merge update

.github/workflows/main.yml

@@ -2,16 +2,8 @@
 
 name: CI
 
-# Controls when the action will run. 
-on:
-  # Triggers the workflow on push and pull request events
-  push:
-    branches: [ $default-branch ]
-  pull_request:
-    branches: [ $default-branch ]
-
-  # Allows you to run this workflow manually from the Actions tab
-  workflow_dispatch:
+# Controls when the action will run.
+on: [push, pull_request, workflow_dispatch]
 
 # A workflow run is made up of one or more jobs that can run sequentially or in parallel
 jobs:
@@ -21,27 +13,30 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: [2.7, 3.5, 3.9]
+        python-version: ["2.7", "3.8", "3.9", "3.10"]
 
     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 [[ ${{ matrix.python-version }} != "2.7" ]]; then conda config --add channels conda-forge; fi
         conda create --yes -n test python=${{ matrix.python-version }}
         source activate test
-        conda install --yes numpy scipy nose pyparsing biopython
-        if [[ ${{ matrix.python-version }} == "2.7" ]]; then conda install --yes unittest2; fi
+        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
+        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 +22,8 @@ __pycache__
 *.nmd
 *.pdb
 *.pdb.gz
+*.cif
+*.cif.gz
 
 # Docs
 /docs/_build/

CONTRIBUTING.md

@@ -72,11 +72,11 @@ $ git commit -a
 This command will open a text editor for you to describe the changes that you just committed.
 Push and Pull Request
 
-After you have committed your changes, you will need to push them to your Bitbucket account:
+After you have committed your changes, you will need to push them to your GitHub account:
 
 git push origin master
 
-This step will ask for your account user name. If you are going to push to your GitHub/Bitbucket account frequently, you may add an SSH key for automatic authentication. To add an SSH key for your system, go to Edit Your Profile ‣ SSH keys page on GitHub or Manage Account ‣ SSH keys page on Bitbucket.
+This step will ask for your account user name. If you are going to push to your GitHub account frequently, you may add an SSH key for automatic authentication. To add an SSH key for your system, go to Edit Your Profile ‣ SSH keys page on GitHub.
 
 After pushing your changes, you will need to make a pull request from your to notify ProDy developers of the changes you made and facilitate their incorporation to ProDy.
 Update Local Copy
@@ -86,11 +86,6 @@ You can also keep an up-to-date copy of ProDy by pulling changes from the master
 $ cd prody
 $ git remote add prodymaster [email protected]:abakan/ProDy.git
 
-or:
-
-$ cd prody
-$ git remote add prodymaster [email protected]:abakan/prody.git
-
 You may use any name other than prodymaster, but origin, which points to the ProDy fork in your account.
 
 After setting up this remote, calling git pull command will fetch latest changes from ProDy master repository and merge them to your local copy:

INSTALL.rst

@@ -6,7 +6,7 @@ Installation
 Required Software
 -----------------
 
-* `Python`_ 2.7, 3.5 or later. We recommend using `Anaconda`_, which provides the conda package and environment manager as well as many useful packages. 
+* `Python`_ 2.7, 3.6 or later. We recommend using `Anaconda`_, which provides the conda package and environment manager as well as many useful packages. 
 
 .. _Anaconda: https://www.anaconda.com/products/individual
 
@@ -91,7 +91,7 @@ Recommended Software
   Scipy linear algebra module is more flexible and can be faster.
 * `IPython`_ is a must have for interactive ProDy sessions.
 * `PyReadline`_ for colorful IPython sessions on Windows.
-* `MDAnalysis`_ for reading molecular dynamics trajectories.
+* `MDAnalysis`_ or `MDTraj`_ for reading molecular dynamics trajectories.
 
 
 .. _PyReadline: http://ipython.org/pyreadline.html

PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 1.1
 Name: ProDy
-Version: 2.0
+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
@@ -95,4 +95,4 @@ Requires: numpy (>=1.10)
 Requires: pyparsing
 Requires: biopython
 Requires: scipy
-Provides: prody (2.0)
+Provides: prody (2.1.2)

README.rst

@@ -72,3 +72,19 @@ 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/_theme/howtocite.html

@@ -12,12 +12,18 @@
           <i>ProDy</i>: Protein Dynamics Inferred from Theory and Experiments</a> <br/>
           <em>Bioinformatics</em> <strong>2011</strong> 27(11):1575-1577.
         </small></p>
-	<p><small>
+	      <p><small>
           Bakan A, Dutta A, Mao W, Liu Y, Chennubhotla C, Lezon TR, Bahar I
           <a class="reference external" href="http://bioinformatics.oxfordjournals.org/content/30/18/2681" target="_blank">
           <i>Evol</i> and <i>ProDy</i> for Bridging Protein Sequence Evolution and Structural Dynamics</a> <br/>
           <em>Bioinformatics</em> <strong>2014</strong> 30(18):2681-2683.
         </small></p>
+        <p><small>
+          Zhang S, Krieger JM, Zhang Y, Kaya C, Kaynak B, Mikulska-Ruminska K, Doruker P, Li H, Bahar I
+          <a class="reference external" href="https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btab187/6211036" target="_blank">
+          <i>ProDy</i> 2.0: Increased Scale and Scope after 10 Years of Protein Dynamics Modelling with Python</a> <br/>
+          <em>Bioinformatics</em> <strong>2021</strong> 37(20):3657-3659
+        </small></p>
       </div>
     </div>
   </div>

docs/about/citing.rst

@@ -6,9 +6,17 @@ Citing
 When using *ProDy* or *NMWiz* in published work, please cite:
 
   | Bakan A, Meireles LM, Bahar I.
-  | ProDy: Protein Dynamics Inferred from Theory and Experiments.
+  | *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.
+
 When using *pairwise2* or *KDTree* modules in published work, please cite:
 
   | Cock PJ, Antao T, Chang JT, Chapman BA, Cox CJ, Dalke A, Friedberg I,

docs/apps/docapps.py

@@ -2,9 +2,10 @@
 
 import os
 import imp
+import importlib
 from subprocess import Popen, PIPE
 
-path = [imp.find_module('prody')[1]]
+path = [importlib.util.find_spec("prody").submodule_search_locations[0]]
 apps = imp.load_module('prody.apps',
                            *imp.find_module('apps', path))
 

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/conf.py

@@ -107,8 +107,8 @@
     'issue': ('https://github.com/prody/ProDy/issues/%s', 'issue '),
     'pdb': ('http://www.pdb.org/pdb/explore/explore.do?structureId=%s', ''),
     'wiki': ('http://en.wikipedia.org/wiki/%s', ''),
-    'pfam': ('http://pfam.xfam.org/family/%s', ''),
-    'pfamprotein': ('http://pfam.xfam.org/protein/%s', ''),
+    'pfam': ('http://pfam-legacy.xfam.org/family/%s', ''),
+    'pfamprotein': ('http://pfam-legacy.xfam.org/protein/%s', ''),
     'uniprot': ('http://www.uniprot.org/uniprot/%s', ''),
     'pdbhet': ('http://www.pdb.org/pdb/ligand/ligandsummary.do?hetId=%s', ''),
 }
@@ -170,7 +170,8 @@
 .. _PDB: http://www.pdb.org
 .. _pip: https://pypi.python.org/pypi/pip
 
-.. _MDAnalysis: http://code.google.com/p/mdanalysis
+.. _MDAnalysis: https://www.mdanalysis.org
+.. _MDTraj: https://www.mdtraj.org
 .. _pyparsing: http://pyparsing.wikispaces.com
 .. _Matplotlib: http://matplotlib.org
 .. _Biopython: http://biopython.org

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::
 
@@ -117,15 +117,14 @@ Push and Pull Request
 ---------------------
 
 After you have committed your changes, you will need to push them to your
-Bitbucket account::
+GitHub account::
 
   git push origin master
 
 This step will ask for your account user name.  If you are going to push
-to your GitHub/Bitbucket account frequently, you may add an SSH key for
+to your GitHub account frequently, you may add an SSH key for
 automatic authentication.  To add an SSH key for your system, go to
-:menuselection:`Edit Your Profile --> SSH keys` page on GitHub or
-:menuselection:`Manage Account --> SSH keys` page on Bitbucket.
+:menuselection:`Edit Your Profile --> SSH keys` page on GitHub.
 
 After pushing your changes, you will need to make a pull request from your
 to notify ProDy developers of the changes you made and facilitate their
@@ -141,15 +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
-
-or::
-
-  $ 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/docs

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

docs/reference/apps/prody_clustenm.rst

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

docs/reference/proteins/interactions.rst

@@ -0,0 +1,6 @@
+Interactions Tools
+======================
+
+.. automodule:: prody.proteins.interactions
+   :members:
+   :undoc-members: