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

.github/workflows/main.yml

@@ -13,29 +13,30 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["2.7", "3.7", "3.8", "3.9", "3.10"]
+        python-version: ["2.7", "3.8", "3.9", "3.10", "3.11"]
 
     steps:
     - uses: actions/checkout@v2
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
+      uses: MatteoH2O1999/setup-python@v2
       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
+        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 biopython requests
-        if [[ ${{ matrix.python-version }} == "2.7" ]]; then conda install --yes unittest2; 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
     - name: Test with pytest
       run: |
         source activate test
         conda install --yes pytest
         pytest
-        
+        

.gitignore

@@ -22,6 +22,12 @@ __pycache__
 *.nmd
 *.pdb
 *.pdb.gz
+*.cif
+*.cif.gz
+*.mmtf
+*.map
+*.mrc
+*.dcd
 
 # Docs
 /docs/_build/

CONTRIBUTING.md

@@ -1,4 +1,4 @@
-This is a first draft, which is based on the ProDy website page http://prody.csb.pitt.edu/manual/devel/develop.html. Please see that page for updates.
+This is a first draft, which is based on the ProDy website page http://www.bahargroup.org/prody/manual/devel/develop.html. Please see that page for updates.
 
 
 Install Git and a GUI

MANIFEST.in

@@ -9,6 +9,7 @@ include prody/*/*.cpp
 include prody/*/*/*.cpp
 include prody/*/*.h
 include prody/*/*/*.h
+include prody/*/*/*/*.so
 include prody/tests/*/*.py
 include prody/tests/datafiles/*.coo
 include prody/tests/datafiles/*.dcd
@@ -20,3 +21,4 @@ include prody/utilities/datafiles/*.dat
 include prody/utilities/datafiles/*.txt
 include scripts/prody*
 include scripts/evol*
+include prody/protein/tabulated_energies.txt

PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 1.1
 Name: ProDy
-Version: 2.3.1
+Version: 2.5.0
 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
@@ -32,23 +32,23 @@ Description: .. image:: https://secure.travis-ci.org/prody/ProDy.png?branch=mast
         You can run ProDy on all major platforms.  For download and installation
         instructions see:
 
-        * http://prody.csb.pitt.edu/downloads
+        * http://www.bahargroup.org/prody/downloads
 
 
         DOCUMENTATION
         -------------
 
-        * Homepage: http://prody.csb.pitt.edu/
+        * Homepage: http://www.bahargroup.org/prody/
 
-        * Tutorials: http://prody.csb.pitt.edu/tutorials
+        * Tutorials: http://www.bahargroup.org/prody/tutorials
 
-        * Reference: http://prody.csb.pitt.edu/manual
+        * Reference: http://www.bahargroup.org/prody/manual
 
-        * Applications: http://prody.csb.pitt.edu/manual/apps
+        * Applications: http://www.bahargroup.org/prody/manual/apps
 
-        * NMWiz GUI: http://prody.csb.pitt.edu/nmwiz
+        * NMWiz GUI: http://www.bahargroup.org/prody/nmwiz
 
-        * Changes: http://prody.csb.pitt.edu/manual/release
+        * Changes: http://www.bahargroup.org/prody/manual/release
 
 
         SOURCE CODE
@@ -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

@@ -1,5 +1,5 @@
-.. image:: https://img.shields.io/travis/prody/ProDy.svg
-   :target: http://travis-ci.org/#!/prody/ProDy
+.. image:: https://img.shields.io/github/actions/workflow/status/prody/prody/main.yml
+   :target: https://github.com/prody/ProDy/actions/workflows/main.yml
 
 .. image:: https://img.shields.io/pypi/v/ProDy.svg
    :target: https://pypi.org/project/ProDy/
@@ -8,7 +8,7 @@
    :target: https://github.com/prody/ProDy/commits/master
 
 .. image:: https://img.shields.io/pypi/dm/ProDy.svg
-   :target: http://prody.csb.pitt.edu/downloads/
+   :target: http://www.bahargroup.org/prody/downloads/
 
 SYNOPSIS
 --------
@@ -20,30 +20,83 @@ 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
 -------------
 
 You can run ProDy on all major platforms.  For download and installation
 instructions see:
 
-* http://prody.csb.pitt.edu/downloads
+* http://www.bahargroup.org/prody/downloads/
 
 
 DOCUMENTATION
 -------------
 
-* Homepage: http://prody.csb.pitt.edu/
+* Homepage: http://www.bahargroup.org/prody/
+
+* Tutorials: http://www.bahargroup.org/prody/tutorials
 
-* Tutorials: http://prody.csb.pitt.edu/tutorials
+* Reference: http://www.bahargroup.org/prody/manual
 
-* Reference: http://prody.csb.pitt.edu/manual
+* Applications: http://www.bahargroup.org/prody/manual/apps
 
-* Applications: http://prody.csb.pitt.edu/manual/apps
+* NMWiz GUI: http://www.bahargroup.org/prody/nmwiz
 
-* NMWiz GUI: http://prody.csb.pitt.edu/nmwiz
+* Changes: http://www.bahargroup.org/prody/manual/release
 
-* Changes: http://prody.csb.pitt.edu/manual/release
+See also https://github.com/prody/ProDy-website for latest versions.
 
 
 SOURCE CODE
@@ -72,3 +125,20 @@ with ProDy. The original CE method was developed by Ilya Shindyalov and Philip
 Bourne. The Python version which is used by ProDy is developed by Jason Vertrees 
 and available under the New BSD license. 
 
+Hbp module: The calculation of hydrophobic interactions, solvent accessible surface 
+area (SASA) and volume for each residue is using geometric methods based on the 
+information of the atoms in the molecule. The methods have been programmed in C++ 
+and can be compiled as a python module “hpb.so” which is then used by ProDy.
+Files for compilation are stored at prody/proteins/hpbmodule folder and
+required C++ and Fortran compiler. After compilation hpb.so file can be
+stored in prody/proteins folder in ProDy or in the local directory which
+is used to perform calulations. The precompiled versions for Python 2.7,
+3.8, 3.9, and 3.10 are availabe in prody/proteins/hpbmodule. The user can
+choose the correct version of hpb.so and copy to the prody/proteins or
+local directory.
+
+C++ code of hpb.so was developed by Xin Cao and Fortran code by Xin Cao, 
+Michelle H. Hummel, Bihua Yu, and Evangelos A. Coutsias (License in 
+prody/proteins/hpbmodule folder). Details of the method can be found 
+in the Supplementary Material of InSty manuscript 
+(soon will be submitted for publication). 

docs/about/people.rst

@@ -21,16 +21,25 @@ Development Team
 `James Krieger`_ was helping develop *ProDy* from 2017 and became the main 
 overseer and developer in mid 2020.
 
-`Hongchun Li`_ is currently maintaining and developing ANM and GNM servers, 
+`Hongchun Li`_ has helped maintain and develop ANM and GNM servers, 
 and made significant contributions to :mod:`.database` and :mod:`.dynamics` 
 including *SignDy* and Adaptive ANM.
 
+`JiYoung Lee`_ is the main developer of :mod:`.Pharmmaker`, for constructing pharmacophore models using the outputs from :mod:`.DruGUI`.
+
 `Yan Zhang`_ contributed significantly to the development of 
 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`_ is one of the main developers since 2022, with the addition of the new modules 
+:mod:`.protein.interactions` (*InSty*), :mod:`.protein.waterbridges`
+(*WatFinder*), in addition to being the developer of :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.
@@ -43,6 +52,12 @@ Blocks and Membrane ENM.
 `Lidio Meireles`_ provided insightful comments on the design of *ProDy*,
 and contributed to the development of :ref:`prody-apps`.
 
+`Mustafa Tekpinar`_ contributed to the development of MechStiff.
+
+`Luca Ponzoni`_ contributed to the development of SignDy.
+
+`David Koes`_ contributed to the development of drug discovery tools.
+
 Contributors
 ------------
 
@@ -52,6 +67,8 @@ 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
@@ -60,18 +77,25 @@ 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
+.. _Ying Liu: https://www.linkedin.com/in/yingliu03/
 .. _Kian Ho: https://github.com/kianho
-.. _Gökçen Eraslan: http://blog.yeredusuncedernegi.com/
-.. _Tim Lezon: http://www.csb.pitt.edu/Faculty/Lezon/
+.. _Gökçen Eraslan: https://github.com/gokceneraslan
+.. _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
+.. _JiYoung Lee: https://scholar.google.com/citations?user=odKQmZcAAAAJ&hl=en
+.. _David Koes: https://bits.csb.pitt.edu/
+.. _Luca Ponzoni: https://scholar.google.it/citations?user=8vfPOYUAAAAJ&hl=en
+.. _Mustafa Tekpinar: https://scholar.google.com/citations?user=qeVv6o8AAAAJ&hl=en   

docs/apps/prody/index.rst

@@ -40,4 +40,4 @@ the output files are prefixed with :file:`p38_anm`::
 
 The output file :file:`p38_anm.nmd` can be visualized using `NMWiz`_.
 
-.. _NMWiz: http://prody.csb.pitt.edu/nmwiz/
+.. _NMWiz: http://www.bahargroup.org/prody/nmwiz/

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
 
@@ -10,8 +8,8 @@ optional arguments:
   -v, --version         print ProDy version and exit
 
 subcommands:
-  {anm,gnm,pca,eda,align,blast,biomol,catdcd,contacts,fetch,select}
-    anm                 perform anisotropic network model calculations
+  {anm,gnm,pca,eda,align,blast,biomol,catdcd,contacts,fetch,select,energy,clustenm}
+    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
@@ -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/conf.py

@@ -158,13 +158,13 @@
     'numpy': ('http://docs.scipy.org/doc/numpy/', None),
     'scipy': ('http://docs.scipy.org/doc/scipy/reference/', None),
     'matplotlib': ('http://matplotlib.sourceforge.net/', None),
-    'prodywebsite': ('http://prody.csb.pitt.edu/', None),
+    'prodywebsite': ('http://www.bahargroup.org/prody/', None),
 }
 
 rst_epilog = u"""
 
-.. _ProDy: http://prody.csb.pitt.edu
-.. _Tutorials: http://prody.csb.pitt.edu/tutorials
+.. _ProDy: http://www.bahargroup.org/prody
+.. _Tutorials: http://www.bahargroup.org/prody/tutorials
 .. _NMWiz: http://csb.pitt.edu/NMWiz
 .. _VMD: http://www.ks.uiuc.edu/Research/vmd
 .. _PDB: http://www.pdb.org