Recent ProDy updates to Cavi-Finder branch

.github/ISSUE_TEMPLATE/config.yml

@@ -0,0 +1 @@
+blank_issues_enabled: false

.github/ISSUE_TEMPLATE/prody-bug-report.md

@@ -0,0 +1,31 @@
+---
+name: ProDy Bug Report
+about: Please let us know about a bug you encountered when using ProDy.
+title: ''
+labels: ''
+assignees: AnthonyBogetti
+
+---
+
+**Note: *Our GitHub Issues are for bug reports ONLY*. Please post any feature requests and other topics to the Discussions tab. Thank you.**
+
+**Please read the following before posting an issue.**
+Hello, we are sorry that you have run into a problem while using ProDy. We will do our best to address your issues in a timely and comprehensive manner. In return, we ask that you completely fill out this bug report. Do not leave any section blank. Filling this form out ensures that we can help you most efficiently and saves us (and you) time and energy. Also, please search old issues and discussions before opening a new Issue. Chances are, someone in the past had your issue and the solution was described there.
+
+## Description of the bug.
+Below, please describe the error you encountered and what you were trying to do with ProDy.
+
+## Do you have any error messages or logs?
+Below, please post the error you got and text from any relevant log files.
+
+## What is your setup?
+Below, please describe your setup. What operating system are you using (MacOS, Linux, etc.).
+
+## How did you install ProDy?
+Below, please say whether you installed from source, with conda or with pip. Please also add what version of ProDy you are using.
+
+## What did your code look like?
+Below, if possible, please post the exact code you ran that led to the error you received. Please also attach any relevant input files. This will help us more quickly respond you your issue.
+
+## Anything else?
+Below, please write any other details you would like us to know about.

.github/workflows/main.yml

@@ -1,42 +1,97 @@
-# This is a basic workflow to help you get started with Actions
-
 name: CI
+on:
+  - push
+  - pull_request
+  - 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:
-  # This workflow contains a single job called "build"
   build:
-    runs-on: ubuntu-latest
+    runs-on: ${{ matrix.os }}
+
+    # ENVIRONMENT SETTINGS TO PREVENT HANGS
+    env:
+      OMP_NUM_THREADS: "1"
+      MKL_NUM_THREADS: "1"
+      OPENBLAS_NUM_THREADS: "1"
+      VECLIB_MAXIMUM_THREADS: "1"
+      NUMEXPR_NUM_THREADS: "1"
+      # Agg backend is critical for headless CI
+      MPLBACKEND: "Agg"
+      # Prevent ProDy from checking online for updates during import
+      PRODY_NO_UPDATE_CHECK: "1"
+
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["2.7", "3.8", "3.9", "3.10", "3.11", "3.12"]
+        os: [ubuntu-latest, macos-latest]
+        python-version: ["3.10", "3.11", "3.12"]
 
     steps:
-    - uses: actions/checkout@v2
-    - name: Set up Python ${{ matrix.python-version }}
-      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 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
-
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Cache Matplotlib
+        uses: actions/cache@v4
+        with:
+          path: ~/.cache/matplotlib
+          key: ${{ runner.os }}-matplotlib-${{ hashFiles('environment.yml') }}
+          restore-keys: |
+            ${{ runner.os }}-matplotlib-
+
+      - name: Set up Micromamba
+        uses: mamba-org/setup-micromamba@v1
+        with:
+          environment-file: environment.yml
+          cache-environment: true
+          create-args: >-
+            python=${{ matrix.python-version }}
+
+      - name: Verify Environment
+        shell: bash -l {0}
+        run: |
+          micromamba info
+          micromamba list
+
+      - name: Build & compile HPB (Linux)
+        if: runner.os == 'Linux'
+        shell: bash -l {0}
+        run: |
+          pip install -e .
+          python setup.py build_ext --inplace --force
+          ls -lh prody/proteins/hpb.so || { echo "hpb.so missing"; exit 1; }
+
+      - name: Build & compile HPB (macOS)
+        if: runner.os == 'macOS'
+        shell: bash -l {0}
+        run: |
+          export CFLAGS="${CFLAGS} -D__NO_FLOAT16"
+          export CPPFLAGS="${CPPFLAGS} -D__NO_FLOAT16"
+
+          pushd prody/proteins/hpbmodule
+
+          gfortran -O3 -fPIC -c reg_tet.f || exit 1
+
+          PYINC=$(python -c "import sysconfig; print(sysconfig.get_path('include'))")
+          PYLIBDIR=$(python -c "import sysconfig; print(sysconfig.get_config_var('LIBDIR'))")
+          export LIBRARY_PATH="$CONDA_PREFIX/lib:$PYLIBDIR:$LIBRARY_PATH"
+
+          g++ -O3 -g -fPIC -I"${PYINC}" -c hpbmodule.cpp -o hpbmodule.o || exit 1
+
+          g++ -dynamiclib -undefined dynamic_lookup \
+              -o hpb.so hpbmodule.o reg_tet.o \
+              -L"${PYLIBDIR}" -L"$CONDA_PREFIX/lib" -lgfortran || exit 1
+
+          cp hpb.so ../
+          popd
+
+          pip install -e .
+          python setup.py build_ext --inplace --force
+
+      - name: Run tests
+        shell: bash -l {0}
+        run: |
+          # Warm up imports to trigger font cache build (if needed) before tests start
+          python -c "import matplotlib.pyplot"
+
+          # Run tests without debug flags
+          pytest -v -k "not testCommandExample19 and not testCommandExample20"

.gitignore

@@ -17,6 +17,7 @@ sdist
 develop-eggs
 .installed.cfg
 __pycache__
+.DS_Store
 
 # ProDy
 *.nmd

.readthedocs.yaml

@@ -0,0 +1,17 @@
+version: 2
+
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.12"
+
+python:
+  install:
+    - method: pip
+      path: .
+      extra_requirements:
+        - docs  # Ensure setup.py has this or use requirements.txt
+    - requirements: docs/requirements.txt
+
+sphinx:
+  configuration: docs/conf.py

INSTALL.rst

@@ -6,7 +6,7 @@ Installation
 Required Software
 -----------------
 
-* `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. 
+* `Python`_ 3.10 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
 
@@ -32,24 +32,14 @@ this package.
 Quick Install
 -------------
 
-If you have pip_ installed, type the following::
 
-  pip install -U ProDy
+We officially recommend installing through conda::
 
-If you don't have pip_, please download an installation file and
-follow the instructions.
+  conda install -c conda-forge prody
 
-If you have conda installed, you can also type the following instead::
 
-  conda install ProDy
-
-
-Download & Install
-------------------
-
-After installing the required packages, you will need to download a suitable
-ProDy source or installation file from http://python.org/pypi/ProDy.
-For changes and list of new features see :ref:`changes`.
+Installing From Source (not recommended)
+----------------------------------------
 
 **Linux**
 
@@ -72,23 +62,9 @@ schemes in `Installing Python Modules`_.
 
 For installing ProDy, please follow the Linux installation instructions.
 
-**Windows**
-
-Remove previously installed ProDy release from :program:`Uninstall a program`
-in :guilabel:`Control Panel`.
-
-Download :file:`ProDy-1.{x}.{y}.win32-py2.{z}.exe` and run to install ProDy.
-
-To be able use :ref:`prody-apps` and :ref:`evol-apps` in command prompt
-(:program:`cmd.exe`), append Python and scripts folders (e.g.
-:file:`C:\\Python27` and :file:`C:\\Python27\\Scripts`) to :envvar:`PATH`
-environment variable.
-
 Recommended Software
 --------------------
 
-* `Scipy`_, when installed, replaces linear algebra module of Numpy.
-  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`_ or `MDTraj`_ for reading molecular dynamics trajectories.
@@ -109,6 +85,9 @@ Following software is included in the ProDy installation packages:
 * `argparse`_ is used to implement applications and provided for
   compatibility with Python 2.6.
 
+* `Scipy`_, when installed, replaces linear algebra module of Numpy.
+  Scipy linear algebra module is more flexible and can be faster.
+
 .. _argparse: http://code.google.com/p/argparse/
 
 

MANIFEST.in

@@ -21,4 +21,5 @@ include prody/utilities/datafiles/*.dat
 include prody/utilities/datafiles/*.txt
 include scripts/prody*
 include scripts/evol*
-include prody/protein/tabulated_energies.txt
+include prody/protein/tabulated_energies.txt
+recursive-include prody/drugui/DruGUI-script *

PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 1.1
 Name: ProDy
-Version: 2.5.0
+Version: 2.6.1
 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
@@ -84,10 +84,8 @@ Classifier: Intended Audience :: Education
 Classifier: Intended Audience :: Science/Research
 Classifier: License :: OSI Approved :: MIT License
 Classifier: Operating System :: MacOS
-Classifier: Operating System :: Microsoft :: Windows
 Classifier: Operating System :: POSIX
 Classifier: Programming Language :: Python
-Classifier: Programming Language :: Python :: 2
 Classifier: Programming Language :: Python :: 3
 Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
 Classifier: Topic :: Scientific/Engineering :: Chemistry

README.md

@@ -0,0 +1,89 @@
+[![ProDy workflow status](https://img.shields.io/github/actions/workflow/status/prody/prody/main.yml)](https://github.com/prody/ProDy/actions/workflows/main.yml)
+[![ProDy conda-forge page](https://anaconda.org/conda-forge/prody/badges/version.svg)](https://anaconda.org/conda-forge/prody)
+[![ProDy pypi page](https://img.shields.io/pypi/v/ProDy.svg)](https://pypi.org/project/ProDy/)
+[![Docs](https://img.shields.io/readthedocs/prody-official.svg?logo=read-the-docs&logoColor=white)](https://prody-official.readthedocs.io/en/latest/)
+
+## Synopsis
+
+ProDy is a free and open-source Python package for protein structure, dynamics, and sequence analysis. It allows for comparative analysis and modeling of protein structural dynamics and sequence co-evolution. The fast and flexible ProDy API is designed 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.
+
+## Installing ProDy
+
+We recommend downloading and installing the Anaconda package manager to handle dependencies in controlled environments. ProDy can be installed with the following command:
+
+```bash
+conda install -c conda-forge ProDy
+```
+
+ProDy is under active development. Install it from the source on GitHub if you want the most recent fixes.
+
+First, download the ProDy code either as a zipped folder or using Git. For example, if you have Git installed, you can do the following:
+
+```bash
+git clone https://github.com/prody/ProDy.git
+```
+
+Then, change into the ProDy directory and install it by running the following commands:
+
+```bash
+cd ProDy  
+python setup.py build\_ext \--inplace \--force  
+pip install \-Ue .
+```
+
+More instructions can be found at [http://bahargroup.org/prody/downloads/](http://bahargroup.org/prody/downloads/) and [http://bahargroup.org/prody/manual/devel/develop.html](http://bahargroup.org/prody/manual/devel/develop.html).
+
+## MODULES
+
+ProDy has a modular structure with modules inside various subpackages.
+
+The main ones are:
+
+* **prody.atomic**: handles all Atomic objects including AtomGroup and Selection  
+* **prody.database**: interfaces with databases such as CATH, DALI, UniProt and Pfam  
+* **prody.dynamics**: provides all the modules for normal mode analysis with various elastic network models, as well as PCA, SignDy (prody.dynamics.signature), hybrid methods such as prody.dynamics.clustenm, allosteric signal propagation methods prody.dynamics.perturb (PRS) and calcHitTime (Markovian hitting time), and various analysis and plotting functions.  
+* **prody.ensemble**: enables construction of heterogeneous structural ensembles for exploring dynamics from experiments and simulations  
+* **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 prody.proteins.interactions within and between proteins (InSty) and find prody.proteins.waterbridges (WatFinder).  
+* **prody.sequence**: has all the sequence alignment and evolutionary analysis tools of Evol
+
+Smaller ones include:
+
+* **prody.chromatin**: specific to chromatin dynamics (ChromDy) including prody.chromatin.hic and prody.chromatin.cluster  
+* **prody.compounds**: for parsing small molecule compounds/ligands from the PDB and related databases  
+* **prody.domain\_decomposition**: for Spectrus dynamical domain decomposition  
+* **prody.trajectory**: for trajectories in DCD format  
+* **prody.utilities**
+
+## GETTING PRODY
+
+You can run ProDy on all major platforms. For download and installation instructions see: [http://www.bahargroup.org/prody/downloads/](http://www.bahargroup.org/prody/downloads/)
+
+## DOCUMENTATION
+
+* **Homepage**: [http://www.bahargroup.org/prody/](http://www.bahargroup.org/prody/)  
+* **Tutorials**: [http://www.bahargroup.org/prody/tutorials](http://www.bahargroup.org/prody/tutorials)  
+* **Reference**: [http://www.bahargroup.org/prody/manual](http://www.bahargroup.org/prody/manual)  
+* **Applications**: [http://www.bahargroup.org/prody/manual/apps](http://www.bahargroup.org/prody/manual/apps)  
+* **NMWiz GUI**: [http://www.bahargroup.org/prody/nmwiz](http://www.bahargroup.org/prody/nmwiz)  
+* **Changes**: [http://www.bahargroup.org/prody/manual/release](http://www.bahargroup.org/prody/manual/release)  
+* See also [https://github.com/prody/ProDy-website](https://github.com/prody/ProDy-website) for latest versions.
+
+## SOURCE CODE
+
+* **Source code**: [https://github.com/prody/ProDy](https://github.com/prody/ProDy)  
+* **Issue tracker**: [https://github.com/prody/ProDy/issues](https://github.com/prody/ProDy/issues)
+
+## LICENSE
+
+ProDy is available under the MIT License. See LICENSE.txt for more details.
+
+* **Biopython**: ([http://biopython.org/](http://biopython.org/)) KDTree and TreeConstruction modules are distributed with ProDy. Biopython is developed by The Biopython Consortium and is available under the Biopython license ([http://www.biopython.org/DIST/LICENSE](http://www.biopython.org/DIST/LICENSE)).  
+* **Pyparsing**: ([https://github.com/pyparsing/pyparsing](https://github.com/pyparsing/pyparsing)) module is distributed with ProDy. Pyparsing is developed by Paul T. McGuire and is available under the MIT license ([http://www.opensource.org/licenses/mit-license.php](http://www.opensource.org/licenses/mit-license.php)).  
+* **CEalign module**: ([https://pymolwiki.org/index.php/Cealign\_plugin](https://pymolwiki.org/index.php/Cealign_plugin)) is distributed 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 ([https://doi.org/10.1016/j.jmb.2025.169009](https://doi.org/10.1016/j.jmb.2025.169009)).