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

.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
@@ -29,8 +29,8 @@ 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
+        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

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/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_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

@@ -87,7 +87,7 @@ def prody_clustenm(pdb, **kwargs):
     model = kwargs.pop('model')
     altloc = kwargs.pop('altloc')
     turbo = kwargs.pop('turbo')
-    nproc = kwargs.get('nproc')
+    nproc = kwargs.pop('nproc')
 
     ngens = kwargs.pop('ngens')
     nconfs = kwargs.pop('nconfs')

prody/atomic/flags.py

@@ -132,8 +132,15 @@
 
     'nucleobase': set(['GUN', 'ADE', 'CYT', 'THY', 'URA']),
     'nucleotide': set(['DA', 'DC', 'DG', 'DT', 'DU', 'A', 'C', 'G', 'T', 'U']),
-    'nucleoside': set(['AMP', 'ADP', 'ATP', 'CDP', 'CTP', 'GMP', 'GDP', 'GTP',
-                       'TMP', 'TTP', 'UMP', 'UDP', 'UTP']),
+    'nucleoside': set(['ADN', 'AMP', 'ADP', 'ATP',
+                       'CMP', # cyclic AMP
+                       'A2P', 'A3P', # multi site diphosphates
+                       'AGS', # ATP-gamma-S
+                       'CTN', 'C5P', 'CDP', 'CTP',
+                       'C2P', 'C3P', # other site monophosphates
+                       'GMP', '5GP', 'GDP', 'GTP',
+                       'THM', 'TMP', 'TPP', 'TTP',
+                       'URI', 'UMP', 'UDP', 'UTP']),
 
     'at': set(['ADE', 'A', 'THY', 'T']),
     'cg': set(['CYT', 'C', 'GUN', 'G']),
@@ -418,19 +425,36 @@ def changeBackbone(flag, names):
       =======  ==================================
 
    nucleoside
-      indicates following nucleoside derivatives that are recognized by *PDB*:
+      indicates following nucleosides and their derivatives that are recognized by *PDB*:
 
       =======  ================================
-      `AMP`_   adenosine monophosphate
+      `ADN`_   adenosine
+      `AMP`_   adenosine-5'-monophosphate
       `ADP`_   adenosine-5'-diphosphate
       `ATP`_   adenosine-5'-triphosphate
+      `AGS`_   adenosine-5'-triphosphate-gamma-S
+      `CMP`_   cyclic adenosine-3',5'-monophosphate
+      `A2P`_   adenosine-2',5'-diphosphate
+      `A3P`_   adenosine-3',5'-diphosphate
+
+      `CTN`_   cytidine
+      `C2P`_   cytidine-2'-monophosphate
+      `C3P`_   cytidine-3'-monophosphate
+      `C5P`_   cytidine-5'-monophosphate
       `CDP`_   cytidine-5'-diphosphate
       `CTP`_   cytidine-5'-triphosphate
+
       `GMP`_   guanosine
+      `5GP`_   guanosine-5'-monophosphate
       `GDP`_   guanosine-5'-diphosphate
       `GTP`_   guanosine-5'-triphosphate
-      `TMP`_   thymidine-5'-phosphate
+
+      `THM`_   thymidine
+      `TMP`_   thymidine-5'-monophosphate
+      `TPP`_   thymidine-5'-diphosphate
       `TTP`_   thymidine-5'-triphosphate
+
+      `URI`_   uridine (uracil plus ribose)
       `UMP`_   2'-deoxyuridine 5'-monophosphate
       `UDP`_   uridine 5'-diphosphate
       `UTP`_   uridine 5'-triphosphate

prody/compounds/pdbligands.py

@@ -158,9 +158,9 @@ def fetchPDBLigand(cci, filename=None):
     resnums = np.ones(n_atoms, dtype=ATOMIC_FIELDS['charge'].dtype)
 
     alternate_atomnames = np.zeros(n_atoms, dtype=ATOMIC_FIELDS['name'].dtype)
-    leaving_atom_flags = np.zeros(n_atoms, np.bool)
-    aromatic_flags = np.zeros(n_atoms, np.bool)
-    stereo_configs = np.zeros(n_atoms, np.bool)
+    leaving_atom_flags = np.zeros(n_atoms, bool)
+    aromatic_flags = np.zeros(n_atoms, bool)
+    stereo_configs = np.zeros(n_atoms, bool)
     ordinals = np.zeros(n_atoms, int)
 
     name2index = {}

prody/database/__init__.py

@@ -72,11 +72,21 @@
 Interpro
 ====
 
-The following functions can be used to search and retrieve Pfam_ data:
+The following functions can be used to search and retrieve Interpro_ data:
 
   * :func:`.searchInterpro` - search for domain families of a protein
 
-.. _Pfam: https://www.ebi.ac.uk/interpro/
+.. _Interpro: https://www.ebi.ac.uk/interpro/
+
+BioExcel-CV19
+====
+
+The following functions can be used to retrieve BioExcel-CV19_ data:
+
+  * :func:`.fetchBioexcelPDB` - fetch PDB files for starting structures for trajectories
+
+.. _BioExcel-CV19: https://bioexcel-cv19-dev.bsc.es/
+
 """
 
 __all__ = []
@@ -108,3 +118,7 @@
 from . import interpro
 from .interpro import *
 __all__.extend(interpro.__all__)
+
+from . import bioexcel
+from .bioexcel import *
+__all__.extend(bioexcel.__all__)