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Commit d46870ae authored by Fabrice ALLAIN's avatar Fabrice ALLAIN
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*: update tutorial doc & fix logger issue during cache data due to the previous rolleback

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docs/configuration.rst
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Configuration
Configuration
=============
The following tables list the available parameters with the corresponding
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docs/contents.rst
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......@@ -6,20 +6,8 @@
installation
configuration
usage
contributing
.. toctree::
:maxdepth: 2
:caption: Tutorial
tutorial
.. toctree::
:maxdepth: 2
:caption: Examples
examples/bpt1/bpt1
examples/malecoli/malecoli
contributing
.. toctree::
:maxdepth: 4
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docs/examples/bpt1/bpt1.rst deleted 100644 → 0
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docs/examples/malecoli/malecoli.rst deleted 100644 → 0
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MALE_ECOLI folding with EC and NMR restraints
=============================================
We show an example of structure calculation combining sparse NMR data and
evolutionary restraints from EVFold_ server. The files related to this example
can be found in the ``docs`` folder or :download:`here <../../examples.tar.gz>`
Setup
-----
.. warning::
We actually need an ARIA project file in the setup step if we want to mix
evolutionary with experimental restraints. Only the data section is
conserved actually. You still needs to give a configuration file for the
other project parameters.
.. code-block:: console
> ariaec setup examples/malecoli/data/MALE_ECOLI.fa examples/malecoli/data/MALE_ECOLI_contacts.evfold.out -t plmev -o examples/malecoli/out -c examples/malecoli/data/config.ini -p examples/malecoli/data/ariaproject_nmr.xml
**Output**
.. code-block:: console
================================================================================
ARIA Evolutive Contact toolbox
================================================================================
INFO Initialize settings
INFO Updating settings according to config file
INFO Making output directories
reading FASTA file examples/malecoli/data/MALE_ECOLI.fa
INFO Amino acid sequence: KIEEGKLVIWINGDKGYNGLAEVGKKFEKDTGIKVTVEHPDKLEEKFPQVAATGDGPDIIFWAHDRFGGYAQSGLLAEITPDKAFQDKLYPFTWDAVRYNGKLIAYPIAVEALSLIYNKDLLPNPPKTWEEIPALDKELKAKGKSALMFNLQEPYFTWPLIAADGGYAFKYENGKYDIKDVGVDNAGAKAGLTFLVDLIKNKHMNADTDYSIAEAAFNKGETAMTINGPWAWSNIDTSKVNYGVTVLPTFKGQPSKPFVGVLSAGINAASPNKELAKEFLENYLLTDEGLEAVNKDKPLGAVALKSYEEELAKDPRIAATMENAQKGEIMPNIPQMSAFWYAVRTAVINAASGRQTVDEALKDAQTRITK
INFO Reader focused on file(s) ['examples/malecoli/data/MALE_ECOLI_contacts.evfold.out'] ['evcoupling']
INFO Conkit doesn't support evcoupling
INFO Checking if file examples/malecoli/data/MALE_ECOLI_contacts.evfold.out correspond to evcoupling format
INFO Format type correct
INFO Reading examples/malecoli/data/MALE_ECOLI_contacts.evfold.out file
INFO Loading contact file
INFO Filtering evcoupling contact map
INFO ...Position filter
INFO ...Conservation filter
WARNING No conservation information. Can't use related filter
INFO ...Secondary structure clash filter
WARNING No secondary structure information. Can't use secondary structure filter
INFO ...Disulfure bridge unicity filter
INFO Setting contact number with treshold 1.0
INFO Update evcoupling maplot
INFO Update evcoupling scoremap
INFO Select top 370 contacts according to scoremap
writing to the file: examples/malecoli/out/etc/MALE_ECOLI.seq
INFO Load molecule file and convert it into xml format
MESSAGE [SequenceList]: reading sequence examples/malecoli/out/etc/
MALE_ECOLI.seq
reading examples/malecoli/out/etc/MALE_ECOLI.seq
INFO Writing tbl files ...
INFO Writing evcoupling ARIA XML distance restraints
INFO Using contact scores as selection criteria
INFO Selecting 370 contacts
INFO 0%| | 0/370 [00:00<?, ?it/s]
INFO 100%|##########| 370/370 [00:00<00:00, 855.92it/s]
INFO Write 370 xml distance restraints in examples/malecoli/out/xml/MALE_ECOLI_evcoupling.xml
INFO Loading aria template file aria/conbox/templates/aria_project_v2.3.4.xml
INFO Directory /tmp/MALE_ECOLI/evcoupling doesn't exist.
INFO Create new directory /tmp/MALE_ECOLI/evcoupling
WARNING No output file defined in host_command. You should add the output option (-o) to your command.
INFO Writing ARIA project file (examples/malecoli/out/ariaproject.xml)
INFO Reading ARIA project file
INFO Update spectrum data in project
INFO Update sequence data in project
INFO Update dihedrals data in project
INFO Update rdcs data in project
INFO Update rdcs annealing parameters
INFO Writing new ARIA xml file (examples/malecoli/out/ariaproject.xml)
INFO Generate contact file (examples/malecoli/out/etc/MALE_ECOLI_evcoupling_filtered.contact.txt)
.. _EVFold: http://evfold.org/evfold-web/evfold.do
\ No newline at end of file
docs/tutorial.rst
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src/aria/core/ariabase.py
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......@@ -258,8 +258,8 @@ class AriaBaseClass:
d['logger'] = logging.getLogger(self.__module__)
self.__dict__.update(d)
if self.__class__.display_debug:
logging.getLogger().setLevel(logging.DEBUG)
# if self.__class__.display_debug:
# logging.getLogger().setLevel(logging.DEBUG)
def __getstate__(self):
"""
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src/aria/core/tools.py
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......@@ -84,10 +84,13 @@ def Dump(this, filename, mode='w', as_string=0, gzip=0):
# Issues if we try to dump the logger since it contains the log file instance
# TODO: do better testing
def remove_logger(this):
if hasattr(elt, "items"):
for foo in elt.items():
if hasattr(this, "items"):
for foo in this.items():
if hasattr(foo, "logger"):
delattr(foo, "logger")
else:
if hasattr(this, "logger"):
delattr(this, "logger")
if type(this) == list:
for elt in this:
......
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