Merge branch 'master' of github.com:prody/ProDy into writeScipion_norm

.github/workflows/main.yml

@@ -13,27 +13,30 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: [2.7, 3.5, 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 [[ ${{ matrix.python-version }} != "2.7" ]]; then conda config --add channels conda-forge; fi
         conda create --yes -n test python=${{ 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 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/

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
 

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
@@ -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 (2.0)
+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
 -----------
@@ -72,3 +125,19 @@ 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/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
 
@@ -10,8 +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

@@ -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', ''),
 }

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::
 
@@ -140,10 +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
+  $ 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
+.

docs/reference/apps/prody_clustenm.rst

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

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

@@ -0,0 +1,6 @@
+Interactions and Stability (InSty)
+===================================
+
+.. automodule:: prody.proteins.interactions
+   :members:
+   :undoc-members:

docs/reference/proteins/waterbridges.rst

@@ -0,0 +1,6 @@
+Water bridge finder (WatFinder)
+===================================
+
+.. automodule:: prody.proteins.waterbridges
+   :members:
+   :undoc-members:

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