Updated API doc

aria/conbox/analysis.py

 # coding=utf-8
-"""
-Created on 4/7/17
-
-@author: fallain
-"""
+"""Analysis tools for protein ensembles"""
 import logging
 import matplotlib.pyplot as plt
 import numpy as np
 import os
 import re
-import sys
 import seaborn as sns
 from Bio.PDB.Residue import Residue
 from Bio.PDB import PDBParser, PDBIO
@@ -37,29 +32,27 @@ def colscatter(X, axe, colors, ndim=2, axtitle="", xlabel="x",
 
     Parameters
     ----------
-    X :
-
-    axe :
-
-    colors :
-
-    ndim :
-         (Default value = 2)
+    X : array-like, shape (n_samples, n_components)
+        matrix used for plotting
+    axe : matplotlib.Axes
+        Axes object containing the plot
+    colors : list of int
+        color indexes
+    ndim : int
+         Number of components extracted for the plot (Default value = 2)
     axtitle :
-         (Default value = "")
-    xlabel :
-         (Default value = "x")
-    ylabel :
-         (Default value = "y")
-    zlabel :
-         (Default value = "z")
-    legend_prefix :
-         (Default value = "")
-    others :
-         (Default value = False)
-
-    Returns
-    -------
+         Plot title (Default value = "")
+    xlabel : str
+         X axis label (Default value = "x")
+    ylabel : str
+         Y axis label (Default value = "y")
+    zlabel : str
+         Z axis label (Default value = "z")
+    legend_prefix : str
+         Add a prefix to the legend (Default value = "")
+    others : bool
+         If the last legend label should contain or not `prefix` (Default
+         value = False)
 
     """
     palette = sns.color_palette("hls", len(set(colors)))
@@ -107,8 +100,9 @@ class EnsembleAnalysis(object):
 
         Returns
         -------
+        list_of_pdb : list of str
+            List of pdb file path
 
-        
         """
         # Get the list of all the generated structures in iteration path if no
         # clustering. Otherwise, get the list of all generated structures
@@ -140,7 +134,7 @@ class EnsembleAnalysis(object):
         Parameters
         ----------
         clusteridx
-        project : aria.Project.Project object
+        project : :class:`aria.core.Project.Project` object
         iteration_id : 
         restraints :
             
@@ -411,8 +405,6 @@ class EnsembleAnalysis(object):
             LOG.info("Reading native structure")
             logging.captureWarnings(True)
             parser = PDBParser()
-            from aria.core.Chain import Chain
-            from aria.core.Molecule import Molecule
 
             # Since segids can be unfilled in the native pdb file, we check here
             # the values according to segid in molecule object

aria/conbox/common.py

@@ -62,6 +62,7 @@ class TqdmToLogger(io.StringIO):
         """
         self.logger.log(self.level, self.buf)
 
+
 # Code below adapated from an answer of klaus se on stackoverflow
 # (http://stackoverflow.com/a/16071616)
 def worker(f, task_queue, done_queue):

aria/conbox/converter.py

@@ -51,7 +51,7 @@ class AriaEcBbConverter(object):
         self.outprefix = ''
 
     def run(self):
-        """BBConverter command"""
+        """BBConverter main command"""
         # Check input
         """
         main method
@@ -101,28 +101,30 @@ class AriaEcBbConverter(object):
     @staticmethod
     def compute_diversityvalue(msa, seqlen):
         """
-        Compute bbcontacts diversity value
+        Compute diversity score related to multiple sequence alignment
 
         Parameters
         ----------
-        msa : `str`
+        msa : str
             multiple sequence alignment file path
-        seqlen : `int`
+        seqlen : int
             protein sequence length
 
         Returns
         -------
-        diversity_score : `float`
-            
+        diversity_score : float
+            Diversity score
 
         Notes
         -----
-            Diversity score correspond to the square root of the multiple
-            sequence alignment length (:math:`m`) over the length of the protein
-            sequence (:math:`l`)
-        
-            .. math:: Divscore = \frac{\sqrt{m}}{l}
+        Diversity score correspond to the square root of the multiple
+        sequence alignment length (:math:`m`) over the length of the protein
+        sequence (:math:`l`)
+
+        .. math:: Divscore = \\frac{\\sqrt{m}}{l}
+
         """
+
         msa_reg = re.compile(r"^>[A-Za-z0-9]+_[A-Za-z0-9]+")
         msalen = 0
 
@@ -1819,6 +1821,10 @@ class AriaEcXMLConverter(AriaXMLConverter):
 
 
 class AriaEcConfigConverter(object):
+    """
+    Configuration file converter
+    """
+
     OUTFILE = "configs.csv"
 
     def __init__(self, settings):
@@ -1855,6 +1861,7 @@ class AriaEcConfigConverter(object):
         ----------
         path: str
             Path to the config file
+        data :
 
         Returns
         -------

aria/core/__init__.py

 # coding=utf-8
 """
-
-          ARIA -- Ambiguous Restraints for Iterative Assignment
-
-                 A software for automated NOE assignment
-
-                               Version 2.3
-
-
-Copyright (C) Benjamin Bardiaux, Michael Habeck, Therese Malliavin,
-              Wolfgang Rieping, and Michael Nilges
-
-All rights reserved.
-
-
-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.
-
-Distribution of substantively modified versions of this module is
-prohibited without the explicit permission of the copyright holders.
-
-$Author: bardiaux $
-$Revision: 1.1.1.1 $
-$Date: 2010/03/23 15:27:24 $
+            ARIA - Ambiguous Restraints for Iterative Assignment
+                A software for automated NOE assignment
 """
 
 __all__ = ["Analyser", "ariabase", "AriaPeak", "AriaXML", "Assignment",

docs/_static/mycss.css

+/* MAKE figures float left to emulate multi-figure environments */
+
+div.figure {
+    float:left;
+    margin: 10px;
+    border: 1px dashed;
+    padding: 10px;
+}
+
+div.figure p.caption {
+    text-align: center;
+}
+
+
+/* necessary to have line-break between last figure and text. */
+
+div.section p {
+    clear: left;
+}
\ No newline at end of file

docs/api/aria.aria2.rst

+
+:autogenerated:
+
+aria.aria2 module
+=================
+
+.. currentmodule:: aria.aria2
+
+.. automodule:: aria.aria2
+    :members: check_numeric_slice, check_python, convert, convert_data, default_printer, get_path, get_project_name, invalid_args, load_project, main, parse_args, print_sequence, print_spectrum, print_template_structure, project_info, run_aria, run_gui, setup_aria, show_help, welcome, write_project_template
+    :undoc-members:
+    :show-inheritance:
+    :member-order: bysource
+
+    Summary
+    -------
+
+    Functions:
+
+    .. autosummary::
+        :nosignatures:
+
+        check_numeric_slice
+        check_python
+        convert
+        convert_data
+        default_printer
+        get_path
+        get_project_name
+        invalid_args
+        load_project
+        main
+        parse_args
+        print_sequence
+        print_spectrum
+        print_template_structure
+        project_info
+        run_aria
+        run_gui
+        setup_aria
+        show_help
+        welcome
+        write_project_template
+
+
+
+
+
+    Reference
+    ---------
\ No newline at end of file

docs/api/aria.check.rst

+
+:autogenerated:
+
+aria.check module
+=================
+
+.. currentmodule:: aria.check
+
+.. automodule:: aria.check
+    :members: check_ccpn, check_numeric, check_numeric_slice, check_pylab, check_python, check_scientific, check_tix
+    :undoc-members:
+    :show-inheritance:
+    :member-order: bysource
+
+    Summary
+    -------
+
+    Functions:
+
+    .. autosummary::
+        :nosignatures:
+
+        check_ccpn
+        check_numeric
+        check_numeric_slice
+        check_pylab
+        check_python
+        check_scientific
+        check_tix
+
+
+
+
+
+    Reference
+    ---------
\ No newline at end of file

docs/api/aria.conbox.analysis.rst

+
+:autogenerated:
+
+aria.conbox.analysis module
+===========================
+
+.. currentmodule:: aria.conbox.analysis
+
+.. automodule:: aria.conbox.analysis
+    :members: EnsembleAnalysis, colscatter
+    :undoc-members:
+    :show-inheritance:
+    :member-order: bysource
+
+    Summary
+    -------
+
+    Classes:
+
+    .. autosummary::
+        :nosignatures:
+
+        EnsembleAnalysis
+
+    Functions:
+
+    .. autosummary::
+        :nosignatures:
+
+        colscatter
+
+
+
+
+
+    Reference
+    ---------
\ No newline at end of file

docs/api/aria.conbox.commands.rst

+
+:autogenerated:
+
+aria.conbox.commands module
+===========================
+
+.. currentmodule:: aria.conbox.commands
+
+.. automodule:: aria.conbox.commands
+    :members: AriaEcCommands, ReadableFile, check_file, main, seqrange_type
+    :undoc-members:
+    :show-inheritance:
+    :member-order: bysource
+
+    Summary
+    -------
+
+    Classes:
+
+    .. autosummary::
+        :nosignatures:
+
+        AriaEcCommands
+        ReadableFile
+
+    Functions:
+
+    .. autosummary::
+        :nosignatures:
+
+        check_file
+        main
+        seqrange_type
+
+
+
+
+
+    Reference
+    ---------
\ No newline at end of file

docs/api/aria.conbox.common.rst

+
+:autogenerated:
+
+aria.conbox.common module
+=========================
+
+.. currentmodule:: aria.conbox.common
+
+.. automodule:: aria.conbox.common
+    :members: Capturing, CommandProtocol, CustomLogging, NotDisordered, RedirectStdStreams, TqdmToLogger, addtup, cart_dist, format_dict, format_str, get_filename, parmap, ppdict, reg_load, sort_2dict, tickmin, tickrot, titleprint, worker
+    :undoc-members:
+    :show-inheritance:
+    :member-order: bysource
+
+    Summary
+    -------
+
+    Classes:
+
+    .. autosummary::
+        :nosignatures:
+
+        Capturing
+        CommandProtocol
+        CustomLogging
+        NotDisordered
+        RedirectStdStreams
+        TqdmToLogger
+
+    Functions:
+
+    .. autosummary::
+        :nosignatures:
+
+        addtup
+        cart_dist
+        format_dict
+        format_str
+        get_filename
+        parmap
+        ppdict
+        reg_load
+        sort_2dict
+        tickmin
+        tickrot
+        titleprint
+        worker
+
+
+
+
+
+    Reference
+    ---------
\ No newline at end of file

docs/api/aria.conbox.converter.rst

+
+:autogenerated:
+
+aria.conbox.converter module
+============================
+
+.. currentmodule:: aria.conbox.converter
+
+.. automodule:: aria.conbox.converter
+    :members: AriaEcBbConverter, AriaEcConfigConverter, AriaEcXMLConverter, AriaXMLConverter
+    :undoc-members:
+    :show-inheritance:
+    :member-order: bysource
+
+    Summary
+    -------
+
+    Classes:
+
+    .. autosummary::
+        :nosignatures:
+
+        AriaEcBbConverter
+        AriaEcConfigConverter
+        AriaEcXMLConverter
+        AriaXMLConverter
+
+
+
+
+
+    Reference
+    ---------
\ No newline at end of file

docs/api/aria.conbox.maplot.rst

+
+:autogenerated:
+
+aria.conbox.maplot module
+=========================
+
+.. currentmodule:: aria.conbox.maplot
+
+.. automodule:: aria.conbox.maplot
+    :members: AriaEcContactMap
+    :undoc-members:
+    :show-inheritance:
+    :member-order: bysource
+
+    Summary
+    -------
+
+    Classes:
+
+    .. autosummary::
+        :nosignatures:
+
+        AriaEcContactMap
+
+
+
+
+
+    Reference
+    ---------
\ No newline at end of file

docs/api/aria.conbox.ndconv.rst

+
+:autogenerated:
+
+aria.conbox.ndconv module
+=========================
+
+.. currentmodule:: aria.conbox.ndconv
+
+.. automodule:: aria.conbox.ndconv
+    :members: net_deconv
+    :undoc-members:
+    :show-inheritance:
+    :member-order: bysource
+
+    Summary
+    -------
+
+    Functions:
+
+    .. autosummary::
+        :nosignatures:
+
+        net_deconv
+
+
+
+
+
+    Reference
+    ---------
\ No newline at end of file

docs/api/aria.conbox.pdbdist.rst

+
+:autogenerated:
+
+aria.conbox.pdbdist module
+==========================
+
+.. currentmodule:: aria.conbox.pdbdist
+
+.. automodule:: aria.conbox.pdbdist
+    :members: PDBDist
+    :undoc-members:
+    :show-inheritance:
+    :member-order: bysource
+
+    Summary
+    -------
+
+    Classes:
+
+    .. autosummary::
+        :nosignatures:
+
+        PDBDist
+
+
+
+
+
+    Reference
+    ---------
\ No newline at end of file

docs/api/aria.conbox.pdbqual.rst

+
+:autogenerated:
+
+aria.conbox.pdbqual module
+==========================
+
+.. currentmodule:: aria.conbox.pdbqual
+
+.. automodule:: aria.conbox.pdbqual
+    :members: AriaEcPdbqual
+    :undoc-members:
+    :show-inheritance:
+    :member-order: bysource
+
+    Summary
+    -------
+
+    Classes:
+
+    .. autosummary::
+        :nosignatures:
+
+        AriaEcPdbqual
+
+
+
+
+
+    Reference
+    ---------
\ No newline at end of file

docs/api/aria.conbox.pdbstat.rst

+
+:autogenerated:
+
+aria.conbox.pdbstat module
+==========================
+
+.. currentmodule:: aria.conbox.pdbstat
+
+.. automodule:: aria.conbox.pdbstat
+    :members: PDBStat
+    :undoc-members:
+    :show-inheritance:
+    :member-order: bysource
+
+    Summary
+    -------
+
+    Classes:
+
+    .. autosummary::
+        :nosignatures:
+
+        PDBStat
+
+
+
+
+
+    Reference
+    ---------
\ No newline at end of file

docs/api/aria.conbox.protein.rst

+
+:autogenerated:
+
+aria.conbox.protein module
+==========================