese Malliavin,</dt>
-<dd>Wolfgang Rieping, and Michael Nilges</dd>
-</dl>
-<p>All rights reserved.</p>
-<p>NO WARRANTY. This software package is provided ‘as is’ without warranty of
-any kind, expressed or implied, including, but not limited to the implied
-warranties of merchantability and fitness for a particular purpose or
-a warranty of non-infringement.</p>
-<p>Distribution of substantively modified versions of this module is
-prohibited without the explicit permission of the copyright holders.</p>
-<p>$Author: bardiaux $
-$Revision: 1.1.1.1 $
-$Date: 2010/03/23 15:27:16 $
-“â€â€œ</p>
-</div>
+
+ <h1>Python Module Index</h1>
+
+ <div class="modindex-jumpbox">
+ <a href="#cap-a"><strong>a</strong></a>
+ </div>
+
+ <table class="indextable modindextable">
+ <tr class="pcap"><td></td><td> </td><td></td></tr>
+ <tr class="cap" id="cap-a"><td></td><td>
+ <strong>a</strong></td><td></td></tr>
+ <tr>
+ <td><img src="_static/minus.png" class="toggler"
+ id="toggle-1" style="display: none" alt="-" /></td>
+ <td>
+ <code class="xref">aria</code></td><td>
+ <em></em></td></tr>
+ <tr class="cg-1">
+ <td></td>
+ <td>   
+ <a href="ariaec.html#module-aria.conbox"><code class="xref">aria.conbox</code></a></td><td>
+ <em></em></td></tr>
+ <tr class="cg-1">
+ <td></td>
+ <td>   
+ <a href="ariaec.html#module-aria.conbox.analysis"><code class="xref">aria.conbox.analysis</code></a></td><td>
+ <em></em></td></tr>
+ <tr class="cg-1">
+ <td></td>
+ <td>   
+ <a href="ariaec.html#module-aria.conbox.commands"><code class="xref">aria.conbox.commands</code></a></td><td>
+ <em></em></td></tr>
+ <tr class="cg-1">
+ <td></td>
+ <td>   
+ <a href="ariaec.html#module-aria.conbox.converter"><code class="xref">aria.conbox.converter</code></a></td><td>
+ <em></em></td></tr>
+ <tr class="cg-1">
+ <td></td>
+ <td>   
+ <a href="ariaec.html#module-aria.conbox.maplot"><code class="xref">aria.conbox.maplot</code></a></td><td>
+ <em></em></td></tr>
+ <tr class="cg-1">
+ <td></td>
+ <td>   
+ <a href="ariaec.html#module-aria.conbox.ndconv"><code class="xref">aria.conbox.ndconv</code></a></td><td>
+ <em></em></td></tr>
+ <tr class="cg-1">
+ <td></td>
+ <td>   
+ <a href="ariaec.html#module-aria.conbox.pdbdist"><code class="xref">aria.conbox.pdbdist</code></a></td><td>
+ <em></em></td></tr>
+ <tr class="cg-1">
+ <td></td>
+ <td>   
+ <a href="ariaec.html#module-aria.conbox.pdbqual"><code class="xref">aria.conbox.pdbqual</code></a></td><td>
+ <em></em></td></tr>
+ <tr class="cg-1">
+ <td></td>
+ <td>   
+ <a href="ariaec.html#module-aria.conbox.protein"><code class="xref">aria.conbox.protein</code></a></td><td>
+ <em></em></td></tr>
+ <tr class="cg-1">
+ <td></td>
+ <td>   
+ <a href="ariaec.html#module-aria.conbox.protmap"><code class="xref">aria.conbox.protmap</code></a></td><td>
+ <em></em></td></tr>
+ <tr class="cg-1">
+ <td></td>
+ <td>   
+ <a href="ariaec.html#module-aria.conbox.reader"><code class="xref">aria.conbox.reader</code></a></td><td>
+ <em></em></td></tr>
+ <tr class="cg-1">
+ <td></td>
+ <td>   
+ <a href="ariaec.html#module-aria.conbox.settings"><code class="xref">aria.conbox.settings</code></a></td><td>
+ <em></em></td></tr>
+ <tr class="cg-1">
+ <td></td>
+ <td>   
+ <a href="ariaec.html#module-aria.conbox.setup"><code class="xref">aria.conbox.setup</code></a></td><td>
+ <em></em></td></tr>
+ </table>
</div>
@@ -195,7 +249,7 @@ $Date: 2010/03/23 15:27:16 $
<div role="contentinfo">
<p>
- © <a href="#">Copyright</a> 2017, Benjamin Bardiaux, Michael Habeck, Therese Malliavin, Wolfgang Rieping, and Michael Nilges.
+ © Copyright 2017, Fabrice Allain, Benjamin Bardiaux, Michael Habeck, Therese Malliavin, Wolfgang Rieping, and Michael Nilges.
</p>
</div>
@@ -217,7 +271,7 @@ $Date: 2010/03/23 15:27:16 $
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
- VERSION:'4',
+ VERSION:'0.3',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
HAS_SOURCE: true,
diff --git a/docs/_build/html/search.html b/examples-dev/olds/_build/html/search.html
similarity index 89%
rename from docs/_build/html/search.html
rename to examples-dev/olds/_build/html/search.html
index f65054604e9dbd9c848d59ff6142e3ec26bf77fe..392f0e7a1590618b0ef7a0569d69fb6c16bd7497 100644
--- a/docs/_build/html/search.html
+++ b/examples-dev/olds/_build/html/search.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>Search — ARIA 4 documentation</title>
+ <title>Search — Aria-EC 0.3 documentation</title>
@@ -35,8 +35,7 @@
<link rel="index" title="Index"
href="genindex.html"/>
<link rel="search" title="Search" href="#"/>
- <link rel="copyright" title="Copyright" href="copyright.html"/>
- <link rel="top" title="ARIA 4 documentation" href="index.html"/>
+ <link rel="top" title="Aria-EC 0.3 documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script>
@@ -55,7 +54,7 @@
- <a href="index.html" class="icon icon-home"> ARIA
+ <a href="index.html" class="icon icon-home"> Aria-EC
@@ -65,7 +64,7 @@
<div class="version">
- 2
+ 0.3
</div>
@@ -103,7 +102,7 @@
<nav class="wy-nav-top" role="navigation" aria-label="top navigation">
<i data-toggle="wy-nav-top" class="fa fa-bars"></i>
- <a href="index.html">ARIA</a>
+ <a href="index.html">Aria-EC</a>
</nav>
@@ -174,7 +173,7 @@
<div role="contentinfo">
<p>
- © <a href="copyright.html">Copyright</a> 2017, Benjamin Bardiaux, Michael Habeck, Therese Malliavin, Wolfgang Rieping, and Michael Nilges.
+ © Copyright 2017, Fabrice Allain, Benjamin Bardiaux, Michael Habeck, Therese Malliavin, Wolfgang Rieping, and Michael Nilges.
</p>
</div>
@@ -196,7 +195,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
- VERSION:'4',
+ VERSION:'0.3',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
HAS_SOURCE: true,
diff --git a/examples-dev/olds/_build/html/searchindex.js b/examples-dev/olds/_build/html/searchindex.js
new file mode 100644
index 0000000000000000000000000000000000000000..f7428e485f4292058f1b09149dbed003ffaab010
--- /dev/null
+++ b/examples-dev/olds/_build/html/searchindex.js
@@ -0,0 +1 @@
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0,observ:0,off:0,offset:0,one:0,onli:0,option:0,ordereddict:0,other:0,out_fil:0,outdir:0,outdir_path:0,outfil:0,outprefix:0,output:0,over:0,page:2,pair:0,pair_list:0,pairdict:0,palett:0,panda:0,paper:0,param:0,paramet:0,pars:0,path:0,pbxplore:0,pca:0,pca_project:0,pconsc1:0,pconsc2:0,pconsc:0,pdb:0,pdbfile:0,pdbid:0,pdbparser:0,pdbpath:0,pdbreg:0,pdbstat:0,pdf:0,phe1:0,phi:0,physic:0,pickler:0,pics:0,pisc:0,pkg:0,plm:0,plm_score:0,plmc:0,plmdca:0,plmev:0,plot:0,plot_dpi:0,plot_ext:0,plotag:0,plotdir:0,plotflush:0,pos:0,pos_filt:0,posit:0,predict:0,prefix:0,pro:0,process:0,product:0,product_typ:0,program:0,project:0,prospective_fil:0,proteinmap:0,protmapcollect:0,protocol:0,provid:0,proxim:0,psi:0,psicov:0,psipred2_reg:0,psipred3_reg:0,psipred_reg:0,python:0,qual:0,qualiti:0,rac:0,read:0,read_indextableplu:0,read_pdb:0,read_psipr:0,read_seq:0,read_ssdist:0,readabl:0,readablefil:0,readtopo:0,reduc:0,reduct:0,refer:0,regex:0,regexfil:0,regulatori:0,rel:0,relat:0,relev:0,remov:0,report:0,repres:0,res1:0,res2:0,res:0,resatmmap:0,residu:0,resmap:0,restatement_reg:0,restraint:0,rm_list:0,root:0,rosenth:0,rtype:0,run:0,run_tbl2xml:0,save:0,save_fig:0,saveplot:0,scale:0,scale_scor:0,scatter:0,score:0,score_field:0,scoremap:0,scratch:0,script:0,scsc:0,scsc_min:0,search:2,sec_struct:0,secondari:0,secstruct:0,section:0,see:0,select:0,self:0,seq:0,seq_po:0,seq_sublist:0,seqfil:0,seqidx:0,seqlen:0,seqpath:0,sequenc:0,sequencelist:0,seri:0,server:0,set_aa_sequ:0,set_sec_struct:0,set_valu:0,sett:0,should:0,side:0,similar:0,size_fig:0,soheil:0,sort:0,sortedset:0,sourc:0,spec:0,specif:0,sqrt:0,squar:0,sre_pattern:0,ss2:0,ss_dist:0,ss_dist_reg:0,ss_type:0,ssaaatmmap:0,ssclash:0,ssclash_filt:0,ssdist:0,ssdist_fil:0,ssdist_filenam:0,ssdistpath:0,ssidx:0,sslist:0,start:0,startres_reg:0,step:0,str:0,string:0,structur:0,subcommand:0,subfil:0,supplementari:0,sym:0,symmetr:0,sync_index:0,target:0,targetdist:0,targetdistmap:0,targetmap:0,tbl2xml:0,tbl:0,tbl_file:0,tbl_path:0,tbldist:0,tbldistfil:0,templat:0,test:[],them:0,thi:0,threshold:0,titl:0,to_seri:0,tool:0,toolbox:0,top:0,topallhdg5:0,topmap:0,topo:0,topolog:0,topologyfil:0,translat:0,treshold:0,triangl:0,tupl:0,txt:0,type:0,unic:0,upd_mol:0,updat:0,update_map:0,upper:0,upperbound:0,usag:0,use:0,used:0,using:0,valu:0,violation_analysi:0,visual:0,wang:0,weight:0,where:0,which:0,write:0,write_ariaproject:0,write_config:0,write_contact:0,write_dihedral_tbl:0,write_dist_xml:0,write_filtout:0,write_hb_tbl:0,write_map_restraint:0,write_maplist_restraint:0,write_optional_fil:0,write_seq:0,write_ssdist_tbl:0,write_ssfasta:0,write_tbl_restraint:0,write_xmlseq:0,xlabel:0,xml:0,xml_path:0,y_pred:0,y_score:0,y_true:0,ylabel:0,zlabel:0},titles:["aria.conbox package","ariaec.test package","Welcome to Aria-EC\u2019s documentation!","ariaec"],titleterms:{analysi:0,aria:[0,2],ariaec:[1,3],base:0,command:0,conbox:0,content:[0,1],convert:0,document:2,indic:2,maplot:0,modul:[0,1],ndconv:0,packag:[0,1],pdbdist:0,pdbqual:0,protein:0,protmap:0,reader:0,set:0,setup:0,submodul:0,subpackag:0,tabl:2,test:1,welcom:2}})
\ No newline at end of file
diff --git a/examples-dev/olds/ariaec.rst b/examples-dev/olds/ariaec.rst
new file mode 100644
index 0000000000000000000000000000000000000000..36ab6ad0b679be8e09552c381ea7607bf629deac
--- /dev/null
+++ b/examples-dev/olds/ariaec.rst
@@ -0,0 +1,114 @@
+Conbox module
+============
+
+.. toctree::
+
+.. automodule:: aria.conbox
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+Analysis
+--------
+
+.. automodule:: aria.conbox.analysis
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+Base
+----
+
+.. automodule:: aria.conbox.base
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+Commands
+--------
+
+.. automodule:: aria.conbox.commands
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+Converter
+---------
+
+.. automodule:: aria.conbox.converter
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+Maplot
+------
+
+.. automodule:: aria.conbox.maplot
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+aria.conbox.ndconv module
+-------------------------
+
+.. automodule:: aria.conbox.ndconv
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+aria.conbox.pdbdist module
+--------------------------
+
+.. automodule:: aria.conbox.pdbdist
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+aria.conbox.pdbqual module
+--------------------------
+
+.. automodule:: aria.conbox.pdbqual
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+aria.conbox.protein module
+--------------------------
+
+.. automodule:: aria.conbox.protein
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+aria.conbox.protmap module
+--------------------------
+
+.. automodule:: aria.conbox.protmap
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+aria.conbox.reader module
+-------------------------
+
+.. automodule:: aria.conbox.reader
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+aria.conbox.settings module
+---------------------------
+
+.. automodule:: aria.conbox.settings
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+aria.conbox.setup module
+------------------------
+
+.. automodule:: aria.conbox.setup
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
diff --git a/examples-dev/olds/ariaec.test.rst b/examples-dev/olds/ariaec.test.rst
new file mode 100644
index 0000000000000000000000000000000000000000..8813337fd0c5d4145318936b602a55b20912fba0
--- /dev/null
+++ b/examples-dev/olds/ariaec.test.rst
@@ -0,0 +1,10 @@
+ariaec.test package
+===================
+
+Module contents
+---------------
+
+.. automodule:: ariaec.test
+ :members:
+ :undoc-members:
+ :show-inheritance:
diff --git a/examples-dev/olds/index.rst b/examples-dev/olds/index.rst
new file mode 100644
index 0000000000000000000000000000000000000000..c213df6f85ef924e67d93b9ad7c0bb1d687239bf
--- /dev/null
+++ b/examples-dev/olds/index.rst
@@ -0,0 +1,20 @@
+.. AriaEc documentation master file, created by
+ sphinx-quickstart on Fri Apr 21 16:27:42 2017.
+ You can adapt this file completely to your liking, but it should at least
+ contain the root `toctree` directive.
+
+Welcome to Aria-EC's documentation!
+===================================
+
+.. toctree::
+ :maxdepth: 2
+ :caption: Contents:
+
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`
diff --git a/examples-dev/olds/make.bat b/examples-dev/olds/make.bat
new file mode 100644
index 0000000000000000000000000000000000000000..b024aeae70b3da1d99c1c6e0f1ce9cfdf0d87196
--- /dev/null
+++ b/examples-dev/olds/make.bat
@@ -0,0 +1,36 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+ set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=.
+set BUILDDIR=_build
+set SPHINXPROJ=AriaEc
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+ echo.
+ echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+ echo.installed, then set the SPHINXBUILD environment variable to point
+ echo.to the full path of the 'sphinx-build' executable. Alternatively you
+ echo.may add the Sphinx directory to PATH.
+ echo.
+ echo.If you don't have Sphinx installed, grab it from
+ echo.http://sphinx-doc.org/
+ exit /b 1
+)
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS%
+
+:end
+popd
diff --git a/docs/modules.rst b/examples-dev/olds/modules.rst
similarity index 100%
rename from docs/modules.rst
rename to examples-dev/olds/modules.rst
diff --git a/setup.py b/setup.py
index a9c197330e981b9dff7d843d03548089320bc15a..e49af7d5ba0e015ae40abbcb7eb5f2e483305b45 100644
--- a/setup.py
+++ b/setup.py
@@ -111,7 +111,7 @@ class CleanCommand(Command):
'./*.egg-info ./*.egg')
-def get_version():
+def get_version(full=True):
"""
Returns
@@ -119,7 +119,7 @@ def get_version():
"""
d = dirname(__file__)
-
+ # TODO: actually no warning when git command is not available !!
if isdir(join(d, '.git')):
# Get the version using "git describe".
cmd = 'git describe --tags'.split()
@@ -130,8 +130,11 @@ def get_version():
sys.exit(1)
# PEP 386 compatibility
- if '-' in version:
+
+ if '-' in version and full:
version = '.post'.join(version.split('-')[:2])
+ else:
+ version = version.split('-')[0]
# Don't declare a version "dirty" merely because a time stamp has
# changed. If it is dirty, append a ".dev1" suffix to indicate a
@@ -147,7 +150,7 @@ def get_version():
print('Unable to get git index status')
sys.exit(1)
- if dirty != '':
+ if dirty != '' and full:
version += '.dev1'
else:
@@ -206,6 +209,7 @@ def setup_package():
'six>=1.10',
'Sphinx',
'sphinx_rtd_theme',
+ # 'sphinx_bootstrap_theme',
'sphinxcontrib-napoleon',
'configparser',
'mako',