Commit 3ee31409 authored by Fabrice  ALLAIN's avatar Fabrice ALLAIN
Browse files

Updated toctree & ariaec setup command within sphinx documentation

parent c650124c
examples/dev/
examples*dev/
examples/tmp/
docs/olds/
*.simg
......
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)
=====================================================
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/
......@@ -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
......
.. _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
:tocdepth: 2
.. _copyright:
Sphinx authors
==============
.. include:: ../COPYRIGHT
@import url("basic.css");
/* -- page layout ----------------------------------------------------------- */
body {
font-family: 'goudy old style', 'minion pro', 'bell mt', Georgia, 'Hiragino Mincho Pro', serif;
font-size: 17px;
background-color: #fff;
color: #000;
margin: 0;
padding: 0;
}
div.document {
width: 940px;
margin: 30px auto 0 auto;
}
div.documentwrapper {
float: left;
width: 100%;
}
div.bodywrapper {
margin: 0 0 0 220px;
}
div.sphinxsidebar {
width: 220px;
font-size: 14px;
line-height: 1.5;
}
hr {
border: 1px solid #B1B4B6;
}
div.body {
background-color: #fff;
color: #3E4349;
padding: 0 30px 0 30px;
}
div.body > .section {
text-align: left;
}
div.footer {
width: 940px;
margin: 20px auto 30px auto;
font-size: 14px;
color: #888;
text-align: right;
}
div.footer a {
color: #888;
}
p.caption {
font-family: inherit;
font-size: inherit;
}
div.relations {
display: none;
}
div.sphinxsidebar a {
color: #444;
text-decoration: none;
border-bottom: 1px dotted #999;
}
div.sphinxsidebar a:hover {
border-bottom: 1px solid #999;
}
div.sphinxsidebarwrapper {
padding: 18px 10px;
}
div.sphinxsidebarwrapper p.logo {
padding: 0;
margin: -10px 0 0 0px;
text-align: center;
}
div.sphinxsidebarwrapper h1.logo {
margin-top: -10px;
text-align: center;
margin-bottom: 5px;
text-align: left;
}
div.sphinxsidebarwrapper h1.logo-name {
margin-top: 0px;
}
div.sphinxsidebarwrapper p.blurb {
margin-top: 0;
font-style: normal;
}
div.sphinxsidebar h3,
div.sphinxsidebar h4 {
font-family: 'Garamond', 'Georgia', serif;
color: #444;
font-size: 24px;
font-weight: normal;
margin: 0 0 5px 0;
padding: 0;
}
div.sphinxsidebar h4 {
font-size: 20px;
}
div.sphinxsidebar h3 a {
color: #444;
}
div.sphinxsidebar p.logo a,
div.sphinxsidebar h3 a,
div.sphinxsidebar p.logo a:hover,
div.sphinxsidebar h3 a:hover {
border: none;
}
div.sphinxsidebar p {
color: #555;
margin: 10px 0;
}
div.sphinxsidebar ul {
margin: 10px 0;
padding: 0;
color: #000;
}
div.sphinxsidebar ul li.toctree-l1 > a {
font-size: 120%;
}
div.sphinxsidebar ul li.toctree-l2 > a {
font-size: 110%;
}
div.sphinxsidebar input {
border: 1px solid #CCC;
font-family: 'goudy old style', 'minion pro', 'bell mt', Georgia, 'Hiragino Mincho Pro', serif;
font-size: 1em;
}
div.sphinxsidebar hr {
border: none;
height: 1px;
color: #AAA;
background: #AAA;
text-align: left;
margin-left: 0;
width: 50%;
}
/* -- body styles ----------------------------------------------------------- */
a {
color: #004B6B;
text-decoration: underline;
}
a:hover {
color: #6D4100;
text-decoration: underline;
}
div.body h1,
div.body h2,
div.body h3,
div.body h4,
div.body h5,
div.body h6 {
font-family: 'Garamond', 'Georgia', serif;
font-weight: normal;
margin: 30px 0px 10px 0px;
padding: 0;
}
div.body h1 { margin-top: 0; padding-top: 0; font-size: 240%; }
div.body h2 { font-size: 180%; }
div.body h3 { font-size: 150%; }
div.body h4 { font-size: 130%; }
div.body h5 { font-size: 100%; }
div.body h6 { font-size: 100%; }
a.headerlink {
color: #DDD;
padding: 0 4px;
text-decoration: none;
}
a.headerlink:hover {
color: #444;
background: #EAEAEA;
}
div.body p, div.body dd, div.body li {
line-height: 1.4em;
}
div.admonition {
margin: 20px 0px;
padding: 10px 30px;
background-color: #EEE;
border: 1px solid #CCC;
}
div.admonition tt.xref, div.admonition code.xref, div.admonition a tt {
background-color: #FBFBFB;
border-bottom: 1px solid #fafafa;
}
div.admonition p.admonition-title {
font-family: 'Garamond', 'Georgia', serif;
font-weight: normal;
font-size: 24px;
margin: 0 0 10px 0;
padding: 0;
line-height: 1;
}
div.admonition p.last {
margin-bottom: 0;
}
div.highlight {
background-color: #fff;
}
dt:target, .highlight {
background: #FAF3E8;
}
div.warning {
background-color: #FCC;
border: 1px solid #FAA;
}
div.danger {
background-color: #FCC;
border: 1px solid #FAA;
-moz-box-shadow: 2px 2px 4px #D52C2C;
-webkit-box-shadow: 2px 2px 4px #D52C2C;
box-shadow: 2px 2px 4px #D52C2C;
}
div.error {
background-color: #FCC;
border: 1px solid #FAA;
-moz-box-shadow: 2px 2px 4px #D52C2C;
-webkit-box-shadow: 2px 2px 4px #D52C2C;
box-shadow: 2px 2px 4px #D52C2C;
}
div.caution {
background-color: #FCC;
border: 1px solid #FAA;
}
div.attention {
background-color: #FCC;
border: 1px solid #FAA;
}
div.important {
background-color: #EEE;
border: 1px solid #CCC;
}
div.note {
background-color: #EEE;
border: 1px solid #CCC;
}
div.tip {
background-color: #EEE;
border: 1px solid #CCC;
}
div.hint {
background-color: #EEE;
border: 1px solid #CCC;
}
div.seealso {
background-color: #EEE;
border: 1px solid #CCC;
}
div.topic {
background-color: #EEE;
}
p.admonition-title {
display: inline;
}
p.admonition-title:after {
content: ":";
}
pre, tt, code {
font-family: 'Consolas', 'Menlo', 'Deja Vu Sans Mono', 'Bitstream Vera Sans Mono', monospace;
font-size: 0.9em;
}
.hll {
background-color: #FFC;
margin: 0 -12px;
padding: 0 12px;
display: block;
}
img.screenshot {
}
tt.descname, tt.descclassname, code.descname, code.descclassname {
font-size: 0.95em;
}
tt.descname, code.descname {
padding-right: 0.08em;
}
img.screenshot {
-moz-box-shadow: 2px 2px 4px #EEE;
-webkit-box-shadow: 2px 2px 4px #EEE;
box-shadow: 2px 2px 4px #EEE;
}
table.docutils {
border: 1px solid #888;
-moz-box-shadow: 2px 2px 4px #EEE;
-webkit-box-shadow: 2px 2px 4px #EEE;
box-shadow: 2px 2px 4px #EEE;
}
table.docutils td, table.docutils th {
border: 1px solid #888;
padding: 0.25em 0.7em;
}