diff --git a/README.rst b/README.rst
index fa6ddae9a54b09bf8f49b3424e4cc340773967a4..293444deabcb16a531bf2f97f0d0fa0d5d1fd36b 100644
--- a/README.rst
+++ b/README.rst
@@ -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 .``
diff --git a/aria/__init__.py b/aria/__init__.py
index b2fcc05667fddc12312af1e8850bbb2e533364bb..dc70bf95bcbf30009bbba5fd516178f8685bb35c 100644
--- a/aria/__init__.py
+++ b/aria/__init__.py
@@ -1,30 +1,30 @@
# 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
diff --git a/aria/aria2.py b/aria/aria2.py
index 25e3ea2b582fa39df6dc299ec5c9d0ba04389cf3..808524b38e29b6666ce24ee1e9b39fcfdbda783e 100644
--- a/aria/aria2.py
+++ b/aria/aria2.py
@@ -1,31 +1,31 @@
#!/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
diff --git a/aria/check.py b/aria/check.py
index ca334b0d111d17cf518aa5e970e67371bb5241f9..80bf21f0620c1ba51d1df2c0622e76a4422496fd 100644
--- a/aria/check.py
+++ b/aria/check.py
@@ -1,31 +1,31 @@
#!/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 $ ..
+.. .......................................................................... ..
"""
diff --git a/aria/conbox/ndconv.py b/aria/conbox/ndconv.py
index bba9fb32fb3828bfbd73dbaab2d0363c64b42947..6ab66df4537291f16abe21eef1e9aee696261077 100644
--- a/aria/conbox/ndconv.py
+++ b/aria/conbox/ndconv.py
@@ -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:
diff --git a/aria/conbox/protmap.py b/aria/conbox/protmap.py
index 8076ceb4f0980f2c85929c5041b189b987685d01..d78299837971022b01ed98e0eaf38eef649ecc9d 100644
--- a/aria/conbox/protmap.py
+++ b/aria/conbox/protmap.py
@@ -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):
diff --git a/aria/core/Analyser.py b/aria/core/Analyser.py
index f27fa2f2448e63a20649bee574d599e1c42285d7..291d9a9c219d2b8a612d77e07258eb03c69b956e 100644
--- a/aria/core/Analyser.py
+++ b/aria/core/Analyser.py
@@ -1,30 +1,30 @@
# 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
diff --git a/aria/core/AriaPeak.py b/aria/core/AriaPeak.py
index 5eb02a1499ea7e8d4cc6ecb4713aa27b3d5478cc..5056c79b475782991eda8e8d94fc672f28124e98 100644
--- a/aria/core/AriaPeak.py
+++ b/aria/core/AriaPeak.py
@@ -1,30 +1,30 @@
# 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
diff --git a/aria/core/AriaXML.py b/aria/core/AriaXML.py
index 06466c99956076b5172580b368a6bb82df65c3db..ea2ea9b71d48265c0eb5a5e463cd44a72843e45b 100644
--- a/aria/core/AriaXML.py
+++ b/aria/core/AriaXML.py
@@ -1,30 +1,30 @@
# 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
diff --git a/aria/core/Assignment.py b/aria/core/Assignment.py
index 6a5a5d1ce7a9f1744a62f9aa39606fd97001afbd..63022e47050b8a3eaf43235005b60e9f8f5036f7 100644
--- a/aria/core/Assignment.py
+++ b/aria/core/Assignment.py
@@ -1,29 +1,29 @@
"""
-
- 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 $ ..
+.. .......................................................................... ..
"""
diff --git a/aria/core/AssignmentFilter.py b/aria/core/AssignmentFilter.py
index f329e704582af55c09d02d401fb5b022d7f6d05d..50e4867f96969f6c0e78b1a05f0f0e07111f6d2d 100644
--- a/aria/core/AssignmentFilter.py
+++ b/aria/core/AssignmentFilter.py
@@ -1,29 +1,29 @@
"""
-
- 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 $ ..
+.. .......................................................................... ..
"""
diff --git a/aria/core/Atom.py b/aria/core/Atom.py
index af6c6cdb1ba32f4c5bc4d8b50d1b6a1d1be7f843..a25ddd9a213efbdd4df078a0d25766a998132bb6 100644
--- a/aria/core/Atom.py
+++ b/aria/core/Atom.py
@@ -1,29 +1,29 @@
"""
-
- 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
diff --git a/aria/core/Calibrator.py b/aria/core/Calibrator.py
index 4674a36ec39f0fea8380c98fc51323ec224c290c..f83773a00bdb3dd1467008640278baed797bc451 100644
--- a/aria/core/Calibrator.py
+++ b/aria/core/Calibrator.py
@@ -1,29 +1,29 @@
"""
-
- 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 .ariabase import AriaBaseClass
diff --git a/aria/core/Chain.py b/aria/core/Chain.py
index 2261a3034c266cb1c08a67f736972ff771b1db6b..87cda60405bdaad7f6244f5fedae65a59b01b8b7 100644
--- a/aria/core/Chain.py
+++ b/aria/core/Chain.py
@@ -1,30 +1,30 @@
# 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
diff --git a/aria/core/ChemicalShiftFilter.py b/aria/core/ChemicalShiftFilter.py
index cc9e6fa781808e4e04671b2234a7908968539787..c7286f0aedc07be96253dfc49688be933461d82f 100644
--- a/aria/core/ChemicalShiftFilter.py
+++ b/aria/core/ChemicalShiftFilter.py
@@ -1,29 +1,29 @@
"""
-
- 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 $ ..
+.. .......................................................................... ..
"""
diff --git a/aria/core/ChemicalShiftList.py b/aria/core/ChemicalShiftList.py
index 72b3c8604b8ae9b083ebc6fa500b99387cc6289c..dbfe678d5ef7b94f4eb3555b02c8d741e5fd10af 100644
--- a/aria/core/ChemicalShiftList.py
+++ b/aria/core/ChemicalShiftList.py
@@ -1,29 +1,29 @@
"""
-
- 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 $ ..
+.. .......................................................................... ..
"""
diff --git a/aria/core/Cluster.py b/aria/core/Cluster.py
index a477a2b67e482413bb4665139fef3f6980b717cc..1cb630cdd1aa3692609eae6e2a21bd5d5f26b4ff 100644
--- a/aria/core/Cluster.py
+++ b/aria/core/Cluster.py
@@ -1,30 +1,30 @@
# 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 .ariabase import AriaBaseClass, NO
@@ -317,8 +317,8 @@ class Clustering(AriaBaseClass, object):
def getLowestEnergyClusterEnsemble(self):
"""
Select ensemble with the lowest average total energy. If the density of
- the cluster is lowest or equal than the number of best structures option
- it select another cluster
+ the cluster is lowest or equal than the number of best structures
+ option it another cluster has been selected
Parameters
----------
@@ -435,4 +435,5 @@ class Clustering(AriaBaseClass, object):
return report
+
ClusteringSettings._xml_state = ClusteringXMLPickler()._xml_state
diff --git a/aria/core/Contribution.py b/aria/core/Contribution.py
index f61db454673738a250e2683e6ee57e3694245e3e..73aac4fce61e5fb3629588ebbdd5d387c0b7fa0c 100644
--- a/aria/core/Contribution.py
+++ b/aria/core/Contribution.py
@@ -1,29 +1,29 @@
"""
-
- 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 .ariabase import AriaBaseClass
diff --git a/aria/core/ContributionAssigner.py b/aria/core/ContributionAssigner.py
index 892be42db4f54cd0b06e15031c3ddbdf24ec9bb0..1d7834b7ff894fb9589473e561e99111ee142d94 100644
--- a/aria/core/ContributionAssigner.py
+++ b/aria/core/ContributionAssigner.py
@@ -1,29 +1,29 @@
"""
-
- 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 .ariabase import AriaBaseClass
diff --git a/aria/core/ConversionTable.py b/aria/core/ConversionTable.py
index 8caa567be531fde5b249f77172850752209a7388..5cdd7ad756e82fff3b8e006863890b3995d8b6dd 100644
--- a/aria/core/ConversionTable.py
+++ b/aria/core/ConversionTable.py
@@ -1,30 +1,30 @@
# 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 .ariabase import AriaBaseClass
@@ -48,19 +48,10 @@ class ConversionTable(AriaBaseClass):
"""
Molecule conversion table for atom names
- Class Attributes
- ----------
- formats: list
- atom name conventions
-
- Parameters
- ----------
-
- Returns
- -------
-
Attributes
----------
+ formats : list
+ atom name conventions
table: dict
conversion table for amino acids, dna or rna molecules
"""
diff --git a/aria/core/CovalentDistances.py b/aria/core/CovalentDistances.py
index 9fb5dfa56e46bf42eb6be2ef1f33b21e8af46370..a2e3085a03702544f43612b89f6b78a9c165df59 100644
--- a/aria/core/CovalentDistances.py
+++ b/aria/core/CovalentDistances.py
@@ -1,29 +1,29 @@
"""
-
- 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 $ ..
+.. .......................................................................... ..
"""
diff --git a/aria/core/CrossPeak.py b/aria/core/CrossPeak.py
index 7f608392ba7219338d300870929a9d5a92efc824..da0af3f61f9d069ff54bf01b17d24309728f2637 100644
--- a/aria/core/CrossPeak.py
+++ b/aria/core/CrossPeak.py
@@ -1,29 +1,29 @@
"""
-
- 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 $ ..
+.. .......................................................................... ..
"""
diff --git a/aria/core/CrossPeakFilter.py b/aria/core/CrossPeakFilter.py
index e8b761cacfffc5cfe44fdafe07c8ac467b81881f..123e2540fbd7b381e624dad2543b225ca345a65e 100644
--- a/aria/core/CrossPeakFilter.py
+++ b/aria/core/CrossPeakFilter.py
@@ -1,29 +1,29 @@
"""
-
- 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 $ ..
+.. .......................................................................... ..
"""
diff --git a/aria/core/DataContainer.py b/aria/core/DataContainer.py
index 0411e304fcfd6c79ed542b57eed874a774b098a0..f0812cab1f353ef6812910c3b0dcf59edec5d6cd 100644
--- a/aria/core/DataContainer.py
+++ b/aria/core/DataContainer.py
@@ -1,30 +1,30 @@
# 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 .ariabase import *
diff --git a/aria/core/Datum.py b/aria/core/Datum.py
index b13575ee5261c85ac1b8ccdef81a7115ea7b3f08..3ce511a5e257c996b8e4e87845cbf2b82f2fbf5d 100644
--- a/aria/core/Datum.py
+++ b/aria/core/Datum.py
@@ -1,29 +1,29 @@
"""
-
- 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 $ ..
+.. .......................................................................... ..
"""
diff --git a/aria/core/Experiment.py b/aria/core/Experiment.py
index f8d25056193ca445f3b09699607da6b0d9b97c01..25cc355743049a43cb564eaa72c5c1b27322d304 100644
--- a/aria/core/Experiment.py
+++ b/aria/core/Experiment.py
@@ -1,29 +1,29 @@
"""
-
- 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 $ ..
+.. .......................................................................... ..
"""
diff --git a/aria/core/Factory.py b/aria/core/Factory.py
index 9305880b5a7bedc5e9220aee5014c0dd65728359..f04ac37b0ebd6a9dd5664a75fda65843b710a184 100644
--- a/aria/core/Factory.py
+++ b/aria/core/Factory.py
@@ -1,29 +1,29 @@
"""
-
- 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 .ariabase import AriaBaseClass
diff --git a/aria/core/FloatFile.py b/aria/core/FloatFile.py
index d703e5db8710d597f1ff4d90f4f8eb48652ffb6f..5b751738e14dc11bf2e0981336cc4f17e8a27640 100644
--- a/aria/core/FloatFile.py
+++ b/aria/core/FloatFile.py
@@ -1,29 +1,29 @@
"""
-
- 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 $ ..
+.. .......................................................................... ..
"""
diff --git a/aria/core/Infrastructure.py b/aria/core/Infrastructure.py
index 8a69260c4adc75fd263b540a5217235077aab35d..a1a2252ac0e77bd6288a1ab1f4628e56b7f0f6d6 100644
--- a/aria/core/Infrastructure.py
+++ b/aria/core/Infrastructure.py
@@ -1,30 +1,30 @@
# 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 .ariabase import *
diff --git a/aria/core/Iteration.py b/aria/core/Iteration.py
index 58fed38d284b54cb69996d2ad5db96e90552e317..f5961b8dccd0f275c920f028721d2717bc481732 100644
--- a/aria/core/Iteration.py
+++ b/aria/core/Iteration.py
@@ -1,30 +1,30 @@
# 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 functools import reduce
diff --git a/aria/core/JobManager.py b/aria/core/JobManager.py
index 74a83a642d32fe0d145438c108fbfd846ff37189..4f9a6b6c97a43697315cf15aa9442de35a3a028a 100644
--- a/aria/core/JobManager.py
+++ b/aria/core/JobManager.py
@@ -1,29 +1,29 @@
"""
-
- 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 .TypeChecking import *
diff --git a/aria/core/Merger.py b/aria/core/Merger.py
index c74511e831b1799b23d7c625426f97d3a4b32f28..013d72c14ea3f1b6d2f325fbf5a61953a813500d 100644
--- a/aria/core/Merger.py
+++ b/aria/core/Merger.py
@@ -1,29 +1,29 @@
"""
-
- 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 .ariabase import AriaBaseClass
diff --git a/aria/core/MolMol.py b/aria/core/MolMol.py
index fd8e632446a37b6af2fab917ce19accad7fcc82a..5aabacbeb5cf4b0528bb37dd0742df44312edf40 100644
--- a/aria/core/MolMol.py
+++ b/aria/core/MolMol.py
@@ -1,29 +1,29 @@
"""
-
- 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 $ ..
+.. .......................................................................... ..
"""
diff --git a/aria/core/Molecule.py b/aria/core/Molecule.py
index de2842786096ce51f08489f89f50386755f67125..d04ba57c60072706a56e1f502f2c846277bfaa95 100644
--- a/aria/core/Molecule.py
+++ b/aria/core/Molecule.py
@@ -1,30 +1,30 @@
# 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 $ ..
+.. .......................................................................... ..
"""
diff --git a/aria/core/Molprobity.py b/aria/core/Molprobity.py
index 532e41abb6e6b5906f61aa724bb466f367073474..a6a1f8bf0d680934f7d3456cbc54f5d14fd51074 100644
--- a/aria/core/Molprobity.py
+++ b/aria/core/Molprobity.py
@@ -1,14 +1,29 @@
"""
-Authors: Bardiaux Benjamin
- Structural Biology Unit, FMP, Berlin
-
- Copyright (C) Benjamin Bardiaux
- No warranty implied or expressed.
- All rights reserved.
-
-$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 ..
+.. Structural Biology Unit, FMP, Berlin ..
+.. ..
+.. 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 os
diff --git a/aria/core/NOEModel.py b/aria/core/NOEModel.py
index 244dbfb5b550ed5b8075dade812ec0869a576269..375d84ac5e8625addc4126a263c81a0618df41b1 100644
--- a/aria/core/NOEModel.py
+++ b/aria/core/NOEModel.py
@@ -1,29 +1,29 @@
"""
-
- 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 $ ..
+.. .......................................................................... ..
"""
diff --git a/aria/core/NOESYSpectrum.py b/aria/core/NOESYSpectrum.py
index 84264c3dbc4f9b3a4829482b4acb6c0d12959e0f..74c386aec6c7f85437110dc7a18f2b6b0c797a34 100644
--- a/aria/core/NOESYSpectrum.py
+++ b/aria/core/NOESYSpectrum.py
@@ -1,29 +1,29 @@
"""
-
- 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 $ ..
+.. .......................................................................... ..
"""
diff --git a/aria/core/NOESYSpectrumFilter.py b/aria/core/NOESYSpectrumFilter.py
index 62857493b1aac47d07191965e8924e1bbdf79f4c..cd28dbc65f7200f91233b0e8360cc50a3b0467ed 100644
--- a/aria/core/NOESYSpectrumFilter.py
+++ b/aria/core/NOESYSpectrumFilter.py
@@ -1,29 +1,29 @@
"""
-
- 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 .ariabase import AriaBaseClass
diff --git a/aria/core/Network.py b/aria/core/Network.py
index f291834589d3b85bfe033ae534bf710d3ae7620f..621fbfc7caa6472dde3c96afe630802995fd7989 100644
--- a/aria/core/Network.py
+++ b/aria/core/Network.py
@@ -1,16 +1,29 @@
"""
-Authors: Bardiaux Benjamin
- Institut Pasteur, Paris
- IBPC, Paris
-
- Copyright (C) 2005 Michael Habeck,
- Wolfgang Rieping and Benjamin Bardiaux
- No warranty implied or expressed.
- All rights reserved.
-
-$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 .ariabase import *
@@ -944,9 +957,8 @@ class NetworkAnchoring(AriaBaseClass):
def create_network(self):
"""
- create the network itself
- dictionnary : key = spid
- value = Set of gammas
+ create the network itself where key = spid & value = Set of gammas
+ within the dictionnary
Parameters
----------
diff --git a/aria/core/OrderedDict.py b/aria/core/OrderedDict.py
index 746f6b9766ef771914c40b20d0323c3b51dac6f5..c0c6b58a81d2335e81770e3846609524632c3545 100644
--- a/aria/core/OrderedDict.py
+++ b/aria/core/OrderedDict.py
@@ -1,29 +1,29 @@
"""
-
- 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 $ ..
+.. .......................................................................... ..
"""
# TODO: get rid of UserDict
diff --git a/aria/core/PDBReader.py b/aria/core/PDBReader.py
index eab2b58962341a96e1693f11ff305ab86ff69770..ef19d7e2b96afc7f079ffeefb9d35f74b34666a5 100644
--- a/aria/core/PDBReader.py
+++ b/aria/core/PDBReader.py
@@ -1,30 +1,30 @@
# 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
from .ariabase import AriaBaseClass
@@ -140,9 +140,10 @@ class PDBReader(AriaBaseClass):
"""
Reads all (het)atoms in a PDB-file and returns a dict
of dicts of the following hierachy:
- * segment level (keys are SEGIDs)
- * residue level (keys are residue numbers)
- * atom level (keys are atom names)
+
+ * segment level (keys are SEGIDs)
+ * residue level (keys are residue numbers)
+ * atom level (keys are atom names)
Parameters
----------
@@ -323,11 +324,8 @@ class PDBReader(AriaBaseClass):
def write(self, dict, filename, input_format=IUPAC_CONVENTION,
output_format=IUPAC_CONVENTION):
"""
- Writes a dict of dicts of the hierarchy
- {<seg_id>:
- {<residue_number>:
- {'residue_type': <three-letter-code>,
- <atom-name>: <coordinates>}}}
+ Writes a dict of dicts of the hierarchy {<seg_id>: {<residue_number>:
+ {'residue_type': <three-letter-code>, <atom-name>: <coordinates>}}}
to a file in PDB format.
Parameters
@@ -432,11 +430,8 @@ class PDBReader(AriaBaseClass):
input_format=IUPAC_CONVENTION,
output_format=IUPAC_CONVENTION):
"""
- Writes a dict of dicts of the hierarchy
- {<seg_id>:
- {<residue_number>:
- {'residue_type': <three-letter-code>,
- <atom-name>: <coordinates>}}}
+ Writes a dict of dicts of the hierarchy {<seg_id>: {<residue_number>:
+ {'residue_type': <three-letter-code>, <atom-name>: <coordinates>}}}
to a pdbfile in PDB format.
Parameters
diff --git a/aria/core/PeakAssigner.py b/aria/core/PeakAssigner.py
index 7fa0ce1799afb1d951fda4139b88701433cb3743..63f8f1ed0f1e207e7b04e482535e2d47eb227cb0 100644
--- a/aria/core/PeakAssigner.py
+++ b/aria/core/PeakAssigner.py
@@ -1,29 +1,29 @@
"""
-
- 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 .ariabase import *
diff --git a/aria/core/Project.py b/aria/core/Project.py
index 23e966747d688b21ba5ef1ac6090c231da8557f2..2983cf76fec7f88008ccaf9bb5b0241381ee9228 100644
--- a/aria/core/Project.py
+++ b/aria/core/Project.py
@@ -1,30 +1,30 @@
# 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
diff --git a/aria/core/Protocol.py b/aria/core/Protocol.py
index 01c1db3a79647bc4cac1882c056cdf918df3b462..af99c04612519c5eeb0357299fe49d24a0e3deb1 100644
--- a/aria/core/Protocol.py
+++ b/aria/core/Protocol.py
@@ -1,32 +1,32 @@
-from __future__ import print_function
-
"""
-
- 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 print_function
+
from .ariabase import *
from .Settings import Settings
diff --git a/aria/core/Relaxation.py b/aria/core/Relaxation.py
index 70d8ad58c721c6b84829b78f11a6b6854545dbf1..4212e29371612675c44f0e85a139ab3d9f2763d3 100644
--- a/aria/core/Relaxation.py
+++ b/aria/core/Relaxation.py
@@ -1,29 +1,29 @@
"""
-
- 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 $ ..
+.. .......................................................................... ..
"""
diff --git a/aria/core/Report.py b/aria/core/Report.py
index 9714e004819b63ca9151dbf684dd0e4408d9099b..b7810a0e56fd34058cf23e6789db77653e95cf77 100644
--- a/aria/core/Report.py
+++ b/aria/core/Report.py
@@ -1,29 +1,29 @@
"""
-
- 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 $ ..
+.. .......................................................................... ..
"""
diff --git a/aria/core/Residue.py b/aria/core/Residue.py
index 18e1d40966aac2643cff3c62c48544b26899f884..4b746c5f02b967ed616d31426de56bc5e6235b8d 100644
--- a/aria/core/Residue.py
+++ b/aria/core/Residue.py
@@ -1,29 +1,29 @@
"""
-
- 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 $ ..
+.. .......................................................................... ..
"""
diff --git a/aria/core/RmsReport.py b/aria/core/RmsReport.py
index 38ec7aa4bb9d5accdfc36b4f20d15d344d10c9df..177a1295cf92583f456234ddffd08cb84d1cf797 100644
--- a/aria/core/RmsReport.py
+++ b/aria/core/RmsReport.py
@@ -1,15 +1,30 @@
# coding=utf-8
"""
-Authors: Bardiaux Benjamin
- Structural Bioinformatics, Institut Pasteur, Paris
-
- Copyright (C) Benjamin Bardiaux
- No warranty implied or expressed.
- All rights reserved.
-
-$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 ..
+.. 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 .ariabase import AriaBaseClass
import os
diff --git a/aria/core/Settings.py b/aria/core/Settings.py
index d7ba4415834bd91b7561cb0ef600f22979ec0232..de36c01ae30d2a43911ac5884aa0c83fa3ee9e22 100644
--- a/aria/core/Settings.py
+++ b/aria/core/Settings.py
@@ -1,30 +1,30 @@
# 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 UserDict import UserDict
diff --git a/aria/core/ShiftAssignment.py b/aria/core/ShiftAssignment.py
index 05975db7830e3b84b0a055b462f1c5ddf86a23d5..f9c036d19096d95b8bdea1139e475d9265a0df35 100644
--- a/aria/core/ShiftAssignment.py
+++ b/aria/core/ShiftAssignment.py
@@ -1,29 +1,29 @@
"""
-
- 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 $ ..
+.. .......................................................................... ..
"""
# TODO:
diff --git a/aria/core/ShiftAssignmentFilter.py b/aria/core/ShiftAssignmentFilter.py
index da99a116ec85cb86e2aea616a2df4ee19ec989d4..0543017e1e8f7bc6d35622205de682563cfdad0a 100644
--- a/aria/core/ShiftAssignmentFilter.py
+++ b/aria/core/ShiftAssignmentFilter.py
@@ -1,29 +1,29 @@
"""
-
- 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 .ariabase import AriaBaseClass
diff --git a/aria/core/Singleton.py b/aria/core/Singleton.py
index 6bc830fa006ee76952b9da2bea5112cbcb06ca21..f810c448cf847f309a2b3f8207d4ef70733e8567 100644
--- a/aria/core/Singleton.py
+++ b/aria/core/Singleton.py
@@ -1,30 +1,30 @@
# 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 $ ..
+.. .......................................................................... ..
"""
diff --git a/aria/core/SpinPair.py b/aria/core/SpinPair.py
index 2a72d173754aaa71b82b353cd24872c9448deca3..f1fecf0832e4659a6f772607dc27176a855445a7 100644
--- a/aria/core/SpinPair.py
+++ b/aria/core/SpinPair.py
@@ -1,29 +1,29 @@
"""
-
- 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 $ ..
+.. .......................................................................... ..
"""
diff --git a/aria/core/StructureEnsemble.py b/aria/core/StructureEnsemble.py
index a8c809919baf5a65c0b569334a42e857b8596df5..e5dc1b3041e1b3cdfceb03d4680e207428b22fd8 100644
--- a/aria/core/StructureEnsemble.py
+++ b/aria/core/StructureEnsemble.py
@@ -1,30 +1,30 @@
# 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 .ariabase import AriaBaseClass
diff --git a/aria/core/SuperImposer.py b/aria/core/SuperImposer.py
index f0eb5642f9891ecdd2f716f4d493838b0859f4e0..e62fa7c01d5a43ec4dd4b2fd3ecae8eb9092245d 100644
--- a/aria/core/SuperImposer.py
+++ b/aria/core/SuperImposer.py
@@ -1,28 +1,29 @@
"""
-
- ARIA -- Ambiguous Restraints for Iterative Assignment
-
- A software for automated NOE assignment
-
- Version 2.3
-
-
-Copyright (C) Benjamin Bardiaux, Aymeric Bernard
-
-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 .ariabase import AriaBaseClass
diff --git a/aria/core/Topology.py b/aria/core/Topology.py
index b790e3e1a4502cc04399edf042bc3a8075429430..023cbd210ebce5774c5eadfaae8f7e1ca9e1c314 100644
--- a/aria/core/Topology.py
+++ b/aria/core/Topology.py
@@ -1,32 +1,32 @@
-from __future__ import print_function
-
"""
-
- 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 print_function
+
from .ariabase import *
from .xmlutils import XMLElement, XMLBasePickler
diff --git a/aria/core/TypeChecking.py b/aria/core/TypeChecking.py
index b269c25158a319c5ab11ce5f4a835c2edf37e9de..236348527b2ea2875340d1bbe130a08de9287a4c 100644
--- a/aria/core/TypeChecking.py
+++ b/aria/core/TypeChecking.py
@@ -1,30 +1,30 @@
# 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
diff --git a/aria/core/ViolationAnalyser.py b/aria/core/ViolationAnalyser.py
index e44bbc771e3677ffb1e89cf32c3fb5b1ac21f339..0380573cb8026417059196c39aff20713c6b0899 100644
--- a/aria/core/ViolationAnalyser.py
+++ b/aria/core/ViolationAnalyser.py
@@ -1,30 +1,30 @@
# 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 .ariabase import *
from .Settings import Settings
diff --git a/aria/core/WhatifProfile.py b/aria/core/WhatifProfile.py
index 9e4cc8be7408b8aa1c520e97bcf19ad1e1f49b63..c5d50f6d0844affed846aa8f3272b2dbf3e4ed6f 100644
--- a/aria/core/WhatifProfile.py
+++ b/aria/core/WhatifProfile.py
@@ -1,17 +1,31 @@
-from __future__ import print_function
-
"""
-Authors: Bardiaux Benjamin
- Structural Bioinformatics, Institut Pasteur, Paris
-
- Copyright (C) Benjamin Bardiaux
- No warranty implied or expressed.
- All rights reserved.
-
-$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 ..
+.. 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 print_function
import time
@@ -20,32 +34,31 @@ CHECK_LIST = ['QUACHK', 'NQACHK', 'RAMCHK', 'C12CHK',
OTHER = ['BNDCHK', 'ANGCHK', 'PLNCHK', 'INOCHK']
-LEGEND_LIST_I = {'1st generation packing quality Z-score' : 'QUACHK',
- '2nd generation packing quality Z-score' : 'NQACHK',
- 'Ramachandran plot appearance Z-score' : 'RAMCHK',
- 'Chi-1 chi-2 rotamer normality Z-score' : 'C12CHK',
- 'Backbone conformation Z-score' : 'BBCCHK',
- 'Bond lengths RMS Z-score' : 'BNDCHK',
- 'Bond angles RMS Z-score' : 'ANGCHK',
- 'Side chain planarity RMS Z-score' : 'PLNCHK',
- 'Improper dihedral distribution RMS Z-score' : 'HNDCHK',
- 'Inside/outside distribution RMS Z-score' : 'INOCHK',
- 'Inter-atomic bumps' : 'BMPCHK'}
+LEGEND_LIST_I = {'1st generation packing quality Z-score': 'QUACHK',
+ '2nd generation packing quality Z-score': 'NQACHK',
+ 'Ramachandran plot appearance Z-score': 'RAMCHK',
+ 'Chi-1 chi-2 rotamer normality Z-score': 'C12CHK',
+ 'Backbone conformation Z-score': 'BBCCHK',
+ 'Bond lengths RMS Z-score': 'BNDCHK',
+ 'Bond angles RMS Z-score': 'ANGCHK',
+ 'Side chain planarity RMS Z-score': 'PLNCHK',
+ 'Improper dihedral distribution RMS Z-score': 'HNDCHK',
+ 'Inside/outside distribution RMS Z-score': 'INOCHK',
+ 'Inter-atomic bumps': 'BMPCHK'}
LEGEND_LIST = dict(zip(LEGEND_LIST_I.values(), LEGEND_LIST_I.keys()))
-SCORES_THRE = {'QUACHK' : (-5., -3.),
- 'NQACHK' : (-3., -2.5),
- 'C12CHK' : (-4., -3.),
- 'BBCCHK' : (5., 10.),
- 'BMPCHK' : (0., 0.1),
- 'RAMCHK' : (-4., -3.)}
-
+SCORES_THRE = {'QUACHK': (-5., -3.),
+ 'NQACHK': (-3., -2.5),
+ 'C12CHK': (-4., -3.),
+ 'BBCCHK': (5., 10.),
+ 'BMPCHK': (0., 0.1),
+ 'RAMCHK': (-4., -3.)}
BAD = 'r'
GOOD = 'g'
POOR = 'orange'
-
+
FILENAME_WHATIF_PROFILE = 'whatif_profiles'
FILENAME_WHATIF_PROFILE_EPS = FILENAME_WHATIF_PROFILE + '.eps'
FILENAME_WHATIF_PROFILE_PS = FILENAME_WHATIF_PROFILE + '.ps'
@@ -55,18 +68,19 @@ _use_matplotlib = 0
try:
import matplotlib
+
_use_matplotlib = 1
matplotlib.use('pdf', warn=False)
except:
pass
-#FILENAME_WHATIF_PROFILE_TEX = FILENAME_WHATIF_PROFILE + '.tex'
-
+# FILENAME_WHATIF_PROFILE_TEX = FILENAME_WHATIF_PROFILE + '.tex'
+
class WhatifProfile:
- def __init__(self, wdir, whatIfExe = 'whatif'):
-
+ def __init__(self, wdir, whatIfExe='whatif'):
+
self.checks = None
self.data = None
self.wdir = wdir
@@ -74,23 +88,22 @@ class WhatifProfile:
if os.path.split(whatIfExe)[1] in ['whatcheck', 'DO_WHATCHECK.COM']:
self.is_whatcheck = 1
-
def parseWhatifChecks(self):
from legacy.QualityChecks.QualityChecks import FILENAME_REPORT_WHATIF
import re
-
+
input = open(os.path.join(self.wdir, FILENAME_REPORT_WHATIF))
-
- fileID = re.compile("^ID\s+\:\s+(\S+)")
+
+ fileID = re.compile("^ID\s+\:\s+(\S+)")
checkID = re.compile("^CheckID\s+\:\s+(\S+)")
- resid = re.compile("\s+Name\s+\:\s(\S*)\-?\s*(\d+)\-(\w+)(\-\s*(CA))?")
+ resid = re.compile("\s+Name\s+\:\s(\S*)\-?\s*(\d+)\-(\w+)(\-\s*(CA))?")
if self.is_whatcheck:
resid = re.compile(
"\s+Name\s+\:\s+(\d+)\s+;\s+\S*\s+;\s+(\d+)\s+;\s+(\w+)\s+;"
"\s+\S*\s*(;\s+CA)?")
- value = re.compile("\s+Value\s+\:\s+(\-?\d+\.\d+)")
+ value = re.compile("\s+Value\s+\:\s+(\-?\d+\.\d+)")
checks = {}
@@ -102,11 +115,10 @@ class WhatifProfile:
fID = fileID.search(line)
cID = checkID.search(line)
- res = resid.search(line)
+ res = resid.search(line)
val = value.search(line)
if fID:
-
file = fID.group(1)
checks.setdefault(file, {})
@@ -136,18 +148,17 @@ class WhatifProfile:
break
self.checks = checks
-
-
def getProfilesData(self):
-
+
import numpy
self.plength = len(self.checks[self.checks.keys()[0]]['NQACHK'])
- self.pids = map(lambda a: int(a), self.checks[self.checks.keys()[0]]['NQACHK'].keys())
+ self.pids = map(lambda a: int(a),
+ self.checks[self.checks.keys()[0]]['NQACHK'].keys())
self.pids.sort()
-
- #print self.plength
+
+ # print self.plength
scores = {}
extrem = {}
@@ -155,47 +166,47 @@ class WhatifProfile:
for elt in self.check_list:
- score = numpy.array([ cv for k,v in self.checks.items() for ck, cv in v.items() if ck == elt])
+ score = numpy.array(
+ [cv for k, v in self.checks.items() for ck, cv in v.items() if
+ ck == elt])
new_score = []
- #print elt
+ # print elt
for s in score:
struc_score = numpy.zeros(self.plength, numpy.float)
-
+
for g in range(self.plength):
try:
- #struc_score[g] = s[str(g+1)]
+ # struc_score[g] = s[str(g+1)]
struc_score[g] = s[str(self.pids[g])]
-
+
except:
pass
new_score.append(struc_score)
-
+
new_score = numpy.array(new_score)
- #if new_score
- #print new_score
+ # if new_score
+ # print new_score
scores[elt] = numpy.mean(new_score, 0)
extrem[elt] = [numpy.min(new_score, 0), numpy.max(new_score, 0)]
if len(new_score) > 1:
- sd[elt] = numpy.std(new_score, 0)
+ sd[elt] = numpy.std(new_score, 0)
else:
sd[elt] = numpy.zeros(len(new_score[0]), numpy.float)
-
-
- self.data = [scores, extrem, sd]
+ self.data = [scores, extrem, sd]
def plotProfiles(self, output_ps):
-
- #import biggles
+
+ # import biggles
from matplotlib.backends.backend_pdf import PdfPages
import matplotlib.pylab as pylab
from matplotlib import rcParams
- #from numpy import ma
- #rcParams['numerix'] = 'numpy'
+ # from numpy import ma
+ # rcParams['numerix'] = 'numpy'
from math import ceil
@@ -203,22 +214,22 @@ class WhatifProfile:
n_l = len(self.check_list)
pdf = PdfPages(output_ps)
-
- f = pylab.figure(figsize=(8.27,11.69))
+
+ f = pylab.figure(figsize=(8.27, 11.69))
titles = "Whatif scores residue profiles"
- #pylab.figtext(0.1,0.95, titles)
+ # pylab.figtext(0.1,0.95, titles)
f.suptitle(titles, fontsize=14, fontweight='bold')
- pylab.figtext(0.35,0.95, "Good", color=GOOD, fontweight='bold')
- pylab.figtext(0.45,0.95, "Poor", color=POOR, fontweight='bold')
- pylab.figtext(0.55,0.95, "Bad", color=BAD, fontweight='bold')
-
+ pylab.figtext(0.35, 0.95, "Good", color=GOOD, fontweight='bold')
+ pylab.figtext(0.45, 0.95, "Poor", color=POOR, fontweight='bold')
+ pylab.figtext(0.55, 0.95, "Bad", color=BAD, fontweight='bold')
+
titles = "%s - %s" % (time.ctime(), output_ps)
- pylab.figtext(0.05,0.02, titles, fontsize=8)
-
+ pylab.figtext(0.05, 0.02, titles, fontsize=8)
+
for e in range(len(self.check_list)):
-
+
name = self.check_list[e]
if e >= n_l:
x = e - n_l
@@ -233,43 +244,43 @@ class WhatifProfile:
# TODO[FALLAIN]: x & y actually not used
scores = self.data[0]
- splotax = pylab.subplot(len(self.check_list), 1, e+1)
+ splotax = pylab.subplot(len(self.check_list), 1, e + 1)
# TODO[FALLAIN] unitaryPlot return nothing actually
pp = self.unitaryPlot(name, scores[name], splotax)
-
+
pylab.subplots_adjust(hspace=0.5)
- #t1.write_eps(output_ps)
- #pylab.savefig(output_ps, papertype='a4')
+ # t1.write_eps(output_ps)
+ # pylab.savefig(output_ps, papertype='a4')
pylab.savefig(pdf, papertype='a4', format='pdf')
pdf.close()
def unitaryPlot(self, t, data, ax):
- #import biggles
+ # import biggles
import matplotlib.pylab as pylab
from matplotlib.ticker import MultipleLocator
from numpy import array, putmask, ma
from numpy import less, greater_equal, greater, less_equal
cutoffs = SCORES_THRE[t]
-
- majorLocator = MultipleLocator(10)
- minorLocator = MultipleLocator(1)
+
+ majorLocator = MultipleLocator(10)
+ minorLocator = MultipleLocator(1)
# TODO[FALLAIN]: linet not used
linet = ['dotted', 'solid']
profile = []
if type(data) == type([]):
- profile = data
+ profile = data
else:
profile.append(data)
x = self.pids
n = 1
-
+
for d in profile:
colors = array([POOR] * len(x))
@@ -281,30 +292,30 @@ class WhatifProfile:
putmask(colors, greater_equal(d, cutoffs[1]), GOOD)
pylab.vlines(x, [0], d, colors=colors, lw=2)
- #if t == 'BMPCHK':
+ # if t == 'BMPCHK':
# pylab.plot(x, ma.masked_where(colors <> 'g', d),
# marker=".", c= 'g', ms=5)
pylab.grid(True)
if min(d) < 0:
- pylab.axhline(y=0, c = 'black', zorder=1)
- ax.set_axisbelow(True)
+ pylab.axhline(y=0, c='black', zorder=1)
+ ax.set_axisbelow(True)
pylab.ylabel(t)
pylab.title(LEGEND_LIST[t])
- pylab.xlim(x[0]-1, x[-1]+1)
+ pylab.xlim(x[0] - 1, x[-1] + 1)
ax.xaxis.set_major_locator(majorLocator)
ax.xaxis.set_minor_locator(minorLocator)
ax.tick_params(axis='y', which='major', labelsize=8)
ax.tick_params(axis='x', which='major', labelsize=10)
-
- n+=1
+ n += 1
def writeTextProfiles(self, dst):
"""
write profiles in text file
- resid check1 check2
- avg max min sd avg max min sd
+
+ .. resid check1 check2
+ .. avg max min sd avg max min sd
Parameters
----------
@@ -315,7 +326,7 @@ class WhatifProfile:
-------
"""
-
+
line = """# Whatif scores residues profiles
# Check : name of the whatif analysis
@@ -326,22 +337,22 @@ class WhatifProfile:
# Min : minimum score
"""
-
-
- line += '#%6s\t%3s\t%6s\t%6s\t%6s\t%6s\n\n' % ('Check', 'Res', 'Mean', 'Sd', 'Min', 'Max')
-
+
+ line += '#%6s\t%3s\t%6s\t%6s\t%6s\t%6s\n\n' % (
+ 'Check', 'Res', 'Mean', 'Sd', 'Min', 'Max')
+
for e in self.check_list:
for r in range(self.plength):
-
idn = self.pids[r]
-
- line += '%6s\t%3d\t%6.3f\t%6.3f\t%6.3f\t%6.3f\n' % (e,idn,self.data[0][e][r],self.data[2][e][r], self.data[1][e][0][r], self.data[1][e][1][r])
+
+ line += '%6s\t%3d\t%6.3f\t%6.3f\t%6.3f\t%6.3f\n' % (
+ e, idn, self.data[0][e][r], self.data[2][e][r],
+ self.data[1][e][0][r], self.data[1][e][1][r])
line += '\n'
f = open(dst, 'w')
f.write(line)
f.close()
-
def makeProfiles(self):
@@ -351,7 +362,7 @@ class WhatifProfile:
# average scores on all
self.getProfilesData()
- #try:
+ # try:
# plot all checks profiles
if _use_matplotlib:
output_ps = os.path.join(self.wdir, FILENAME_WHATIF_PROFILE_PDF)
@@ -361,7 +372,8 @@ class WhatifProfile:
# to /graphics
from .tools import copy_file
src = output_ps
- dst = os.path.join(os.path.join(self.wdir, 'graphics'), FILENAME_WHATIF_PROFILE_PDF)
+ dst = os.path.join(os.path.join(self.wdir, 'graphics'),
+ FILENAME_WHATIF_PROFILE_PDF)
if os.path.exists(os.path.join(self.wdir, 'graphics')):
try:
copy_file(src, dst)
@@ -369,8 +381,8 @@ class WhatifProfile:
except IOError:
s = 'File "%s" does not exist or cannot be accessed.'
print(IOError, s % src)
-
- #except:
+
+ # except:
# print "Plotting abording. Check if module biggles/ps installed."
# write ASCII whatif residue profiles
@@ -378,16 +390,13 @@ class WhatifProfile:
self.writeTextProfiles(output)
-
-
-
if __name__ == '__main__':
import sys
import os
path = os.environ['ARIA2']
- sys.path.insert(0, path+'/src/py')
+ sys.path.insert(0, path + '/src/py')
p = WhatifProfile(sys.argv[1])
p.makeProfiles()
diff --git a/aria/core/_PDBReader.py b/aria/core/_PDBReader.py
index bf378948f178ab87a88862ed1ebb986fa226a4e1..0541634a4fb6affea9b81827e41ab85a7c929ac8 100644
--- a/aria/core/_PDBReader.py
+++ b/aria/core/_PDBReader.py
@@ -1,30 +1,30 @@
# 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 $ ..
+.. .......................................................................... ..
"""
diff --git a/aria/core/ariabase.py b/aria/core/ariabase.py
index 3fd923ac1cbe990f70f865d1ae42e5f48d6e5d8d..576ef1f10e965e1d78f2e6cc1983f0e6b5801c7e 100644
--- a/aria/core/ariabase.py
+++ b/aria/core/ariabase.py
@@ -1,30 +1,30 @@
# 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
from future.builtins import input
diff --git a/aria/core/ccpn2top.py b/aria/core/ccpn2top.py
index 0f7f7cb97e10ae2adb890b775d33b9d8be8e5ffd..4e6c0ee9962559cb1f61914a8ab27a59a14ad8cf 100644
--- a/aria/core/ccpn2top.py
+++ b/aria/core/ccpn2top.py
@@ -1,31 +1,30 @@
# 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.
-
-Updated and almost completely recoded by Tim Stevens on 1st Nov 2006
-
-$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 os
diff --git a/aria/core/ccpn_conversion.py b/aria/core/ccpn_conversion.py
index ff386223f0fe72b7f613af91a4d3f4933756d5a0..df32d622052a53818a3edaf5f8f30cd86389168a 100644
--- a/aria/core/ccpn_conversion.py
+++ b/aria/core/ccpn_conversion.py
@@ -1,30 +1,30 @@
# 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 .ariabase import AriaBaseClass
diff --git a/aria/core/cns.py b/aria/core/cns.py
index 84c6fac1c5a62218a1862997ebc6dee3e6a5f714..ffc040188feb248dced497e73a4dff1ed764bc68 100644
--- a/aria/core/cns.py
+++ b/aria/core/cns.py
@@ -1,30 +1,30 @@
# 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 string
diff --git a/aria/core/conversion.py b/aria/core/conversion.py
index 4efc644d8388d9b8cdb14db6a1cbd6699aba95e8..2f01ad67dcc4862076cceabd493f86375c89fef8 100644
--- a/aria/core/conversion.py
+++ b/aria/core/conversion.py
@@ -1,29 +1,29 @@
"""
-
- 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 $ ..
+.. .......................................................................... ..
"""
# TODO: is the residue number checked in PPM list conversion?
diff --git a/aria/core/exportToCcpn.py b/aria/core/exportToCcpn.py
index 5042b39840375b65fe363cf92e5e351c63090d84..769a2e0dfe0699706154840ecdcefc00f153165f 100644
--- a/aria/core/exportToCcpn.py
+++ b/aria/core/exportToCcpn.py
@@ -1,4 +1,31 @@
# 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 $ ..
+.. .......................................................................... ..
+"""
from ccpnmr.analysis.core.ConstraintBasic import makeNmrConstraintStore, \
makeStructureGeneration, getFixedResonance
from ccpnmr.analysis.core.ExperimentBasic import getOnebondDataDims, \
diff --git a/aria/core/gui/AriaViewer.py b/aria/core/gui/AriaViewer.py
index 62b423f420d48daa04757ebceaa67acd5f7a9c46..c2236580b2ff4662b48cbf2d17dbf0fd00463ef7 100644
--- a/aria/core/gui/AriaViewer.py
+++ b/aria/core/gui/AriaViewer.py
@@ -1,29 +1,29 @@
"""
-
- 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 ..
+.. 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
diff --git a/aria/core/gui/decorators.py b/aria/core/gui/decorators.py
index d94c336844eeb1e1595771aa90c866476c7011b0..3aa9db7b7c172a1fdcb04362e0c204ff8d571eff 100644
--- a/aria/core/gui/decorators.py
+++ b/aria/core/gui/decorators.py
@@ -1,29 +1,29 @@
"""
-
- 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 ..
+.. 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
diff --git a/aria/core/gui/gui.py b/aria/core/gui/gui.py
index 4d9d5281c2f91719c4046d9cbe01106a173a7761..64679e548b9ef80bff197df6e8a6653c30a64685 100644
--- a/aria/core/gui/gui.py
+++ b/aria/core/gui/gui.py
@@ -1,29 +1,29 @@
"""
-
- 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 ..
+.. 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
diff --git a/aria/core/gui/panels.py b/aria/core/gui/panels.py
index 3567d7209d2baebd5e7e55d5676a66fcd270ff9d..a8cd3efba593320d2662169cffd0373e5a00e41b 100644
--- a/aria/core/gui/panels.py
+++ b/aria/core/gui/panels.py
@@ -1,29 +1,29 @@
"""
-
- 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 ..
+.. 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
diff --git a/aria/core/gui/widgets.py b/aria/core/gui/widgets.py
index 4576ab4c4224a8167dece978bcbca007d6f2419a..5b09e696ac3f0aae87f0dcb4232a70b8c54a69b4 100644
--- a/aria/core/gui/widgets.py
+++ b/aria/core/gui/widgets.py
@@ -1,29 +1,29 @@
"""
-
- 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 ..
+.. 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
from future.utils import PY3
diff --git a/aria/core/importFromCcpn.py b/aria/core/importFromCcpn.py
index 36c1bc324e67fdb33050b7fc68c5f91c2dca70bd..8ac9df0f6b076a8625d4a93feee0b6aa96d682c4 100644
--- a/aria/core/importFromCcpn.py
+++ b/aria/core/importFromCcpn.py
@@ -1,3 +1,30 @@
+"""
+.. .......................................................................... ..
+.. 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 .Assignment import Assignment, ASSIGNMENT_TYPE_MANUAL
from .Atom import Atom, AtomSettings
from .Chain import TYPE_PROTEIN, TYPE_DNA, TYPE_RNA, TYPE_NONPOLYMER, Chain, \
diff --git a/aria/core/mathutils.py b/aria/core/mathutils.py
index 9691b80510da68796db512862a4ec11848a9f4cb..4392f27ba0cf718a5aa7ef4397ea1af7d14130b0 100644
--- a/aria/core/mathutils.py
+++ b/aria/core/mathutils.py
@@ -1,29 +1,29 @@
"""
-
- 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 $ ..
+.. .......................................................................... ..
"""
diff --git a/aria/core/scientific/FortranFormat.py b/aria/core/scientific/FortranFormat.py
index 83ba9cbdc0c45b2bc67131acb4af0061bb8656b5..6b05b5125e88b0e82f3b6dc9953494166f1092ff 100644
--- a/aria/core/scientific/FortranFormat.py
+++ b/aria/core/scientific/FortranFormat.py
@@ -21,26 +21,26 @@
#
"""
- Fortran-style formatted input/output
-
- This module provides two classes that aid in reading and writing
- Fortran-formatted text files.
-
- :Example:
-
-
- >>> s = ' 59999'
- >>> format = FortranFormat('2I4')
- >>> line = FortranLine(s, format)
- >>> print(line[0])
- 5
- >>> print(line[1])
- 9999
-
- >>> format = FortranFormat('2D15.5')
- >>> line = FortranLine([3.1415926, 2.71828], format)
- >>> print(str(line))
- 3.14159D+00 2.71828D+00
+Fortran-style formatted input/output
+
+This module provides two classes that aid in reading and writing
+Fortran-formatted text files.
+
+Example
+---------
+
+>>> s = ' 59999'
+>>> format = FortranFormat('2I4')
+>>> line = FortranLine(s, format)
+>>> print(line[0])
+5
+>>> print(line[1])
+9999
+
+>>> format = FortranFormat('2D15.5')
+>>> line = FortranLine([3.1415926, 2.71828], format)
+>>> print(str(line))
+ 3.14159D+00 2.71828D+00
"""
diff --git a/aria/core/scientific/PDB.py b/aria/core/scientific/PDB.py
index 3bddac2e626f8d25960210a616c9a34b54c2c99a..e23fbdc78d5d65bf7ce16d4951cd5adc0c76b404 100644
--- a/aria/core/scientific/PDB.py
+++ b/aria/core/scientific/PDB.py
@@ -6,68 +6,56 @@
#
"""
- Parsing and writing of Protein Data Bank (PDB) files
-
- This module provides classes that represent PDB (Protein Data Bank)
- files and configurations contained in PDB files. It provides access to
- PDB files on two levels: low-level (line by line) and high-level
- (chains, residues, and atoms).
-
- Caution: The PDB file format has been heavily abused, and it is
- probably impossible to write code that can deal with all variants
- correctly. This modules tries to read the widest possible range of PDB
- files, but gives priority to a correct interpretation of the PDB
- format as defined by the Brookhaven National Laboratory.
-
- A special problem are atom names. The PDB file format specifies that
- the first two letters contain the right-justified chemical element
- name. A later modification allowed the initial space in hydrogen names
- to be replaced by a digit. Many programs ignore all this and treat the
- name as an arbitrary left-justified four-character name. This makes it
- difficult to extract the chemical element accurately; most programs
- write the '"CA"' for C_alpha in such a way that it actually stands for
- a calcium atom. For this reason a special element field has been added
- later, but only few files use it. In the absence of an element field,
- the code in this module attempts to guess the element using all information
- available.
-
- The low-level routines in this module do not try to deal with the atom
- name problem; they return and expect four-character atom names
- including spaces in the correct positions. The high-level routines use
- atom names without leading or trailing spaces, but provide and use the
- element field whenever possible. For output, they use the element
- field to place the atom name correctly, and for input, they construct
- the element field content from the atom name if no explicit element
- field is found in the file.
-
- Except where indicated, numerical values use the same units and
- conventions as specified in the PDB format description.
-
- :Example:
-
- >>> conf = Structure('docs/examples/werner/result/hrdc_10_water.pdb')
- >>> print(conf)
- Structure('docs/examples/werner/result/hrdc_10_water.pdb'):
- Peptide chain of length 91
- <BLANKLINE>
- >>> for residue in conf.residues:
- ... for atom in residue:
- ... pass
- >>> print(atom)
- Atom OT2 at [7.831 6.168 6.392]
-
-@undocumented: atom_format
-@undocumented: anisou_format
-@undocumented: conect_format
-@undocumented: ter_format
-@undocumented: model_format
-@undocumented: header_format
-@undocumented: cryst1_format
-@undocumented: scalen_format
-@undocumented: mtrixn_format
-@undocumented: generic_format
-@undocumented: export_filters
-@undocumented: DummyChain
+Parsing and writing of Protein Data Bank (PDB) files
+
+This module provides classes that represent PDB (Protein Data Bank)
+files and configurations contained in PDB files. It provides access to
+PDB files on two levels: low-level (line by line) and high-level
+(chains, residues, and atoms).
+
+Caution: The PDB file format has been heavily abused, and it is
+probably impossible to write code that can deal with all variants
+correctly. This modules tries to read the widest possible range of PDB
+files, but gives priority to a correct interpretation of the PDB
+format as defined by the Brookhaven National Laboratory.
+
+A special problem are atom names. The PDB file format specifies that
+the first two letters contain the right-justified chemical element
+name. A later modification allowed the initial space in hydrogen names
+to be replaced by a digit. Many programs ignore all this and treat the
+name as an arbitrary left-justified four-character name. This makes it
+difficult to extract the chemical element accurately; most programs
+write the '"CA"' for C_alpha in such a way that it actually stands for
+a calcium atom. For this reason a special element field has been added
+later, but only few files use it. In the absence of an element field,
+the code in this module attempts to guess the element using all information
+available.
+
+The low-level routines in this module do not try to deal with the atom
+name problem; they return and expect four-character atom names
+including spaces in the correct positions. The high-level routines use
+atom names without leading or trailing spaces, but provide and use the
+element field whenever possible. For output, they use the element
+field to place the atom name correctly, and for input, they construct
+the element field content from the atom name if no explicit element
+field is found in the file.
+
+Except where indicated, numerical values use the same units and
+conventions as specified in the PDB format description.
+
+Example
+-------
+
+>>> conf = Structure('docs/examples/werner/result/hrdc_10_water.pdb')
+>>> print(conf)
+Structure('docs/examples/werner/result/hrdc_10_water.pdb'):
+ Peptide chain of length 91
+<BLANKLINE>
+>>> for residue in conf.residues:
+... for atom in residue:
+... pass
+>>> print(atom)
+Atom OT2 at [7.831 6.168 6.392]
"""
# from Scientific.Geometry import Vector, Tensor
# from Scientific import N
diff --git a/aria/core/tools.py b/aria/core/tools.py
index 23a2526dc6bad999185096fd2c23fbacf2c5e2ea..9c4bf188af8d804d9d9dfdd4df01107f5f24e43b 100644
--- a/aria/core/tools.py
+++ b/aria/core/tools.py
@@ -1,30 +1,30 @@
# 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 $ ..
+.. .......................................................................... ..
"""
diff --git a/aria/core/xmlparser.py b/aria/core/xmlparser.py
index 9c47ff9a4b1f15284dd227bdf3244d2f8e88ac45..e562a901b4c122d75738cf10d1505d51a3b763c1 100644
--- a/aria/core/xmlparser.py
+++ b/aria/core/xmlparser.py
@@ -1,29 +1,29 @@
"""
-
- 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 ..
+.. 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 print_function
diff --git a/aria/core/xmlutils.py b/aria/core/xmlutils.py
index d5fdb7c5932390200e3bdaa766fe7f9f3de5cc6b..1f83eb4c2bfe4b6335cd506dfee9602d187de890 100644
--- a/aria/core/xmlutils.py
+++ b/aria/core/xmlutils.py
@@ -1,30 +1,30 @@
# 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 ..
+.. 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 print_function
diff --git a/docs/_static/theme_overrides.css b/docs/_static/theme_overrides.css
index 174fade5f219b8b87141bae4c0f68f1ab10aba79..4211d478ea009d6e3561d6ee605afe666977e2b2 100644
--- a/docs/_static/theme_overrides.css
+++ b/docs/_static/theme_overrides.css
@@ -10,4 +10,14 @@
.wy-table-responsive {
overflow: visible !important;
}
+}
+
+p {
+ font-size: 100%; /* Get rid of RTD rule that assumes nobody changes their browser font size */
+}
+
+/* Get rid of rtd theme max width */
+.wy-nav-content {
+ /*background-color: #fff;*/
+ max-width: none;
}
\ No newline at end of file
diff --git a/docs/_templates/module.rst b/docs/_templates/module.rst
index 907b3fe2c6e46d9e41719b9ef1d5664496fc34af..ab9695d30832ca479da160b53695532d9f0dd7e2 100644
--- a/docs/_templates/module.rst
+++ b/docs/_templates/module.rst
@@ -7,67 +7,67 @@
.. currentmodule:: {{ fullname }}
.. automodule:: {{ fullname }}
- {% if members -%}
- :members: {{ members|join(", ") }}
- :undoc-members:
- :show-inheritance:
- :member-order: bysource
+ {% if members -%}
+ :members: {{ members|join(", ") }}
+ :undoc-members:
+ :show-inheritance:
+ :member-order: bysource
- Summary
- -------
+Summary
+-------
- {%- if exceptions %}
+{%- if exceptions %}
- Exceptions:
+Exceptions:
- .. autosummary::
- :nosignatures:
+.. autosummary::
+ :nosignatures:
{% for item in exceptions %}
- {{ item }}
+ {{ item }}
{%- endfor %}
- {%- endif %}
+{%- endif %}
- {%- if classes %}
+{%- if classes %}
- Classes:
+Classes:
- .. autosummary::
- :nosignatures:
+.. autosummary::
+ :nosignatures:
{% for item in classes %}
- {{ item }}
+ {{ item }}
{%- endfor %}
- {%- endif %}
+{%- endif %}
- {%- if functions %}
+{%- if functions %}
- Functions:
+Functions:
- .. autosummary::
- :nosignatures:
+.. autosummary::
+ :nosignatures:
{% for item in functions %}
- {{ item }}
+ {{ item }}
{%- endfor %}
- {%- endif %}
+{%- endif %}
{%- endif %}
- {%- if data %}
+{%- if data %}
- Data:
+Data:
- .. autosummary::
- :nosignatures:
+.. autosummary::
+ :nosignatures:
{% for item in data %}
- {{ item }}
+ {{ item }}
{%- endfor %}
- {%- endif %}
+{%- endif %}
{% if all_refs %}
- ``__all__``: {{ all_refs|join(", ") }}
+``__all__``: {{ all_refs|join(", ") }}
{%- endif %}
{% if members %}
- Reference
- ---------
+Reference
+---------
{%- endif %}
diff --git a/docs/_templates/package.rst b/docs/_templates/package.rst
index bfb4c25a143d02aa15fe95b5993fc668e66f30f0..1c522caf302e7dd057d98ebe8be477094f6d5842 100644
--- a/docs/_templates/package.rst
+++ b/docs/_templates/package.rst
@@ -5,80 +5,82 @@
{% for item in range(8 + fullname|length) -%}={%- endfor %}
.. automodule:: {{ fullname }}
- {% if members -%}
- :members: {{ members|join(", ") }}
- :undoc-members:
- :show-inheritance:
- {%- endif %}
+ {% if members -%}
+ :members: {{ members|join(", ") }}
+ :undoc-members:
+ :show-inheritance:
+ {%- endif %}
{% if submodules %}
- Submodules:
- .. toctree::
- :maxdepth: 1
+Submodules:
+
+.. toctree::
+ :maxdepth: 1
{% for item in submodules %}
- {{ fullname }}.{{ item }}
- {%- endfor %}
- {%- endif -%}
+ {{ fullname }}.{{ item }}
+{%- endfor %}
+{%- endif -%}
{% if subpackages %}
- Subpackages:
- .. toctree::
- :maxdepth: 1
+Subpackages:
+
+.. toctree::
+ :maxdepth: 1
{% for item in subpackages %}
- {{ fullname }}.{{ item }}
- {%- endfor %}
- {%- endif %}
+ {{ fullname }}.{{ item }}
+{%- endfor %}
+{%- endif %}
{% if members %}
- Summary
- -------
+Summary
+-------
- {%- if exceptions %}
+{%- if exceptions %}
- Exceptions:
+Exceptions:
- .. autosummary::
- :nosignatures:
+.. autosummary::
+ :nosignatures:
{% for item in exceptions %}
- {{ item }}
+ {{ item }}
{%- endfor %}
- {%- endif %}
+{%- endif %}
- {%- if classes %}
+{%- if classes %}
- Classes:
+Classes:
- .. autosummary::
- :nosignatures:
+.. autosummary::
+ :nosignatures:
{% for item in classes %}
- {{ item }}
+ {{ item }}
{%- endfor %}
- {%- endif %}
+{%- endif %}
- {%- if functions %}
+{%- if functions %}
- Functions:
+Functions:
- .. autosummary::
- :nosignatures:
+.. autosummary::
+ :nosignatures:
{% for item in functions %}
- {{ item }}
+ {{ item }}
{%- endfor %}
- {%- endif %}
+{%- endif %}
{%- endif %}
- {%- if data %}
+{%- if data %}
- Data:
+Data:
- .. autosummary::
- :nosignatures:
+.. autosummary::
+ :nosignatures:
{% for item in data %}
- {{ item }}
+ {{ item }}
{%- endfor %}
- {%- endif %}
+{%- endif %}
{% if all_refs %}
``__all__``: {{ all_refs|join(", ") }}
@@ -86,7 +88,7 @@
{% if members %}
- Reference
- ---------
+Reference
+---------
{%- endif %}
diff --git a/docs/api/aria.conbox.analysis.rst b/docs/api/aria.conbox.analysis.rst
index 205c7919fcbf336982006ee2cc8657a79d3934db..ced5db791a4d850e63174e5419ff9cec2dc22324 100644
--- a/docs/api/aria.conbox.analysis.rst
+++ b/docs/api/aria.conbox.analysis.rst
@@ -7,31 +7,31 @@ aria.conbox.analysis module
.. currentmodule:: aria.conbox.analysis
.. automodule:: aria.conbox.analysis
- :members: EnsembleAnalysis, colscatter
- :undoc-members:
- :show-inheritance:
- :member-order: bysource
+ :members: EnsembleAnalysis, colscatter
+ :undoc-members:
+ :show-inheritance:
+ :member-order: bysource
- Summary
- -------
+Summary
+-------
- Classes:
+Classes:
- .. autosummary::
- :nosignatures:
+.. autosummary::
+ :nosignatures:
- EnsembleAnalysis
+ EnsembleAnalysis
- Functions:
+Functions:
- .. autosummary::
- :nosignatures:
+.. autosummary::
+ :nosignatures:
- colscatter
+ colscatter
- Reference
- ---------
\ No newline at end of file
+Reference
+---------
\ No newline at end of file
diff --git a/docs/api/aria.conbox.commands.rst b/docs/api/aria.conbox.commands.rst
index 5208fa25a1129d15e6053d9907a48875d16fb3d2..4e0e39adaf1f828dec185e7c01e29dbd10b32ec7 100644
--- a/docs/api/aria.conbox.commands.rst
+++ b/docs/api/aria.conbox.commands.rst
@@ -7,34 +7,34 @@ 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
+ :members: AriaEcCommands, ReadableFile, check_file, main, seqrange_type
+ :undoc-members:
+ :show-inheritance:
+ :member-order: bysource
- Summary
- -------
+Summary
+-------
- Classes:
+Classes:
- .. autosummary::
- :nosignatures:
+.. autosummary::
+ :nosignatures:
- AriaEcCommands
- ReadableFile
+ AriaEcCommands
+ ReadableFile
- Functions:
+Functions:
- .. autosummary::
- :nosignatures:
+.. autosummary::
+ :nosignatures:
- check_file
- main
- seqrange_type
+ check_file
+ main
+ seqrange_type
- Reference
- ---------
\ No newline at end of file
+Reference
+---------
\ No newline at end of file
diff --git a/docs/api/aria.conbox.common.rst b/docs/api/aria.conbox.common.rst
index 9006fdb96c1befc5fe2d8a97e9060542b7ca4d2c..183df3cf84bf74a2671afadd6a65d86b23f58c2e 100644
--- a/docs/api/aria.conbox.common.rst
+++ b/docs/api/aria.conbox.common.rst
@@ -7,48 +7,48 @@ 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
+ :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
- -------
+Summary
+-------
- Classes:
+Classes:
- .. autosummary::
- :nosignatures:
+.. autosummary::
+ :nosignatures:
- Capturing
- CommandProtocol
- CustomLogging
- NotDisordered
- RedirectStdStreams
- TqdmToLogger
+ Capturing
+ CommandProtocol
+ CustomLogging
+ NotDisordered
+ RedirectStdStreams
+ TqdmToLogger
- Functions:
+Functions:
- .. autosummary::
- :nosignatures:
+.. autosummary::
+ :nosignatures:
- addtup
- cart_dist
- format_dict
- format_str
- get_filename
- parmap
- ppdict
- reg_load
- sort_2dict
- tickmin
- tickrot
- titleprint
- worker
+ 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
+Reference
+---------
\ No newline at end of file
diff --git a/docs/api/aria.conbox.converter.rst b/docs/api/aria.conbox.converter.rst
index 20748d3293c2d74adfff8c1f39cf73966089fd0e..f2bcd85ab4288f60a888f451c59ff72b105aa3f7 100644
--- a/docs/api/aria.conbox.converter.rst
+++ b/docs/api/aria.conbox.converter.rst
@@ -7,27 +7,27 @@ aria.conbox.converter module
.. currentmodule:: aria.conbox.converter
.. automodule:: aria.conbox.converter
- :members: AriaEcBbConverter, AriaEcConfigConverter, AriaEcXMLConverter, AriaXMLConverter
- :undoc-members:
- :show-inheritance:
- :member-order: bysource
+ :members: AriaEcBbConverter, AriaEcConfigConverter, AriaEcXMLConverter, AriaXMLConverter
+ :undoc-members:
+ :show-inheritance:
+ :member-order: bysource
- Summary
- -------
+Summary
+-------
- Classes:
+Classes:
- .. autosummary::
- :nosignatures:
+.. autosummary::
+ :nosignatures:
- AriaEcBbConverter
- AriaEcConfigConverter
- AriaEcXMLConverter
- AriaXMLConverter
+ AriaEcBbConverter
+ AriaEcConfigConverter
+ AriaEcXMLConverter
+ AriaXMLConverter
- Reference
- ---------
\ No newline at end of file
+Reference
+---------
\ No newline at end of file
diff --git a/docs/api/aria.conbox.maplot.rst b/docs/api/aria.conbox.maplot.rst
index d712a98e3096ed8ddd3a7a9348a6a89c25221b9b..f8b5c2e5edb57b027a147efcb6ec097a6884e320 100644
--- a/docs/api/aria.conbox.maplot.rst
+++ b/docs/api/aria.conbox.maplot.rst
@@ -7,24 +7,24 @@ aria.conbox.maplot module
.. currentmodule:: aria.conbox.maplot
.. automodule:: aria.conbox.maplot
- :members: AriaEcContactMap
- :undoc-members:
- :show-inheritance:
- :member-order: bysource
+ :members: AriaEcContactMap
+ :undoc-members:
+ :show-inheritance:
+ :member-order: bysource
- Summary
- -------
+Summary
+-------
- Classes:
+Classes:
- .. autosummary::
- :nosignatures:
+.. autosummary::
+ :nosignatures:
- AriaEcContactMap
+ AriaEcContactMap
- Reference
- ---------
\ No newline at end of file
+Reference
+---------
\ No newline at end of file
diff --git a/docs/api/aria.conbox.ndconv.rst b/docs/api/aria.conbox.ndconv.rst
index cdfadf2400d06204ecf04636d051f5162b97a31b..50681ae30218c2e70d4db781522d9b0d84e38e61 100644
--- a/docs/api/aria.conbox.ndconv.rst
+++ b/docs/api/aria.conbox.ndconv.rst
@@ -7,24 +7,24 @@ aria.conbox.ndconv module
.. currentmodule:: aria.conbox.ndconv
.. automodule:: aria.conbox.ndconv
- :members: net_deconv
- :undoc-members:
- :show-inheritance:
- :member-order: bysource
+ :members: net_deconv
+ :undoc-members:
+ :show-inheritance:
+ :member-order: bysource
- Summary
- -------
+Summary
+-------
- Functions:
+Functions:
- .. autosummary::
- :nosignatures:
+.. autosummary::
+ :nosignatures:
- net_deconv
+ net_deconv
- Reference
- ---------
\ No newline at end of file
+Reference
+---------
\ No newline at end of file
diff --git a/docs/api/aria.conbox.pdbdist.rst b/docs/api/aria.conbox.pdbdist.rst
index 6a6b908cc7ea7f53a9611f4b6a8f0049fcad2b4e..f8bf81df88a09f6784ae7e4dbf46a362e07886bf 100644
--- a/docs/api/aria.conbox.pdbdist.rst
+++ b/docs/api/aria.conbox.pdbdist.rst
@@ -7,24 +7,24 @@ aria.conbox.pdbdist module
.. currentmodule:: aria.conbox.pdbdist
.. automodule:: aria.conbox.pdbdist
- :members: PDBDist
- :undoc-members:
- :show-inheritance:
- :member-order: bysource
+ :members: PDBDist
+ :undoc-members:
+ :show-inheritance:
+ :member-order: bysource
- Summary
- -------
+Summary
+-------
- Classes:
+Classes:
- .. autosummary::
- :nosignatures:
+.. autosummary::
+ :nosignatures:
- PDBDist
+ PDBDist
- Reference
- ---------
\ No newline at end of file
+Reference
+---------
\ No newline at end of file
diff --git a/docs/api/aria.conbox.pdbqual.rst b/docs/api/aria.conbox.pdbqual.rst
index d5708e82baf053b5dfcf75ea405ea9702fac4aa4..2c6c297e4310907a3f85cb4b61d8e7012ef66837 100644
--- a/docs/api/aria.conbox.pdbqual.rst
+++ b/docs/api/aria.conbox.pdbqual.rst
@@ -7,24 +7,24 @@ aria.conbox.pdbqual module
.. currentmodule:: aria.conbox.pdbqual
.. automodule:: aria.conbox.pdbqual
- :members: AriaEcPdbqual
- :undoc-members:
- :show-inheritance:
- :member-order: bysource
+ :members: AriaEcPdbqual
+ :undoc-members:
+ :show-inheritance:
+ :member-order: bysource
- Summary
- -------
+Summary
+-------
- Classes:
+Classes:
- .. autosummary::
- :nosignatures:
+.. autosummary::
+ :nosignatures:
- AriaEcPdbqual
+ AriaEcPdbqual
- Reference
- ---------
\ No newline at end of file
+Reference
+---------
\ No newline at end of file
diff --git a/docs/api/aria.conbox.pdbstat.rst b/docs/api/aria.conbox.pdbstat.rst
index 7e2f88292af305b6dc85fb58cf94e98c794daded..4e718404cd52bb5c27c7784baead1f86bb32e96b 100644
--- a/docs/api/aria.conbox.pdbstat.rst
+++ b/docs/api/aria.conbox.pdbstat.rst
@@ -7,24 +7,24 @@ aria.conbox.pdbstat module
.. currentmodule:: aria.conbox.pdbstat
.. automodule:: aria.conbox.pdbstat
- :members: PDBStat
- :undoc-members:
- :show-inheritance:
- :member-order: bysource
+ :members: PDBStat
+ :undoc-members:
+ :show-inheritance:
+ :member-order: bysource
- Summary
- -------
+Summary
+-------
- Classes:
+Classes:
- .. autosummary::
- :nosignatures:
+.. autosummary::
+ :nosignatures:
- PDBStat
+ PDBStat
- Reference
- ---------
\ No newline at end of file
+Reference
+---------
\ No newline at end of file
diff --git a/docs/api/aria.conbox.protein.rst b/docs/api/aria.conbox.protein.rst
index a0c5cdce6a54279e77d3990c68cf18238a77198f..b475aa1d109809e00cef90ce3cc75f35c61d188c 100644
--- a/docs/api/aria.conbox.protein.rst
+++ b/docs/api/aria.conbox.protein.rst
@@ -7,26 +7,26 @@ aria.conbox.protein module
.. currentmodule:: aria.conbox.protein
.. automodule:: aria.conbox.protein
- :members: AminoAcidSequence, Protein, SsList
- :undoc-members:
- :show-inheritance:
- :member-order: bysource
+ :members: AminoAcidSequence, Protein, SsList
+ :undoc-members:
+ :show-inheritance:
+ :member-order: bysource
- Summary
- -------
+Summary
+-------
- Classes:
+Classes:
- .. autosummary::
- :nosignatures:
+.. autosummary::
+ :nosignatures:
- AminoAcidSequence
- Protein
- SsList
+ AminoAcidSequence
+ Protein
+ SsList
- Reference
- ---------
\ No newline at end of file
+Reference
+---------
\ No newline at end of file
diff --git a/docs/api/aria.conbox.protmap.rst b/docs/api/aria.conbox.protmap.rst
index 0ce6d201a8cfd938c81da354b53544ae46608351..881660942749e59234eccf5f4ffa134af313523b 100644
--- a/docs/api/aria.conbox.protmap.rst
+++ b/docs/api/aria.conbox.protmap.rst
@@ -7,33 +7,33 @@ aria.conbox.protmap module
.. currentmodule:: aria.conbox.protmap
.. automodule:: aria.conbox.protmap
- :members: AaAtmMap, AaMap, AtmMap, Map, MapFilter, ProtMapCollection, ProteinMap, ResAtmMap, ResMap, SsAaAtmMap
- :undoc-members:
- :show-inheritance:
- :member-order: bysource
+ :members: AaAtmMap, AaMap, AtmMap, Map, MapFilter, ProtMapCollection, ProteinMap, ResAtmMap, ResMap, SsAaAtmMap
+ :undoc-members:
+ :show-inheritance:
+ :member-order: bysource
- Summary
- -------
+Summary
+-------
- Classes:
+Classes:
- .. autosummary::
- :nosignatures:
+.. autosummary::
+ :nosignatures:
- AaAtmMap
- AaMap
- AtmMap
- Map
- MapFilter
- ProtMapCollection
- ProteinMap
- ResAtmMap
- ResMap
- SsAaAtmMap
+ AaAtmMap
+ AaMap
+ AtmMap
+ Map
+ MapFilter
+ ProtMapCollection
+ ProteinMap
+ ResAtmMap
+ ResMap
+ SsAaAtmMap
- Reference
- ---------
\ No newline at end of file
+Reference
+---------
\ No newline at end of file
diff --git a/docs/api/aria.conbox.reader.rst b/docs/api/aria.conbox.reader.rst
index 76285cd97f1cfc111dae5e7e165280621ee7efd9..6482f4da64368bb4595bd0f2e822a1ca1a930dd2 100644
--- a/docs/api/aria.conbox.reader.rst
+++ b/docs/api/aria.conbox.reader.rst
@@ -7,32 +7,32 @@ aria.conbox.reader module
.. currentmodule:: aria.conbox.reader
.. automodule:: aria.conbox.reader
- :members: Atom, ContactMapFile, CulledPdbFile, DistanceMapFile, MapFile, MapFileListReader, PDBFile, RegexFile, TblDistFile
- :undoc-members:
- :show-inheritance:
- :member-order: bysource
+ :members: Atom, ContactMapFile, CulledPdbFile, DistanceMapFile, MapFile, MapFileListReader, PDBFile, RegexFile, TblDistFile
+ :undoc-members:
+ :show-inheritance:
+ :member-order: bysource
- Summary
- -------
+Summary
+-------
- Classes:
+Classes:
- .. autosummary::
- :nosignatures:
+.. autosummary::
+ :nosignatures:
- Atom
- ContactMapFile
- CulledPdbFile
- DistanceMapFile
- MapFile
- MapFileListReader
- PDBFile
- RegexFile
- TblDistFile
+ Atom
+ ContactMapFile
+ CulledPdbFile
+ DistanceMapFile
+ MapFile
+ MapFileListReader
+ PDBFile
+ RegexFile
+ TblDistFile
- Reference
- ---------
\ No newline at end of file
+Reference
+---------
\ No newline at end of file
diff --git a/docs/api/aria.conbox.rst b/docs/api/aria.conbox.rst
index 91c9cbcdf9302ebd7d8f9b8c70fd29d6c03d1333..7a78c6d0beee9f4e0f0474106fe03d60de38686e 100644
--- a/docs/api/aria.conbox.rst
+++ b/docs/api/aria.conbox.rst
@@ -5,28 +5,29 @@ aria.conbox package
===================
.. automodule:: aria.conbox
-
-
-
- Submodules:
-
- .. toctree::
- :maxdepth: 1
-
- aria.conbox.analysis
- aria.conbox.commands
- aria.conbox.common
- aria.conbox.converter
- aria.conbox.maplot
- aria.conbox.ndconv
- aria.conbox.pdbdist
- aria.conbox.pdbqual
- aria.conbox.pdbstat
- aria.conbox.protein
- aria.conbox.protmap
- aria.conbox.reader
- aria.conbox.settings
- aria.conbox.setup
+
+
+
+
+Submodules:
+
+.. toctree::
+ :maxdepth: 1
+
+ aria.conbox.analysis
+ aria.conbox.commands
+ aria.conbox.common
+ aria.conbox.converter
+ aria.conbox.maplot
+ aria.conbox.ndconv
+ aria.conbox.pdbdist
+ aria.conbox.pdbqual
+ aria.conbox.pdbstat
+ aria.conbox.protein
+ aria.conbox.protmap
+ aria.conbox.reader
+ aria.conbox.settings
+ aria.conbox.setup
diff --git a/docs/api/aria.conbox.settings.rst b/docs/api/aria.conbox.settings.rst
index 438fd8244257ad0f5dd876fa16bee3760535fcbb..87bc6a7adddc985808fa97d0b2011b0e182ba492 100644
--- a/docs/api/aria.conbox.settings.rst
+++ b/docs/api/aria.conbox.settings.rst
@@ -7,26 +7,26 @@ aria.conbox.settings module
.. currentmodule:: aria.conbox.settings
.. automodule:: aria.conbox.settings
- :members: AriaEcSettings, Setting, Settings
- :undoc-members:
- :show-inheritance:
- :member-order: bysource
+ :members: AriaEcSettings, Setting, Settings
+ :undoc-members:
+ :show-inheritance:
+ :member-order: bysource
- Summary
- -------
+Summary
+-------
- Classes:
+Classes:
- .. autosummary::
- :nosignatures:
+.. autosummary::
+ :nosignatures:
- AriaEcSettings
- Setting
- Settings
+ AriaEcSettings
+ Setting
+ Settings
- Reference
- ---------
\ No newline at end of file
+Reference
+---------
\ No newline at end of file
diff --git a/docs/api/aria.conbox.setup.rst b/docs/api/aria.conbox.setup.rst
index 0fffd500533a25308f237e69656f9e5450bd87ef..29858d0746108868b86506629b4ae9a61e12e835 100644
--- a/docs/api/aria.conbox.setup.rst
+++ b/docs/api/aria.conbox.setup.rst
@@ -7,24 +7,24 @@ aria.conbox.setup module
.. currentmodule:: aria.conbox.setup
.. automodule:: aria.conbox.setup
- :members: AriaEcSetup
- :undoc-members:
- :show-inheritance:
- :member-order: bysource
+ :members: AriaEcSetup
+ :undoc-members:
+ :show-inheritance:
+ :member-order: bysource
- Summary
- -------
+Summary
+-------
- Classes:
+Classes:
- .. autosummary::
- :nosignatures:
+.. autosummary::
+ :nosignatures:
- AriaEcSetup
+ AriaEcSetup
- Reference
- ---------
\ No newline at end of file
+Reference
+---------
\ No newline at end of file
diff --git a/docs/api/aria.core.Analyser.rst b/docs/api/aria.core.Analyser.rst
index bcb8f566de52e8cd96063fde3a514c1a540f2eec..1592a58b6e285be5581f6cb9462d5b486f9a2c1f 100644
--- a/docs/api/aria.core.Analyser.rst
+++ b/docs/api/aria.core.Analyser.rst
@@ -7,26 +7,26 @@ aria.core.Analyser module
.. currentmodule:: aria.core.Analyser
.. automodule:: aria.core.Analyser
- :members: Analyser, AnalyserXMLPickler, AnalysisParameters
- :undoc-members:
- :show-inheritance:
- :member-order: bysource
+ :members: Analyser, AnalyserXMLPickler, AnalysisParameters
+ :undoc-members:
+ :show-inheritance:
+ :member-order: bysource
- Summary
- -------
+Summary
+-------
- Classes:
+Classes:
- .. autosummary::
- :nosignatures:
+.. autosummary::
+ :nosignatures:
- Analyser
- AnalyserXMLPickler
- AnalysisParameters
+ Analyser
+ AnalyserXMLPickler
+ AnalysisParameters
- Reference
- ---------
\ No newline at end of file
+Reference
+---------
\ No newline at end of file
diff --git a/docs/api/aria.core.AriaPeak.rst b/docs/api/aria.core.AriaPeak.rst
index c43f387b7e2fb5c8a885e848431d843ff640f935..9dd2f0be56a5a4fa5cb2aa05679eb47445b253e2 100644
--- a/docs/api/aria.core.AriaPeak.rst
+++ b/docs/api/aria.core.AriaPeak.rst
@@ -7,35 +7,35 @@ aria.core.AriaPeak module
.. currentmodule:: aria.core.AriaPeak
.. automodule:: aria.core.AriaPeak
- :members: AbstractPeak, AriaPeak, AriaPeakAnalysis, AriaPeakAnalysisXMLPickler, AriaPeakListTextPickler, AriaPeakListTextPicklerSettings, AriaPeakTextPickler, AriaPeakXMLPickler, ContributionTextPickler, DistanceRestraint, DistanceRestraintXMLPickler, TextPickler
- :undoc-members:
- :show-inheritance:
- :member-order: bysource
+ :members: AbstractPeak, AriaPeak, AriaPeakAnalysis, AriaPeakAnalysisXMLPickler, AriaPeakListTextPickler, AriaPeakListTextPicklerSettings, AriaPeakTextPickler, AriaPeakXMLPickler, ContributionTextPickler, DistanceRestraint, DistanceRestraintXMLPickler, TextPickler
+ :undoc-members:
+ :show-inheritance:
+ :member-order: bysource
- Summary
- -------
+Summary
+-------
- Classes:
+Classes:
- .. autosummary::
- :nosignatures:
+.. autosummary::
+ :nosignatures:
- AbstractPeak
- AriaPeak
- AriaPeakAnalysis
- AriaPeakAnalysisXMLPickler
- AriaPeakListTextPickler
- AriaPeakListTextPicklerSettings
- AriaPeakTextPickler
- AriaPeakXMLPickler
- ContributionTextPickler
- DistanceRestraint
- DistanceRestraintXMLPickler
- TextPickler
+ AbstractPeak
+ AriaPeak
+ AriaPeakAnalysis
+ AriaPeakAnalysisXMLPickler
+ AriaPeakListTextPickler
+ AriaPeakListTextPicklerSettings
+ AriaPeakTextPickler
+ AriaPeakXMLPickler
+ ContributionTextPickler
+ DistanceRestraint
+ DistanceRestraintXMLPickler
+ TextPickler
- Reference
- ---------
\ No newline at end of file
+Reference
+---------
\ No newline at end of file
diff --git a/docs/api/aria.core.AriaXML.rst b/docs/api/aria.core.AriaXML.rst
index 0752cb5a7a605b33472d2d5ebcd66ac14b6b6ed4..5163197859d011b7d9ea02324464145cbee48a3d 100644
--- a/docs/api/aria.core.AriaXML.rst
+++ b/docs/api/aria.core.AriaXML.rst
@@ -7,26 +7,26 @@ aria.core.AriaXML module
.. currentmodule:: aria.core.AriaXML
.. automodule:: aria.core.AriaXML
- :members: AriaXMLContentHandler, AriaXMLPickler, DOCManager
- :undoc-members:
- :show-inheritance:
- :member-order: bysource
+ :members: AriaXMLContentHandler, AriaXMLPickler, DOCManager
+ :undoc-members:
+ :show-inheritance:
+ :member-order: bysource
- Summary
- -------
+Summary
+-------
- Classes:
+Classes:
- .. autosummary::
- :nosignatures:
+.. autosummary::
+ :nosignatures:
- AriaXMLContentHandler
- AriaXMLPickler
- DOCManager
+ AriaXMLContentHandler
+ AriaXMLPickler
+ DOCManager
- Reference
- ---------
\ No newline at end of file
+Reference
+---------
\ No newline at end of file
diff --git a/docs/api/aria.core.Assignment.rst b/docs/api/aria.core.Assignment.rst
index e99db796aeb3b271c7ab9fb1eeb9b134d19d0f77..bdbae3f1ee8e7a09415829fa1762ed20b432a0a0 100644
--- a/docs/api/aria.core.Assignment.rst
+++ b/docs/api/aria.core.Assignment.rst
@@ -7,25 +7,25 @@ aria.core.Assignment module
.. currentmodule:: aria.core.Assignment
.. automodule:: aria.core.Assignment
- :members: Assignment, AssignmentXMLPickler
- :undoc-members:
- :show-inheritance:
- :member-order: bysource
+ :members: Assignment, AssignmentXMLPickler
+ :undoc-members:
+ :show-inheritance:
+ :member-order: bysource
- Summary
- -------
+Summary
+-------
- Classes:
+Classes:
- .. autosummary::
- :nosignatures:
+.. autosummary::
+ :nosignatures:
- Assignment
- AssignmentXMLPickler
+ Assignment
+ AssignmentXMLPickler
- Reference
- ---------
\ No newline at end of file
+Reference
+---------
\ No newline at end of file
diff --git a/docs/api/aria.core.AssignmentFilter.rst b/docs/api/aria.core.AssignmentFilter.rst
index 62a04a0763d075c0e578ae08dc9f71f585f0b62f..c7b6865d45d2c96bd21a9ed7e1b5495bda80ceeb 100644
--- a/docs/api/aria.core.AssignmentFilter.rst
+++ b/docs/api/aria.core.AssignmentFilter.rst
@@ -7,24 +7,24 @@ aria.core.AssignmentFilter module
.. currentmodule:: aria.core.AssignmentFilter
.. automodule:: aria.core.AssignmentFilter
- :members: AssignmentFilter
- :undoc-members:
- :show-inheritance:
- :member-order: bysource
+ :members: AssignmentFilter
+ :undoc-members:
+ :show-inheritance:
+ :member-order: bysource
- Summary
- -------
+Summary
+-------
- Classes:
+Classes:
- .. autosummary::
- :nosignatures:
+.. autosummary::
+ :nosignatures:
- AssignmentFilter
+ AssignmentFilter
- Reference
- ---------
\ No newline at end of file
+Reference
+---------
\ No newline at end of file
diff --git a/docs/api/aria.core.Atom.rst b/docs/api/aria.core.Atom.rst
index 498373dc7262be557e513689ba5512c528954a51..027d3c704514a59885e7038cd588eab5f8f918f7 100644
--- a/docs/api/aria.core.Atom.rst
+++ b/docs/api/aria.core.Atom.rst
@@ -7,26 +7,26 @@ aria.core.Atom module
.. currentmodule:: aria.core.Atom
.. automodule:: aria.core.Atom
- :members: Atom, AtomSettings, AtomXMLPickler
- :undoc-members:
- :show-inheritance:
- :member-order: bysource
+ :members: Atom, AtomSettings, AtomXMLPickler
+ :undoc-members:
+ :show-inheritance:
+ :member-order: bysource
- Summary
- -------
+Summary
+-------
- Classes:
+Classes:
- .. autosummary::
- :nosignatures:
+.. autosummary::
+ :nosignatures:
- Atom
- AtomSettings
- AtomXMLPickler
+ Atom
+ AtomSettings
+ AtomXMLPickler
- Reference
- ---------
\ No newline at end of file
+Reference
+---------
\ No newline at end of file
diff --git a/docs/api/aria.core.Calibrator.rst b/docs/api/aria.core.Calibrator.rst
index d96cb7ffcaa2cc67bae2b2db662c47b4a2a48dcf..fa42d074fc46d9329c989cabe067c3d58d99b7d5 100644
--- a/docs/api/aria.core.Calibrator.rst
+++ b/docs/api/aria.core.Calibrator.rst
@@ -7,27 +7,27 @@ aria.core.Calibrator module
.. currentmodule:: aria.core.Calibrator
.. automodule:: aria.core.Calibrator
- :members: Calibrator, CalibratorSettings, CalibratorXMLPickler, DistanceCutoffEntity
- :undoc-members:
- :show-inheritance:
- :member-order: bysource
+ :members: Calibrator, CalibratorSettings, CalibratorXMLPickler, DistanceCutoffEntity
+ :undoc-members:
+ :show-inheritance:
+ :member-order: bysource
- Summary
- -------
+Summary
+-------
- Classes:
+Classes:
- .. autosummary::
- :nosignatures:
+.. autosummary::
+ :nosignatures:
- Calibrator
- CalibratorSettings
- CalibratorXMLPickler
- DistanceCutoffEntity
+ Calibrator
+ CalibratorSettings
+ CalibratorXMLPickler
+ DistanceCutoffEntity
- Reference
- ---------
\ No newline at end of file
+Reference
+---------
\ No newline at end of file
diff --git a/docs/api/aria.core.Chain.rst b/docs/api/aria.core.Chain.rst
index 13cf61b2c63c2d47508ecba0336d31581f8f4e9a..5ede965ac1c4683441bcff9f2bec625d87cfde77 100644
--- a/docs/api/aria.core.Chain.rst
+++ b/docs/api/aria.core.Chain.rst
@@ -7,27 +7,27 @@ aria.core.Chain module
.. currentmodule:: aria.core.Chain
.. automodule:: aria.core.Chain
- :members: AtomNomenclatureEntity, Chain, ChainSettings, ChainXMLPickler
- :undoc-members:
- :show-inheritance:
- :member-order: bysource
+ :members: AtomNomenclatureEntity, Chain, ChainSettings, ChainXMLPickler
+ :undoc-members:
+ :show-inheritance:
+ :member-order: bysource
- Summary
- -------
+Summary
+-------
- Classes:
+Classes:
- .. autosummary::
- :nosignatures:
+.. autosummary::
+ :nosignatures:
- AtomNomenclatureEntity
- Chain
- ChainSettings
- ChainXMLPickler
+ AtomNomenclatureEntity
+ Chain
+ ChainSettings
+ ChainXMLPickler
- Reference
- ---------
\ No newline at end of file
+Reference
+---------
\ No newline at end of file
diff --git a/docs/api/aria.core.ChemicalShiftFilter.rst b/docs/api/aria.core.ChemicalShiftFilter.rst
index 5703f827f97bf2383e366daa61249bab84a687b2..c45096ca8848d527fdb0175c8428f692371bd09c 100644
--- a/docs/api/aria.core.ChemicalShiftFilter.rst
+++ b/docs/api/aria.core.ChemicalShiftFilter.rst
@@ -7,25 +7,25 @@ aria.core.ChemicalShiftFilter module
.. currentmodule:: aria.core.ChemicalShiftFilter
.. automodule:: aria.core.ChemicalShiftFilter
- :members: ChemicalShiftFilter, ChemicalShiftFilterSettings
- :undoc-members:
- :show-inheritance:
- :member-order: bysource
+ :members: ChemicalShiftFilter, ChemicalShiftFilterSettings
+ :undoc-members:
+ :show-inheritance:
+ :member-order: bysource
- Summary
- -------
+Summary
+-------
- Classes:
+Classes:
- .. autosummary::
- :nosignatures:
+.. autosummary::
+ :nosignatures:
- ChemicalShiftFilter
- ChemicalShiftFilterSettings
+ ChemicalShiftFilter
+ ChemicalShiftFilterSettings
- Reference
- ---------
\ No newline at end of file
+Reference
+---------
\ No newline at end of file
diff --git a/docs/api/aria.core.ChemicalShiftList.rst b/docs/api/aria.core.ChemicalShiftList.rst
index 1d273b23c7a39e090d61863cdc1e555491976b8f..b6752a18713b82f1ee32c221a5b461666b6445c5 100644
--- a/docs/api/aria.core.ChemicalShiftList.rst
+++ b/docs/api/aria.core.ChemicalShiftList.rst
@@ -7,25 +7,25 @@ aria.core.ChemicalShiftList module
.. currentmodule:: aria.core.ChemicalShiftList
.. automodule:: aria.core.ChemicalShiftList
- :members: ChemicalShiftList, ChemicalShiftListXMLPickler
- :undoc-members:
- :show-inheritance:
- :member-order: bysource
+ :members: ChemicalShiftList, ChemicalShiftListXMLPickler
+ :undoc-members:
+ :show-inheritance:
+ :member-order: bysource
- Summary
- -------
+Summary
+-------
- Classes:
+Classes:
- .. autosummary::
- :nosignatures:
+.. autosummary::
+ :nosignatures:
- ChemicalShiftList
- ChemicalShiftListXMLPickler
+ ChemicalShiftList
+ ChemicalShiftListXMLPickler
- Reference
- ---------
\ No newline at end of file
+Reference
+---------
\ No newline at end of file
diff --git a/docs/api/aria.core.Cluster.rst b/docs/api/aria.core.Cluster.rst
index 989a2b71c2b5a4c76c4bab73133fac025b6f38fe..b0fe4493ea0ffba404d2a971c5545341e9f56342 100644
--- a/docs/api/aria.core.Cluster.rst
+++ b/docs/api/aria.core.Cluster.rst
@@ -7,26 +7,26 @@ aria.core.Cluster module
.. currentmodule:: aria.core.Cluster
.. automodule:: aria.core.Cluster
- :members: Clustering, ClusteringSettings, ClusteringXMLPickler
- :undoc-members:
- :show-inheritance:
- :member-order: bysource
+ :members: Clustering, ClusteringSettings, ClusteringXMLPickler
+ :undoc-members:
+ :show-inheritance:
+ :member-order: bysource
- Summary
- -------
+Summary
+-------
- Classes:
+Classes:
- .. autosummary::
- :nosignatures:
+.. autosummary::
+ :nosignatures:
- Clustering
- ClusteringSettings
- ClusteringXMLPickler
+ Clustering
+ ClusteringSettings
+ ClusteringXMLPickler
- Reference
- ---------
\ No newline at end of file
+Reference
+---------
\ No newline at end of file
diff --git a/docs/api/aria.core.Contribution.rst b/docs/api/aria.core.Contribution.rst
index 2d0fa0fc455659d923920800dddd36268a0df2b0..e12df9523c6090ddb2a35981ae1ed9bfd9cd0452 100644
--- a/docs/api/aria.core.Contribution.rst
+++ b/docs/api/aria.core.Contribution.rst
@@ -7,27 +7,27 @@ aria.core.Contribution module
.. currentmodule:: aria.core.Contribution
.. automodule:: aria.core.Contribution
- :members: Contribution, Contribution2XMLPickler, ContributionEvaluator, ContributionXMLPickler
- :undoc-members:
- :show-inheritance:
- :member-order: bysource
+ :members: Contribution, Contribution2XMLPickler, ContributionEvaluator, ContributionXMLPickler
+ :undoc-members:
+ :show-inheritance:
+ :member-order: bysource
- Summary
- -------
+Summary
+-------
- Classes:
+Classes:
- .. autosummary::
- :nosignatures:
+.. autosummary::
+ :nosignatures:
- Contribution
- Contribution2XMLPickler
- ContributionEvaluator
- ContributionXMLPickler
+ Contribution
+ Contribution2XMLPickler
+ ContributionEvaluator
+ ContributionXMLPickler
- Reference
- ---------
\ No newline at end of file
+Reference
+---------
\ No newline at end of file
diff --git a/docs/api/aria.core.ContributionAssigner.rst b/docs/api/aria.core.ContributionAssigner.rst
index ae944d8123a565972b3aacff87b86067ac30332f..bd0dc52932735c19e94f12ddd408cd7d17b1e549 100644
--- a/docs/api/aria.core.ContributionAssigner.rst
+++ b/docs/api/aria.core.ContributionAssigner.rst
@@ -7,27 +7,27 @@ aria.core.ContributionAssigner module
.. currentmodule:: aria.core.ContributionAssigner
.. automodule:: aria.core.ContributionAssigner
- :members: ContributionAssigner, ContributionAssignerSettings, ContributionAssignerXMLPickler, WeightCutoff
- :undoc-members:
- :show-inheritance:
- :member-order: bysource
+ :members: ContributionAssigner, ContributionAssignerSettings, ContributionAssignerXMLPickler, WeightCutoff
+ :undoc-members:
+ :show-inheritance:
+ :member-order: bysource
- Summary
- -------
+Summary
+-------
- Classes:
+Classes:
- .. autosummary::
- :nosignatures:
+.. autosummary::
+ :nosignatures:
- ContributionAssigner
- ContributionAssignerSettings
- ContributionAssignerXMLPickler
- WeightCutoff
+ ContributionAssigner
+ ContributionAssignerSettings
+ ContributionAssignerXMLPickler
+ WeightCutoff
- Reference
- ---------
\ No newline at end of file
+Reference
+---------
\ No newline at end of file
diff --git a/docs/api/aria.core.ConversionTable.rst b/docs/api/aria.core.ConversionTable.rst
index da25e5447e0239c80495e5749c4c65ab52a304bb..f2b63253de83143c79472d1e1e51fabb4cab2682 100644
--- a/docs/api/aria.core.ConversionTable.rst
+++ b/docs/api/aria.core.ConversionTable.rst
@@ -7,31 +7,31 @@ aria.core.ConversionTable module
.. currentmodule:: aria.core.ConversionTable
.. automodule:: aria.core.ConversionTable
- :members: AtomnameConversionError, ConversionTable
- :undoc-members:
- :show-inheritance:
- :member-order: bysource
+ :members: AtomnameConversionError, ConversionTable
+ :undoc-members:
+ :show-inheritance:
+ :member-order: bysource
- Summary
- -------
+Summary
+-------
- Exceptions:
+Exceptions:
- .. autosummary::
- :nosignatures:
+.. autosummary::
+ :nosignatures:
- AtomnameConversionError
+ AtomnameConversionError
- Classes:
+Classes:
- .. autosummary::
- :nosignatures:
+.. autosummary::
+ :nosignatures:
- ConversionTable
+ ConversionTable
- Reference
- ---------
\ No newline at end of file
+Reference
+---------
\ No newline at end of file
diff --git a/docs/api/aria.core.CovalentDistances.rst b/docs/api/aria.core.CovalentDistances.rst
index 36423c2e6b8bb8d89c5a39124316b9b290035770..2062ce5d4fa9655aeb8e910c84e1f3b1fb03d0f3 100644
--- a/docs/api/aria.core.CovalentDistances.rst
+++ b/docs/api/aria.core.CovalentDistances.rst
@@ -7,24 +7,24 @@ aria.core.CovalentDistances module
.. currentmodule:: aria.core.CovalentDistances
.. automodule:: aria.core.CovalentDistances
- :members: CovalentDistances
- :undoc-members:
- :show-inheritance:
- :member-order: bysource
+ :members: CovalentDistances
+ :undoc-members:
+ :show-inheritance:
+ :member-order: bysource
- Summary
- -------
+Summary
+-------
- Classes:
+Classes:
- .. autosummary::
- :nosignatures:
+.. autosummary::
+ :nosignatures:
- CovalentDistances
+ CovalentDistances
- Reference
- ---------
\ No newline at end of file
+Reference
+---------
\ No newline at end of file
diff --git a/docs/api/aria.core.CrossPeak.rst b/docs/api/aria.core.CrossPeak.rst
index 8476733ab127e1fcfeb4bc0ba07978cc816901f3..5c553c6a482de29e4674b48e69668c06a0fd3213 100644
--- a/docs/api/aria.core.CrossPeak.rst
+++ b/docs/api/aria.core.CrossPeak.rst
@@ -7,25 +7,25 @@ aria.core.CrossPeak module
.. currentmodule:: aria.core.CrossPeak
.. automodule:: aria.core.CrossPeak
- :members: CrossPeak, CrossPeakXMLPickler
- :undoc-members:
- :show-inheritance:
- :member-order: bysource
+ :members: CrossPeak, CrossPeakXMLPickler
+ :undoc-members:
+ :show-inheritance:
+ :member-order: bysource
- Summary
- -------
+Summary
+-------
- Classes:
+Classes:
- .. autosummary::
- :nosignatures:
+.. autosummary::
+ :nosignatures:
- CrossPeak
- CrossPeakXMLPickler
+ CrossPeak
+ CrossPeakXMLPickler
- Reference
- ---------
\ No newline at end of file
+Reference
+---------
\ No newline at end of file
diff --git a/docs/api/aria.core.CrossPeakFilter.rst b/docs/api/aria.core.CrossPeakFilter.rst
index 222e10878977c56de1f87142d3f3e067f1fe8e20..3dc46dc22a1485a3974698c85fc95654cc2e74c6 100644
--- a/docs/api/aria.core.CrossPeakFilter.rst
+++ b/docs/api/aria.core.CrossPeakFilter.rst
@@ -7,25 +7,25 @@ aria.core.CrossPeakFilter module
.. currentmodule:: aria.core.CrossPeakFilter
.. automodule:: aria.core.CrossPeakFilter
- :members: CrossPeakFilter, CrossPeakFilterSettings
- :undoc-members:
- :show-inheritance:
- :member-order: bysource
+ :members: CrossPeakFilter, CrossPeakFilterSettings
+ :undoc-members:
+ :show-inheritance:
+ :member-order: bysource
- Summary
- -------
+Summary
+-------
- Classes:
+Classes:
- .. autosummary::
- :nosignatures:
+.. autosummary::
+ :nosignatures:
- CrossPeakFilter
- CrossPeakFilterSettings
+ CrossPeakFilter
+ CrossPeakFilterSettings
- Reference
- ---------
\ No newline at end of file
+Reference
+---------
\ No newline at end of file
diff --git a/docs/api/aria.core.DataContainer.rst b/docs/api/aria.core.DataContainer.rst
index 41de9116751be58966dee27aefcf10fc018cb312..16e001a4c31cd56ea433a7dc15d3d8f5a7982f86 100644
--- a/docs/api/aria.core.DataContainer.rst
+++ b/docs/api/aria.core.DataContainer.rst
@@ -7,112 +7,112 @@ aria.core.DataContainer module
.. currentmodule:: aria.core.DataContainer
.. automodule:: aria.core.DataContainer
- :members: AmbiguousDistanceData, AmbiguousDistanceDataXMLPickler, AmbiguousParameters, AmbiguousParametersXMLPickler, AnnealingParameters, AnnealingParametersXMLPickler, BASE, BoundCorrection, BoundCorrectionXMLPickler, CCPNData, CCPNDataXMLPickler, CisProPatch, CisProPatchXMLPickler, CysPatch, CysPatchXMLPickler, DRParametersXMLPickler, DataContainer, DataContainerXMLPickler, DihedralData, DihedralDataXMLPickler, DihedralParameters, DihedralParametersXMLPickler, DistanceDataXMLPickler, ExperimentData, ExperimentDataXMLPickler, FBHWParameters, FBHWParametersXMLPickler, FFP, FileFormatXMLPickler, HBDBParameters, HBDBParametersXMLPickler, HBondData, HBondDataXMLPickler, HBondParameters, HBondParametersXMLPickler, HisPatch, HisPatchXMLPickler, InitialStructureData, InitialStructureDataXMLPickler, IsoPeptidePatch, IsoPeptidePatchXMLPickler, KarplusData, KarplusDataXMLPickler, KarplusParameters, KarplusParametersXMLPickler, LogHarmonicParameters, LogHarmonicParametersXMLPickler, LowerBoundCorrection, MDParameters, MDParametersXMLPickler, OtherData, OtherDataXMLPickler, PeakData, PeakDataXMLPickler, RDCData, RDCDataXMLPickler, RDCParameters, RDCParametersXMLPickler, RamaParameters, RamaParametersXMLPickler, SSBondData, SSBondDataXMLPickler, SSBridge, SSBridgeXMLPickler, ScoringParameters, ScoringParametersXMLPickler, SequenceData, SequenceDataXMLPickler, ShiftData, ShiftDataXMLPickler, SimpleDCXMLPickler, SimpleDataContainer, SpectrumData, SpectrumDataXMLPickler, Symmetry, SymmetryParameters, SymmetryParametersXMLPickler, SymmetryXMLPickler, TemplateData, TemplateDataXMLPickler, UnambiguousDistanceData, UnambiguousDistanceDataXMLPickler, UnambiguousParameters, UnambiguousParametersXMLPickler, UpperBoundCorrection, WaterRefinementParameters, WaterRefinementXMLPickler, ZnPatch, ZnPatchXMLPickler
- :undoc-members:
- :show-inheritance:
- :member-order: bysource
+ :members: AmbiguousDistanceData, AmbiguousDistanceDataXMLPickler, AmbiguousParameters, AmbiguousParametersXMLPickler, AnnealingParameters, AnnealingParametersXMLPickler, BASE, BoundCorrection, BoundCorrectionXMLPickler, CCPNData, CCPNDataXMLPickler, CisProPatch, CisProPatchXMLPickler, CysPatch, CysPatchXMLPickler, DRParametersXMLPickler, DataContainer, DataContainerXMLPickler, DihedralData, DihedralDataXMLPickler, DihedralParameters, DihedralParametersXMLPickler, DistanceDataXMLPickler, ExperimentData, ExperimentDataXMLPickler, FBHWParameters, FBHWParametersXMLPickler, FFP, FileFormatXMLPickler, HBDBParameters, HBDBParametersXMLPickler, HBondData, HBondDataXMLPickler, HBondParameters, HBondParametersXMLPickler, HisPatch, HisPatchXMLPickler, InitialStructureData, InitialStructureDataXMLPickler, IsoPeptidePatch, IsoPeptidePatchXMLPickler, KarplusData, KarplusDataXMLPickler, KarplusParameters, KarplusParametersXMLPickler, LogHarmonicParameters, LogHarmonicParametersXMLPickler, LowerBoundCorrection, MDParameters, MDParametersXMLPickler, OtherData, OtherDataXMLPickler, PeakData, PeakDataXMLPickler, RDCData, RDCDataXMLPickler, RDCParameters, RDCParametersXMLPickler, RamaParameters, RamaParametersXMLPickler, SSBondData, SSBondDataXMLPickler, SSBridge, SSBridgeXMLPickler, ScoringParameters, ScoringParametersXMLPickler, SequenceData, SequenceDataXMLPickler, ShiftData, ShiftDataXMLPickler, SimpleDCXMLPickler, SimpleDataContainer, SpectrumData, SpectrumDataXMLPickler, Symmetry, SymmetryParameters, SymmetryParametersXMLPickler, SymmetryXMLPickler, TemplateData, TemplateDataXMLPickler, UnambiguousDistanceData, UnambiguousDistanceDataXMLPickler, UnambiguousParameters, UnambiguousParametersXMLPickler, UpperBoundCorrection, WaterRefinementParameters, WaterRefinementXMLPickler, ZnPatch, ZnPatchXMLPickler
+ :undoc-members:
+ :show-inheritance:
+ :member-order: bysource
- Summary
- -------
+Summary
+-------
- Classes:
+Classes:
- .. autosummary::
- :nosignatures:
+.. autosummary::
+ :nosignatures:
- AmbiguousDistanceData
- AmbiguousDistanceDataXMLPickler
- AmbiguousParameters
- AmbiguousParametersXMLPickler
- AnnealingParameters
- AnnealingParametersXMLPickler
- BASE
- BoundCorrection
- BoundCorrectionXMLPickler
- CCPNData
- CCPNDataXMLPickler
- CisProPatch
- CisProPatchXMLPickler
- CysPatch
- CysPatchXMLPickler
- DRParametersXMLPickler
- DataContainer
- DataContainerXMLPickler
- DihedralData
- DihedralDataXMLPickler
- DihedralParameters
- DihedralParametersXMLPickler
- DistanceDataXMLPickler
- ExperimentData
- ExperimentDataXMLPickler
- FBHWParameters
- FBHWParametersXMLPickler
- FFP
- FileFormatXMLPickler
- HBDBParameters
- HBDBParametersXMLPickler
- HBondData
- HBondDataXMLPickler
- HBondParameters
- HBondParametersXMLPickler
- HisPatch
- HisPatchXMLPickler
- InitialStructureData
- InitialStructureDataXMLPickler
- IsoPeptidePatch
- IsoPeptidePatchXMLPickler
- KarplusData
- KarplusDataXMLPickler
- KarplusParameters
- KarplusParametersXMLPickler
- LogHarmonicParameters
- LogHarmonicParametersXMLPickler
- LowerBoundCorrection
- MDParameters
- MDParametersXMLPickler
- OtherData
- OtherDataXMLPickler
- PeakData
- PeakDataXMLPickler
- RDCData
- RDCDataXMLPickler
- RDCParameters
- RDCParametersXMLPickler
- RamaParameters
- RamaParametersXMLPickler
- SSBondData
- SSBondDataXMLPickler
- SSBridge
- SSBridgeXMLPickler
- ScoringParameters
- ScoringParametersXMLPickler
- SequenceData
- SequenceDataXMLPickler
- ShiftData
- ShiftDataXMLPickler
- SimpleDCXMLPickler
- SimpleDataContainer
- SpectrumData
- SpectrumDataXMLPickler
- Symmetry
- SymmetryParameters
- SymmetryParametersXMLPickler
- SymmetryXMLPickler
- TemplateData
- TemplateDataXMLPickler
- UnambiguousDistanceData
- UnambiguousDistanceDataXMLPickler
- UnambiguousParameters
- UnambiguousParametersXMLPickler
- UpperBoundCorrection
- WaterRefinementParameters
- WaterRefinementXMLPickler
- ZnPatch
- ZnPatchXMLPickler
+ AmbiguousDistanceData
+ AmbiguousDistanceDataXMLPickler
+ AmbiguousParameters
+ AmbiguousParametersXMLPickler
+ AnnealingParameters
+ AnnealingParametersXMLPickler
+ BASE
+ BoundCorrection
+ BoundCorrectionXMLPickler
+ CCPNData
+ CCPNDataXMLPickler
+ CisProPatch
+ CisProPatchXMLPickler
+ CysPatch
+ CysPatchXMLPickler
+ DRParametersXMLPickler
+ DataContainer
+ DataContainerXMLPickler
+ DihedralData
+ DihedralDataXMLPickler
+ DihedralParameters
+ DihedralParametersXMLPickler
+ DistanceDataXMLPickler
+ ExperimentData
+ ExperimentDataXMLPickler
+ FBHWParameters
+ FBHWParametersXMLPickler
+ FFP
+ FileFormatXMLPickler
+ HBDBParameters
+ HBDBParametersXMLPickler
+ HBondData
+ HBondDataXMLPickler
+ HBondParameters
+ HBondParametersXMLPickler
+ HisPatch
+ HisPatchXMLPickler
+ InitialStructureData
+ InitialStructureDataXMLPickler
+ IsoPeptidePatch
+ IsoPeptidePatchXMLPickler
+ KarplusData
+ KarplusDataXMLPickler
+ KarplusParameters
+ KarplusParametersXMLPickler
+ LogHarmonicParameters
+ LogHarmonicParametersXMLPickler
+ LowerBoundCorrection
+ MDParameters
+ MDParametersXMLPickler
+ OtherData
+ OtherDataXMLPickler
+ PeakData
+ PeakDataXMLPickler
+ RDCData
+ RDCDataXMLPickler
+ RDCParameters
+ RDCParametersXMLPickler
+ RamaParameters
+ RamaParametersXMLPickler
+ SSBondData
+ SSBondDataXMLPickler
+ SSBridge
+ SSBridgeXMLPickler
+ ScoringParameters
+ ScoringParametersXMLPickler
+ SequenceData
+ SequenceDataXMLPickler
+ ShiftData
+ ShiftDataXMLPickler
+ SimpleDCXMLPickler
+ SimpleDataContainer
+ SpectrumData
+ SpectrumDataXMLPickler
+ Symmetry
+ SymmetryParameters
+ SymmetryParametersXMLPickler
+ SymmetryXMLPickler
+ TemplateData
+ TemplateDataXMLPickler
+ UnambiguousDistanceData
+ UnambiguousDistanceDataXMLPickler
+ UnambiguousParameters
+ UnambiguousParametersXMLPickler
+ UpperBoundCorrection
+ WaterRefinementParameters
+ WaterRefinementXMLPickler
+ ZnPatch
+ ZnPatchXMLPickler
- Reference
- ---------
\ No newline at end of file
+Reference
+---------
\ No newline at end of file
diff --git a/docs/api/aria.core.Datum.rst b/docs/api/aria.core.Datum.rst
index 02434ec73cd68773c8ab31578bebf24cf9e3123b..b10e3974d0d9ec21ed0c735bd661509335b3f869 100644
--- a/docs/api/aria.core.Datum.rst
+++ b/docs/api/aria.core.Datum.rst
@@ -7,27 +7,27 @@ aria.core.Datum module
.. currentmodule:: aria.core.Datum
.. automodule:: aria.core.Datum
- :members: ChemicalShift, ChemicalShiftXMLPickler, Datum, DatumXMLPickler
- :undoc-members:
- :show-inheritance:
- :member-order: bysource
+ :members: ChemicalShift, ChemicalShiftXMLPickler, Datum, DatumXMLPickler
+ :undoc-members:
+ :show-inheritance:
+ :member-order: bysource
- Summary
- -------
+Summary
+-------
- Classes:
+Classes:
- .. autosummary::
- :nosignatures:
+.. autosummary::
+ :nosignatures:
- ChemicalShift
- ChemicalShiftXMLPickler
- Datum
- DatumXMLPickler
+ ChemicalShift
+ ChemicalShiftXMLPickler
+ Datum
+ DatumXMLPickler
- Reference
- ---------
\ No newline at end of file
+Reference
+---------
\ No newline at end of file
diff --git a/docs/api/aria.core.Experiment.rst b/docs/api/aria.core.Experiment.rst
index 4b483355bfad7e2495cb7773798a13508f0b6b4f..5d31fd58d9ef92741f76516b21065a40d6424659 100644
--- a/docs/api/aria.core.Experiment.rst
+++ b/docs/api/aria.core.Experiment.rst
@@ -7,24 +7,24 @@ aria.core.Experiment module
.. currentmodule:: aria.core.Experiment
.. automodule:: aria.core.Experiment
- :members: Experiment
- :undoc-members:
- :show-inheritance:
- :member-order: bysource
+ :members: Experiment
+ :undoc-members:
+ :show-inheritance:
+ :member-order: bysource
- Summary
- -------
+Summary
+-------
- Classes:
+Classes:
- .. autosummary::
- :nosignatures:
+.. autosummary::
+ :nosignatures:
- Experiment
+ Experiment
- Reference
- ---------
\ No newline at end of file
+Reference
+---------
\ No newline at end of file
diff --git a/docs/api/aria.core.Factory.rst b/docs/api/aria.core.Factory.rst
index 92028606e14bf752edfe1dad3e12662e666c1824..eecf70e1408b127c899bfe2c1b8d0aa631a136b6 100644
--- a/docs/api/aria.core.Factory.rst
+++ b/docs/api/aria.core.Factory.rst
@@ -7,26 +7,26 @@ aria.core.Factory module
.. currentmodule:: aria.core.Factory
.. automodule:: aria.core.Factory
- :members: AtomFactory, SpinPairFactory, SpinPairListFactory
- :undoc-members:
- :show-inheritance:
- :member-order: bysource
+ :members: AtomFactory, SpinPairFactory, SpinPairListFactory
+ :undoc-members:
+ :show-inheritance:
+ :member-order: bysource
- Summary
- -------
+Summary
+-------
- Classes:
+Classes:
- .. autosummary::
- :nosignatures:
+.. autosummary::
+ :nosignatures:
- AtomFactory
- SpinPairFactory
- SpinPairListFactory
+ AtomFactory
+ SpinPairFactory
+ SpinPairListFactory
- Reference
- ---------
\ No newline at end of file
+Reference
+---------
\ No newline at end of file
diff --git a/docs/api/aria.core.FloatFile.rst b/docs/api/aria.core.FloatFile.rst
index d4ea8bbb83012762ba714ec8676c7bc8e914a68d..fabba81ff5e1563ff47f15e1cbf367f33b37d938 100644
--- a/docs/api/aria.core.FloatFile.rst
+++ b/docs/api/aria.core.FloatFile.rst
@@ -7,24 +7,24 @@ aria.core.FloatFile module
.. currentmodule:: aria.core.FloatFile
.. automodule:: aria.core.FloatFile
- :members: FloatFile
- :undoc-members:
- :show-inheritance:
- :member-order: bysource
+ :members: FloatFile
+ :undoc-members:
+ :show-inheritance:
+ :member-order: bysource
- Summary
- -------
+Summary
+-------
- Classes:
+Classes:
- .. autosummary::
- :nosignatures:
+.. autosummary::
+ :nosignatures:
- FloatFile
+ FloatFile
- Reference
- ---------
\ No newline at end of file
+Reference
+---------
\ No newline at end of file
diff --git a/docs/api/aria.core.Infrastructure.rst b/docs/api/aria.core.Infrastructure.rst
index a95c82da02691fd77cd28fc12111a31f3ce9b1f2..06b5b1e62304feb8fd908dedbfd9f0a3fd3396f4 100644
--- a/docs/api/aria.core.Infrastructure.rst
+++ b/docs/api/aria.core.Infrastructure.rst
@@ -7,31 +7,31 @@ aria.core.Infrastructure module
.. currentmodule:: aria.core.Infrastructure
.. automodule:: aria.core.Infrastructure
- :members: AriaDirectoryCreationError, Infrastructure
- :undoc-members:
- :show-inheritance:
- :member-order: bysource
+ :members: AriaDirectoryCreationError, Infrastructure
+ :undoc-members:
+ :show-inheritance:
+ :member-order: bysource
- Summary
- -------
+Summary
+-------
- Exceptions:
+Exceptions:
- .. autosummary::
- :nosignatures:
+.. autosummary::
+ :nosignatures:
- AriaDirectoryCreationError
+ AriaDirectoryCreationError
- Classes:
+Classes:
- .. autosummary::
- :nosignatures:
+.. autosummary::
+ :nosignatures:
- Infrastructure
+ Infrastructure
- Reference
- ---------
\ No newline at end of file
+Reference
+---------
\ No newline at end of file
diff --git a/docs/api/aria.core.Iteration.rst b/docs/api/aria.core.Iteration.rst
index 2b295e8903741eefd24a673cb84a007a7398c64a..006d07b089d0af59890e3efcb35e3e9be78e516c 100644
--- a/docs/api/aria.core.Iteration.rst
+++ b/docs/api/aria.core.Iteration.rst
@@ -7,25 +7,25 @@ aria.core.Iteration module
.. currentmodule:: aria.core.Iteration
.. automodule:: aria.core.Iteration
- :members: Iteration, IterationTextPickler
- :undoc-members:
- :show-inheritance:
- :member-order: bysource
+ :members: Iteration, IterationTextPickler
+ :undoc-members:
+ :show-inheritance:
+ :member-order: bysource
- Summary
- -------
+Summary
+-------
- Classes:
+Classes:
- .. autosummary::
- :nosignatures:
+.. autosummary::
+ :nosignatures:
- Iteration
- IterationTextPickler
+ Iteration
+ IterationTextPickler
- Reference
- ---------
\ No newline at end of file
+Reference
+---------
\ No newline at end of file
diff --git a/docs/api/aria.core.JobManager.rst b/docs/api/aria.core.JobManager.rst
index 53d1688f234684db9df6f5e71a782a7225eea18e..fcfef227a7f7fcbe8ca6da58f7d402b9e1295f65 100644
--- a/docs/api/aria.core.JobManager.rst
+++ b/docs/api/aria.core.JobManager.rst
@@ -7,32 +7,32 @@ aria.core.JobManager module
.. currentmodule:: aria.core.JobManager
.. automodule:: aria.core.JobManager
- :members: HostSettings, HostSettingsXMLPickler, Job, JobManager, JobManagerXMLPickler, JobScheduler, JobSchedulerSettings, JobSettings, PartlyUsedNodesFinder
- :undoc-members:
- :show-inheritance:
- :member-order: bysource
+ :members: HostSettings, HostSettingsXMLPickler, Job, JobManager, JobManagerXMLPickler, JobScheduler, JobSchedulerSettings, JobSettings, PartlyUsedNodesFinder
+ :undoc-members:
+ :show-inheritance:
+ :member-order: bysource
- Summary
- -------
+Summary
+-------
- Classes:
+Classes:
- .. autosummary::
- :nosignatures:
+.. autosummary::
+ :nosignatures:
- HostSettings
- HostSettingsXMLPickler
- Job
- JobManager
- JobManagerXMLPickler
- JobScheduler
- JobSchedulerSettings
- JobSettings
- PartlyUsedNodesFinder
+ HostSettings
+ HostSettingsXMLPickler
+ Job
+ JobManager
+ JobManagerXMLPickler
+ JobScheduler
+ JobSchedulerSettings
+ JobSettings
+ PartlyUsedNodesFinder
- Reference
- ---------
\ No newline at end of file
+Reference
+---------
\ No newline at end of file
diff --git a/docs/api/aria.core.Merger.rst b/docs/api/aria.core.Merger.rst
index bd1a15a43047adbed352500190c9e59bf91cd7e1..ed8f360aec8ab9f8325af3f4473b0986d463e7c6 100644
--- a/docs/api/aria.core.Merger.rst
+++ b/docs/api/aria.core.Merger.rst
@@ -7,27 +7,27 @@ aria.core.Merger module
.. currentmodule:: aria.core.Merger
.. automodule:: aria.core.Merger
- :members: Merger, MergerSettings, MergerTextPickler, MergerXMLPickler
- :undoc-members:
- :show-inheritance:
- :member-order: bysource
+ :members: Merger, MergerSettings, MergerTextPickler, MergerXMLPickler
+ :undoc-members:
+ :show-inheritance:
+ :member-order: bysource
- Summary
- -------
+Summary
+-------
- Classes:
+Classes:
- .. autosummary::
- :nosignatures:
+.. autosummary::
+ :nosignatures:
- Merger
- MergerSettings
- MergerTextPickler
- MergerXMLPickler
+ Merger
+ MergerSettings
+ MergerTextPickler
+ MergerXMLPickler
- Reference
- ---------
\ No newline at end of file
+Reference
+---------
\ No newline at end of file
diff --git a/docs/api/aria.core.MolMol.rst b/docs/api/aria.core.MolMol.rst
index 81f0e64916aa63a58feb2a94ee22415188546efe..75d88798dff2872492d7f4d53a99bb43e2bef156 100644
--- a/docs/api/aria.core.MolMol.rst
+++ b/docs/api/aria.core.MolMol.rst
@@ -7,31 +7,31 @@ aria.core.MolMol module
.. currentmodule:: aria.core.MolMol
.. automodule:: aria.core.MolMol
- :members: MolMolPickler, write_noe_restraints
- :undoc-members:
- :show-inheritance:
- :member-order: bysource
+ :members: MolMolPickler, write_noe_restraints
+ :undoc-members:
+ :show-inheritance:
+ :member-order: bysource
- Summary
- -------
+Summary
+-------
- Classes:
+Classes:
- .. autosummary::
- :nosignatures:
+.. autosummary::
+ :nosignatures:
- MolMolPickler
+ MolMolPickler
- Functions:
+Functions:
- .. autosummary::
- :nosignatures:
+.. autosummary::
+ :nosignatures:
- write_noe_restraints
+ write_noe_restraints
- Reference
- ---------
\ No newline at end of file
+Reference
+---------
\ No newline at end of file
diff --git a/docs/api/aria.core.Molecule.rst b/docs/api/aria.core.Molecule.rst
index c4e4dd9a9a89b457fece784e2acb1e684734b8a9..d9f59de89df3f9820ac0d62de0a94027094af023 100644
--- a/docs/api/aria.core.Molecule.rst
+++ b/docs/api/aria.core.Molecule.rst
@@ -7,25 +7,25 @@ aria.core.Molecule module
.. currentmodule:: aria.core.Molecule
.. automodule:: aria.core.Molecule
- :members: Molecule, MoleculeXMLPickler
- :undoc-members:
- :show-inheritance:
- :member-order: bysource
+ :members: Molecule, MoleculeXMLPickler
+ :undoc-members:
+ :show-inheritance:
+ :member-order: bysource
- Summary
- -------
+Summary
+-------
- Classes:
+Classes:
- .. autosummary::
- :nosignatures:
+.. autosummary::
+ :nosignatures:
- Molecule
- MoleculeXMLPickler
+ Molecule
+ MoleculeXMLPickler
- Reference
- ---------
\ No newline at end of file
+Reference
+---------
\ No newline at end of file
diff --git a/docs/api/aria.core.Molprobity.rst b/docs/api/aria.core.Molprobity.rst
index 985327f9a544a960d7ec1e95af6e4f1d042457b6..d0223061830e0766357cf84ba06b8ebbc044f0bd 100644
--- a/docs/api/aria.core.Molprobity.rst
+++ b/docs/api/aria.core.Molprobity.rst
@@ -7,24 +7,24 @@ aria.core.Molprobity module
.. currentmodule:: aria.core.Molprobity
.. automodule:: aria.core.Molprobity
- :members: MolprobityClashlist
- :undoc-members:
- :show-inheritance:
- :member-order: bysource
+ :members: MolprobityClashlist
+ :undoc-members:
+ :show-inheritance:
+ :member-order: bysource
- Summary
- -------
+Summary
+-------
- Classes:
+Classes:
- .. autosummary::
- :nosignatures:
+.. autosummary::
+ :nosignatures:
- MolprobityClashlist
+ MolprobityClashlist
- Reference
- ---------
\ No newline at end of file
+Reference
+---------
\ No newline at end of file
diff --git a/docs/api/aria.core.NOEModel.rst b/docs/api/aria.core.NOEModel.rst
index 1523460f2c7d7a37f4eca241d2a74c648b02561e..07db14d226f41e57cb593eb6b5e7e1d611c9d5ce 100644
--- a/docs/api/aria.core.NOEModel.rst
+++ b/docs/api/aria.core.NOEModel.rst
@@ -7,26 +7,26 @@ aria.core.NOEModel module
.. currentmodule:: aria.core.NOEModel
.. automodule:: aria.core.NOEModel
- :members: ISPA, NOEModel, SpinDiffusionCorrection
- :undoc-members:
- :show-inheritance:
- :member-order: bysource
+ :members: ISPA, NOEModel, SpinDiffusionCorrection
+ :undoc-members:
+ :show-inheritance:
+ :member-order: bysource
- Summary
- -------
+Summary
+-------
- Classes:
+Classes:
- .. autosummary::
- :nosignatures:
+.. autosummary::
+ :nosignatures:
- ISPA
- NOEModel
- SpinDiffusionCorrection
+ ISPA
+ NOEModel
+ SpinDiffusionCorrection
- Reference
- ---------
\ No newline at end of file
+Reference
+---------
\ No newline at end of file
diff --git a/docs/api/aria.core.NOESYSpectrum.rst b/docs/api/aria.core.NOESYSpectrum.rst
index bb008f2d11547edf26cfc499da766d7a16c5c998..e8c60a000256bcb97b1b6f887a28a397eec11de4 100644
--- a/docs/api/aria.core.NOESYSpectrum.rst
+++ b/docs/api/aria.core.NOESYSpectrum.rst
@@ -7,26 +7,26 @@ aria.core.NOESYSpectrum module
.. currentmodule:: aria.core.NOESYSpectrum
.. automodule:: aria.core.NOESYSpectrum
- :members: ConstraintList, NOESYSpectrum, NOESYSpectrumXMLPickler
- :undoc-members:
- :show-inheritance:
- :member-order: bysource
+ :members: ConstraintList, NOESYSpectrum, NOESYSpectrumXMLPickler
+ :undoc-members:
+ :show-inheritance:
+ :member-order: bysource
- Summary
- -------
+Summary
+-------
- Classes:
+Classes:
- .. autosummary::
- :nosignatures:
+.. autosummary::
+ :nosignatures:
- ConstraintList
- NOESYSpectrum
- NOESYSpectrumXMLPickler
+ ConstraintList
+ NOESYSpectrum
+ NOESYSpectrumXMLPickler
- Reference
- ---------
\ No newline at end of file
+Reference
+---------
\ No newline at end of file
diff --git a/docs/api/aria.core.NOESYSpectrumFilter.rst b/docs/api/aria.core.NOESYSpectrumFilter.rst
index 999c9183e25d9333b642bf282d2be0afd60e0670..dda45644fbe69cd3d869733869acec8d5585ea20 100644
--- a/docs/api/aria.core.NOESYSpectrumFilter.rst
+++ b/docs/api/aria.core.NOESYSpectrumFilter.rst
@@ -7,26 +7,26 @@ aria.core.NOESYSpectrumFilter module
.. currentmodule:: aria.core.NOESYSpectrumFilter
.. automodule:: aria.core.NOESYSpectrumFilter
- :members: NOESYSpectrumFilter, NOESYSpectrumFilterSettings, NOESYSpectrumFilterTextPickler
- :undoc-members:
- :show-inheritance:
- :member-order: bysource
+ :members: NOESYSpectrumFilter, NOESYSpectrumFilterSettings, NOESYSpectrumFilterTextPickler
+ :undoc-members:
+ :show-inheritance:
+ :member-order: bysource
- Summary
- -------
+Summary
+-------
- Classes:
+Classes:
- .. autosummary::
- :nosignatures:
+.. autosummary::
+ :nosignatures:
- NOESYSpectrumFilter
- NOESYSpectrumFilterSettings
- NOESYSpectrumFilterTextPickler
+ NOESYSpectrumFilter
+ NOESYSpectrumFilterSettings
+ NOESYSpectrumFilterTextPickler
- Reference
- ---------
\ No newline at end of file
+Reference
+---------
\ No newline at end of file
diff --git a/docs/api/aria.core.Network.rst b/docs/api/aria.core.Network.rst
index 870b438fbc56afdc57d7aa3ec4b2ce1c97734d80..cb629472b7005068d24bd568950c56bc5af576ba 100644
--- a/docs/api/aria.core.Network.rst
+++ b/docs/api/aria.core.Network.rst
@@ -7,30 +7,30 @@ aria.core.Network module
.. currentmodule:: aria.core.Network
.. automodule:: aria.core.Network
- :members: CovalentConstraint, NetworkAnchoring, NetworkAnchoringTextPickler, NetworkPsPickler, NetworkScoreTextPickler, NetworkSettings, NetworkXMLPickler
- :undoc-members:
- :show-inheritance:
- :member-order: bysource
+ :members: CovalentConstraint, NetworkAnchoring, NetworkAnchoringTextPickler, NetworkPsPickler, NetworkScoreTextPickler, NetworkSettings, NetworkXMLPickler
+ :undoc-members:
+ :show-inheritance:
+ :member-order: bysource
- Summary
- -------
+Summary
+-------
- Classes:
+Classes:
- .. autosummary::
- :nosignatures:
+.. autosummary::
+ :nosignatures:
- CovalentConstraint
- NetworkAnchoring
- NetworkAnchoringTextPickler
- NetworkPsPickler
- NetworkScoreTextPickler
- NetworkSettings
- NetworkXMLPickler
+ CovalentConstraint
+ NetworkAnchoring
+ NetworkAnchoringTextPickler
+ NetworkPsPickler
+ NetworkScoreTextPickler
+ NetworkSettings
+ NetworkXMLPickler
- Reference
- ---------
\ No newline at end of file
+Reference
+---------
\ No newline at end of file
diff --git a/docs/api/aria.core.OrderedDict.rst b/docs/api/aria.core.OrderedDict.rst
index 6214f986f50eee09309de5ab660e44a26677874f..acf79c4b0f5420e107c06fa7c313ecd91981c826 100644
--- a/docs/api/aria.core.OrderedDict.rst
+++ b/docs/api/aria.core.OrderedDict.rst
@@ -7,24 +7,24 @@ aria.core.OrderedDict module
.. currentmodule:: aria.core.OrderedDict
.. automodule:: aria.core.OrderedDict
- :members: OrderedDict
- :undoc-members:
- :show-inheritance:
- :member-order: bysource
+ :members: OrderedDict
+ :undoc-members:
+ :show-inheritance:
+ :member-order: bysource
- Summary
- -------
+Summary
+-------
- Classes:
+Classes:
- .. autosummary::
- :nosignatures:
+.. autosummary::
+ :nosignatures:
- OrderedDict
+ OrderedDict
- Reference
- ---------
\ No newline at end of file
+Reference
+---------
\ No newline at end of file
diff --git a/docs/api/aria.core.PDBReader.rst b/docs/api/aria.core.PDBReader.rst
index 5694d8de1f663528e561682800374da6b4ed59fc..3af4cf2dc213d4859b98bdb7abb29e985cd06485 100644
--- a/docs/api/aria.core.PDBReader.rst
+++ b/docs/api/aria.core.PDBReader.rst
@@ -7,24 +7,24 @@ aria.core.PDBReader module
.. currentmodule:: aria.core.PDBReader
.. automodule:: aria.core.PDBReader
- :members: PDBReader
- :undoc-members:
- :show-inheritance:
- :member-order: bysource
+ :members: PDBReader
+ :undoc-members:
+ :show-inheritance:
+ :member-order: bysource
- Summary
- -------
+Summary
+-------
- Classes:
+Classes:
- .. autosummary::
- :nosignatures:
+.. autosummary::
+ :nosignatures:
- PDBReader
+ PDBReader
- Reference
- ---------
\ No newline at end of file
+Reference
+---------
\ No newline at end of file
diff --git a/docs/api/aria.core.PeakAssigner.rst b/docs/api/aria.core.PeakAssigner.rst
index a63fdc5ab8199b78f15cc23a5d65067f8c6389ba..a0fae07520db5ed25daf0955c47ab21966673bcc 100644
--- a/docs/api/aria.core.PeakAssigner.rst
+++ b/docs/api/aria.core.PeakAssigner.rst
@@ -7,34 +7,34 @@ aria.core.PeakAssigner module
.. currentmodule:: aria.core.PeakAssigner
.. automodule:: aria.core.PeakAssigner
- :members: PeakAssigner, PeakAssignerSettings, PeakAssignerTextPickler, PeakAssignerXMLPickler, peak_shape
- :undoc-members:
- :show-inheritance:
- :member-order: bysource
+ :members: PeakAssigner, PeakAssignerSettings, PeakAssignerTextPickler, PeakAssignerXMLPickler, peak_shape
+ :undoc-members:
+ :show-inheritance:
+ :member-order: bysource
- Summary
- -------
+Summary
+-------
- Classes:
+Classes:
- .. autosummary::
- :nosignatures:
+.. autosummary::
+ :nosignatures:
- PeakAssigner
- PeakAssignerSettings
- PeakAssignerTextPickler
- PeakAssignerXMLPickler
+ PeakAssigner
+ PeakAssignerSettings
+ PeakAssignerTextPickler
+ PeakAssignerXMLPickler
- Functions:
+Functions:
- .. autosummary::
- :nosignatures:
+.. autosummary::
+ :nosignatures:
- peak_shape
+ peak_shape
- Reference
- ---------
\ No newline at end of file
+Reference
+---------
\ No newline at end of file
diff --git a/docs/api/aria.core.Project.rst b/docs/api/aria.core.Project.rst
index 4bcb7e55f87a82df8197dd5a46dcdd21039fc78b..e6daf3757fa7908667ca2188525c06afee956c60 100644
--- a/docs/api/aria.core.Project.rst
+++ b/docs/api/aria.core.Project.rst
@@ -7,35 +7,35 @@ aria.core.Project module
.. currentmodule:: aria.core.Project
.. automodule:: aria.core.Project
- :members: Project, ProjectSettings, ProjectSingleton, ProjectThread, ProjectXMLPickler, checksum
- :undoc-members:
- :show-inheritance:
- :member-order: bysource
+ :members: Project, ProjectSettings, ProjectSingleton, ProjectThread, ProjectXMLPickler, checksum
+ :undoc-members:
+ :show-inheritance:
+ :member-order: bysource
- Summary
- -------
+Summary
+-------
- Classes:
+Classes:
- .. autosummary::
- :nosignatures:
+.. autosummary::
+ :nosignatures:
- Project
- ProjectSettings
- ProjectSingleton
- ProjectThread
- ProjectXMLPickler
+ Project
+ ProjectSettings
+ ProjectSingleton
+ ProjectThread
+ ProjectXMLPickler
- Functions:
+Functions:
- .. autosummary::
- :nosignatures:
+.. autosummary::
+ :nosignatures:
- checksum
+ checksum
- Reference
- ---------
\ No newline at end of file
+Reference
+---------
\ No newline at end of file
diff --git a/docs/api/aria.core.Protocol.rst b/docs/api/aria.core.Protocol.rst
index 137bfadc4c6c4e63e093d50607f10f2ba0fd967d..e944a9043f6a3a76eb0c7fb9e0a42a7fccd1e7a3 100644
--- a/docs/api/aria.core.Protocol.rst
+++ b/docs/api/aria.core.Protocol.rst
@@ -7,36 +7,36 @@ aria.core.Protocol module
.. currentmodule:: aria.core.Protocol
.. automodule:: aria.core.Protocol
- :members: IterationSettings, IterationSettingsXMLPickler, Protocol, ProtocolSettings, ProtocolXMLPickler, dump_peaks_as_text, files_exist
- :undoc-members:
- :show-inheritance:
- :member-order: bysource
+ :members: IterationSettings, IterationSettingsXMLPickler, Protocol, ProtocolSettings, ProtocolXMLPickler, dump_peaks_as_text, files_exist
+ :undoc-members:
+ :show-inheritance:
+ :member-order: bysource
- Summary
- -------
+Summary
+-------
- Classes:
+Classes:
- .. autosummary::
- :nosignatures:
+.. autosummary::
+ :nosignatures:
- IterationSettings
- IterationSettingsXMLPickler
- Protocol
- ProtocolSettings
- ProtocolXMLPickler
+ IterationSettings
+ IterationSettingsXMLPickler
+ Protocol
+ ProtocolSettings
+ ProtocolXMLPickler
- Functions:
+Functions:
- .. autosummary::
- :nosignatures:
+.. autosummary::
+ :nosignatures:
- dump_peaks_as_text
- files_exist
+ dump_peaks_as_text
+ files_exist
- Reference
- ---------
\ No newline at end of file
+Reference
+---------
\ No newline at end of file
diff --git a/docs/api/aria.core.Relaxation.rst b/docs/api/aria.core.Relaxation.rst
index b30de21959d05298112f4f4457d80399fe6643f4..f9b4b135bd83d23fe36dfd266f02ff4bf591b2cf 100644
--- a/docs/api/aria.core.Relaxation.rst
+++ b/docs/api/aria.core.Relaxation.rst
@@ -7,24 +7,24 @@ aria.core.Relaxation module
.. currentmodule:: aria.core.Relaxation
.. automodule:: aria.core.Relaxation
- :members: Relaxation
- :undoc-members:
- :show-inheritance:
- :member-order: bysource
+ :members: Relaxation
+ :undoc-members:
+ :show-inheritance:
+ :member-order: bysource
- Summary
- -------
+Summary
+-------
- Classes:
+Classes:
- .. autosummary::
- :nosignatures:
+.. autosummary::
+ :nosignatures:
- Relaxation
+ Relaxation
- Reference
- ---------
\ No newline at end of file
+Reference
+---------
\ No newline at end of file
diff --git a/docs/api/aria.core.Report.rst b/docs/api/aria.core.Report.rst
index 71b58d6026e5a686927cc95d3b88e35776a96a05..38c2655ea68a0a628411f29a6504b51e671f0743 100644
--- a/docs/api/aria.core.Report.rst
+++ b/docs/api/aria.core.Report.rst
@@ -7,35 +7,35 @@ aria.core.Report module
.. currentmodule:: aria.core.Report
.. automodule:: aria.core.Report
- :members: CCPNSettings, CCPNSettingsXMLPickler, MolMolSettings, MolMolSettingsXMLPickler, NOEListSettings, NOEListSettingsXMLPickler, ReportBaseSettings, ReportBaseXMLPickler, ReportSettings, ReportXMLPickler, UpSpecSettings, UpSpecSettingsXMLPickler
- :undoc-members:
- :show-inheritance:
- :member-order: bysource
+ :members: CCPNSettings, CCPNSettingsXMLPickler, MolMolSettings, MolMolSettingsXMLPickler, NOEListSettings, NOEListSettingsXMLPickler, ReportBaseSettings, ReportBaseXMLPickler, ReportSettings, ReportXMLPickler, UpSpecSettings, UpSpecSettingsXMLPickler
+ :undoc-members:
+ :show-inheritance:
+ :member-order: bysource
- Summary
- -------
+Summary
+-------
- Classes:
+Classes:
- .. autosummary::
- :nosignatures:
+.. autosummary::
+ :nosignatures:
- CCPNSettings
- CCPNSettingsXMLPickler
- MolMolSettings
- MolMolSettingsXMLPickler
- NOEListSettings
- NOEListSettingsXMLPickler
- ReportBaseSettings
- ReportBaseXMLPickler
- ReportSettings
- ReportXMLPickler
- UpSpecSettings
- UpSpecSettingsXMLPickler
+ CCPNSettings
+ CCPNSettingsXMLPickler
+ MolMolSettings
+ MolMolSettingsXMLPickler
+ NOEListSettings
+ NOEListSettingsXMLPickler
+ ReportBaseSettings
+ ReportBaseXMLPickler
+ ReportSettings
+ ReportXMLPickler
+ UpSpecSettings
+ UpSpecSettingsXMLPickler
- Reference
- ---------
\ No newline at end of file
+Reference
+---------
\ No newline at end of file
diff --git a/docs/api/aria.core.Residue.rst b/docs/api/aria.core.Residue.rst
index 6295912c26b529615141a770bf704680f2f1155c..dc991a8c07c69c30a39c6dc261f0fa3b0c462305 100644
--- a/docs/api/aria.core.Residue.rst
+++ b/docs/api/aria.core.Residue.rst
@@ -7,25 +7,25 @@ aria.core.Residue module
.. currentmodule:: aria.core.Residue
.. automodule:: aria.core.Residue
- :members: Residue, ResidueXMLPickler
- :undoc-members:
- :show-inheritance:
- :member-order: bysource
+ :members: Residue, ResidueXMLPickler
+ :undoc-members:
+ :show-inheritance:
+ :member-order: bysource
- Summary
- -------
+Summary
+-------
- Classes:
+Classes:
- .. autosummary::
- :nosignatures:
+.. autosummary::
+ :nosignatures:
- Residue
- ResidueXMLPickler
+ Residue
+ ResidueXMLPickler
- Reference
- ---------
\ No newline at end of file
+Reference
+---------
\ No newline at end of file
diff --git a/docs/api/aria.core.RmsReport.rst b/docs/api/aria.core.RmsReport.rst
index 65dbe93c8e73d9f266b25f0227d0357438b3279a..51678e4f46d466459d683ad925dfa6a2a8c203e6 100644
--- a/docs/api/aria.core.RmsReport.rst
+++ b/docs/api/aria.core.RmsReport.rst
@@ -7,24 +7,24 @@ aria.core.RmsReport module
.. currentmodule:: aria.core.RmsReport
.. automodule:: aria.core.RmsReport
- :members: RmsReport
- :undoc-members:
- :show-inheritance:
- :member-order: bysource
+ :members: RmsReport
+ :undoc-members:
+ :show-inheritance:
+ :member-order: bysource
- Summary
- -------
+Summary
+-------
- Classes:
+Classes:
- .. autosummary::
- :nosignatures:
+.. autosummary::
+ :nosignatures:
- RmsReport
+ RmsReport
- Reference
- ---------
\ No newline at end of file
+Reference
+---------
\ No newline at end of file
diff --git a/docs/api/aria.core.Settings.rst b/docs/api/aria.core.Settings.rst
index 478368eb91653e2e356b1f3d585db78709a8572f..e6f176a583559f062190d70f9b356b2d3a68f15f 100644
--- a/docs/api/aria.core.Settings.rst
+++ b/docs/api/aria.core.Settings.rst
@@ -7,55 +7,55 @@ aria.core.Settings module
.. currentmodule:: aria.core.Settings
.. automodule:: aria.core.Settings
- :members: AbsolutePath, AutoFixChoice, AutoInteger, ChoiceEntity, Entity, EntityCastError, EntityError, EntityValueError, Float, FourLetterString, GZipChoice, Integer, MultiTypeEntity, NonEmptyString, NonNegativeFloat, NonNegativeInt, Path, PeakType, PositiveFloat, PositiveInteger, Settings, String, TrueFalseChoice, TypeEntity, Weight, YesNoChoice
- :undoc-members:
- :show-inheritance:
- :member-order: bysource
-
- Summary
- -------
-
- Exceptions:
-
- .. autosummary::
- :nosignatures:
-
- EntityCastError
- EntityError
- EntityValueError
-
- Classes:
-
- .. autosummary::
- :nosignatures:
-
- AbsolutePath
- AutoFixChoice
- AutoInteger
- ChoiceEntity
- Entity
- Float
- FourLetterString
- GZipChoice
- Integer
- MultiTypeEntity
- NonEmptyString
- NonNegativeFloat
- NonNegativeInt
- Path
- PeakType
- PositiveFloat
- PositiveInteger
- Settings
- String
- TrueFalseChoice
- TypeEntity
- Weight
- YesNoChoice
-
-
-
-
-
- Reference
- ---------
\ No newline at end of file
+ :members: AbsolutePath, AutoFixChoice, AutoInteger, ChoiceEntity, Entity, EntityCastError, EntityError, EntityValueError, Float, FourLetterString, GZipChoice, Integer, MultiTypeEntity, NonEmptyString, NonNegativeFloat, NonNegativeInt, Path, PeakType, PositiveFloat, PositiveInteger, Settings, String, TrueFalseChoice, TypeEntity, Weight, YesNoChoice
+ :undoc-members:
+ :show-inheritance:
+ :member-order: bysource
+
+Summary
+-------
+
+Exceptions:
+
+.. autosummary::
+ :nosignatures:
+
+ EntityCastError
+ EntityError
+ EntityValueError
+
+Classes:
+
+.. autosummary::
+ :nosignatures:
+
+ AbsolutePath
+ AutoFixChoice
+ AutoInteger
+ ChoiceEntity
+ Entity
+ Float
+ FourLetterString
+ GZipChoice
+ Integer
+ MultiTypeEntity
+ NonEmptyString
+ NonNegativeFloat
+ NonNegativeInt
+ Path
+ PeakType
+ PositiveFloat
+ PositiveInteger
+ Settings
+ String
+ TrueFalseChoice
+ TypeEntity
+ Weight
+ YesNoChoice
+
+
+
+
+
+Reference
+---------
\ No newline at end of file
diff --git a/docs/api/aria.core.ShiftAssignment.rst b/docs/api/aria.core.ShiftAssignment.rst
index 06cca39f6bb3321af30e9493b50913204b42c1ec..11c31b353b39c8bc2793bc923f63e5d34e42778a 100644
--- a/docs/api/aria.core.ShiftAssignment.rst
+++ b/docs/api/aria.core.ShiftAssignment.rst
@@ -7,28 +7,28 @@ aria.core.ShiftAssignment module
.. currentmodule:: aria.core.ShiftAssignment
.. automodule:: aria.core.ShiftAssignment
- :members: ShiftAssignment, ShiftAssignmentXMLPickler, SpinSystem, SpinSystem2XMLPickler, SpinSystemXMLPickler
- :undoc-members:
- :show-inheritance:
- :member-order: bysource
+ :members: ShiftAssignment, ShiftAssignmentXMLPickler, SpinSystem, SpinSystem2XMLPickler, SpinSystemXMLPickler
+ :undoc-members:
+ :show-inheritance:
+ :member-order: bysource
- Summary
- -------
+Summary
+-------
- Classes:
+Classes:
- .. autosummary::
- :nosignatures:
+.. autosummary::
+ :nosignatures:
- ShiftAssignment
- ShiftAssignmentXMLPickler
- SpinSystem
- SpinSystem2XMLPickler
- SpinSystemXMLPickler
+ ShiftAssignment
+ ShiftAssignmentXMLPickler
+ SpinSystem
+ SpinSystem2XMLPickler
+ SpinSystemXMLPickler
- Reference
- ---------
\ No newline at end of file
+Reference
+---------
\ No newline at end of file
diff --git a/docs/api/aria.core.ShiftAssignmentFilter.rst b/docs/api/aria.core.ShiftAssignmentFilter.rst
index 4a93668885c37f32edd9a2db4971ae9644fece8e..f1aaebf13d95e4a3f77081defce71928148e707f 100644
--- a/docs/api/aria.core.ShiftAssignmentFilter.rst
+++ b/docs/api/aria.core.ShiftAssignmentFilter.rst
@@ -7,29 +7,29 @@ aria.core.ShiftAssignmentFilter module
.. currentmodule:: aria.core.ShiftAssignmentFilter
.. automodule:: aria.core.ShiftAssignmentFilter
- :members: ChemicalShiftListFilter, ChemicalShiftListFilterSettings, ShiftAssignmentFilter, ShiftAssignmentFilterSettings, SpinSystemFilter, SpinSystemFilterSettings
- :undoc-members:
- :show-inheritance:
- :member-order: bysource
+ :members: ChemicalShiftListFilter, ChemicalShiftListFilterSettings, ShiftAssignmentFilter, ShiftAssignmentFilterSettings, SpinSystemFilter, SpinSystemFilterSettings
+ :undoc-members:
+ :show-inheritance:
+ :member-order: bysource
- Summary
- -------
+Summary
+-------
- Classes:
+Classes:
- .. autosummary::
- :nosignatures:
+.. autosummary::
+ :nosignatures:
- ChemicalShiftListFilter
- ChemicalShiftListFilterSettings
- ShiftAssignmentFilter
- ShiftAssignmentFilterSettings
- SpinSystemFilter
- SpinSystemFilterSettings
+ ChemicalShiftListFilter
+ ChemicalShiftListFilterSettings
+ ShiftAssignmentFilter
+ ShiftAssignmentFilterSettings
+ SpinSystemFilter
+ SpinSystemFilterSettings
- Reference
- ---------
\ No newline at end of file
+Reference
+---------
\ No newline at end of file
diff --git a/docs/api/aria.core.Singleton.rst b/docs/api/aria.core.Singleton.rst
index 8f7d187ba09e7e1641c3fba818e96b7f325a67c7..fdf39e7b91849206ce22abd8298af1a7a6eae748 100644
--- a/docs/api/aria.core.Singleton.rst
+++ b/docs/api/aria.core.Singleton.rst
@@ -7,35 +7,35 @@ aria.core.Singleton module
.. currentmodule:: aria.core.Singleton
.. automodule:: aria.core.Singleton
- :members: AtomFactory, ProjectSingleton, Singleton, SpinPairFactory, SpinPairListFactory, instantiate
- :undoc-members:
- :show-inheritance:
- :member-order: bysource
+ :members: AtomFactory, ProjectSingleton, Singleton, SpinPairFactory, SpinPairListFactory, instantiate
+ :undoc-members:
+ :show-inheritance:
+ :member-order: bysource
- Summary
- -------
+Summary
+-------
- Classes:
+Classes:
- .. autosummary::
- :nosignatures:
+.. autosummary::
+ :nosignatures:
- Singleton
+ Singleton
- Functions:
+Functions:
- .. autosummary::
- :nosignatures:
+.. autosummary::
+ :nosignatures:
- AtomFactory
- ProjectSingleton
- SpinPairFactory
- SpinPairListFactory
- instantiate
+ AtomFactory
+ ProjectSingleton
+ SpinPairFactory
+ SpinPairListFactory
+ instantiate
- Reference
- ---------
\ No newline at end of file
+Reference
+---------
\ No newline at end of file
diff --git a/docs/api/aria.core.SpinPair.rst b/docs/api/aria.core.SpinPair.rst
index 279e4d62a2a32a1b7e9e07fad1ed5e510fa4a06f..9c31a8085526e4320dbee482d05a6ce00f4a7e1c 100644
--- a/docs/api/aria.core.SpinPair.rst
+++ b/docs/api/aria.core.SpinPair.rst
@@ -7,25 +7,25 @@ aria.core.SpinPair module
.. currentmodule:: aria.core.SpinPair
.. automodule:: aria.core.SpinPair
- :members: SpinPair, SpinPairXMLPickler
- :undoc-members:
- :show-inheritance:
- :member-order: bysource
+ :members: SpinPair, SpinPairXMLPickler
+ :undoc-members:
+ :show-inheritance:
+ :member-order: bysource
- Summary
- -------
+Summary
+-------
- Classes:
+Classes:
- .. autosummary::
- :nosignatures:
+.. autosummary::
+ :nosignatures:
- SpinPair
- SpinPairXMLPickler
+ SpinPair
+ SpinPairXMLPickler
- Reference
- ---------
\ No newline at end of file
+Reference
+---------
\ No newline at end of file
diff --git a/docs/api/aria.core.StructureEnsemble.rst b/docs/api/aria.core.StructureEnsemble.rst
index 11cc39e5902cf7524021d968a7eb2130cf1edce7..1b5392a2b5dbb411aae9de96360d4212cbfcbb57 100644
--- a/docs/api/aria.core.StructureEnsemble.rst
+++ b/docs/api/aria.core.StructureEnsemble.rst
@@ -7,26 +7,26 @@ aria.core.StructureEnsemble module
.. currentmodule:: aria.core.StructureEnsemble
.. automodule:: aria.core.StructureEnsemble
- :members: NumberOfBestStructures, StructureEnsemble, StructureEnsembleSettings
- :undoc-members:
- :show-inheritance:
- :member-order: bysource
+ :members: NumberOfBestStructures, StructureEnsemble, StructureEnsembleSettings
+ :undoc-members:
+ :show-inheritance:
+ :member-order: bysource
- Summary
- -------
+Summary
+-------
- Classes:
+Classes:
- .. autosummary::
- :nosignatures:
+.. autosummary::
+ :nosignatures:
- NumberOfBestStructures
- StructureEnsemble
- StructureEnsembleSettings
+ NumberOfBestStructures
+ StructureEnsemble
+ StructureEnsembleSettings
- Reference
- ---------
\ No newline at end of file
+Reference
+---------
\ No newline at end of file
diff --git a/docs/api/aria.core.SuperImposer.rst b/docs/api/aria.core.SuperImposer.rst
index e762b1d5b768dfbd07d5b6dd9a80ad5ef5bfb88a..24b429ee47779cef16009b4fe2bdf1e6a9d07d14 100644
--- a/docs/api/aria.core.SuperImposer.rst
+++ b/docs/api/aria.core.SuperImposer.rst
@@ -7,24 +7,24 @@ aria.core.SuperImposer module
.. currentmodule:: aria.core.SuperImposer
.. automodule:: aria.core.SuperImposer
- :members: SuperImposer
- :undoc-members:
- :show-inheritance:
- :member-order: bysource
+ :members: SuperImposer
+ :undoc-members:
+ :show-inheritance:
+ :member-order: bysource
- Summary
- -------
+Summary
+-------
- Classes:
+Classes:
- .. autosummary::
- :nosignatures:
+.. autosummary::
+ :nosignatures:
- SuperImposer
+ SuperImposer
- Reference
- ---------
\ No newline at end of file
+Reference
+---------
\ No newline at end of file
diff --git a/docs/api/aria.core.Topology.rst b/docs/api/aria.core.Topology.rst
index 5aaa550cdb178cd7d23bcbec8887ef109c9b05c8..dd17b4f07ce5fe47e1cdfd3a48e8014e54d823df 100644
--- a/docs/api/aria.core.Topology.rst
+++ b/docs/api/aria.core.Topology.rst
@@ -7,47 +7,47 @@ aria.core.Topology module
.. currentmodule:: aria.core.Topology
.. automodule:: aria.core.Topology
- :members: AtomGroup, AtomGroupSettings, AtomGroupXMLPickler, BaseAtom, BaseAtomSettings, BaseAtomXMLPickler, BaseResidue, BaseResidueSettings, BaseResidueXMLPickler, EquivalentGroup, EquivalentGroupSettings, EquivalentGroupXMLPickler, Terminus, TerminusSettings, TerminusXMLPickler, Topology, TopologyXMLPickler, load_topology
- :undoc-members:
- :show-inheritance:
- :member-order: bysource
+ :members: AtomGroup, AtomGroupSettings, AtomGroupXMLPickler, BaseAtom, BaseAtomSettings, BaseAtomXMLPickler, BaseResidue, BaseResidueSettings, BaseResidueXMLPickler, EquivalentGroup, EquivalentGroupSettings, EquivalentGroupXMLPickler, Terminus, TerminusSettings, TerminusXMLPickler, Topology, TopologyXMLPickler, load_topology
+ :undoc-members:
+ :show-inheritance:
+ :member-order: bysource
- Summary
- -------
+Summary
+-------
- Classes:
+Classes:
- .. autosummary::
- :nosignatures:
+.. autosummary::
+ :nosignatures:
- AtomGroup
- AtomGroupSettings
- AtomGroupXMLPickler
- BaseAtom
- BaseAtomSettings
- BaseAtomXMLPickler
- BaseResidue
- BaseResidueSettings
- BaseResidueXMLPickler
- EquivalentGroup
- EquivalentGroupSettings
- EquivalentGroupXMLPickler
- Terminus
- TerminusSettings
- TerminusXMLPickler
- Topology
- TopologyXMLPickler
+ AtomGroup
+ AtomGroupSettings
+ AtomGroupXMLPickler
+ BaseAtom
+ BaseAtomSettings
+ BaseAtomXMLPickler
+ BaseResidue
+ BaseResidueSettings
+ BaseResidueXMLPickler
+ EquivalentGroup
+ EquivalentGroupSettings
+ EquivalentGroupXMLPickler
+ Terminus
+ TerminusSettings
+ TerminusXMLPickler
+ Topology
+ TopologyXMLPickler
- Functions:
+Functions:
- .. autosummary::
- :nosignatures:
+.. autosummary::
+ :nosignatures:
- load_topology
+ load_topology
- Reference
- ---------
\ No newline at end of file
+Reference
+---------
\ No newline at end of file
diff --git a/docs/api/aria.core.TypeChecking.rst b/docs/api/aria.core.TypeChecking.rst
index c91ad3cb3650c8f56246f4ed28804322273d7c16..1841aed61f2cbb07e8438063bf1a93faf4380cfe 100644
--- a/docs/api/aria.core.TypeChecking.rst
+++ b/docs/api/aria.core.TypeChecking.rst
@@ -7,41 +7,41 @@ aria.core.TypeChecking module
.. currentmodule:: aria.core.TypeChecking
.. automodule:: aria.core.TypeChecking
- :members: check_array, check_bool, check_dict, check_elements, check_file, check_float, check_int, check_list, check_string, check_tuple, check_type, is_type
- :undoc-members:
- :show-inheritance:
- :member-order: bysource
+ :members: check_array, check_bool, check_dict, check_elements, check_file, check_float, check_int, check_list, check_string, check_tuple, check_type, is_type
+ :undoc-members:
+ :show-inheritance:
+ :member-order: bysource
- Summary
- -------
+Summary
+-------
- Functions:
+Functions:
- .. autosummary::
- :nosignatures:
+.. autosummary::
+ :nosignatures:
- check_array
- check_bool
- check_dict
- check_file
- check_float
- check_int
- check_list
- check_string
- check_tuple
+ check_array
+ check_bool
+ check_dict
+ check_file
+ check_float
+ check_int
+ check_list
+ check_string
+ check_tuple
- Data:
+Data:
- .. autosummary::
- :nosignatures:
+.. autosummary::
+ :nosignatures:
- check_elements
- check_type
- is_type
+ check_elements
+ check_type
+ is_type
- Reference
- ---------
\ No newline at end of file
+Reference
+---------
\ No newline at end of file
diff --git a/docs/api/aria.core.ViolationAnalyser.rst b/docs/api/aria.core.ViolationAnalyser.rst
index 810aca11fffd61deef5cb2365218facd9ac7b156..e7ed2a9c84f4c12aa0775c36c9907b2787a481b4 100644
--- a/docs/api/aria.core.ViolationAnalyser.rst
+++ b/docs/api/aria.core.ViolationAnalyser.rst
@@ -7,26 +7,26 @@ aria.core.ViolationAnalyser module
.. currentmodule:: aria.core.ViolationAnalyser
.. automodule:: aria.core.ViolationAnalyser
- :members: ViolationAnalyser, ViolationAnalyserSettings, ViolationAnalyserXMLPickler
- :undoc-members:
- :show-inheritance:
- :member-order: bysource
+ :members: ViolationAnalyser, ViolationAnalyserSettings, ViolationAnalyserXMLPickler
+ :undoc-members:
+ :show-inheritance:
+ :member-order: bysource
- Summary
- -------
+Summary
+-------
- Classes:
+Classes:
- .. autosummary::
- :nosignatures:
+.. autosummary::
+ :nosignatures:
- ViolationAnalyser
- ViolationAnalyserSettings
- ViolationAnalyserXMLPickler
+ ViolationAnalyser
+ ViolationAnalyserSettings
+ ViolationAnalyserXMLPickler
- Reference
- ---------
\ No newline at end of file
+Reference
+---------
\ No newline at end of file
diff --git a/docs/api/aria.core.WhatifProfile.rst b/docs/api/aria.core.WhatifProfile.rst
index f08c71acf5088b54d01ebd3c24d9036de66606d0..b1544afde27f84821818127d5b4a5d5cbc93fd61 100644
--- a/docs/api/aria.core.WhatifProfile.rst
+++ b/docs/api/aria.core.WhatifProfile.rst
@@ -7,24 +7,24 @@ aria.core.WhatifProfile module
.. currentmodule:: aria.core.WhatifProfile
.. automodule:: aria.core.WhatifProfile
- :members: WhatifProfile
- :undoc-members:
- :show-inheritance:
- :member-order: bysource
+ :members: WhatifProfile
+ :undoc-members:
+ :show-inheritance:
+ :member-order: bysource
- Summary
- -------
+Summary
+-------
- Classes:
+Classes:
- .. autosummary::
- :nosignatures:
+.. autosummary::
+ :nosignatures:
- WhatifProfile
+ WhatifProfile
- Reference
- ---------
\ No newline at end of file
+Reference
+---------
\ No newline at end of file
diff --git a/docs/api/aria.core.ariabase.rst b/docs/api/aria.core.ariabase.rst
index 78fa4c12f3430764cdfb483ecea7685f186f5964..b5e70dde5f6fe4ae96c9f7331a5abe410c9277d8 100644
--- a/docs/api/aria.core.ariabase.rst
+++ b/docs/api/aria.core.ariabase.rst
@@ -7,32 +7,32 @@ aria.core.ariabase module
.. currentmodule:: aria.core.ariabase
.. automodule:: aria.core.ariabase
- :members: AriaBaseClass, get_aria_root, get_path
- :undoc-members:
- :show-inheritance:
- :member-order: bysource
+ :members: AriaBaseClass, get_aria_root, get_path
+ :undoc-members:
+ :show-inheritance:
+ :member-order: bysource
- Summary
- -------
+Summary
+-------
- Classes:
+Classes:
- .. autosummary::
- :nosignatures:
+.. autosummary::
+ :nosignatures:
- AriaBaseClass
+ AriaBaseClass
- Functions:
+Functions:
- .. autosummary::
- :nosignatures:
+.. autosummary::
+ :nosignatures:
- get_aria_root
- get_path
+ get_aria_root
+ get_path
- Reference
- ---------
\ No newline at end of file
+Reference
+---------
\ No newline at end of file
diff --git a/docs/api/aria.core.ccpn2top.rst b/docs/api/aria.core.ccpn2top.rst
index 4c353f92a9fde61df31cd6a4a5a61a976cd406a1..e4243afbf5ae73e0ad08f5dfb158e6d94d4174d0 100644
--- a/docs/api/aria.core.ccpn2top.rst
+++ b/docs/api/aria.core.ccpn2top.rst
@@ -7,27 +7,27 @@ aria.core.ccpn2top module
.. currentmodule:: aria.core.ccpn2top
.. automodule:: aria.core.ccpn2top
- :members: createAriaAtom, createAriaResidue, createAriaTopology, setupEquivalentGroup
- :undoc-members:
- :show-inheritance:
- :member-order: bysource
+ :members: createAriaAtom, createAriaResidue, createAriaTopology, setupEquivalentGroup
+ :undoc-members:
+ :show-inheritance:
+ :member-order: bysource
- Summary
- -------
+Summary
+-------
- Functions:
+Functions:
- .. autosummary::
- :nosignatures:
+.. autosummary::
+ :nosignatures:
- createAriaAtom
- createAriaResidue
- createAriaTopology
- setupEquivalentGroup
+ createAriaAtom
+ createAriaResidue
+ createAriaTopology
+ setupEquivalentGroup
- Reference
- ---------
\ No newline at end of file
+Reference
+---------
\ No newline at end of file
diff --git a/docs/api/aria.core.ccpn_conversion.rst b/docs/api/aria.core.ccpn_conversion.rst
index f439be8cc3e6205c106abeb2f9f3cd17988da3a6..fbf8fd68fd8640043777f20ec844b74c84eb3524 100644
--- a/docs/api/aria.core.ccpn_conversion.rst
+++ b/docs/api/aria.core.ccpn_conversion.rst
@@ -7,33 +7,33 @@ aria.core.ccpn_conversion module
.. currentmodule:: aria.core.ccpn_conversion
.. automodule:: aria.core.ccpn_conversion
- :members: CCPNConverter, find_ccpn_atom, map_aria_atoms, map_dimensions
- :undoc-members:
- :show-inheritance:
- :member-order: bysource
+ :members: CCPNConverter, find_ccpn_atom, map_aria_atoms, map_dimensions
+ :undoc-members:
+ :show-inheritance:
+ :member-order: bysource
- Summary
- -------
+Summary
+-------
- Classes:
+Classes:
- .. autosummary::
- :nosignatures:
+.. autosummary::
+ :nosignatures:
- CCPNConverter
+ CCPNConverter
- Functions:
+Functions:
- .. autosummary::
- :nosignatures:
+.. autosummary::
+ :nosignatures:
- find_ccpn_atom
- map_aria_atoms
- map_dimensions
+ find_ccpn_atom
+ map_aria_atoms
+ map_dimensions
- Reference
- ---------
\ No newline at end of file
+Reference
+---------
\ No newline at end of file
diff --git a/docs/api/aria.core.cns.rst b/docs/api/aria.core.cns.rst
index c18ec5181a1b59135b8aa70f8f6dda45719a3fcb..3fb4d1149cd62073dc136f3a96a629b5fb819e21 100644
--- a/docs/api/aria.core.cns.rst
+++ b/docs/api/aria.core.cns.rst
@@ -7,27 +7,27 @@ aria.core.cns module
.. currentmodule:: aria.core.cns
.. automodule:: aria.core.cns
- :members: CNS, CNSSettings, CNSXMLPickler, StructureEngine
- :undoc-members:
- :show-inheritance:
- :member-order: bysource
+ :members: CNS, CNSSettings, CNSXMLPickler, StructureEngine
+ :undoc-members:
+ :show-inheritance:
+ :member-order: bysource
- Summary
- -------
+Summary
+-------
- Classes:
+Classes:
- .. autosummary::
- :nosignatures:
+.. autosummary::
+ :nosignatures:
- CNS
- CNSSettings
- CNSXMLPickler
- StructureEngine
+ CNS
+ CNSSettings
+ CNSXMLPickler
+ StructureEngine
- Reference
- ---------
\ No newline at end of file
+Reference
+---------
\ No newline at end of file
diff --git a/docs/api/aria.core.conversion.rst b/docs/api/aria.core.conversion.rst
index 4cb902d1c70db73c94dd419334b943c4c884a108..db899f8d3b59a908fe497cf3d4a43acc0ac82abb 100644
--- a/docs/api/aria.core.conversion.rst
+++ b/docs/api/aria.core.conversion.rst
@@ -7,49 +7,49 @@ aria.core.conversion module
.. currentmodule:: aria.core.conversion
.. automodule:: aria.core.conversion
- :members: Base, ChemicalShiftsSettings, ChemicalShiftsSettingsXMLPickler, Converter, ConverterSettings, ConverterSettingsXMLPickler, CrossPeaksSettings, CrossPeaksSettingsXMLPickler, MoleculeSettings, MoleculeSettingsXMLPickler, NoeList, PpmList, SequenceList, SpectrumSettings, SpectrumSettingsXMLPickler, abspath, convert_atomname, convert_value, is_pseudo, test_sparky
- :undoc-members:
- :show-inheritance:
- :member-order: bysource
+ :members: Base, ChemicalShiftsSettings, ChemicalShiftsSettingsXMLPickler, Converter, ConverterSettings, ConverterSettingsXMLPickler, CrossPeaksSettings, CrossPeaksSettingsXMLPickler, MoleculeSettings, MoleculeSettingsXMLPickler, NoeList, PpmList, SequenceList, SpectrumSettings, SpectrumSettingsXMLPickler, abspath, convert_atomname, convert_value, is_pseudo, test_sparky
+ :undoc-members:
+ :show-inheritance:
+ :member-order: bysource
- Summary
- -------
+Summary
+-------
- Classes:
+Classes:
- .. autosummary::
- :nosignatures:
+.. autosummary::
+ :nosignatures:
- Base
- ChemicalShiftsSettings
- ChemicalShiftsSettingsXMLPickler
- Converter
- ConverterSettings
- ConverterSettingsXMLPickler
- CrossPeaksSettings
- CrossPeaksSettingsXMLPickler
- MoleculeSettings
- MoleculeSettingsXMLPickler
- NoeList
- PpmList
- SequenceList
- SpectrumSettings
- SpectrumSettingsXMLPickler
+ Base
+ ChemicalShiftsSettings
+ ChemicalShiftsSettingsXMLPickler
+ Converter
+ ConverterSettings
+ ConverterSettingsXMLPickler
+ CrossPeaksSettings
+ CrossPeaksSettingsXMLPickler
+ MoleculeSettings
+ MoleculeSettingsXMLPickler
+ NoeList
+ PpmList
+ SequenceList
+ SpectrumSettings
+ SpectrumSettingsXMLPickler
- Functions:
+Functions:
- .. autosummary::
- :nosignatures:
+.. autosummary::
+ :nosignatures:
- abspath
- convert_atomname
- convert_value
- is_pseudo
- test_sparky
+ abspath
+ convert_atomname
+ convert_value
+ is_pseudo
+ test_sparky
- Reference
- ---------
\ No newline at end of file
+Reference
+---------
\ No newline at end of file
diff --git a/docs/api/aria.core.exportToCcpn.rst b/docs/api/aria.core.exportToCcpn.rst
index c146ae2e685ab9200cdce9b2043c0adf565d3a8a..0481e8346207cb1bb2d6268f2ca374a5010a32a5 100644
--- a/docs/api/aria.core.exportToCcpn.rst
+++ b/docs/api/aria.core.exportToCcpn.rst
@@ -7,44 +7,44 @@ aria.core.exportToCcpn module
.. currentmodule:: aria.core.exportToCcpn
.. automodule:: aria.core.exportToCcpn
- :members: copyFixedResonance, getAria2AtomSetPairs, getAria2ObjectsFromPickle, getAria2SpinSystems, getAriaRun, getBoundResonance, getCcpnSeqfromAriaChain, getChainFromAria2, getChainFromAria2Atom, getChainsFromAria2, getConstraintFromAria2, getConstraintsFromAria2, getFixedAtomSet, getFixedResonanceFromAria2Atom, getPeakAssignmentsFromAria2, getResonanceFromAria2Atom, getStructuresFromAria2Dir, getStructuresFromAria2Dir_Analysis, getStructuresFromAria2Dir_Format, getViolationFromAria2, importAria2RunData
- :undoc-members:
- :show-inheritance:
- :member-order: bysource
-
- Summary
- -------
-
- Functions:
-
- .. autosummary::
- :nosignatures:
-
- copyFixedResonance
- getAria2AtomSetPairs
- getAria2ObjectsFromPickle
- getAria2SpinSystems
- getAriaRun
- getBoundResonance
- getCcpnSeqfromAriaChain
- getChainFromAria2
- getChainFromAria2Atom
- getChainsFromAria2
- getConstraintFromAria2
- getConstraintsFromAria2
- getFixedAtomSet
- getFixedResonanceFromAria2Atom
- getPeakAssignmentsFromAria2
- getResonanceFromAria2Atom
- getStructuresFromAria2Dir
- getStructuresFromAria2Dir_Analysis
- getStructuresFromAria2Dir_Format
- getViolationFromAria2
- importAria2RunData
-
-
-
-
-
- Reference
- ---------
\ No newline at end of file
+ :members: copyFixedResonance, getAria2AtomSetPairs, getAria2ObjectsFromPickle, getAria2SpinSystems, getAriaRun, getBoundResonance, getCcpnSeqfromAriaChain, getChainFromAria2, getChainFromAria2Atom, getChainsFromAria2, getConstraintFromAria2, getConstraintsFromAria2, getFixedAtomSet, getFixedResonanceFromAria2Atom, getPeakAssignmentsFromAria2, getResonanceFromAria2Atom, getStructuresFromAria2Dir, getStructuresFromAria2Dir_Analysis, getStructuresFromAria2Dir_Format, getViolationFromAria2, importAria2RunData
+ :undoc-members:
+ :show-inheritance:
+ :member-order: bysource
+
+Summary
+-------
+
+Functions:
+
+.. autosummary::
+ :nosignatures:
+
+ copyFixedResonance
+ getAria2AtomSetPairs
+ getAria2ObjectsFromPickle
+ getAria2SpinSystems
+ getAriaRun
+ getBoundResonance
+ getCcpnSeqfromAriaChain
+ getChainFromAria2
+ getChainFromAria2Atom
+ getChainsFromAria2
+ getConstraintFromAria2
+ getConstraintsFromAria2
+ getFixedAtomSet
+ getFixedResonanceFromAria2Atom
+ getPeakAssignmentsFromAria2
+ getResonanceFromAria2Atom
+ getStructuresFromAria2Dir
+ getStructuresFromAria2Dir_Analysis
+ getStructuresFromAria2Dir_Format
+ getViolationFromAria2
+ importAria2RunData
+
+
+
+
+
+Reference
+---------
\ No newline at end of file
diff --git a/docs/api/aria.core.gui.AriaViewer.rst b/docs/api/aria.core.gui.AriaViewer.rst
index 1663186cf3209402efacaaac8c586ea4a6d30cc1..f384556a45db444fe2544e7a6ca2666a96b42a4e 100644
--- a/docs/api/aria.core.gui.AriaViewer.rst
+++ b/docs/api/aria.core.gui.AriaViewer.rst
@@ -7,40 +7,40 @@ aria.core.gui.AriaViewer module
.. currentmodule:: aria.core.gui.AriaViewer
.. automodule:: aria.core.gui.AriaViewer
- :members: CmapSettings, ContribListSettings, ContribSettings, DisplaySettings, Exporter, PeakListSettings, PeakSettings, get_cmap_list, pseudoString, setContrib, setPeak
- :undoc-members:
- :show-inheritance:
- :member-order: bysource
+ :members: CmapSettings, ContribListSettings, ContribSettings, DisplaySettings, Exporter, PeakListSettings, PeakSettings, get_cmap_list, pseudoString, setContrib, setPeak
+ :undoc-members:
+ :show-inheritance:
+ :member-order: bysource
- Summary
- -------
+Summary
+-------
- Classes:
+Classes:
- .. autosummary::
- :nosignatures:
+.. autosummary::
+ :nosignatures:
- CmapSettings
- ContribListSettings
- ContribSettings
- DisplaySettings
- Exporter
- PeakListSettings
- PeakSettings
+ CmapSettings
+ ContribListSettings
+ ContribSettings
+ DisplaySettings
+ Exporter
+ PeakListSettings
+ PeakSettings
- Functions:
+Functions:
- .. autosummary::
- :nosignatures:
+.. autosummary::
+ :nosignatures:
- get_cmap_list
- pseudoString
- setContrib
- setPeak
+ get_cmap_list
+ pseudoString
+ setContrib
+ setPeak
- Reference
- ---------
\ No newline at end of file
+Reference
+---------
\ No newline at end of file
diff --git a/docs/api/aria.core.gui.ccpnGui.rst b/docs/api/aria.core.gui.ccpnGui.rst
index afe5e054f4a3e4a5699dd0fd443e2b4747de6663..4796d0e2b086a9189922d31a6821533ed40a9026 100644
--- a/docs/api/aria.core.gui.ccpnGui.rst
+++ b/docs/api/aria.core.gui.ccpnGui.rst
@@ -7,34 +7,34 @@ aria.core.gui.ccpnGui module
.. currentmodule:: aria.core.gui.ccpnGui
.. automodule:: aria.core.gui.ccpnGui
- :members: gui_select_constraintList, gui_select_constraintStore, gui_select_ensemble, gui_select_model, gui_select_molSystem, gui_select_peakList, gui_select_shiftList, gui_select_structureGeneration, selectConstraintList, setupDialog, setupDialogAndSelect
- :undoc-members:
- :show-inheritance:
- :member-order: bysource
+ :members: gui_select_constraintList, gui_select_constraintStore, gui_select_ensemble, gui_select_model, gui_select_molSystem, gui_select_peakList, gui_select_shiftList, gui_select_structureGeneration, selectConstraintList, setupDialog, setupDialogAndSelect
+ :undoc-members:
+ :show-inheritance:
+ :member-order: bysource
- Summary
- -------
+Summary
+-------
- Functions:
+Functions:
- .. autosummary::
- :nosignatures:
+.. autosummary::
+ :nosignatures:
- gui_select_constraintList
- gui_select_constraintStore
- gui_select_ensemble
- gui_select_model
- gui_select_molSystem
- gui_select_peakList
- gui_select_shiftList
- gui_select_structureGeneration
- selectConstraintList
- setupDialog
- setupDialogAndSelect
+ gui_select_constraintList
+ gui_select_constraintStore
+ gui_select_ensemble
+ gui_select_model
+ gui_select_molSystem
+ gui_select_peakList
+ gui_select_shiftList
+ gui_select_structureGeneration
+ selectConstraintList
+ setupDialog
+ setupDialogAndSelect
- Reference
- ---------
\ No newline at end of file
+Reference
+---------
\ No newline at end of file
diff --git a/docs/api/aria.core.gui.decorators.rst b/docs/api/aria.core.gui.decorators.rst
index 6f0866b5b1365f8ae081b548bb757c6ddee677a0..105127cb1c427ed72c63fe8cde3aac6b2ce4c636 100644
--- a/docs/api/aria.core.gui.decorators.rst
+++ b/docs/api/aria.core.gui.decorators.rst
@@ -7,45 +7,45 @@ aria.core.gui.decorators module
.. currentmodule:: aria.core.gui.decorators
.. automodule:: aria.core.gui.decorators
- :members: CCPNProjectBrowser, DBrowseEntry, DCell, DCheckbutton, DComboBox, DEntry, DFileEntry, DIntOptionMenu, DLabelEntry, DListBox, DOptionMenu, DPathEntry, DTable, DText, WidgetDecorator, WidgetSaveError
- :undoc-members:
- :show-inheritance:
- :member-order: bysource
+ :members: CCPNProjectBrowser, DBrowseEntry, DCell, DCheckbutton, DComboBox, DEntry, DFileEntry, DIntOptionMenu, DLabelEntry, DListBox, DOptionMenu, DPathEntry, DTable, DText, WidgetDecorator, WidgetSaveError
+ :undoc-members:
+ :show-inheritance:
+ :member-order: bysource
- Summary
- -------
+Summary
+-------
- Exceptions:
+Exceptions:
- .. autosummary::
- :nosignatures:
+.. autosummary::
+ :nosignatures:
- WidgetSaveError
+ WidgetSaveError
- Classes:
+Classes:
- .. autosummary::
- :nosignatures:
+.. autosummary::
+ :nosignatures:
- CCPNProjectBrowser
- DBrowseEntry
- DCell
- DCheckbutton
- DComboBox
- DEntry
- DFileEntry
- DIntOptionMenu
- DLabelEntry
- DListBox
- DOptionMenu
- DPathEntry
- DTable
- DText
- WidgetDecorator
+ CCPNProjectBrowser
+ DBrowseEntry
+ DCell
+ DCheckbutton
+ DComboBox
+ DEntry
+ DFileEntry
+ DIntOptionMenu
+ DLabelEntry
+ DListBox
+ DOptionMenu
+ DPathEntry
+ DTable
+ DText
+ WidgetDecorator
- Reference
- ---------
\ No newline at end of file
+Reference
+---------
\ No newline at end of file
diff --git a/docs/api/aria.core.gui.gui.rst b/docs/api/aria.core.gui.gui.rst
index 0029260f2b92408f5d8f3f41bc6d4cf5c6f19776..0a9bfc758224d4a51816061aaf346fbd0f91d55c 100644
--- a/docs/api/aria.core.gui.gui.rst
+++ b/docs/api/aria.core.gui.gui.rst
@@ -7,37 +7,37 @@ aria.core.gui.gui module
.. currentmodule:: aria.core.gui.gui
.. automodule:: aria.core.gui.gui
- :members: AboutBox, DiscardDialog, EntriesMissingDialog, GUI, GUISettings, NotSavedDialog, go, popup
- :undoc-members:
- :show-inheritance:
- :member-order: bysource
+ :members: AboutBox, DiscardDialog, EntriesMissingDialog, GUI, GUISettings, NotSavedDialog, go, popup
+ :undoc-members:
+ :show-inheritance:
+ :member-order: bysource
- Summary
- -------
+Summary
+-------
- Classes:
+Classes:
- .. autosummary::
- :nosignatures:
+.. autosummary::
+ :nosignatures:
- GUI
- GUISettings
+ GUI
+ GUISettings
- Functions:
+Functions:
- .. autosummary::
- :nosignatures:
+.. autosummary::
+ :nosignatures:
- AboutBox
- DiscardDialog
- EntriesMissingDialog
- NotSavedDialog
- go
- popup
+ AboutBox
+ DiscardDialog
+ EntriesMissingDialog
+ NotSavedDialog
+ go
+ popup
- Reference
- ---------
\ No newline at end of file
+Reference
+---------
\ No newline at end of file
diff --git a/docs/api/aria.core.gui.panels.rst b/docs/api/aria.core.gui.panels.rst
index 384f433e5f5268ab425baf64a1467e35a3563c1a..99d9ea3442bcca2bf281a8c356b8da9917e096f0 100644
--- a/docs/api/aria.core.gui.panels.rst
+++ b/docs/api/aria.core.gui.panels.rst
@@ -7,80 +7,80 @@ aria.core.gui.panels module
.. currentmodule:: aria.core.gui.panels
.. automodule:: aria.core.gui.panels
- :members: AnalysisPanel, AnnealingAmbigPanel, AnnealingDihedralPanel, AnnealingFBHWPanel, AnnealingHBondPanel, AnnealingKarplusPanel, AnnealingRDCPanel, AnnealingSymmetryPanel, AnnealingUnambigPanel, CCPNPanel, CNSPanel, ChainCodeSelector, CisProPatchPanel, CmapOptionsPanel, ContactMapPanel, ContribPanel, ControlPanel, ControlPanelSettings, DataAmbigPanel, DataDihedralPanel, DataHBondPanel, DataIsoPeptidePatchPanel, DataKarplusPanel, DataOtherPanel, DataPanel, DataRDCPanel, DataSSBondPanel, DataSequencePanel, DataSpectrumPanel, DataTemplatePanel, DataUnambigPanel, DataZnPatchPanel, DynamicsPanel, HBDBPanel, HisPatchPanel, IterationPanel, JobManagerPanel, LogHarmonicPanel, Panel, PanelEx, PlotPanel, PreferencesPanel, ProjectPanel, ProtocolPanel, RamaPanel, ReportPanel, SSBridgePanel, SSBridgePanel2, SymmetryPanel, WaterRefinementPanel, file_and_format
- :undoc-members:
- :show-inheritance:
- :member-order: bysource
-
- Summary
- -------
-
- Classes:
-
- .. autosummary::
- :nosignatures:
-
- AnalysisPanel
- AnnealingAmbigPanel
- AnnealingDihedralPanel
- AnnealingFBHWPanel
- AnnealingHBondPanel
- AnnealingKarplusPanel
- AnnealingRDCPanel
- AnnealingSymmetryPanel
- AnnealingUnambigPanel
- CCPNPanel
- CNSPanel
- ChainCodeSelector
- CisProPatchPanel
- CmapOptionsPanel
- ContactMapPanel
- ContribPanel
- ControlPanel
- ControlPanelSettings
- DataAmbigPanel
- DataDihedralPanel
- DataHBondPanel
- DataIsoPeptidePatchPanel
- DataKarplusPanel
- DataOtherPanel
- DataPanel
- DataRDCPanel
- DataSSBondPanel
- DataSequencePanel
- DataSpectrumPanel
- DataTemplatePanel
- DataUnambigPanel
- DataZnPatchPanel
- DynamicsPanel
- HBDBPanel
- HisPatchPanel
- IterationPanel
- JobManagerPanel
- LogHarmonicPanel
- Panel
- PanelEx
- PlotPanel
- PreferencesPanel
- ProjectPanel
- ProtocolPanel
- RamaPanel
- ReportPanel
- SSBridgePanel
- SSBridgePanel2
- SymmetryPanel
- WaterRefinementPanel
-
- Functions:
-
- .. autosummary::
- :nosignatures:
-
- file_and_format
-
-
-
-
-
- Reference
- ---------
\ No newline at end of file
+ :members: AnalysisPanel, AnnealingAmbigPanel, AnnealingDihedralPanel, AnnealingFBHWPanel, AnnealingHBondPanel, AnnealingKarplusPanel, AnnealingRDCPanel, AnnealingSymmetryPanel, AnnealingUnambigPanel, CCPNPanel, CNSPanel, ChainCodeSelector, CisProPatchPanel, CmapOptionsPanel, ContactMapPanel, ContribPanel, ControlPanel, ControlPanelSettings, DataAmbigPanel, DataDihedralPanel, DataHBondPanel, DataIsoPeptidePatchPanel, DataKarplusPanel, DataOtherPanel, DataPanel, DataRDCPanel, DataSSBondPanel, DataSequencePanel, DataSpectrumPanel, DataTemplatePanel, DataUnambigPanel, DataZnPatchPanel, DynamicsPanel, HBDBPanel, HisPatchPanel, IterationPanel, JobManagerPanel, LogHarmonicPanel, Panel, PanelEx, PlotPanel, PreferencesPanel, ProjectPanel, ProtocolPanel, RamaPanel, ReportPanel, SSBridgePanel, SSBridgePanel2, SymmetryPanel, WaterRefinementPanel, file_and_format
+ :undoc-members:
+ :show-inheritance:
+ :member-order: bysource
+
+Summary
+-------
+
+Classes:
+
+.. autosummary::
+ :nosignatures:
+
+ AnalysisPanel
+ AnnealingAmbigPanel
+ AnnealingDihedralPanel
+ AnnealingFBHWPanel
+ AnnealingHBondPanel
+ AnnealingKarplusPanel
+ AnnealingRDCPanel
+ AnnealingSymmetryPanel
+ AnnealingUnambigPanel
+ CCPNPanel
+ CNSPanel
+ ChainCodeSelector
+ CisProPatchPanel
+ CmapOptionsPanel
+ ContactMapPanel
+ ContribPanel
+ ControlPanel
+ ControlPanelSettings
+ DataAmbigPanel
+ DataDihedralPanel
+ DataHBondPanel
+ DataIsoPeptidePatchPanel
+ DataKarplusPanel
+ DataOtherPanel
+ DataPanel
+ DataRDCPanel
+ DataSSBondPanel
+ DataSequencePanel
+ DataSpectrumPanel
+ DataTemplatePanel
+ DataUnambigPanel
+ DataZnPatchPanel
+ DynamicsPanel
+ HBDBPanel
+ HisPatchPanel
+ IterationPanel
+ JobManagerPanel
+ LogHarmonicPanel
+ Panel
+ PanelEx
+ PlotPanel
+ PreferencesPanel
+ ProjectPanel
+ ProtocolPanel
+ RamaPanel
+ ReportPanel
+ SSBridgePanel
+ SSBridgePanel2
+ SymmetryPanel
+ WaterRefinementPanel
+
+Functions:
+
+.. autosummary::
+ :nosignatures:
+
+ file_and_format
+
+
+
+
+
+Reference
+---------
\ No newline at end of file
diff --git a/docs/api/aria.core.gui.rst b/docs/api/aria.core.gui.rst
index feb64599ad4ae12573f292a7db1c72abf46d3d96..ca33520c1c53561e47a35628d13f90bd2368eacf 100644
--- a/docs/api/aria.core.gui.rst
+++ b/docs/api/aria.core.gui.rst
@@ -5,20 +5,21 @@ aria.core.gui package
=====================
.. automodule:: aria.core.gui
-
+
- Submodules:
- .. toctree::
- :maxdepth: 1
+Submodules:
- aria.core.gui.AriaViewer
- aria.core.gui.ccpnGui
- aria.core.gui.decorators
- aria.core.gui.gui
- aria.core.gui.panels
- aria.core.gui.widgets
+.. toctree::
+ :maxdepth: 1
+
+ aria.core.gui.AriaViewer
+ aria.core.gui.ccpnGui
+ aria.core.gui.decorators
+ aria.core.gui.gui
+ aria.core.gui.panels
+ aria.core.gui.widgets
diff --git a/docs/api/aria.core.gui.widgets.rst b/docs/api/aria.core.gui.widgets.rst
index dbed8a89cdb8375767d432b28f4144e8f4b68097..1982aefd6a4285e9c839ad8e45e97c8d5be3374e 100644
--- a/docs/api/aria.core.gui.widgets.rst
+++ b/docs/api/aria.core.gui.widgets.rst
@@ -7,40 +7,40 @@ aria.core.gui.widgets module
.. currentmodule:: aria.core.gui.widgets
.. automodule:: aria.core.gui.widgets
- :members: BrowseEntry, Cell, DefaultButton, DefaultButtonBox, Dialog, DirChooser, Menu, MessageBox, MyPanedWindow, MyScrolledText, Node, OKDialog, Table, Tree, YesNoCancelDialog, YesNoDialog, ariaPopup
- :undoc-members:
- :show-inheritance:
- :member-order: bysource
+ :members: BrowseEntry, Cell, DefaultButton, DefaultButtonBox, Dialog, DirChooser, Menu, MessageBox, MyPanedWindow, MyScrolledText, Node, OKDialog, Table, Tree, YesNoCancelDialog, YesNoDialog, ariaPopup
+ :undoc-members:
+ :show-inheritance:
+ :member-order: bysource
- Summary
- -------
+Summary
+-------
- Classes:
+Classes:
- .. autosummary::
- :nosignatures:
+.. autosummary::
+ :nosignatures:
- BrowseEntry
- Cell
- DefaultButton
- DefaultButtonBox
- Dialog
- DirChooser
- Menu
- MessageBox
- MyPanedWindow
- MyScrolledText
- Node
- OKDialog
- Table
- Tree
- YesNoCancelDialog
- YesNoDialog
- ariaPopup
+ BrowseEntry
+ Cell
+ DefaultButton
+ DefaultButtonBox
+ Dialog
+ DirChooser
+ Menu
+ MessageBox
+ MyPanedWindow
+ MyScrolledText
+ Node
+ OKDialog
+ Table
+ Tree
+ YesNoCancelDialog
+ YesNoDialog
+ ariaPopup
- Reference
- ---------
\ No newline at end of file
+Reference
+---------
\ No newline at end of file
diff --git a/docs/api/aria.core.importFromCcpn.rst b/docs/api/aria.core.importFromCcpn.rst
index 7ebbfc7b3abe77d98e8938f14acb859563340125..649e0564e70694328828193a9b06c01649790937 100644
--- a/docs/api/aria.core.importFromCcpn.rst
+++ b/docs/api/aria.core.importFromCcpn.rst
@@ -7,57 +7,57 @@ aria.core.importFromCcpn module
.. currentmodule:: aria.core.importFromCcpn
.. automodule:: aria.core.importFromCcpn
- :members: addSecStrucToAriaRes, checkExpTransfers, dumpModel, dumpRestraintsList, findCcpnDataDim, getAcqRefExpDimRef, getAriaAtomsFromResonance, getAriaDistanceRestraintsList, getCcpnChain, getCcpnChains, getCcpnConstraintList, getCcpnConstraintLists, getCcpnExperimentData, getCcpnExperimentShiftList, getCcpnModel, getCcpnModels, getCcpnPeakAndShiftLists, getCcpnPeakList, getCcpnShiftList, getKeysFromString, getModels, getNoesyPeakLists, getObjectKeyString, getObjectKeys, getObjectsKeyString, getShiftLists, getStructureEnsembles, makeAriaAtom, makeAriaChain, makeAriaChemicalShift, makeAriaMolecule, makeAriaResidue, makeAriaShiftList, makeAriaSpectrum
- :undoc-members:
- :show-inheritance:
- :member-order: bysource
-
- Summary
- -------
-
- Functions:
-
- .. autosummary::
- :nosignatures:
-
- addSecStrucToAriaRes
- checkExpTransfers
- dumpModel
- dumpRestraintsList
- findCcpnDataDim
- getAcqRefExpDimRef
- getAriaAtomsFromResonance
- getAriaDistanceRestraintsList
- getCcpnChain
- getCcpnChains
- getCcpnConstraintList
- getCcpnConstraintLists
- getCcpnExperimentData
- getCcpnExperimentShiftList
- getCcpnModel
- getCcpnModels
- getCcpnPeakAndShiftLists
- getCcpnPeakList
- getCcpnShiftList
- getKeysFromString
- getModels
- getNoesyPeakLists
- getObjectKeyString
- getObjectKeys
- getObjectsKeyString
- getShiftLists
- getStructureEnsembles
- makeAriaAtom
- makeAriaChain
- makeAriaChemicalShift
- makeAriaMolecule
- makeAriaResidue
- makeAriaShiftList
- makeAriaSpectrum
-
-
-
-
-
- Reference
- ---------
\ No newline at end of file
+ :members: addSecStrucToAriaRes, checkExpTransfers, dumpModel, dumpRestraintsList, findCcpnDataDim, getAcqRefExpDimRef, getAriaAtomsFromResonance, getAriaDistanceRestraintsList, getCcpnChain, getCcpnChains, getCcpnConstraintList, getCcpnConstraintLists, getCcpnExperimentData, getCcpnExperimentShiftList, getCcpnModel, getCcpnModels, getCcpnPeakAndShiftLists, getCcpnPeakList, getCcpnShiftList, getKeysFromString, getModels, getNoesyPeakLists, getObjectKeyString, getObjectKeys, getObjectsKeyString, getShiftLists, getStructureEnsembles, makeAriaAtom, makeAriaChain, makeAriaChemicalShift, makeAriaMolecule, makeAriaResidue, makeAriaShiftList, makeAriaSpectrum
+ :undoc-members:
+ :show-inheritance:
+ :member-order: bysource
+
+Summary
+-------
+
+Functions:
+
+.. autosummary::
+ :nosignatures:
+
+ addSecStrucToAriaRes
+ checkExpTransfers
+ dumpModel
+ dumpRestraintsList
+ findCcpnDataDim
+ getAcqRefExpDimRef
+ getAriaAtomsFromResonance
+ getAriaDistanceRestraintsList
+ getCcpnChain
+ getCcpnChains
+ getCcpnConstraintList
+ getCcpnConstraintLists
+ getCcpnExperimentData
+ getCcpnExperimentShiftList
+ getCcpnModel
+ getCcpnModels
+ getCcpnPeakAndShiftLists
+ getCcpnPeakList
+ getCcpnShiftList
+ getKeysFromString
+ getModels
+ getNoesyPeakLists
+ getObjectKeyString
+ getObjectKeys
+ getObjectsKeyString
+ getShiftLists
+ getStructureEnsembles
+ makeAriaAtom
+ makeAriaChain
+ makeAriaChemicalShift
+ makeAriaMolecule
+ makeAriaResidue
+ makeAriaShiftList
+ makeAriaSpectrum
+
+
+
+
+
+Reference
+---------
\ No newline at end of file
diff --git a/docs/api/aria.core.legacy.AminoAcid.rst b/docs/api/aria.core.legacy.AminoAcid.rst
index 3148a6acef389e1c4d413a09cb32b19b0c55c1ac..c0962c041cbbe7124378d6d0b4705e036734f75c 100644
--- a/docs/api/aria.core.legacy.AminoAcid.rst
+++ b/docs/api/aria.core.legacy.AminoAcid.rst
@@ -7,24 +7,24 @@ aria.core.legacy.AminoAcid module
.. currentmodule:: aria.core.legacy.AminoAcid
.. automodule:: aria.core.legacy.AminoAcid
- :members: AminoAcid
- :undoc-members:
- :show-inheritance:
- :member-order: bysource
+ :members: AminoAcid
+ :undoc-members:
+ :show-inheritance:
+ :member-order: bysource
- Summary
- -------
+Summary
+-------
- Functions:
+Functions:
- .. autosummary::
- :nosignatures:
+.. autosummary::
+ :nosignatures:
- AminoAcid
+ AminoAcid
- Reference
- ---------
\ No newline at end of file
+Reference
+---------
\ No newline at end of file
diff --git a/docs/api/aria.core.legacy.Comparisons.rst b/docs/api/aria.core.legacy.Comparisons.rst
index 831cf75005a134753718806ce4e08e3a8299aea2..c3a2407d9deec983f0ac939299f0bb2e135733ba 100644
--- a/docs/api/aria.core.legacy.Comparisons.rst
+++ b/docs/api/aria.core.legacy.Comparisons.rst
@@ -7,26 +7,26 @@ aria.core.legacy.Comparisons module
.. currentmodule:: aria.core.legacy.Comparisons
.. automodule:: aria.core.legacy.Comparisons
- :members: CmpAttr, CmpColumn, CmpComposite
- :undoc-members:
- :show-inheritance:
- :member-order: bysource
+ :members: CmpAttr, CmpColumn, CmpComposite
+ :undoc-members:
+ :show-inheritance:
+ :member-order: bysource
- Summary
- -------
+Summary
+-------
- Classes:
+Classes:
- .. autosummary::
- :nosignatures:
+.. autosummary::
+ :nosignatures:
- CmpAttr
- CmpColumn
- CmpComposite
+ CmpAttr
+ CmpColumn
+ CmpComposite
- Reference
- ---------
\ No newline at end of file
+Reference
+---------
\ No newline at end of file
diff --git a/docs/api/aria.core.legacy.DeleteCnsComments.rst b/docs/api/aria.core.legacy.DeleteCnsComments.rst
index 807555e9899d7b416d2a71882138ea755b63ecc9..c658ce8f835006c9a0068408477c88bc0758d3ce 100644
--- a/docs/api/aria.core.legacy.DeleteCnsComments.rst
+++ b/docs/api/aria.core.legacy.DeleteCnsComments.rst
@@ -7,25 +7,25 @@ aria.core.legacy.DeleteCnsComments module
.. currentmodule:: aria.core.legacy.DeleteCnsComments
.. automodule:: aria.core.legacy.DeleteCnsComments
- :members: GetFile, GetString
- :undoc-members:
- :show-inheritance:
- :member-order: bysource
+ :members: GetFile, GetString
+ :undoc-members:
+ :show-inheritance:
+ :member-order: bysource
- Summary
- -------
+Summary
+-------
- Functions:
+Functions:
- .. autosummary::
- :nosignatures:
+.. autosummary::
+ :nosignatures:
- GetFile
- GetString
+ GetFile
+ GetString
- Reference
- ---------
\ No newline at end of file
+Reference
+---------
\ No newline at end of file
diff --git a/docs/api/aria.core.legacy.DeleteComments.rst b/docs/api/aria.core.legacy.DeleteComments.rst
index 7ccbc4188f9025c5b24c0b14e5f1d0ff759b0c7e..a9b7d96b7761a5c7760878cae18e5410c68469f3 100644
--- a/docs/api/aria.core.legacy.DeleteComments.rst
+++ b/docs/api/aria.core.legacy.DeleteComments.rst
@@ -7,25 +7,25 @@ aria.core.legacy.DeleteComments module
.. currentmodule:: aria.core.legacy.DeleteComments
.. automodule:: aria.core.legacy.DeleteComments
- :members: GetFile, GetString
- :undoc-members:
- :show-inheritance:
- :member-order: bysource
+ :members: GetFile, GetString
+ :undoc-members:
+ :show-inheritance:
+ :member-order: bysource
- Summary
- -------
+Summary
+-------
- Functions:
+Functions:
- .. autosummary::
- :nosignatures:
+.. autosummary::
+ :nosignatures:
- GetFile
- GetString
+ GetFile
+ GetString
- Reference
- ---------
\ No newline at end of file
+Reference
+---------
\ No newline at end of file
diff --git a/docs/api/aria.core.legacy.DictWithDefault.rst b/docs/api/aria.core.legacy.DictWithDefault.rst
index eaf4f22760fd80c6d08957b949c4aa903855e534..ee70b90b4f3c929055ad2fd0638824c211ffcdf0 100644
--- a/docs/api/aria.core.legacy.DictWithDefault.rst
+++ b/docs/api/aria.core.legacy.DictWithDefault.rst
@@ -7,25 +7,25 @@ aria.core.legacy.DictWithDefault module
.. currentmodule:: aria.core.legacy.DictWithDefault
.. automodule:: aria.core.legacy.DictWithDefault
- :members: DictWithDefault, SafeFormatDict
- :undoc-members:
- :show-inheritance:
- :member-order: bysource
+ :members: DictWithDefault, SafeFormatDict
+ :undoc-members:
+ :show-inheritance:
+ :member-order: bysource
- Summary
- -------
+Summary
+-------
- Classes:
+Classes:
- .. autosummary::
- :nosignatures:
+.. autosummary::
+ :nosignatures:
- DictWithDefault
- SafeFormatDict
+ DictWithDefault
+ SafeFormatDict
- Reference
- ---------
\ No newline at end of file
+Reference
+---------
\ No newline at end of file
diff --git a/docs/api/aria.core.legacy.FortranFormat.rst b/docs/api/aria.core.legacy.FortranFormat.rst
index 83c366dd8f3edd6f273ee582298419150d9b9192..cedfa77057d600c5d4701a57ab4e81cf809c6230 100644
--- a/docs/api/aria.core.legacy.FortranFormat.rst
+++ b/docs/api/aria.core.legacy.FortranFormat.rst
@@ -7,25 +7,25 @@ aria.core.legacy.FortranFormat module
.. currentmodule:: aria.core.legacy.FortranFormat
.. automodule:: aria.core.legacy.FortranFormat
- :members: FortranFormat, FortranLine
- :undoc-members:
- :show-inheritance:
- :member-order: bysource
+ :members: FortranFormat, FortranLine
+ :undoc-members:
+ :show-inheritance:
+ :member-order: bysource
- Summary
- -------
+Summary
+-------
- Classes:
+Classes:
- .. autosummary::
- :nosignatures:
+.. autosummary::
+ :nosignatures:
- FortranFormat
- FortranLine
+ FortranFormat
+ FortranLine
- Reference
- ---------
\ No newline at end of file
+Reference
+---------
\ No newline at end of file
diff --git a/docs/api/aria.core.legacy.HeteronucleusPlusProton.rst b/docs/api/aria.core.legacy.HeteronucleusPlusProton.rst
index f5ab0f08e53bbdd439e9317e5022a9a13f0953d4..804b98f62e33f731e31faa1c1b978b7de2b5774c 100644
--- a/docs/api/aria.core.legacy.HeteronucleusPlusProton.rst
+++ b/docs/api/aria.core.legacy.HeteronucleusPlusProton.rst
@@ -7,24 +7,24 @@ aria.core.legacy.HeteronucleusPlusProton module
.. currentmodule:: aria.core.legacy.HeteronucleusPlusProton
.. automodule:: aria.core.legacy.HeteronucleusPlusProton
- :members: checkProton
- :undoc-members:
- :show-inheritance:
- :member-order: bysource
+ :members: checkProton
+ :undoc-members:
+ :show-inheritance:
+ :member-order: bysource
- Summary
- -------
+Summary
+-------
- Functions:
+Functions:
- .. autosummary::
- :nosignatures:
+.. autosummary::
+ :nosignatures:
- checkProton
+ checkProton
- Reference
- ---------
\ No newline at end of file
+Reference
+---------
\ No newline at end of file
diff --git a/docs/api/aria.core.legacy.NoeList.rst b/docs/api/aria.core.legacy.NoeList.rst
index 70e588582c1517748bd58442d08bec2497fda4c0..5d8b47c8b680e0b27143ac8d28d7359e26c4c383 100644
--- a/docs/api/aria.core.legacy.NoeList.rst
+++ b/docs/api/aria.core.legacy.NoeList.rst
@@ -7,26 +7,26 @@ aria.core.legacy.NoeList module
.. currentmodule:: aria.core.legacy.NoeList
.. automodule:: aria.core.legacy.NoeList
- :members: NoeContribution, NoeList, NoePeak
- :undoc-members:
- :show-inheritance:
- :member-order: bysource
+ :members: NoeContribution, NoeList, NoePeak
+ :undoc-members:
+ :show-inheritance:
+ :member-order: bysource
- Summary
- -------
+Summary
+-------
- Classes:
+Classes:
- .. autosummary::
- :nosignatures:
+.. autosummary::
+ :nosignatures:
- NoeContribution
- NoeList
- NoePeak
+ NoeContribution
+ NoeList
+ NoePeak
- Reference
- ---------
\ No newline at end of file
+Reference
+---------
\ No newline at end of file
diff --git a/docs/api/aria.core.legacy.Nomenclature.rst b/docs/api/aria.core.legacy.Nomenclature.rst
index 95fdde30f5ba787073a0c7aa4710ec7fd800969c..3f4f3cff41b76c894e3e6a92f1f1584f53865bef 100644
--- a/docs/api/aria.core.legacy.Nomenclature.rst
+++ b/docs/api/aria.core.legacy.Nomenclature.rst
@@ -7,25 +7,25 @@ aria.core.legacy.Nomenclature module
.. currentmodule:: aria.core.legacy.Nomenclature
.. automodule:: aria.core.legacy.Nomenclature
- :members: ConvertCnsProtonNames, ConvertCnsPseudoAtomNames
- :undoc-members:
- :show-inheritance:
- :member-order: bysource
+ :members: ConvertCnsProtonNames, ConvertCnsPseudoAtomNames
+ :undoc-members:
+ :show-inheritance:
+ :member-order: bysource
- Summary
- -------
+Summary
+-------
- Functions:
+Functions:
- .. autosummary::
- :nosignatures:
+.. autosummary::
+ :nosignatures:
- ConvertCnsProtonNames
- ConvertCnsPseudoAtomNames
+ ConvertCnsProtonNames
+ ConvertCnsPseudoAtomNames
- Reference
- ---------
\ No newline at end of file
+Reference
+---------
\ No newline at end of file
diff --git a/docs/api/aria.core.legacy.PpmList.rst b/docs/api/aria.core.legacy.PpmList.rst
index 7464348cf298f58e7e8da4a45a3e7ce2089ec4ae..051588b83ba591c8cfe186fd6a5651a05e8e5e3c 100644
--- a/docs/api/aria.core.legacy.PpmList.rst
+++ b/docs/api/aria.core.legacy.PpmList.rst
@@ -7,25 +7,25 @@ aria.core.legacy.PpmList module
.. currentmodule:: aria.core.legacy.PpmList
.. automodule:: aria.core.legacy.PpmList
- :members: Atom, PpmList
- :undoc-members:
- :show-inheritance:
- :member-order: bysource
+ :members: Atom, PpmList
+ :undoc-members:
+ :show-inheritance:
+ :member-order: bysource
- Summary
- -------
+Summary
+-------
- Classes:
+Classes:
- .. autosummary::
- :nosignatures:
+.. autosummary::
+ :nosignatures:
- Atom
- PpmList
+ Atom
+ PpmList
- Reference
- ---------
\ No newline at end of file
+Reference
+---------
\ No newline at end of file
diff --git a/docs/api/aria.core.legacy.PseudoAtom.rst b/docs/api/aria.core.legacy.PseudoAtom.rst
index 58ce3416bce97f86bd3464f1732f976470bbd713..c00ad705a3eba540984c2cb98581a1b69055b2e3 100644
--- a/docs/api/aria.core.legacy.PseudoAtom.rst
+++ b/docs/api/aria.core.legacy.PseudoAtom.rst
@@ -7,27 +7,27 @@ aria.core.legacy.PseudoAtom module
.. currentmodule:: aria.core.legacy.PseudoAtom
.. automodule:: aria.core.legacy.PseudoAtom
- :members: Atom2Pseudo, Pseudo2Atom, Pseudo2IupacTuple, Pseudo2Tuple
- :undoc-members:
- :show-inheritance:
- :member-order: bysource
+ :members: Atom2Pseudo, Pseudo2Atom, Pseudo2IupacTuple, Pseudo2Tuple
+ :undoc-members:
+ :show-inheritance:
+ :member-order: bysource
- Summary
- -------
+Summary
+-------
- Functions:
+Functions:
- .. autosummary::
- :nosignatures:
+.. autosummary::
+ :nosignatures:
- Atom2Pseudo
- Pseudo2Atom
- Pseudo2IupacTuple
- Pseudo2Tuple
+ Atom2Pseudo
+ Pseudo2Atom
+ Pseudo2IupacTuple
+ Pseudo2Tuple
- Reference
- ---------
\ No newline at end of file
+Reference
+---------
\ No newline at end of file
diff --git a/docs/api/aria.core.legacy.QualityChecks.DelTrailingSlash.rst b/docs/api/aria.core.legacy.QualityChecks.DelTrailingSlash.rst
index 210e09084a76898b757aef846cac2f6cee9d6196..8869d2c7d2335de5a3ce08830c01da58a33f4a0e 100644
--- a/docs/api/aria.core.legacy.QualityChecks.DelTrailingSlash.rst
+++ b/docs/api/aria.core.legacy.QualityChecks.DelTrailingSlash.rst
@@ -7,24 +7,24 @@ aria.core.legacy.QualityChecks.DelTrailingSlash module
.. currentmodule:: aria.core.legacy.QualityChecks.DelTrailingSlash
.. automodule:: aria.core.legacy.QualityChecks.DelTrailingSlash
- :members: DelTrailingSlash
- :undoc-members:
- :show-inheritance:
- :member-order: bysource
+ :members: DelTrailingSlash
+ :undoc-members:
+ :show-inheritance:
+ :member-order: bysource
- Summary
- -------
+Summary
+-------
- Functions:
+Functions:
- .. autosummary::
- :nosignatures:
+.. autosummary::
+ :nosignatures:
- DelTrailingSlash
+ DelTrailingSlash
- Reference
- ---------
\ No newline at end of file
+Reference
+---------
\ No newline at end of file
diff --git a/docs/api/aria.core.legacy.QualityChecks.Descriptive.rst b/docs/api/aria.core.legacy.QualityChecks.Descriptive.rst
index 793d99a96e84120386a73c6efa6e0f2b60df1e18..a1d6c209da0574eae396a5ba86cbc119991fcb48 100644
--- a/docs/api/aria.core.legacy.QualityChecks.Descriptive.rst
+++ b/docs/api/aria.core.legacy.QualityChecks.Descriptive.rst
@@ -7,24 +7,24 @@ aria.core.legacy.QualityChecks.Descriptive module
.. currentmodule:: aria.core.legacy.QualityChecks.Descriptive
.. automodule:: aria.core.legacy.QualityChecks.Descriptive
- :members: Descriptive
- :undoc-members:
- :show-inheritance:
- :member-order: bysource
+ :members: Descriptive
+ :undoc-members:
+ :show-inheritance:
+ :member-order: bysource
- Summary
- -------
+Summary
+-------
- Classes:
+Classes:
- .. autosummary::
- :nosignatures:
+.. autosummary::
+ :nosignatures:
- Descriptive
+ Descriptive
- Reference
- ---------
\ No newline at end of file
+Reference
+---------
\ No newline at end of file
diff --git a/docs/api/aria.core.legacy.QualityChecks.QualityChecks.rst b/docs/api/aria.core.legacy.QualityChecks.QualityChecks.rst
index f7eff5ad3bd1f3af969913a08dd675bf16248560..696de296e81e1d67ad5e16186b04a1ad520c6d38 100644
--- a/docs/api/aria.core.legacy.QualityChecks.QualityChecks.rst
+++ b/docs/api/aria.core.legacy.QualityChecks.QualityChecks.rst
@@ -7,25 +7,25 @@ aria.core.legacy.QualityChecks.QualityChecks module
.. currentmodule:: aria.core.legacy.QualityChecks.QualityChecks
.. automodule:: aria.core.legacy.QualityChecks.QualityChecks
- :members: copypdb_for_prosa, runChecks
- :undoc-members:
- :show-inheritance:
- :member-order: bysource
+ :members: copypdb_for_prosa, runChecks
+ :undoc-members:
+ :show-inheritance:
+ :member-order: bysource
- Summary
- -------
+Summary
+-------
- Functions:
+Functions:
- .. autosummary::
- :nosignatures:
+.. autosummary::
+ :nosignatures:
- copypdb_for_prosa
- runChecks
+ copypdb_for_prosa
+ runChecks
- Reference
- ---------
\ No newline at end of file
+Reference
+---------
\ No newline at end of file
diff --git a/docs/api/aria.core.legacy.QualityChecks.ReadCheckDB.rst b/docs/api/aria.core.legacy.QualityChecks.ReadCheckDB.rst
index 654d567125529a6a01b4d29d00a45a4fd2b44e39..46a71a5f9559210d86d30ab7ebe07f0739a1fb4b 100644
--- a/docs/api/aria.core.legacy.QualityChecks.ReadCheckDB.rst
+++ b/docs/api/aria.core.legacy.QualityChecks.ReadCheckDB.rst
@@ -7,24 +7,24 @@ aria.core.legacy.QualityChecks.ReadCheckDB module
.. currentmodule:: aria.core.legacy.QualityChecks.ReadCheckDB
.. automodule:: aria.core.legacy.QualityChecks.ReadCheckDB
- :members: readCheckDB
- :undoc-members:
- :show-inheritance:
- :member-order: bysource
+ :members: readCheckDB
+ :undoc-members:
+ :show-inheritance:
+ :member-order: bysource
- Summary
- -------
+Summary
+-------
- Functions:
+Functions:
- .. autosummary::
- :nosignatures:
+.. autosummary::
+ :nosignatures:
- readCheckDB
+ readCheckDB
- Reference
- ---------
\ No newline at end of file
+Reference
+---------
\ No newline at end of file
diff --git a/docs/api/aria.core.legacy.QualityChecks.RunProcheck.rst b/docs/api/aria.core.legacy.QualityChecks.RunProcheck.rst
index 372262d71cc23ebdd29b06d46534f039865738a0..a18ee49b9b2acd35c392928eb699b848560434b8 100644
--- a/docs/api/aria.core.legacy.QualityChecks.RunProcheck.rst
+++ b/docs/api/aria.core.legacy.QualityChecks.RunProcheck.rst
@@ -7,24 +7,24 @@ aria.core.legacy.QualityChecks.RunProcheck module
.. currentmodule:: aria.core.legacy.QualityChecks.RunProcheck
.. automodule:: aria.core.legacy.QualityChecks.RunProcheck
- :members: RunProcheck
- :undoc-members:
- :show-inheritance:
- :member-order: bysource
+ :members: RunProcheck
+ :undoc-members:
+ :show-inheritance:
+ :member-order: bysource
- Summary
- -------
+Summary
+-------
- Functions:
+Functions:
- .. autosummary::
- :nosignatures:
+.. autosummary::
+ :nosignatures:
- RunProcheck
+ RunProcheck
- Reference
- ---------
\ No newline at end of file
+Reference
+---------
\ No newline at end of file
diff --git a/docs/api/aria.core.legacy.QualityChecks.RunProsa.rst b/docs/api/aria.core.legacy.QualityChecks.RunProsa.rst
index 68df0a9db888053daadbef13f48f3a8fe4c734e6..65fb5a9d8e45a6e1cfbea67ff86c32e086298091 100644
--- a/docs/api/aria.core.legacy.QualityChecks.RunProsa.rst
+++ b/docs/api/aria.core.legacy.QualityChecks.RunProsa.rst
@@ -7,24 +7,24 @@ aria.core.legacy.QualityChecks.RunProsa module
.. currentmodule:: aria.core.legacy.QualityChecks.RunProsa
.. automodule:: aria.core.legacy.QualityChecks.RunProsa
- :members: RunProsa
- :undoc-members:
- :show-inheritance:
- :member-order: bysource
+ :members: RunProsa
+ :undoc-members:
+ :show-inheritance:
+ :member-order: bysource
- Summary
- -------
+Summary
+-------
- Functions:
+Functions:
- .. autosummary::
- :nosignatures:
+.. autosummary::
+ :nosignatures:
- RunProsa
+ RunProsa
- Reference
- ---------
\ No newline at end of file
+Reference
+---------
\ No newline at end of file
diff --git a/docs/api/aria.core.legacy.QualityChecks.RunWhatif.rst b/docs/api/aria.core.legacy.QualityChecks.RunWhatif.rst
index ba8a11ce25166274fa29a8efdde9cd38af1dc3f3..6f81a3bf36963b36b7e7ae9724e62105de9a31ab 100644
--- a/docs/api/aria.core.legacy.QualityChecks.RunWhatif.rst
+++ b/docs/api/aria.core.legacy.QualityChecks.RunWhatif.rst
@@ -7,24 +7,24 @@ aria.core.legacy.QualityChecks.RunWhatif module
.. currentmodule:: aria.core.legacy.QualityChecks.RunWhatif
.. automodule:: aria.core.legacy.QualityChecks.RunWhatif
- :members: RunWhatif
- :undoc-members:
- :show-inheritance:
- :member-order: bysource
+ :members: RunWhatif
+ :undoc-members:
+ :show-inheritance:
+ :member-order: bysource
- Summary
- -------
+Summary
+-------
- Functions:
+Functions:
- .. autosummary::
- :nosignatures:
+.. autosummary::
+ :nosignatures:
- RunWhatif
+ RunWhatif
- Reference
- ---------
\ No newline at end of file
+Reference
+---------
\ No newline at end of file
diff --git a/docs/api/aria.core.legacy.QualityChecks.rst b/docs/api/aria.core.legacy.QualityChecks.rst
index 1fd80441e8e4436902c95f1cb044b74bc7ad0e24..92d1469c04b808d548dd2c680d7bc79fe3930395 100644
--- a/docs/api/aria.core.legacy.QualityChecks.rst
+++ b/docs/api/aria.core.legacy.QualityChecks.rst
@@ -5,21 +5,22 @@ aria.core.legacy.QualityChecks package
======================================
.. automodule:: aria.core.legacy.QualityChecks
-
+
- Submodules:
- .. toctree::
- :maxdepth: 1
+Submodules:
- aria.core.legacy.QualityChecks.DelTrailingSlash
- aria.core.legacy.QualityChecks.Descriptive
- aria.core.legacy.QualityChecks.QualityChecks
- aria.core.legacy.QualityChecks.ReadCheckDB
- aria.core.legacy.QualityChecks.RunProcheck
- aria.core.legacy.QualityChecks.RunProsa
- aria.core.legacy.QualityChecks.RunWhatif
+.. toctree::
+ :maxdepth: 1
+
+ aria.core.legacy.QualityChecks.DelTrailingSlash
+ aria.core.legacy.QualityChecks.Descriptive
+ aria.core.legacy.QualityChecks.QualityChecks
+ aria.core.legacy.QualityChecks.ReadCheckDB
+ aria.core.legacy.QualityChecks.RunProcheck
+ aria.core.legacy.QualityChecks.RunProsa
+ aria.core.legacy.QualityChecks.RunWhatif
diff --git a/docs/api/aria.core.legacy.ReadXeasy.rst b/docs/api/aria.core.legacy.ReadXeasy.rst
index 4d76ff33fbef956623e513380a3beed28bccf424..5d62c77576b7a968552026bc4111697147a105ca 100644
--- a/docs/api/aria.core.legacy.ReadXeasy.rst
+++ b/docs/api/aria.core.legacy.ReadXeasy.rst
@@ -7,29 +7,29 @@ aria.core.legacy.ReadXeasy module
.. currentmodule:: aria.core.legacy.ReadXeasy
.. automodule:: aria.core.legacy.ReadXeasy
- :members: XeasyAssign, XeasyAssignPeak, XeasyPeaks, XeasyPeaksPeak, XeasyProt, XeasyProtAtom
- :undoc-members:
- :show-inheritance:
- :member-order: bysource
+ :members: XeasyAssign, XeasyAssignPeak, XeasyPeaks, XeasyPeaksPeak, XeasyProt, XeasyProtAtom
+ :undoc-members:
+ :show-inheritance:
+ :member-order: bysource
- Summary
- -------
+Summary
+-------
- Classes:
+Classes:
- .. autosummary::
- :nosignatures:
+.. autosummary::
+ :nosignatures:
- XeasyAssign
- XeasyAssignPeak
- XeasyPeaks
- XeasyPeaksPeak
- XeasyProt
- XeasyProtAtom
+ XeasyAssign
+ XeasyAssignPeak
+ XeasyPeaks
+ XeasyPeaksPeak
+ XeasyProt
+ XeasyProtAtom
- Reference
- ---------
\ No newline at end of file
+Reference
+---------
\ No newline at end of file
diff --git a/docs/api/aria.core.legacy.SequenceList.rst b/docs/api/aria.core.legacy.SequenceList.rst
index 54b65ce767cc8a72f259a0c858ecf2487630ce22..c1a1037d7244dc41aebdf8d727d1a401024d72c5 100644
--- a/docs/api/aria.core.legacy.SequenceList.rst
+++ b/docs/api/aria.core.legacy.SequenceList.rst
@@ -7,24 +7,24 @@ aria.core.legacy.SequenceList module
.. currentmodule:: aria.core.legacy.SequenceList
.. automodule:: aria.core.legacy.SequenceList
- :members: SequenceList
- :undoc-members:
- :show-inheritance:
- :member-order: bysource
+ :members: SequenceList
+ :undoc-members:
+ :show-inheritance:
+ :member-order: bysource
- Summary
- -------
+Summary
+-------
- Classes:
+Classes:
- .. autosummary::
- :nosignatures:
+.. autosummary::
+ :nosignatures:
- SequenceList
+ SequenceList
- Reference
- ---------
\ No newline at end of file
+Reference
+---------
\ No newline at end of file
diff --git a/docs/api/aria.core.legacy.Talos2Aria.rst b/docs/api/aria.core.legacy.Talos2Aria.rst
index 2054d26c756572e116c16ab79bfc9c629ea05711..350dd4e8a74d560fb5e6049907142a124fab8c22 100644
--- a/docs/api/aria.core.legacy.Talos2Aria.rst
+++ b/docs/api/aria.core.legacy.Talos2Aria.rst
@@ -7,34 +7,34 @@ aria.core.legacy.Talos2Aria module
.. currentmodule:: aria.core.legacy.Talos2Aria
.. automodule:: aria.core.legacy.Talos2Aria
- :members: ReadTalos, makeBondRestraint, makePhiRestraint, makePsiRestraint, residue
- :undoc-members:
- :show-inheritance:
- :member-order: bysource
+ :members: ReadTalos, makeBondRestraint, makePhiRestraint, makePsiRestraint, residue
+ :undoc-members:
+ :show-inheritance:
+ :member-order: bysource
- Summary
- -------
+Summary
+-------
- Classes:
+Classes:
- .. autosummary::
- :nosignatures:
+.. autosummary::
+ :nosignatures:
- ReadTalos
- residue
+ ReadTalos
+ residue
- Functions:
+Functions:
- .. autosummary::
- :nosignatures:
+.. autosummary::
+ :nosignatures:
- makeBondRestraint
- makePhiRestraint
- makePsiRestraint
+ makeBondRestraint
+ makePhiRestraint
+ makePsiRestraint
- Reference
- ---------
\ No newline at end of file
+Reference
+---------
\ No newline at end of file
diff --git a/docs/api/aria.core.legacy.TextFile.rst b/docs/api/aria.core.legacy.TextFile.rst
index 88d4c059556d13b68ad0cc92c19682b1c3fc91a3..739b9269e3a5cb3992b8f5a47d75d61d1436182f 100644
--- a/docs/api/aria.core.legacy.TextFile.rst
+++ b/docs/api/aria.core.legacy.TextFile.rst
@@ -7,24 +7,24 @@ aria.core.legacy.TextFile module
.. currentmodule:: aria.core.legacy.TextFile
.. automodule:: aria.core.legacy.TextFile
- :members: TextFile
- :undoc-members:
- :show-inheritance:
- :member-order: bysource
+ :members: TextFile
+ :undoc-members:
+ :show-inheritance:
+ :member-order: bysource
- Summary
- -------
+Summary
+-------
- Classes:
+Classes:
- .. autosummary::
- :nosignatures:
+.. autosummary::
+ :nosignatures:
- TextFile
+ TextFile
- Reference
- ---------
\ No newline at end of file
+Reference
+---------
\ No newline at end of file
diff --git a/docs/api/aria.core.legacy.rst b/docs/api/aria.core.legacy.rst
index cdf26672b9cf4d4dc6362b865eeb91be5991db05..aaa5fd872bbcaba2189675c773d8fbaffe060071 100644
--- a/docs/api/aria.core.legacy.rst
+++ b/docs/api/aria.core.legacy.rst
@@ -5,35 +5,37 @@ aria.core.legacy package
========================
.. automodule:: aria.core.legacy
-
-
-
- Submodules:
-
- .. toctree::
- :maxdepth: 1
-
- aria.core.legacy.AminoAcid
- aria.core.legacy.Comparisons
- aria.core.legacy.DeleteCnsComments
- aria.core.legacy.DeleteComments
- aria.core.legacy.DictWithDefault
- aria.core.legacy.FortranFormat
- aria.core.legacy.HeteronucleusPlusProton
- aria.core.legacy.NoeList
- aria.core.legacy.Nomenclature
- aria.core.legacy.PpmList
- aria.core.legacy.PseudoAtom
- aria.core.legacy.ReadXeasy
- aria.core.legacy.SequenceList
- aria.core.legacy.Talos2Aria
- aria.core.legacy.TextFile
- Subpackages:
-
- .. toctree::
- :maxdepth: 1
-
- aria.core.legacy.QualityChecks
+
+
+
+
+Submodules:
+
+.. toctree::
+ :maxdepth: 1
+
+ aria.core.legacy.AminoAcid
+ aria.core.legacy.Comparisons
+ aria.core.legacy.DeleteCnsComments
+ aria.core.legacy.DeleteComments
+ aria.core.legacy.DictWithDefault
+ aria.core.legacy.FortranFormat
+ aria.core.legacy.HeteronucleusPlusProton
+ aria.core.legacy.NoeList
+ aria.core.legacy.Nomenclature
+ aria.core.legacy.PpmList
+ aria.core.legacy.PseudoAtom
+ aria.core.legacy.ReadXeasy
+ aria.core.legacy.SequenceList
+ aria.core.legacy.Talos2Aria
+ aria.core.legacy.TextFile
+
+Subpackages:
+
+.. toctree::
+ :maxdepth: 1
+
+ aria.core.legacy.QualityChecks
diff --git a/docs/api/aria.core.mathutils.rst b/docs/api/aria.core.mathutils.rst
index 8ac0f47711dd939c850c4314e9f3306e8882171d..66aae814d92b1a3f02d2bf39a2cd213abf3ffbfd 100644
--- a/docs/api/aria.core.mathutils.rst
+++ b/docs/api/aria.core.mathutils.rst
@@ -7,27 +7,27 @@ aria.core.mathutils module
.. currentmodule:: aria.core.mathutils
.. automodule:: aria.core.mathutils
- :members: average, confidenceInterval, standardDeviation, variance
- :undoc-members:
- :show-inheritance:
- :member-order: bysource
+ :members: average, confidenceInterval, standardDeviation, variance
+ :undoc-members:
+ :show-inheritance:
+ :member-order: bysource
- Summary
- -------
+Summary
+-------
- Functions:
+Functions:
- .. autosummary::
- :nosignatures:
+.. autosummary::
+ :nosignatures:
- average
- confidenceInterval
- standardDeviation
- variance
+ average
+ confidenceInterval
+ standardDeviation
+ variance
- Reference
- ---------
\ No newline at end of file
+Reference
+---------
\ No newline at end of file
diff --git a/docs/api/aria.core.rst b/docs/api/aria.core.rst
index bb84a2cf4e90431a9fc42ff78061680cbe49efb0..8b937ad574e63fe1fa95b32d831525c60fd15a5d 100644
--- a/docs/api/aria.core.rst
+++ b/docs/api/aria.core.rst
@@ -5,97 +5,99 @@ aria.core package
=================
.. automodule:: aria.core
- :members: Analyser, AriaPeak, AriaXML, Assignment, AssignmentFilter, Atom, Calibrator, Chain, ChemicalShiftFilter, ChemicalShiftList, Cluster, Contribution, ContributionAssigner, ConversionTable, CovalentDistances, CrossPeak, CrossPeakFilter, DataContainer, Datum, Experiment, Factory, FloatFile, Infrastructure, Iteration, JobManager, Merger, MolMol, Molecule, Molprobity, NOEModel, NOESYSpectrum, NOESYSpectrumFilter, Network, OrderedDict, PDBReader, PeakAssigner, Project, Protocol, Relaxation, Report, Residue, RmsReport, Settings, ShiftAssignment, ShiftAssignmentFilter, Singleton, SpinPair, StructureEnsemble, SuperImposer, Topology, TypeChecking, ViolationAnalyser, WhatifProfile, ariabase, cns, conversion, mathutils, tools, xmlparser, xmlutils
- :undoc-members:
- :show-inheritance:
-
-
- Submodules:
-
- .. toctree::
- :maxdepth: 1
-
- aria.core.Analyser
- aria.core.AriaPeak
- aria.core.AriaXML
- aria.core.Assignment
- aria.core.AssignmentFilter
- aria.core.Atom
- aria.core.Calibrator
- aria.core.Chain
- aria.core.ChemicalShiftFilter
- aria.core.ChemicalShiftList
- aria.core.Cluster
- aria.core.Contribution
- aria.core.ContributionAssigner
- aria.core.ConversionTable
- aria.core.CovalentDistances
- aria.core.CrossPeak
- aria.core.CrossPeakFilter
- aria.core.DataContainer
- aria.core.Datum
- aria.core.Experiment
- aria.core.Factory
- aria.core.FloatFile
- aria.core.Infrastructure
- aria.core.Iteration
- aria.core.JobManager
- aria.core.Merger
- aria.core.MolMol
- aria.core.Molecule
- aria.core.Molprobity
- aria.core.NOEModel
- aria.core.NOESYSpectrum
- aria.core.NOESYSpectrumFilter
- aria.core.Network
- aria.core.OrderedDict
- aria.core.PDBReader
- aria.core.PeakAssigner
- aria.core.Project
- aria.core.Protocol
- aria.core.Relaxation
- aria.core.Report
- aria.core.Residue
- aria.core.RmsReport
- aria.core.Settings
- aria.core.ShiftAssignment
- aria.core.ShiftAssignmentFilter
- aria.core.Singleton
- aria.core.SpinPair
- aria.core.StructureEnsemble
- aria.core.SuperImposer
- aria.core.Topology
- aria.core.TypeChecking
- aria.core.ViolationAnalyser
- aria.core.WhatifProfile
- aria.core.ariabase
- aria.core.ccpn2top
- aria.core.ccpn_conversion
- aria.core.cns
- aria.core.conversion
- aria.core.exportToCcpn
- aria.core.importFromCcpn
- aria.core.mathutils
- aria.core.tools
- aria.core.xmlparser
- aria.core.xmlutils
- Subpackages:
-
- .. toctree::
- :maxdepth: 1
-
- aria.core.gui
- aria.core.legacy
- aria.core.scientific
-
-
- Summary
- -------
+ :members: Analyser, AriaPeak, AriaXML, Assignment, AssignmentFilter, Atom, Calibrator, Chain, ChemicalShiftFilter, ChemicalShiftList, Cluster, Contribution, ContributionAssigner, ConversionTable, CovalentDistances, CrossPeak, CrossPeakFilter, DataContainer, Datum, Experiment, Factory, FloatFile, Infrastructure, Iteration, JobManager, Merger, MolMol, Molecule, Molprobity, NOEModel, NOESYSpectrum, NOESYSpectrumFilter, Network, OrderedDict, PDBReader, PeakAssigner, Project, Protocol, Relaxation, Report, Residue, RmsReport, Settings, ShiftAssignment, ShiftAssignmentFilter, Singleton, SpinPair, StructureEnsemble, SuperImposer, Topology, TypeChecking, ViolationAnalyser, WhatifProfile, ariabase, cns, conversion, mathutils, tools, xmlparser, xmlutils
+ :undoc-members:
+ :show-inheritance:
+
+
+
+Submodules:
+
+.. toctree::
+ :maxdepth: 1
+
+ aria.core.Analyser
+ aria.core.AriaPeak
+ aria.core.AriaXML
+ aria.core.Assignment
+ aria.core.AssignmentFilter
+ aria.core.Atom
+ aria.core.Calibrator
+ aria.core.Chain
+ aria.core.ChemicalShiftFilter
+ aria.core.ChemicalShiftList
+ aria.core.Cluster
+ aria.core.Contribution
+ aria.core.ContributionAssigner
+ aria.core.ConversionTable
+ aria.core.CovalentDistances
+ aria.core.CrossPeak
+ aria.core.CrossPeakFilter
+ aria.core.DataContainer
+ aria.core.Datum
+ aria.core.Experiment
+ aria.core.Factory
+ aria.core.FloatFile
+ aria.core.Infrastructure
+ aria.core.Iteration
+ aria.core.JobManager
+ aria.core.Merger
+ aria.core.MolMol
+ aria.core.Molecule
+ aria.core.Molprobity
+ aria.core.NOEModel
+ aria.core.NOESYSpectrum
+ aria.core.NOESYSpectrumFilter
+ aria.core.Network
+ aria.core.OrderedDict
+ aria.core.PDBReader
+ aria.core.PeakAssigner
+ aria.core.Project
+ aria.core.Protocol
+ aria.core.Relaxation
+ aria.core.Report
+ aria.core.Residue
+ aria.core.RmsReport
+ aria.core.Settings
+ aria.core.ShiftAssignment
+ aria.core.ShiftAssignmentFilter
+ aria.core.Singleton
+ aria.core.SpinPair
+ aria.core.StructureEnsemble
+ aria.core.SuperImposer
+ aria.core.Topology
+ aria.core.TypeChecking
+ aria.core.ViolationAnalyser
+ aria.core.WhatifProfile
+ aria.core.ariabase
+ aria.core.ccpn2top
+ aria.core.ccpn_conversion
+ aria.core.cns
+ aria.core.conversion
+ aria.core.exportToCcpn
+ aria.core.importFromCcpn
+ aria.core.mathutils
+ aria.core.tools
+ aria.core.xmlparser
+ aria.core.xmlutils
+
+Subpackages:
+
+.. toctree::
+ :maxdepth: 1
+
+ aria.core.gui
+ aria.core.legacy
+ aria.core.scientific
+
+
+Summary
+-------
``__all__``: :mod:`Analyser <aria.core.Analyser>`, :mod:`AriaPeak <aria.core.AriaPeak>`, :mod:`AriaXML <aria.core.AriaXML>`, :mod:`Assignment <aria.core.Assignment>`, :mod:`AssignmentFilter <aria.core.AssignmentFilter>`, :mod:`Atom <aria.core.Atom>`, :mod:`Calibrator <aria.core.Calibrator>`, :mod:`Chain <aria.core.Chain>`, :mod:`ChemicalShiftFilter <aria.core.ChemicalShiftFilter>`, :mod:`ChemicalShiftList <aria.core.ChemicalShiftList>`, :mod:`Cluster <aria.core.Cluster>`, :mod:`Contribution <aria.core.Contribution>`, :mod:`ContributionAssigner <aria.core.ContributionAssigner>`, :mod:`ConversionTable <aria.core.ConversionTable>`, :mod:`CovalentDistances <aria.core.CovalentDistances>`, :mod:`CrossPeak <aria.core.CrossPeak>`, :mod:`CrossPeakFilter <aria.core.CrossPeakFilter>`, :mod:`DataContainer <aria.core.DataContainer>`, :mod:`Datum <aria.core.Datum>`, :mod:`Experiment <aria.core.Experiment>`, :mod:`Factory <aria.core.Factory>`, :mod:`FloatFile <aria.core.FloatFile>`, :mod:`Infrastructure <aria.core.Infrastructure>`, :mod:`Iteration <aria.core.Iteration>`, :mod:`JobManager <aria.core.JobManager>`, :mod:`Merger <aria.core.Merger>`, :mod:`MolMol <aria.core.MolMol>`, :mod:`Molecule <aria.core.Molecule>`, :mod:`Molprobity <aria.core.Molprobity>`, :mod:`NOEModel <aria.core.NOEModel>`, :mod:`NOESYSpectrum <aria.core.NOESYSpectrum>`, :mod:`NOESYSpectrumFilter <aria.core.NOESYSpectrumFilter>`, :mod:`Network <aria.core.Network>`, :mod:`OrderedDict <aria.core.OrderedDict>`, :mod:`PDBReader <aria.core.PDBReader>`, :mod:`PeakAssigner <aria.core.PeakAssigner>`, :mod:`Project <aria.core.Project>`, :mod:`Protocol <aria.core.Protocol>`, :mod:`Relaxation <aria.core.Relaxation>`, :mod:`Report <aria.core.Report>`, :mod:`Residue <aria.core.Residue>`, :mod:`RmsReport <aria.core.RmsReport>`, :mod:`Settings <aria.core.Settings>`, :mod:`ShiftAssignment <aria.core.ShiftAssignment>`, :mod:`ShiftAssignmentFilter <aria.core.ShiftAssignmentFilter>`, :mod:`Singleton <aria.core.Singleton>`, :mod:`SpinPair <aria.core.SpinPair>`, :mod:`StructureEnsemble <aria.core.StructureEnsemble>`, :mod:`SuperImposer <aria.core.SuperImposer>`, :mod:`Topology <aria.core.Topology>`, :mod:`TypeChecking <aria.core.TypeChecking>`, :mod:`ViolationAnalyser <aria.core.ViolationAnalyser>`, :mod:`WhatifProfile <aria.core.WhatifProfile>`, :mod:`ariabase <aria.core.ariabase>`, :mod:`cns <aria.core.cns>`, :mod:`conversion <aria.core.conversion>`, :mod:`mathutils <aria.core.mathutils>`, :mod:`tools <aria.core.tools>`, :mod:`xmlparser <aria.core.xmlparser>`, :mod:`xmlutils <aria.core.xmlutils>`
- Reference
- ---------
\ No newline at end of file
+Reference
+---------
\ No newline at end of file
diff --git a/docs/api/aria.core.scientific.FortranFormat.rst b/docs/api/aria.core.scientific.FortranFormat.rst
index f5a82b957d9e45256afb157210c35b36beef6086..288043897ab96da2b136dc315981719146ff44f5 100644
--- a/docs/api/aria.core.scientific.FortranFormat.rst
+++ b/docs/api/aria.core.scientific.FortranFormat.rst
@@ -7,25 +7,25 @@ aria.core.scientific.FortranFormat module
.. currentmodule:: aria.core.scientific.FortranFormat
.. automodule:: aria.core.scientific.FortranFormat
- :members: FortranFormat, FortranLine
- :undoc-members:
- :show-inheritance:
- :member-order: bysource
+ :members: FortranFormat, FortranLine
+ :undoc-members:
+ :show-inheritance:
+ :member-order: bysource
- Summary
- -------
+Summary
+-------
- Classes:
+Classes:
- .. autosummary::
- :nosignatures:
+.. autosummary::
+ :nosignatures:
- FortranFormat
- FortranLine
+ FortranFormat
+ FortranLine
- Reference
- ---------
\ No newline at end of file
+Reference
+---------
\ No newline at end of file
diff --git a/docs/api/aria.core.scientific.PDB.rst b/docs/api/aria.core.scientific.PDB.rst
index daf13d5e7724b3be28d3d545196250cddaca21c3..ad7ab08f6ddbae0dbab9f73e1c0065c7367e9bfb 100644
--- a/docs/api/aria.core.scientific.PDB.rst
+++ b/docs/api/aria.core.scientific.PDB.rst
@@ -7,45 +7,45 @@ aria.core.scientific.PDB module
.. currentmodule:: aria.core.scientific.PDB
.. automodule:: aria.core.scientific.PDB
- :members: AminoAcidResidue, Atom, Chain, DummyChain, Group, HetAtom, Molecule, NucleotideChain, NucleotideResidue, PDBFile, PeptideChain, Residue, ResidueNumber, Structure, defineAminoAcidResidue, defineNucleicAcidResidue
- :undoc-members:
- :show-inheritance:
- :member-order: bysource
+ :members: AminoAcidResidue, Atom, Chain, DummyChain, Group, HetAtom, Molecule, NucleotideChain, NucleotideResidue, PDBFile, PeptideChain, Residue, ResidueNumber, Structure, defineAminoAcidResidue, defineNucleicAcidResidue
+ :undoc-members:
+ :show-inheritance:
+ :member-order: bysource
- Summary
- -------
+Summary
+-------
- Classes:
+Classes:
- .. autosummary::
- :nosignatures:
+.. autosummary::
+ :nosignatures:
- AminoAcidResidue
- Atom
- Chain
- DummyChain
- Group
- HetAtom
- Molecule
- NucleotideChain
- NucleotideResidue
- PDBFile
- PeptideChain
- Residue
- ResidueNumber
- Structure
+ AminoAcidResidue
+ Atom
+ Chain
+ DummyChain
+ Group
+ HetAtom
+ Molecule
+ NucleotideChain
+ NucleotideResidue
+ PDBFile
+ PeptideChain
+ Residue
+ ResidueNumber
+ Structure
- Functions:
+Functions:
- .. autosummary::
- :nosignatures:
+.. autosummary::
+ :nosignatures:
- defineAminoAcidResidue
- defineNucleicAcidResidue
+ defineAminoAcidResidue
+ defineNucleicAcidResidue
- Reference
- ---------
\ No newline at end of file
+Reference
+---------
\ No newline at end of file
diff --git a/docs/api/aria.core.scientific.TextFile.rst b/docs/api/aria.core.scientific.TextFile.rst
index 3b81a26dad039622c92756016e6207299208240a..5fe33c8182a771f9261f986ec4b1fb9cf985a7a3 100644
--- a/docs/api/aria.core.scientific.TextFile.rst
+++ b/docs/api/aria.core.scientific.TextFile.rst
@@ -7,24 +7,24 @@ aria.core.scientific.TextFile module
.. currentmodule:: aria.core.scientific.TextFile
.. automodule:: aria.core.scientific.TextFile
- :members: TextFile
- :undoc-members:
- :show-inheritance:
- :member-order: bysource
+ :members: TextFile
+ :undoc-members:
+ :show-inheritance:
+ :member-order: bysource
- Summary
- -------
+Summary
+-------
- Classes:
+Classes:
- .. autosummary::
- :nosignatures:
+.. autosummary::
+ :nosignatures:
- TextFile
+ TextFile
- Reference
- ---------
\ No newline at end of file
+Reference
+---------
\ No newline at end of file
diff --git a/docs/api/aria.core.scientific.rst b/docs/api/aria.core.scientific.rst
index a034355ce026f072fec596b3d2f132bff9501dd7..d9358402b66a26e77b10f04c5ba9f8d433367192 100644
--- a/docs/api/aria.core.scientific.rst
+++ b/docs/api/aria.core.scientific.rst
@@ -5,17 +5,18 @@ aria.core.scientific package
============================
.. automodule:: aria.core.scientific
-
+
- Submodules:
- .. toctree::
- :maxdepth: 1
+Submodules:
- aria.core.scientific.FortranFormat
- aria.core.scientific.PDB
- aria.core.scientific.TextFile
+.. toctree::
+ :maxdepth: 1
+
+ aria.core.scientific.FortranFormat
+ aria.core.scientific.PDB
+ aria.core.scientific.TextFile
diff --git a/docs/api/aria.core.tools.rst b/docs/api/aria.core.tools.rst
index d941048eb8d03195727b946df21bb33a65d35cd6..b67bd83d9ef708bebb561034fd90b0d553fd332a 100644
--- a/docs/api/aria.core.tools.rst
+++ b/docs/api/aria.core.tools.rst
@@ -7,38 +7,38 @@ aria.core.tools module
.. currentmodule:: aria.core.tools
.. automodule:: aria.core.tools
- :members: Dump, Load, as_tuple, cat_files, check_modules, circular_permutation, copy_file, gzip_open, indent, last_traceback, make_block, sortProtonDimensions, string_to_segid, touch, wrap_string
- :undoc-members:
- :show-inheritance:
- :member-order: bysource
+ :members: Dump, Load, as_tuple, cat_files, check_modules, circular_permutation, copy_file, gzip_open, indent, last_traceback, make_block, sortProtonDimensions, string_to_segid, touch, wrap_string
+ :undoc-members:
+ :show-inheritance:
+ :member-order: bysource
- Summary
- -------
+Summary
+-------
- Functions:
+Functions:
- .. autosummary::
- :nosignatures:
+.. autosummary::
+ :nosignatures:
- Dump
- Load
- as_tuple
- cat_files
- check_modules
- circular_permutation
- copy_file
- gzip_open
- indent
- last_traceback
- make_block
- sortProtonDimensions
- string_to_segid
- touch
- wrap_string
+ Dump
+ Load
+ as_tuple
+ cat_files
+ check_modules
+ circular_permutation
+ copy_file
+ gzip_open
+ indent
+ last_traceback
+ make_block
+ sortProtonDimensions
+ string_to_segid
+ touch
+ wrap_string
- Reference
- ---------
\ No newline at end of file
+Reference
+---------
\ No newline at end of file
diff --git a/docs/api/aria.core.xmlparser.rst b/docs/api/aria.core.xmlparser.rst
index b0573363fd5c273e33766dfe7dbbc6806012abe6..5983bbad78f64b1fc75bb9783184399f7c861d95 100644
--- a/docs/api/aria.core.xmlparser.rst
+++ b/docs/api/aria.core.xmlparser.rst
@@ -7,31 +7,31 @@ aria.core.xmlparser module
.. currentmodule:: aria.core.xmlparser
.. automodule:: aria.core.xmlparser
- :members: SelfmadeXMLParser, quote
- :undoc-members:
- :show-inheritance:
- :member-order: bysource
+ :members: SelfmadeXMLParser, quote
+ :undoc-members:
+ :show-inheritance:
+ :member-order: bysource
- Summary
- -------
+Summary
+-------
- Classes:
+Classes:
- .. autosummary::
- :nosignatures:
+.. autosummary::
+ :nosignatures:
- SelfmadeXMLParser
+ SelfmadeXMLParser
- Functions:
+Functions:
- .. autosummary::
- :nosignatures:
+.. autosummary::
+ :nosignatures:
- quote
+ quote
- Reference
- ---------
\ No newline at end of file
+Reference
+---------
\ No newline at end of file
diff --git a/docs/api/aria.core.xmlutils.rst b/docs/api/aria.core.xmlutils.rst
index c1ef34c5c1664d33d2771e288ef6999586eb3f05..2f62dc6c545d224d53c11801adbc3c204617bb3b 100644
--- a/docs/api/aria.core.xmlutils.rst
+++ b/docs/api/aria.core.xmlutils.rst
@@ -7,40 +7,40 @@ aria.core.xmlutils module
.. currentmodule:: aria.core.xmlutils
.. automodule:: aria.core.xmlutils
- :members: BaseReader, ContentConverter, ContentHandler, XMLBasePickler, XMLContentHandler, XMLDocument, XMLElement, XMLPickler, XMLReader, XMLReaderError, XMLTagError
- :undoc-members:
- :show-inheritance:
- :member-order: bysource
+ :members: BaseReader, ContentConverter, ContentHandler, XMLBasePickler, XMLContentHandler, XMLDocument, XMLElement, XMLPickler, XMLReader, XMLReaderError, XMLTagError
+ :undoc-members:
+ :show-inheritance:
+ :member-order: bysource
- Summary
- -------
+Summary
+-------
- Exceptions:
+Exceptions:
- .. autosummary::
- :nosignatures:
+.. autosummary::
+ :nosignatures:
- XMLReaderError
- XMLTagError
+ XMLReaderError
+ XMLTagError
- Classes:
+Classes:
- .. autosummary::
- :nosignatures:
+.. autosummary::
+ :nosignatures:
- BaseReader
- ContentConverter
- ContentHandler
- XMLBasePickler
- XMLContentHandler
- XMLDocument
- XMLElement
- XMLPickler
- XMLReader
+ BaseReader
+ ContentConverter
+ ContentHandler
+ XMLBasePickler
+ XMLContentHandler
+ XMLDocument
+ XMLElement
+ XMLPickler
+ XMLReader
- Reference
- ---------
\ No newline at end of file
+Reference
+---------
\ No newline at end of file
diff --git a/docs/api/aria.rst b/docs/api/aria.rst
index 8b943cfae7126de6c15833e2d876bc0138d8c7bb..b83bd6d10191af020d56f6edf4142fc909fedc2b 100644
--- a/docs/api/aria.rst
+++ b/docs/api/aria.rst
@@ -5,33 +5,34 @@ aria package
============
.. automodule:: aria
- :members: get_version
- :undoc-members:
- :show-inheritance:
+ :members: get_version
+ :undoc-members:
+ :show-inheritance:
- Subpackages:
- .. toctree::
- :maxdepth: 1
+Subpackages:
- aria.conbox
- aria.core
+.. toctree::
+ :maxdepth: 1
+ aria.conbox
+ aria.core
- Summary
- -------
- Functions:
+Summary
+-------
- .. autosummary::
- :nosignatures:
+Functions:
- get_version
+.. autosummary::
+ :nosignatures:
+ get_version
- Reference
- ---------
\ No newline at end of file
+
+Reference
+---------
\ No newline at end of file
diff --git a/docs/conf.py b/docs/conf.py
index 19ce004d86267ed9d2a9dba9ca2e3711ba72bb19..f275657600f163c67f2197c678ec4f1b6e3c5897 100644
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -88,7 +88,7 @@ def run_apidoc(_):
"""Generage API documentation"""
import better_apidoc
better_apidoc.main(
- ['better-apidoc', '-t', './_templates', '--force', '--no-toc',
+ ['better-apidoc', '-t', './_templates', '--force', '--no-toc', '-E',
'--separate', '-o', './api', '../aria', '../*test*',
'../aria/aria2.py', '../aria/check.py'])
diff --git a/docs/contents.rst b/docs/contents.rst
index c57c35f12756f227a9f85e8e030a3f2057038469..fd563b6681068a5955a87ba48fce3c21492a6c37 100644
--- a/docs/contents.rst
+++ b/docs/contents.rst
@@ -9,9 +9,10 @@
contributing
.. toctree::
- :maxdepth: 3
+ :maxdepth: 4
:caption: API
+ api/aria
Core package <api/aria.core>
Conbox package <api/aria.conbox>