Merge branch 'main' of github.com:prody/ProDy into ens_from_sel_ref

.github/workflows/main.yml

@@ -13,7 +13,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["2.7", "3.8", "3.9", "3.10"]
+        python-version: ["2.7", "3.8", "3.9", "3.10", "3.11"]
 
     steps:
     - uses: actions/checkout@v2
@@ -29,9 +29,9 @@ jobs:
         if [[ ${{ matrix.python-version }} != "2.7" ]]; then conda config --add channels conda-forge; fi
         conda create --yes -n test python=${{ matrix.python-version }}
         source activate test
-        conda install --yes numpy scipy nose pyparsing requests
-        if [[ ${{ matrix.python-version }} == "2.7" ]]; then conda install --yes unittest2; else conda install --yes pdbfixer; fi
-        pip install mmtf-python
+        conda install --yes numpy scipy nose requests
+        if [[ ${{ matrix.python-version }} == "2.7" ]]; then conda install --yes unittest2; else conda install --yes pdbfixer mdtraj; fi
+        pip install mmtf-python scikit-learn
         pip install .
         python setup.py build_ext --inplace --force
     - name: Test with pytest

.gitignore

@@ -24,6 +24,10 @@ __pycache__
 *.pdb.gz
 *.cif
 *.cif.gz
+*.mmtf
+*.map
+*.mrc
+*.dcd
 
 # Docs
 /docs/_build/

PKG-INFO

@@ -92,7 +92,7 @@ Classifier: Programming Language :: Python :: 3
 Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
 Classifier: Topic :: Scientific/Engineering :: Chemistry
 Requires: numpy (>=1.10)
-Requires: pyparsing
+Requires: pyparsing (<=3.1.1)
 Requires: biopython
 Requires: scipy
-Provides: prody (2.1.2)
+Provides: prody

README.rst

@@ -20,6 +20,57 @@ API is for interactive usage as well as application development.  ProDy also
 comes with several analysis applications and a graphical user interface for
 visual analysis.
 
+Further details are described in the ProDy papers:
+
+  | Bakan A, Meireles LM, Bahar I.
+  | *ProDy*: Protein Dynamics Inferred from Theory and Experiments.
+  | *Bioinformatics* **2011** 27(11):1575-1577.
+
+  | Bakan A, Dutta A, Mao W, Liu Y, Chennubhotla C, Lezon TR, Bahar I.
+  | *Evol* and *ProDy* for Bridging Protein Sequence Evolution and Structural Dynamics.
+  | *Bioinformatics* **2014** 30(18):2681-2683.
+
+  | Zhang S, Krieger JM, Zhang Y, Kaya C, Kaynak B, Mikulska-Ruminska K, Doruker P, Li H, Bahar I.
+  | *ProDy* 2.0: Increased Scale and Scope after 10 Years of Protein Dynamics Modelling with Python.
+  | *Bioinformatics* **2021** 37(20):3657-3659.
+
+MODULES
+--------
+
+ProDy has a modular structure with modules inside various subpackages.
+
+The main ones are:
+
+- :mod:`~prody.atomic`` handles all :class:`~prody.atomic.Atomic` objects including :class:`~prody.atomic.AtomGroup` and :class:`.Selection`
+
+- :mod:`~prody.database` interfaces with databases such as CATH, DALI, UniProt and Pfam
+
+- :mod:`~prody.dynamics` provides all the modules for normal mode analysis with various elastic network models, 
+as well as PCA, SignDy (:mod:`~prody.dynamics.signature`), hybrid methods such as :mod:`~prody.dynamics.clustenm`, 
+allosteric signal propagation methods :mod:`~prody.dynamics.perturb` (PRS) and :func:`~prody.dynamics.analysis.calcHitTime` (Markovian hitting time),
+and various analysis and plotting functions.
+
+- :mod:`~prody.ensemble` enables construction of heterogeneous structural ensembles for exploring dynamics from experiments and simulations
+
+- :mod:`~prody.proteins` provides various modules for parsing different kinds of protein structure files including PDB, mmCIF, MMTF and maps,
+as well as tools to align and compare structures, and analysis of :mod:`~prody.proteins.interactions` within and between proteins (InSty) and 
+find :mod:`~prody.proteins.waterbridges` (WatFinder).
+
+- :mod:`~prody.sequence` has all the sequence alignment and evolutionary analysis tools of Evol
+
+
+Smaller ones include:
+
+- :mod:`~prody.chromatin` specific to chromatin dynamics (ChromDy) including :mod:`~prody.chromatin.hic` and :mod:`~prody.chromatin.cluster`
+
+- :mod:`~prody.compounds` for parsing small molecule compounds/ligands from the PDB and related databases
+
+- :mod:`~prody.domain_decomposition` for Spectrus dynamical domain decomposition 
+
+- :mod:`~prody.trajectory` for trajectories in DCD format
+
+- :mod:`~prody.utilities`
+
 
 GETTING PRODY
 -------------
@@ -45,6 +96,8 @@ DOCUMENTATION
 
 * Changes: http://prody.csb.pitt.edu/manual/release
 
+See also https://github.com/prody/ProDy-website for latest versions.
+
 
 SOURCE CODE
 -----------

docs/about/people.rst

@@ -29,8 +29,15 @@ including *SignDy* and Adaptive ANM.
 the *cryo-EM* module, :mod:`.protein.emdmap`.
 
 `Burak Kaynak`_ contributed significantly to the development of 
-:mod:`.domain_decomposition` and :mod:`.dynamics.essa`, 
-and is in the process of adding other modules too.
+:mod:`.domain_decomposition`, :mod:`.dynamics.essa`, and
+:mod:`.dynamics.clustenm`. 
+
+`Karolina Mikulska-Ruminska`_ contributed significantly to the development of 
+:mod:`.protein.interactions` (*InSty*), :mod:`.protein.waterbridges`
+(*WatFinder*), and :mod:`.dynamics.mechstiff` (*MechStiff*).
+
+`Anthony Bogetti`_ is overseeing the overall development of *ProDy* since 
+2024.
 
 `Anindita Dutta`_ contributed to the development of *Evol*,
 :mod:`.database` and :mod:`.sequence` modules.
@@ -52,26 +59,32 @@ contributions and feedback from the following individuals:
 
 `Ying Liu`_ provided the code for Perturbation Response Scanning method.
 
+`Frane Doljanin`_ provided the code for the water bridge detection.
+
 `Kian Ho`_ contributed with bug fixes and unit tests for DSSP functions.
 
 `Gökçen Eraslan`_ contributed with bug fixes and development and maintenance
 insights.
 
 
+
 .. _Ahmet Bakan: https://scholar.google.com/citations?user=-QAYVgMAAAAJ&hl=en
 .. _Cihan Kaya: https://www.linkedin.com/in/cihan-kaya/
-.. _Bahar Lab: http://www.ccbb.pitt.edu/faculty/bahar/
+.. _Bahar Lab: http://www.bahargroup.org/Faculty/bahar/
 .. _University of Pittsburgh: http://www.pitt.edu/
 .. _Anindita Dutta: http://www.linkedin.com/pub/anindita-dutta/5a/568/a90
 .. _Wenzhi Mao: http://www.linkedin.com/pub/wenzhi-mao/2a/29a/29
 .. _Lidio Meireles: http://www.linkedin.com/in/lidio
 .. _Ying Liu: http://www.linkedin.com/pub/ying-liu/15/48b/5a9
 .. _Kian Ho: https://github.com/kianho
 .. _Gökçen Eraslan: http://blog.yeredusuncedernegi.com/
-.. _Tim Lezon: http://www.csb.pitt.edu/Faculty/Lezon/
+.. _Tim Lezon: https://scholar.google.pl/citations?user=1MwNI3EAAAAJ&hl=pl&oi=ao
 .. _Chakra Chennubhotla: http://www.csb.pitt.edu/Faculty/Chakra/
 .. _She (John) Zhang: https://www.linkedin.com/in/she-zhang-49164399/
 .. _Hongchun Li: http://www.pitt.edu/~hongchun/
-.. _James Krieger: http://www.csb.pitt.edu/Faculty/bahar/lab.html
-.. _Yan Zhang: https://www.csb.pitt.edu/Faculty/bahar/lab.html
-.. _Burak Kaynak: https://www.csb.pitt.edu/Faculty/bahar/lab.html
+.. _James Krieger: https://scholar.google.pl/citations?user=DoiCjkUAAAAJ&hl=pl
+.. _Yan Zhang: https://scholar.google.pl/citations?user=VxwU0pgAAAAJ&hl=pl&oi=sra
+.. _Burak Kaynak: https://scholar.google.pl/citations?user=gP8RokwAAAAJ&hl=pl&oi=ao
+.. _Karolina Mikulska-Ruminska: https://scholar.google.pl/citations?user=IpyPHRwAAAAJ&hl=pl
+.. _Anthony Bogetti: https://scholar.google.pl/citations?hl=pl&user=9qQClIcAAAAJ
+.. _Frane Doljanin: https://github.com/fdoljanin

docs/apps/prody/prody.txt

@@ -9,7 +9,7 @@ optional arguments:
 
 subcommands:
   {anm,gnm,pca,eda,align,blast,biomol,catdcd,contacts,fetch,select,energy,clustenm}
-    anm                 perform anisotropic network model calculations
+    anm                 perform anisotropic network model normal mode analysis calculations
     gnm                 perform Gaussian network model calculations
     pca                 perform principal component analysis calculations
     eda                 perform essential dynamics analysis calculations

docs/docs

@@ -1 +1 @@
-ProDy/docs
+.

docs/reference/dynamics/signature.rst

@@ -1,5 +1,5 @@
-Signature Dynamics of Protein Families
-======================================
+Signature Dynamics of Protein Families (SignDy)
+===============================================
 
 .. automodule:: prody.dynamics.signature
    :members:

docs/reference/proteins/interactions.rst

@@ -1,5 +1,5 @@
-Interactions Tools
-======================
+Interactions and Stability (InSty)
+===================================
 
 .. automodule:: prody.proteins.interactions
    :members:

docs/reference/proteins/waterbridges.rst

@@ -0,0 +1,6 @@
+Water bridge finder (WatFinder)
+===================================
+
+.. automodule:: prody.proteins.waterbridges
+   :members:
+   :undoc-members:

docs/release/index.rst

@@ -10,6 +10,10 @@ Release Notes
    :maxdepth: 2
    :glob:
 
+   v2.4_series
+   v2.3_series
+   v2.2_series
+   v2.1_series
    v2.0_series
    v1.11_series
    v1.10_series

prody/apps/prody_apps/prody_anm.py

@@ -258,7 +258,7 @@ def prody_anm(pdb, **kwargs):
 def addCommand(commands):
 
     subparser = commands.add_parser('anm',
-        help='perform anisotropic network model calculations')
+        help='perform anisotropic network model normal mode analysis calculations')
 
     subparser.add_argument('--quiet', help="suppress info messages to stderr",
         action=Quiet, nargs=0)

prody/apps/prody_apps/prody_catdcd.py

@@ -80,8 +80,9 @@ def prody_catdcd(*dcd, **kwargs):
     out = prody.DCDFile(output, 'w')
     count = 0
     stride = kwargs.get('stride', 1)
-    goto = stride != 1
-    slc = slice(kwargs.get('first', 0), kwargs.get('last', -1),
+    first = kwargs.get('first', 0)
+    goto = stride != 1 or first != 0
+    slc = slice(first, kwargs.get('last', -1),
                 stride).indices(len(traj)+1)
     for i in range(*slc):
         if goto:

prody/apps/prody_apps/prody_clustenm.py

@@ -41,7 +41,12 @@
     ('t_steps_i', 'number of 2.0 fs MD time steps for initial structure', 1000),
     ('t_steps_g', 'number of 2.0 fs MD time steps in each generation, can be tuple of floats', '7500'),
     ('multiple', 'whether each conformer will be saved as a separate PDB file', False),
-    ('write_params', 'whether to write parameters', False)]:
+    ('write_params', 'whether to write parameters', False),
+    ('fitmap', 'map to fit by filtering conformations like MDeNMD-EMFit', None),
+    ('fit_resolution', 'resolution for blurring structures for fitting cc', 5),
+    ('map_cutoff', 'min_cutoff for passing map for fitting', 0),
+    ('replace_filtered', 'whether to keep sampling again to replace filtered conformers', False),
+    ('platform', 'openmm platform (OpenCL, CUDA, CPU or None)', None)]:
 
     DEFAULTS[key] = val
     HELPTEXT[key] = txt
@@ -67,6 +72,13 @@ def prody_clustenm(pdb, **kwargs):
     import prody
     LOGGER = prody.LOGGER
 
+    fitmap = kwargs.pop('fitmap')
+    map_cutoff = kwargs.pop('map_cutoff')
+    if fitmap is not None:
+        fitmap = prody.parseEMD(fitmap, min_cutoff=map_cutoff)
+
+    fit_resolution = kwargs.pop('fit_resolution')
+
     selstr = kwargs.pop('select')
     prefix = kwargs.pop('prefix')
     sparse = kwargs.pop('sparse')
@@ -75,6 +87,7 @@ def prody_clustenm(pdb, **kwargs):
     model = kwargs.pop('model')
     altloc = kwargs.pop('altloc')
     turbo = kwargs.pop('turbo')
+    nproc = kwargs.pop('nproc')
 
     ngens = kwargs.pop('ngens')
     nconfs = kwargs.pop('nconfs')
@@ -142,7 +155,9 @@ def prody_clustenm(pdb, **kwargs):
             t_steps_g=eval(t_steps_g),
             outlier=outlier, mzscore=mzscore,
             sparse=sparse, kdtree=kdtree, turbo=turbo,
-            parallel=parallel, **kwargs)
+            parallel=parallel, fitmap=fitmap, 
+            fit_resolution=fit_resolution,
+            nproc=nproc, **kwargs)
 
     single = not kwargs.pop('multiple')
     outname = join(outdir, prefix)
@@ -188,7 +203,7 @@ def addCommand(commands):
   $ prody clustenm 1aar -s "calpha and chain A and resnum < 70" -A""",
   test_examples=[0, 1])
 
-    group = addNMAParameters(subparser, include_nproc=False)
+    group = addNMAParameters(subparser, include_nproc=True)
 
     group.add_argument('-c', '--cutoff', dest='cutoff', type=str,
         default=DEFAULTS['cutoff'], metavar='FLOAT',
@@ -256,7 +271,7 @@ def addCommand(commands):
         default=DEFAULTS['ionicStrength'], metavar='FLOAT',
         help=HELPTEXT['ionicStrength'] + ' (default: %(default)s)')
 
-    group.add_argument('-P', '--padding', dest='padding', type=float,
+    group.add_argument('-Q', '--padding', dest='padding', type=float,
         default=DEFAULTS['padding'], metavar='FLOAT',
         help=HELPTEXT['padding'] + ' (default: %(default)s)')
 
@@ -307,6 +322,26 @@ def addCommand(commands):
     group.add_argument('-p', '--file-prefix', dest='prefix', type=str,
         default=DEFAULTS['prefix'], metavar='STR',
         help=HELPTEXT['prefix'] + ' (default: pdb%(default)s)')
+
+    group.add_argument('-q', '--fitmap', dest='fitmap', type=str,
+        default=DEFAULTS['fitmap'], metavar='STR',
+        help=HELPTEXT['fitmap'] + ' (default: %(default)s)')
+
+    group.add_argument('-r', '--fit_resolution', dest='fit_resolution', type=float,
+        default=DEFAULTS['fit_resolution'], metavar='FLOAT',
+        help=HELPTEXT['fit_resolution'] + ' (default: %(default)s)')
+
+    group.add_argument('-u', '--map_cutoff', dest='map_cutoff', type=float,
+        default=DEFAULTS['map_cutoff'], metavar='FLOAT',
+        help=HELPTEXT['map_cutoff'] + ' (default: %(default)s)')
+
+    group.add_argument('-O', '--replace_filtered', dest='replace_filtered',
+        action='store_true',
+        default=DEFAULTS['replace_filtered'], help=HELPTEXT['replace_filtered'])
+
+    group.add_argument('-V', '--platform', dest='platform', type=str,
+        default=DEFAULTS['platform'], metavar='STR',
+        help=HELPTEXT['platform'] + ' (default: %(default)s)')
 
     subparser.add_argument('pdb', help='PDB identifier or filename')
 

prody/apps/prody_apps/prody_select.py

@@ -36,9 +36,10 @@ def prody_select(selstr, *pdbs, **kwargs):
     suffix = kwargs.get('suffix', '_selected')
     output = kwargs.get('output', None)
     altloc = kwargs.get('altloc', 'all')
+    uniteChains = kwargs.get('uniteChains', False)
 
     for pdb in pdbs:
-        pdb = parsePDB(pdb, altloc=altloc)
+        pdb = parsePDB(pdb, altloc=altloc, unite_chains=uniteChains)
 
         pdbselect = pdb.select(selstr)
         if pdbselect is None:
@@ -89,6 +90,10 @@ def addCommand(commands):
         type=str, default='_selected',
         help=('output filename suffix (default: %(default)s)'))
 
+    group.add_argument('-u', '--unite-chains', dest='uniteChains',
+        action='store_true',
+        default=False, help=('unite chains if using mmCIF (default False)'))
+
     subparser.add_argument('select', help='atom selection string')
     subparser.add_argument('pdb', nargs='+',
         help='PDB identifier(s) or filename(s)')

prody/atomic/atom.py

@@ -275,7 +275,7 @@ def toTEMPyAtom(self):
             self.getAltloc(), self.getIcode(),
             self.getCharge(), self.getElement(),
             self.getOccupancy(), self.getResname(),
-            None, self.getACSIndex(), self.getChid(),
+            self.getACSIndex(), self.getChid(),
             self.getResnum())