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:
@@ -21,7 +13,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: [2.7, 3.5, 3.9]
+        python-version: ["2.7", "3.7", "3.8", "3.9", "3.10"]
 
     steps:
     - uses: actions/checkout@v2
@@ -34,10 +26,12 @@ jobs:
         echo $CONDA/bin >> $GITHUB_PATH
     - name: Install dependencies
       run: |
+        if [[ ${{ matrix.python-version }} == "3.11" ]]; then conda config --add channels conda-forge; fi
         conda create --yes -n test python=${{ matrix.python-version }}
         source activate test
-        conda install --yes numpy scipy nose pyparsing biopython
+        conda install --yes numpy scipy nose pyparsing biopython requests
         if [[ ${{ matrix.python-version }} == "2.7" ]]; then conda install --yes unittest2; fi
+        pip install .
         python setup.py build_ext --inplace --force
     - name: Test with pytest
       run: |

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 git@github.com:abakan/ProDy.git
 
-or:
-
-$ cd prody
-$ git remote add prodymaster git@bitbucket.org: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: 2.3.1
 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)

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

@@ -1,14 +1,11 @@
 #!/usr/bin/python
 
 import os
-try:
-    import imp
-except ImportError:
-    import importlib as imp
-
+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/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

@@ -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
@@ -143,11 +142,6 @@ following command from the ProDy project folder::
   $ cd prody
   $ git remote add prodymaster git@github.com:abakan/ProDy.git
 
-or::
-
-  $ cd prody
-  $ git remote add prodymaster git@bitbucket.org:abakan/prody.git
-
 
 You may use any name other than `prodymaster`, but `origin`, which points to
 the ProDy fork in your account.

docs/release/v2.0_series.rst

@@ -4,6 +4,70 @@ ProDy 2.0 Series
 .. contents::
    :local:
 
+2.0.2 (February 17, 2022)
+------------------------------------------------------------------------------
+
+**New Features**:
+
+  * Added :function:`.realignModes` for comparing sets of modes calculated on unaligned 
+  structures
+
+  * New option *by_time* in :function:`.showProjection`, allowing projections onto 1 PC 
+  and the frames sampled over the time course of a simulation or the conformers in an ensemble.
+
+  * Updates to ClustENM(D) to use latest and more efficient OpenMM version, 7.6
+
+  * New :function:`.parseGromacsModes` for parsing NMA and PCA modes calculated in Gromacs, 
+  allowing the use of all-atom force fields and more efficient handling of large trajectories
+
+**Bug Fixes and Improvements**:
+
+  * Bug fixes to searchPfam and fetchPfamMSA, which no longer worked due to some security change.
+
+  * Bug fix to Ensembles and Conformations for weights being indexed twice
+
+  * Bug fix to --quiet option of apps that fixes the VMD ProDy interface
+
+  * General documentation and error improvements
+
+**Full Changelog**: https://github.com/prody/ProDy/compare/v2.0.1...v2.0.2
+
+
+2.0.1 (Dec 20, 2021)
+------------------------------------------------------------------------------
+
+**New Features**:
+
+  * Added :function:`.calcRWSIP` for comparing sets of modes
+
+  * New methods to convert :class:`.Atom`, :class:`.Atomic` and :class:`.EMDMAP` 
+  to TEMPy objects, allowing calculations such as cross-correlation coefficient (CCC) 
+  to EM maps.
+
+  * Added :func:`.calcDynamicFlexibilityIndex` and :func:`.calcDynamicCouplingIndex`
+  for further interpretation of PRS results.
+
+  * Reinstated the option of using forces in PRS as in ProDy v1.8 (`turbo=**False**`)
+
+  * Added GitHub Actions Continuous Integration in place of Travis. 
+
+**Bug Fixes and Improvements**:
+
+  * Compatibility and bug fixes for various functions, including pyparsing for selections.
+
+  * Extended :class:`.AdaptiveANM` to work with other models including explicit membrane 
+  ANM, :class:`.exANM`.
+
+  * Improved capabilities for fetching and parsing mmCIF and EMD files.
+
+  * Improved handling of residue and serial numbers including hexadecimal and hybrid36 formats.
+
+  * Consistency fixes.
+
+  * More non-standard amino acids (MEN, CSB, CME).
+
+**Full Changelog**: https://github.com/prody/ProDy/compare/v2.0...v2.0.1
+
 2.0 (Dec 30, 2020)
 ------------------------------------------------------------------------------
 

docs/release/v2.1_series.rst

@@ -0,0 +1,52 @@
+ProDy 2.1 Series
+===============================================================================
+
+.. contents::
+   :local:
+
+2.1.2 (April 27, 2022)
+------------------------------------------------------------------------------
+
+**Bug Fixes and Improvements**:
+
+  * New :function:`.showRMSFlucts` and :function:`.calcRMSFlucts` for root-mean-square fluctuations
+
+  * fix to :function:`.showAtomicLines` for overlaying multiple chains
+
+2.1.1 (April 18, 2022)
+------------------------------------------------------------------------------
+
+**Bug Fixes and Improvements**:
+
+  * :function:`.parseScipionModes` can handle having a pdb file or not
+
+  * fix to mmCIF header parsing for chemicals in blocks not loops
+
+2.1.0 (April 8, 2022)
+------------------------------------------------------------------------------
+
+**New Features**:
+
+*Integration with Scipion*
+
+  * New functions :function:`.parseScipionModes`, :function:`.writeScipionModes` 
+  and :function:`.calcScipionScore`
+
+  * New argument *--export-scipion* (*-S*) in prody apps
+
+*Other*
+
+  * Added :function:`.assignBlocks` for assigning blocks for RTB
+
+  * Added mmCIF header parsing to create the same header dictionary as PDB header,
+  including secstr information and biomolecular assembly building
+
+  * New arguments for prody apps, including altloc, zeros, sparse, kdtree and turbo
+
+**Bug Fixes and Improvements**:
+
+  * Improvement to cealign mapping to be faster for protein only alignment
+
+  * Bug fix for writing psf files
+
+**Full Changelog**: https://github.com/prody/ProDy/compare/v2.0.2...v2.1.0

docs/release/v2.2_series.rst

@@ -0,0 +1,26 @@
+ProDy 2.2 Series
+===============================================================================
+
+.. contents::
+   :local:
+
+2.2.0 (May 19, 2022)
+------------------------------------------------------------------------------
+
+**Bug Fixes and Improvements**:
+
+  * Updates to :function:`.parseScipionModes`` to use sqlite and xmd metadata files 
+  and handle eigenvalues
+
+  * Actual fix to logging so LOGGER.progress doesn't override logging level
+
+  * Updates to the PCA app to better handle number of modes for Scipion 
+
+  * New arguments sparse, kdtree and turbo for :class:`.ClustENM`, allowing 
+  better control of ANM calculations.
+
+  * Another bug fix for mmCIF header parsing
+
+  * Bug fix for parsing CONECT bond records from PDB files
+
+**Full Changelog**: https://github.com/prody/ProDy/compare/v2.1.2...v2.2.0