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

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: 2.4.1
+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

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
 --------
@@ -78,23 +78,23 @@ 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://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
 
 See also https://github.com/prody/ProDy-website for latest versions.
 
@@ -136,6 +136,7 @@ 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 

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/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

docs/devel/website.rst

@@ -14,7 +14,7 @@ This is a short guide for building the ProDy website.
 Environment Setup
 --------------
 
-First log in to the ProDy webserver (prody.csb.pitt.edu) then run the following::
+First log in to your ProDy webserver and then run the following::
 
   $ conda deactivate
 
@@ -34,7 +34,7 @@ ProDy-website-workdir. You can then copy files back over afterwards.
 
 It's recommended to have the symbolic link called test_prody pointing to 
 your build directory instead and then you can monitor changes by going to 
-http://prody.csb.pitt.edu/test_prody/_build/html/ in your web browser.
+http://yourdomainname/test_prody/_build/html/ in your web browser.
 
 
 Updating from GitHub

docs/docs

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

docs/index.rst

@@ -11,7 +11,7 @@ ProDy Manual
 .. only:: rtd and html
 
     This is a partial copy of ProDy documentation.  Please visit
-    `ProDy Homepage <http://prody.csb.pitt.edu>`_ for complete
+    `ProDy Homepage <http://www.bahargroup.org/prody>`_ for complete
     documentation with tutorials.
 
 

docs/reference/proteins/waterbridges.rst

@@ -3,4 +3,4 @@ Water bridge finder (WatFinder)
 
 .. automodule:: prody.proteins.waterbridges
    :members:
-   :undoc-members:
+   :undoc-members:

docs/release/index.rst

@@ -9,7 +9,12 @@ Release Notes
 .. toctree::
    :maxdepth: 2
    :glob:
-
+
+   v2.5_series
+   v2.4_series
+   v2.3_series
+   v2.2_series
+   v2.1_series
    v2.0_series
    v1.11_series
    v1.10_series

docs/release/v2.5_series.rst

@@ -0,0 +1,39 @@
+ProDy 2.5 Series
+===============================================================================
+
+.. contents::
+   :local:
+
+
+2.5.0 (Aug 14, 2024)
+------------------------------------------------------------------------------
+
+**New Features**:
+
+* InSty module prody/proteins/interactions.py for protein interactions and stability
+* WatFinder module prody/proteins/waterbridges.py for analysing water bridges, chains and clusters
+* Membrane exANM and exGNM apps
+* kmedoid clustering
+* Logistic regression for differences between sub-ensembles
+* MMTF Parser by @vratins
+* Protein-ligand interactions including calcSminaBindingAffinity by @karolamik13
+* New support for Interpro Pfam
+* New modules for accessing Bioexcel cv19 simulation database (precursor to MDDB)
+
+**Bug Fixes and Improvements**:
+
+* add weights to showProjection and fix colors
+* fix catdcd frame selection
+* fix showAtomicLines gaps
+* update pyproject.toml and setup.py to limit scipy
+* fix clustenm saving and loading
+* fix adp matrix by @jamesmkrieger
+* several fixes related to fetching, parsing and writing pdb and cif files
+* limit pyparsing<=3.1.1
+
+**New Contributors**:
+
+* @jyaacoub made their first contribution in https://github.com/prody/ProDy/pull/1750
+* @vratins made their first contribution in https://github.com/prody/ProDy/pull/1752
+
+**Full Changelog**: https://github.com/prody/ProDy/compare/v2.4.1...v2.5.0

prody/__init__.py

@@ -1,6 +1,6 @@
 """ProDy is a package for Protein Dynamics, Sequence, and Structure Analysis"""
 
-__version__ = '2.4.1'
+__version__ = '2.5.0'
 __release__ = __version__ # + '-dev' # comment out '-dev' before a release
 
 import sys

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/chromatin/functions.py

@@ -212,7 +212,7 @@ def showEmbedding(modes, labels=None, trace=True, headtail=True, cmap='prism'):
         X, Y, Z = V[:,:3].T
 
         f = figure()
-        ax = f.add_subplot(projection="3d")
+        ax = f.add_subplot(1,1,1,projection="3d")
         if trace:
             ax.plot(X, Y, Z, ':', color=[0.3, 0.3, 0.3])
         if labels is None:
@@ -240,4 +240,4 @@ def getDomainList(labels):
     ends = sites[1:]
     domains = np.array([starts, ends]).T
 
-    return domains
+    return domains