Merge branch 'master' of github.com:prody/ProDy into remove_numpy_ali…

…as_types

.github/workflows/main.yml

@@ -18,7 +18,7 @@ jobs:
     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

.gitignore

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

PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 1.1
 Name: ProDy
-Version: 2.4.0
+Version: 2.4.1
 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

docs/apps/prody/prody.txt

@@ -1,6 +1,4 @@
-usage: prody [-h] [-c] [-v]
-             {anm,gnm,pca,eda,align,blast,biomol,catdcd,contacts,fetch,select}
-             ...
+usage: prody [-h] [-c] [-v] {anm,gnm,pca,eda,align,blast,biomol,catdcd,contacts,fetch,select,energy,clustenm} ...
 
 ProDy: A Python Package for Protein Dynamics Analysis
 
@@ -10,7 +8,7 @@ optional arguments:
   -v, --version         print ProDy version and exit
 
 subcommands:
-  {anm,gnm,pca,eda,align,blast,biomol,catdcd,contacts,fetch,select}
+  {anm,gnm,pca,eda,align,blast,biomol,catdcd,contacts,fetch,select,energy,clustenm}
     anm                 perform anisotropic network model calculations
     gnm                 perform Gaussian network model calculations
     pca                 perform principal component analysis calculations
@@ -22,5 +20,7 @@ subcommands:
     contacts            identify contacts between a target and ligand(s)
     fetch               fetch a PDB file
     select              select atoms and write a PDB file
+    energy              fix missing atoms, solvate, minimise and calculate energy
+    clustenm            run clustenm(d) simulations
 
 See 'prody <command> -h' for more information on a specific command.

docs/devel/develop.rst

@@ -44,10 +44,10 @@ creating a copy of the repository in your account.  You will see
 a link for this on ProDy_ source code page.  You will have write access to
 this fork and later will use it share your changes with others.
 
-The next step is cloning the fork from your online account to your local
+The next step is cloning the fork from your online account (e.g. jamesmkrieger) to your local
 system.  If you are not using the GitHub software, you can do it as follows::
 
-  $ git clone https://github.com/prody/ProDy.git
+  $ git clone https://github.com/jamesmkrieger/ProDy.git
 
 This will create :file:`ProDy` folder with a copy of the project files in it::
 
@@ -140,10 +140,10 @@ repository as a remote to your local copy.  You can do this running the
 following command from the ProDy project folder::
 
   $ cd prody
-  $ git remote add prodymaster [email protected]:abakan/ProDy.git
+  $ git remote add prodymaster [email protected]:prody/ProDy.git
 
 
-You may use any name other than `prodymaster`, but `origin`, which points to
+You may use any name other than `prodymaster`, except for `origin`, which points to
 the ProDy fork in your account.
 
 After setting up this remote, calling :program:`git pull` command will

docs/reference/apps/prody_clustenm.rst

@@ -0,0 +1,6 @@
+ANM Application
+===============
+
+.. automodule:: prody.apps.prody_apps.prody_clustenm
+   :members:
+   :undoc-members:

docs/release/v2.4_series.rst

@@ -5,6 +5,32 @@ ProDy 2.4 Series
    :local:
 
 
+2.4.1 (Aug 11, 2023)
+------------------------------------------------------------------------------
+
+**New Features**:
+
+* New function writeBILD to write modes in BILD format for viewing in Chimera/ChimeraX
+* New function addMissingAtoms based on PDBFixer or OpenBabel
+* Added Seaborn kernel density estimator (KDE) options to showProjection like Kaynak et al., 2022
+* Added options to control adjust_text for showProjection
+* Added unite_chains option to parseMMCIF to handle splitting over segments
+* New function interpolateModel based on SITUS ModeHunter
+* New ClustENM app
+* New module for analysing water bridges (only for Python 3)
+* New option nproc as a number of processors limit for solveEig, ANM, GNM and PCA calcModes
+
+**Bug Fixes and Improvements**:
+
+* Fixed Trajectory next frame overwriting with atoms linked
+* Important fixes to alignBioPairwise
+* Update to blastpdb to account for changes to on the NCBI side
+* Improvements to apps including writing matrices
+* Improved handling of mmCIF files including those from PDB-REDO
+
+**Full Changelog**: https://github.com/prody/ProDy/compare/v2.4.0...v2.4.1
+
+
 2.4.0 (Feb 2, 2023)
 ------------------------------------------------------------------------------
 

prody/__init__.py

@@ -1,6 +1,6 @@
 """ProDy is a package for Protein Dynamics, Sequence, and Structure Analysis"""
 
-__version__ = '2.4.0'
+__version__ = '2.4.1'
 __release__ = __version__ # + '-dev' # comment out '-dev' before a release
 
 import sys

prody/apps/prody_apps/__init__.py

@@ -19,7 +19,8 @@
 path_apps = imp.find_module('prody_apps', [path_apps])[1]
 
 PRODY_APPS = ['anm', 'gnm', 'pca', 'eda', 'align', 'blast', 'biomol',
-                  'catdcd', 'contacts', 'fetch', 'select', 'energy']
+                  'catdcd', 'contacts', 'fetch', 'select', 'energy', 
+                  'clustenm']
 
 __all__ = ['prody_main']
 

prody/apps/prody_apps/nmaoptions.py

@@ -12,11 +12,13 @@
     ('select', 'atom selection',
          "protein and name CA or nucleic and name P C4' C2"),
     ('nmodes', 'number of non-zero eigenvectors (modes) to calculate', 10),
+    ('membrane', 'whether to include the explicit membrane model', False),
 
     ('outall', 'write all outputs', False),
     ('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),
@@ -47,7 +49,7 @@
            'addNMAFigures', 'addNMAFigureOptions']
 
 
-def addNMAParameters(parser):
+def addNMAParameters(parser, include_nproc=True):
 
     parser = parser.add_argument_group('parameters')
 
@@ -58,6 +60,14 @@ def addNMAParameters(parser):
     parser.add_argument('-s', '--select', dest='select', type=str,
         default=DEFAULTS['select'], metavar='STR',
         help=HELPTEXT['select'] + ' (default: "%(default)s")')
+
+    parser.add_argument('-N', '--membrane', dest='membrane', action='store_true',
+        default=DEFAULTS['membrane'], help=HELPTEXT['membrane'])
+
+    if include_nproc:
+        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
 
@@ -96,17 +106,16 @@ 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)')        
-
     return parser
 
 

prody/apps/prody_apps/prody_anm.py

@@ -13,14 +13,14 @@
 for key, txt, val in [
     ('model', 'index of model that will be used in the calculations', 1),
     ('altloc', 'alternative location identifiers for residues used in the calculations', "A"),
-    ('cutoff', 'cutoff distance (A)', 15.),
+    ('cutoff', 'cutoff distance (A)', '15.'),
     ('gamma', 'spring constant', '1.'),
     ('sparse', 'use sparse matrices', False),
     ('kdtree', 'use kdtree for Hessian', False),    
     ('zeros', 'calculate zero modes', False),
     ('turbo', 'use memory-intensive turbo option for modes', False),
 
-    ('outbeta', 'write beta-factors calculated from GNM modes', False),
+    ('outbeta', 'write beta-factors calculated from ANM modes', False),
     ('hessian', 'write Hessian matrix', False),
     ('kirchhoff', 'write Kirchhoff matrix', False),
     ('figcmap', 'save contact map (Kirchhoff matrix) figure', False),
@@ -43,10 +43,10 @@ def prody_anm(pdb, **kwargs):
     """
 
     for key in DEFAULTS:
-        if not key in kwargs:
+        if key not in kwargs:
             kwargs[key] = DEFAULTS[key]
 
-    from os.path import isdir, join
+    from os.path import isdir, join, exists
     outdir = kwargs.get('outdir')
     if not isdir(outdir):
         raise IOError('{0} is not a valid path'.format(repr(outdir)))
@@ -57,15 +57,17 @@ def prody_anm(pdb, **kwargs):
 
     selstr = kwargs.get('select')
     prefix = kwargs.get('prefix')
-    cutoff = kwargs.get('cutoff')
     sparse = kwargs.get('sparse')
     kdtree = kwargs.get('kdtree')
     nmodes = kwargs.get('nmodes')
-    selstr = kwargs.get('select')
     model = kwargs.get('model')
     altloc = kwargs.get('altloc')
     zeros = kwargs.get('zeros')
     turbo = kwargs.get('turbo')
+    membrane = kwargs.get('membrane')
+
+    if membrane and not exists(pdb):
+        pdb = prody.fetchPDBfromOPM(pdb)
 
     pdb = prody.parsePDB(pdb, model=model, altloc=altloc)
     if prefix == '_anm':
@@ -79,38 +81,45 @@ def prody_anm(pdb, **kwargs):
     LOGGER.info('{0} atoms will be used for ANM calculations.'
                 .format(len(select)))
 
+    if membrane:
+        anm = prody.exANM(pdb.getTitle())
+    else:
+        anm = prody.ANM(pdb.getTitle())
     try:
         gamma = float(kwargs.get('gamma'))
         LOGGER.info("Using gamma {0}".format(gamma))
     except ValueError:
         try:
-            Gamma = eval('prody.' + kwargs.get('gamma'))
-            gamma = Gamma(select)
-            LOGGER.info("Using gamma {0}".format(Gamma))
+            gamma = eval('prody.' + kwargs.get('gamma'))
+            gamma = gamma(select)
+            LOGGER.info("Using gamma {0}".format(gamma))
         except NameError:
             raise NameError("Please provide gamma as a float or ProDy Gamma class")
         except TypeError:
             raise TypeError("Please provide gamma as a float or ProDy Gamma class")
-
-    anm = prody.ANM(pdb.getTitle())
-
-    nproc = kwargs.get('nproc')
-    if nproc:
+        
+    try:
+        cutoff = float(kwargs.get('cutoff'))
+        LOGGER.info("Using cutoff {0}".format(cutoff))
+    except ValueError:
         try:
-            from threadpoolctl import threadpool_limits
-        except ImportError:
-            raise ImportError('Please install threadpoolctl to control threads')
+            import math
+            cutoff = eval(kwargs.get('cutoff'))
+            LOGGER.info("Using cutoff {0}".format(cutoff))
+        except NameError:
+            raise NameError("Please provide cutoff as a float or equation using math")
+        except TypeError:
+            raise TypeError("Please provide cutoff as a float or equation using math")
 
-        with threadpool_limits(limits=nproc, user_api="blas"):
-            anm.buildHessian(select, cutoff, gamma, sparse=sparse, kdtree=kdtree)
-            anm.calcModes(nmodes, zeros=zeros, turbo=turbo)
-    else:
-        anm.buildHessian(select, cutoff, gamma, sparse=sparse, kdtree=kdtree)
-        anm.calcModes(nmodes, zeros=zeros, turbo=turbo)
+    nproc = kwargs.get('nproc')
+    anm.buildHessian(select, cutoff, gamma, sparse=sparse, kdtree=kdtree)
+    anm.calcModes(nmodes, zeros=zeros, turbo=turbo, nproc=nproc)
+
     LOGGER.info('Writing numerical output.')
 
     if kwargs.get('outnpz'):
-        prody.saveModel(anm, join(outdir, prefix))
+        prody.saveModel(anm, join(outdir, prefix), 
+                        matrices=kwargs.get('npzmatrices'))
 
     if kwargs.get('outscipion'):
         prody.writeScipionModes(outdir, anm)
@@ -275,7 +284,7 @@ def addCommand(commands):
 
     group = addNMAParameters(subparser)
 
-    group.add_argument('-c', '--cutoff', dest='cutoff', type=float,
+    group.add_argument('-c', '--cutoff', dest='cutoff', type=str,
         default=DEFAULTS['cutoff'], metavar='FLOAT',
         help=HELPTEXT['cutoff'] + ' (default: %(default)s)')