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Commit feb5e17f authored by Fabrice Allain's avatar Fabrice Allain
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Changed aria header docstrings in rest format

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README.rst
View file @ feb5e17f
......@@ -40,8 +40,6 @@ your python installation or virtual environment.
Then the easiest solution is to call the **pip** command below :
``pip install git+https://gitlab.pasteur.fr/bis-aria/ariaec``
.. TODO change line to code block console when gitlab rst rendering will
be solved
Even though it is not recommanded, another possibility is to download the ZIP_
or TAR_ version from Gitlab_, extract the files and run ``pip install .``
......
aria/__init__.py
View file @ feb5e17f
# 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 ..
.. ..
.. 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 $ ..
.. .......................................................................... ..
"""
import re
......
aria/aria2.py
View file @ feb5e17f
#!/usr/bin/env python
# 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 15:27:16 $
.. .......................................................................... ..
.. ARIA -- Ambiguous Restraints for Iterative Assignment ..
.. ..
.. A software for automated NOE assignment ..
.. ..
.. Version 2.3 ..
.. ..
.. ..
.. Copyright (C) Benjamin Bardiaux ..
.. Structural Bioinformatics, Institut Pasteur, Paris ..
.. ..
.. 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 $ ..
.. .......................................................................... ..
"""
from __future__ import absolute_import, division, print_function
from future.builtins import input
......
aria/check.py
View file @ feb5e17f
#!/usr/bin/env python
# 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 15:27:16 $
.. .......................................................................... ..
.. ARIA -- Ambiguous Restraints for Iterative Assignment ..
.. ..
.. A software for automated NOE assignment ..
.. ..
.. Version 2.3 ..
.. ..
.. ..
.. Copyright (C) Benjamin Bardiaux ..
.. Structural Bioinformatics, Institut Pasteur, Paris ..
.. ..
.. 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/conbox/ndconv.py
View file @ feb5e17f
......@@ -16,32 +16,27 @@ def net_deconv(npmat, beta=0.99, alpha=1, control=0):
This is a python implementation/translation of network deconvolution by
MIT-KELLIS LAB
LICENSE: MIT-KELLIS LAB
LICENSE: MIT-KELLIS LAB
AUTHORS:
AUTHORS:
Algorithm was programmed by Soheil Feizi.
Paper authors are S. Feizi, D. Marbach, M. Medard and M. Kellis
Python implementation: Gideon Rosenthal
REFERENCES:
For more details, see the following paper:
For more details, see the following paper:
Network Deconvolution as a General Method to Distinguish
Direct Dependencies over Networks
By: Soheil Feizi, Daniel Marbach, Muriel Medard and Manolis Kellis
Nature Biotechnology
--------------------------------------------------------------------------
ND.m: network deconvolution
--------------------------------------------------------------------------
DESCRIPTION:
USAGE:
mat_nd = ND(npmat)
mat_nd = ND(npmat,beta)
mat_nd = ND(npmat,beta,alpha,control)
USAGE:
mat_nd = ND(npmat)
mat_nd = ND(npmat,beta)
mat_nd = ND(npmat,beta,alpha,control)
INPUT ARGUMENTS:
......
aria/conbox/protmap.py
View file @ feb5e17f
......@@ -44,6 +44,7 @@ class Map(pd.DataFrame):
Examples
--------
Score/distance matrix
>>> d = Map(index=[0,1,2], columns=[0,1,2])
>>> d
0 1 2
......@@ -983,23 +984,13 @@ class ResAtmMap(ProteinMap):
"""
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
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
Parameters
Attributes
----------
Returns
-------
Examples
--------
"""
# def _constructor_expanddim(self):
......
aria/core/Analyser.py
View file @ feb5e17f
# 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 ..
.. ..
.. 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 $ ..
.. .......................................................................... ..
"""
from __future__ import absolute_import, division, print_function
......
aria/core/AriaPeak.py
View file @ feb5e17f
# 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 ..
.. ..
.. 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 $ ..
.. .......................................................................... ..
"""
# from . import CrossPeak as Xpk
......
aria/core/AriaXML.py
View file @ feb5e17f
# 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 ..
.. ..
.. 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 $ ..
.. .......................................................................... ..
"""
from __future__ import absolute_import
......
aria/core/Assignment.py
View file @ feb5e17f
"""
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 ..
.. ..
.. 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/core/AssignmentFilter.py
View file @ feb5e17f
"""
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 ..
.. ..
.. 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/core/Atom.py
View file @ feb5e17f
"""
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 ..
.. ..
.. 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 $ ..
.. .......................................................................... ..
"""
from .xmlutils import XMLBasePickler, XMLElement
......
aria/core/Calibrator.py
View file @ feb5e17f
"""
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 ..
.. ..
.. Version 2.3 ..
.. ..
.. ..
.. Copyright (C) Benjamin Bardiaux, Michael Habeck, Therese Malliavin, ..