Merge branch 'master' of github.com:prody/ProDy into scipion-clean

.github/workflows/main.yml

@@ -13,23 +13,25 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: [2.7, 3.5, 3.9, '3.10']
+        python-version: ["2.7", "3.7", "3.8", "3.9", "3.10"]
 
     steps:
     - uses: actions/checkout@v2
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
+      uses: MatteoH2O1999/setup-python@v1
       with:
         python-version: ${{ matrix.python-version }}
     - name: Add conda to system path
       run: |
         echo $CONDA/bin >> $GITHUB_PATH
     - name: Install dependencies
       run: |
+        if [[ ${{ matrix.python-version }} == "3.11" ]]; then conda config --add channels conda-forge; fi
         conda create --yes -n test python=${{ matrix.python-version }}
         source activate test
-        conda install --yes numpy scipy nose pyparsing biopython
+        conda install --yes numpy scipy nose pyparsing requests
         if [[ ${{ matrix.python-version }} == "2.7" ]]; then conda install --yes unittest2; fi
+        pip install .
         python setup.py build_ext --inplace --force
     - name: Test with pytest
       run: |

.gitignore

@@ -22,6 +22,8 @@ __pycache__
 *.nmd
 *.pdb
 *.pdb.gz
+*.cif
+*.cif.gz
 
 # Docs
 /docs/_build/

INSTALL.rst

@@ -6,7 +6,7 @@ Installation
 Required Software
 -----------------
 
-* `Python`_ 2.7, 3.5 or later. We recommend using `Anaconda`_, which provides the conda package and environment manager as well as many useful packages. 
+* `Python`_ 2.7, 3.6 or later. We recommend using `Anaconda`_, which provides the conda package and environment manager as well as many useful packages. 
 
 .. _Anaconda: https://www.anaconda.com/products/individual
 

PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 1.1
 Name: ProDy
-Version: 2.0
+Version: 2.4.0
 Summary: A Python Package for Protein Dynamics Analysis
 Home-page: http://www.csb.pitt.edu/ProDy
 Author: James Krieger, She Zhang, Hongchun Li, Cihan Kaya, Ahmet Bakan, and others
@@ -95,4 +95,4 @@ Requires: numpy (>=1.10)
 Requires: pyparsing
 Requires: biopython
 Requires: scipy
-Provides: prody (2.0)
+Provides: prody (2.1.2)

docs/apps/docapps.py

@@ -2,9 +2,10 @@
 
 import os
 import imp
+import importlib
 from subprocess import Popen, PIPE
 
-path = [imp.find_module('prody')[1]]
+path = [importlib.util.find_spec("prody").submodule_search_locations[0]]
 apps = imp.load_module('prody.apps',
                            *imp.find_module('apps', path))
 

docs/conf.py

@@ -107,8 +107,8 @@
     'issue': ('https://github.com/prody/ProDy/issues/%s', 'issue '),
     'pdb': ('http://www.pdb.org/pdb/explore/explore.do?structureId=%s', ''),
     'wiki': ('http://en.wikipedia.org/wiki/%s', ''),
-    'pfam': ('http://pfam.xfam.org/family/%s', ''),
-    'pfamprotein': ('http://pfam.xfam.org/protein/%s', ''),
+    'pfam': ('http://pfam-legacy.xfam.org/family/%s', ''),
+    'pfamprotein': ('http://pfam-legacy.xfam.org/protein/%s', ''),
     'uniprot': ('http://www.uniprot.org/uniprot/%s', ''),
     'pdbhet': ('http://www.pdb.org/pdb/ligand/ligandsummary.do?hetId=%s', ''),
 }

docs/release/v2.1_series.rst

@@ -0,0 +1,52 @@
+ProDy 2.1 Series
+===============================================================================
+
+.. contents::
+   :local:
+
+2.1.2 (April 27, 2022)
+------------------------------------------------------------------------------
+
+**Bug Fixes and Improvements**:
+
+  * New :function:`.showRMSFlucts` and :function:`.calcRMSFlucts` for root-mean-square fluctuations
+
+  * fix to :function:`.showAtomicLines` for overlaying multiple chains
+
+2.1.1 (April 18, 2022)
+------------------------------------------------------------------------------
+
+**Bug Fixes and Improvements**:
+
+  * :function:`.parseScipionModes` can handle having a pdb file or not
+
+  * fix to mmCIF header parsing for chemicals in blocks not loops
+
+2.1.0 (April 8, 2022)
+------------------------------------------------------------------------------
+
+**New Features**:
+
+*Integration with Scipion*
+
+  * New functions :function:`.parseScipionModes`, :function:`.writeScipionModes` 
+  and :function:`.calcScipionScore`
+
+  * New argument *--export-scipion* (*-S*) in prody apps
+
+*Other*
+
+  * Added :function:`.assignBlocks` for assigning blocks for RTB
+
+  * Added mmCIF header parsing to create the same header dictionary as PDB header,
+  including secstr information and biomolecular assembly building
+
+  * New arguments for prody apps, including altloc, zeros, sparse, kdtree and turbo
+
+**Bug Fixes and Improvements**:
+
+  * Improvement to cealign mapping to be faster for protein only alignment
+
+  * Bug fix for writing psf files
+
+**Full Changelog**: https://github.com/prody/ProDy/compare/v2.0.2...v2.1.0

docs/release/v2.2_series.rst

@@ -0,0 +1,26 @@
+ProDy 2.2 Series
+===============================================================================
+
+.. contents::
+   :local:
+
+2.2.0 (May 19, 2022)
+------------------------------------------------------------------------------
+
+**Bug Fixes and Improvements**:
+
+  * Updates to :function:`.parseScipionModes`` to use sqlite and xmd metadata files 
+  and handle eigenvalues
+
+  * Actual fix to logging so LOGGER.progress doesn't override logging level
+
+  * Updates to the PCA app to better handle number of modes for Scipion 
+
+  * New arguments sparse, kdtree and turbo for :class:`.ClustENM`, allowing 
+  better control of ANM calculations.
+
+  * Another bug fix for mmCIF header parsing
+
+  * Bug fix for parsing CONECT bond records from PDB files
+
+**Full Changelog**: https://github.com/prody/ProDy/compare/v2.1.2...v2.2.0

docs/release/v2.3_series.rst

@@ -0,0 +1,32 @@
+ProDy 2.3 Series
+===============================================================================
+
+.. contents::
+   :local:
+
+2.3.1 (Nov 15, 2022)
+------------------------------------------------------------------------------
+
+**Bug Fixes and Improvements**:
+
+* use of 4-char hybrid36 (residue version) for biomol segnames 
+* remove pfam tests
+* remove python 3.5 support
+
+2.3.0 (Nov 12, 2022)
+------------------------------------------------------------------------------
+
+**New Features**:
+
+* new Gamma function class from GOdMD
+* added prody energy app based on ClustENM
+
+**Bug Fixes and Improvements**:
+
+* restored matrix option to dfi and dci
+* pfam migrated to pfam-legacy
+* fix to apps for broken imp.find_module
+* various other fixes including to mmCIF parsing and alignments
+
+
+**Full Changelog**: https://github.com/prody/ProDy/compare/v2.2.0...v2.3.0

docs/release/v2.4_series.rst

@@ -0,0 +1,42 @@
+ProDy 2.4 Series
+===============================================================================
+
+.. contents::
+   :local:
+
+
+2.4.0 (Feb 2, 2023)
+------------------------------------------------------------------------------
+
+**New Features**:
+
+* New function alignBioPairwise to address Biopython deprecation
+* Added gromos rmsd clustering
+* New data_type option for refineEnsemble to use seqid instead of rmsd
+* New ignore_ids option for mergeMSA to use different ids for interacting proteins
+
+**Bug Fixes and Improvements**:
+
+* Fixed error during writeout PQR file
+* Proper handling of fragments when bonds are absent
+* Setting the atoms for ensemble even if the atoms is a subset
+* Allowing setFlags to take scalar values
+* Transpose princ axes matrix to get columns
+* New flag selpdbter to keep ter lines in selections
+* No sorting of strands in writing
+* Add cif datafiles to setup
+* Select app help fix
+* Fixes to mmcif parsing
+* Improvements to cutoffs in Dali filtering
+* Fix to protein definition
+* Set matrix interactive to false and fix to axes3d usage for matplotlib 3.6
+* Improved requirements
+* Fix to fetchPDB for files with two dots but not gz ending
+
+**New Contributors**:
+
+* @changephilip made their first contribution in https://github.com/prody/ProDy/pull/1618
+* @odcambc made their first contribution in https://github.com/prody/ProDy/pull/1634
+* @hrnciar made their first contribution in https://github.com/prody/ProDy/pull/1372
+
+**Full Changelog**: https://github.com/prody/ProDy/compare/v2.3.1...v2.4.0

prody/__init__.py

@@ -1,6 +1,6 @@
 """ProDy is a package for Protein Dynamics, Sequence, and Structure Analysis"""
 
-__version__ = '2.0.2'
+__version__ = '2.4.0'
 __release__ = __version__ # + '-dev' # comment out '-dev' before a release
 
 import sys
@@ -11,8 +11,8 @@
     sys.exit()
 
 if sys.version_info[0] == 3:
-    if sys.version_info[1] < 4:
-        sys.stderr.write('Python 3.4 and older is not supported\n')
+    if sys.version_info[1] < 6:
+        sys.stderr.write('Python 3.5 and older is not supported\n')
         sys.exit()
 
 try:

prody/apps/evol_apps/__init__.py

@@ -1,6 +1,7 @@
 """This module defines some sequence evolution applications."""
 
 import imp
+import importlib
 import sys
 
 try:
@@ -10,7 +11,10 @@
 
 from ..apptools import *
 
-path_prody = imp.find_module('prody')[1]
+if sys.version_info[0] == 2:
+    path_prody = imp.find_module('prody')[1]
+else:
+    path_prody = importlib.util.find_spec("prody").submodule_search_locations[0]
 path_apps = imp.find_module('apps', [path_prody])[1]
 path_apps = imp.find_module('evol_apps', [path_apps])[1]
 

prody/apps/prody_apps/__init__.py

@@ -1,6 +1,7 @@
 """This module defines structure and dynamics analysis applications."""
 
 import imp
+import importlib
 import sys
 
 try:
@@ -10,12 +11,15 @@
 
 from ..apptools import *
 
-path_prody = imp.find_module('prody')[1]
+if sys.version_info[0] == 2:
+    path_prody = imp.find_module('prody')[1]
+else:
+    path_prody = importlib.util.find_spec("prody").submodule_search_locations[0]
 path_apps = imp.find_module('apps', [path_prody])[1]
 path_apps = imp.find_module('prody_apps', [path_apps])[1]
 
 PRODY_APPS = ['anm', 'gnm', 'pca', 'eda', 'align', 'blast', 'biomol',
-                  'catdcd', 'contacts', 'fetch', 'select',]
+                  'catdcd', 'contacts', 'fetch', 'select', 'energy']
 
 __all__ = ['prody_main']
 

prody/apps/prody_apps/nmaoptions.py

@@ -17,6 +17,7 @@
     ('outeig', 'write eigenvalues/vectors', False),
     ('outcov', 'write covariance matrix', False),
     ('outnpz', 'write compressed ProDy data file', False),
+    ('npzmatrices', 'write matrix to compressed ProDy data file', False),
     ('outscipion', 'write continuousflex modes directory and sqlite', False),
     ('outcc', 'write cross-correlations', False),
     ('outhm', 'write cross-correlations heatmap file', False),
@@ -36,7 +37,8 @@
     ('figdpi', 'figure resolution (dpi)', 300),
     ('figall', 'save all figures', False),
     ('figcc', 'save cross-correlations figure', False),
-    ('figsf', 'save square-fluctuations figure', False),]:
+    ('figsf', 'save square-fluctuations figure', False),
+    ('nproc', 'number of processors', 0),]:
 
     DEFAULTS[key] = val
     HELPTEXT[key] = txt
@@ -55,7 +57,7 @@ def addNMAParameters(parser):
         help=HELPTEXT['nmodes'] + ' (default: %(default)s)')
 
     parser.add_argument('-s', '--select', dest='select', type=str,
-        default=DEFAULTS['select'], metavar='SEL',
+        default=DEFAULTS['select'], metavar='STR',
         help=HELPTEXT['select'] + ' (default: "%(default)s")')
 
     return parser
@@ -95,13 +97,20 @@ def addNMAOutput(parser):
     parser.add_argument('-z', '--npz', dest='outnpz', action='store_true',
         default=DEFAULTS['outnpz'], help=HELPTEXT['outnpz'])
 
+    parser.add_argument('-Z', '--npzmatrices', dest='npzmatrices', action='store_true',
+        default=DEFAULTS['npzmatrices'], help=HELPTEXT['npzmatrices'])
+
     parser.add_argument('-S', '--export-scipion', dest='outscipion', action='store_true',
         default=DEFAULTS['outscipion'], help=HELPTEXT['outscipion'])
 
     parser.add_argument('-t', '--extend', dest='extend', type=str,
         metavar='STR', choices=set(['bb', 'all', 'backbone']),
         help=HELPTEXT['extend'])
 
+    parser.add_argument('-P', '--number-of-processors', dest='nproc', type=int,
+        default=DEFAULTS['nproc'], metavar='INT',
+        help=HELPTEXT['nproc'] + ' (default: %(default)s meaning use all)')        
+
     return parser