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Merge branch 'main' of https://github.com/prody/ProDy into fix_fetchPDB_cif
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‎.github/workflows/main.yml‎

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# This is a basic workflow to help you get started with Actions
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name: CI
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on:
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- push
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- pull_request
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- workflow_dispatch
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# Controls when the action will run.
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on: [push, pull_request, workflow_dispatch]
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# A workflow run is made up of one or more jobs that can run sequentially or in parallel
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jobs:
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# This workflow contains a single job called "build"
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build:
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runs-on: ubuntu-latest
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runs-on: ${{ matrix.os }}
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strategy:
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fail-fast: false
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matrix:
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os: [ubuntu-latest, macos-latest]
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python-version: ["3.10", "3.11", "3.12"]
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steps:
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- uses: actions/checkout@v2
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- name: Set up Python ${{ matrix.python-version }}
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uses: MatteoH2O1999/setup-python@v2
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with:
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python-version: ${{ matrix.python-version }}
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- name: Add conda to system path
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run: |
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echo $CONDA/bin >> $GITHUB_PATH
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- name: Install dependencies
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run: |
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conda create --yes -n test python=${{ matrix.python-version }}
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source activate test
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conda config --add channels conda-forge
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conda install --yes numpy scipy nose requests
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conda install --yes pdbfixer mdtraj openmm
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conda install -c bioconda clustalw
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pip install mmtf-python scikit-learn
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pip install .
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python setup.py build_ext --inplace --force
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- name: Test with pytest
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run: |
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source activate test
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conda install --yes pytest
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pytest
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- name: Checkout
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uses: actions/checkout@v2
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- name: Set up Miniconda
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uses: conda-incubator/setup-miniconda@v2
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with:
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miniconda-version: "latest"
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python-version: ${{ matrix.python-version }}
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activate-environment: test
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auto-update-conda: true
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channels: conda-forge
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architecture: ${{ runner.arch }}
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- name: Install deps
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shell: bash -l {0}
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run: |
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conda activate test
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conda install --yes -c conda-forge compilers gfortran
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conda install --yes \
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"numpy" \
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"pyparsing<=3.1.1" \
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scipy nose pytest requests \
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pdbfixer mdtraj openmm
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conda install -c bioconda --yes clustalw
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pip install mmtf-python scikit-learn
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- name: Build & compile HPB (Linux)
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if: runner.os == 'Linux'
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shell: bash -l {0}
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run: |
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conda activate test
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pip install -e .
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python setup.py build_ext --inplace --force
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echo "Verifying hpb.so file properties on Linux:"
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ls -lh prody/proteins/hpb.so || { echo "hpb.so not found on Linux!"; exit 1; }
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file prody/proteins/hpb.so || { echo "file command failed for hpb.so on Linux!"; exit 1; }
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ldd prody/proteins/hpb.so || { echo "ldd failed or found issues on Linux!"; exit 1; }
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- name: Build & compile HPB (macOS)
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if: runner.os == 'macOS'
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shell: bash -l {0}
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run: |
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conda activate test
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echo "Debugging environment variables before compilation:"
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echo "PATH: $PATH"
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echo "CONDA_PREFIX: $CONDA_PREFIX"
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echo "LIBRARY_PATH: $LIBRARY_PATH"
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echo "CPATH: $CPATH"
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echo "DYLD_LIBRARY_PATH: $DYLD_LIBRARY_PATH"
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export CFLAGS="${CFLAGS} -D__NO_FLOAT16"
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export CPPFLAGS="${CPPFLAGS} -D__NO_FLOAT16"
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pushd prody/proteins/hpbmodule
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echo "Contents of hpbmodule directory:"
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ls -l
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echo "Attempting Fortran compilation..."
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gfortran -O3 -fPIC -c reg_tet.f || { echo "Fortran compilation of reg_tet.f failed!"; exit 1; }
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echo "reg_tet.f compiled successfully to reg_tet.o."
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ls -lh reg_tet.o
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file reg_tet.o
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PYINC=$(python -c "import sysconfig; print(sysconfig.get_path('include'))")
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PYLIBDIR=$(python -c "import sysconfig; print(sysconfig.get_config_var('LIBDIR'))")
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echo "Python Include Dir (PYINC): ${PYINC}"
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echo "Python Lib Dir (PYLIBDIR): ${PYLIBDIR}"
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[ -d "${PYINC}" ] || { echo "Python Include Dir '${PYINC}' does not exist!"; exit 1; }
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[ -d "${PYLIBDIR}" ] || { echo "Python Lib Dir '${PYLIBDIR}' does not exist!"; exit 1; }
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export LIBRARY_PATH="$CONDA_PREFIX/lib:$PYLIBDIR:$LIBRARY_PATH"
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echo "Attempting C++ compilation..."
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g++ -O3 -g -fPIC -I"${PYINC}" -c hpbmodule.cpp -o hpbmodule.o || { echo "C++ compilation of hpbmodule.cpp failed!"; exit 1; }
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echo "hpbmodule.cpp compiled successfully to hpbmodule.o."
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ls -lh hpbmodule.o
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file hpbmodule.o
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echo "Attempting HPB linking for macOS..."
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g++ -dynamiclib \
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-undefined dynamic_lookup \
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-o hpb.so hpbmodule.o reg_tet.o \
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-L"${PYLIBDIR}" -L"$CONDA_PREFIX/lib" -lgfortran || { echo "HPB shared library linking failed!"; exit 1; }
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echo "hpb.so linked successfully."
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echo "Verifying hpb.so file properties (macOS):"
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ls -lh hpb.so || { echo "hpb.so not found after linking!"; exit 1; }
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file hpb.so || { echo "File type check failed for hpb.so!"; exit 1; }
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otool -L hpb.so || { echo "otool -L failed or found issues for hpb.so! This usually means it's not a valid Mach-O binary."; exit 1; }
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cp hpb.so ../
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popd
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pip install -e .
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python setup.py build_ext --inplace --force
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- name: Run tests
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shell: bash -l {0}
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run: |
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conda activate test
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pytest

‎INSTALL.rst‎

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Required Software
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-----------------
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* `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.
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* `Python`_ 3.10 or later. We recommend using `Anaconda`_, which provides the conda package and environment manager as well as many useful packages.
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.. _Anaconda: https://www.anaconda.com/products/individual
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Quick Install
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-------------
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If you have pip_ installed, type the following::
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pip install -U ProDy
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We officially recommend installing through conda::
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If you don't have pip_, please download an installation file and
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follow the instructions.
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conda install -c conda-forge prody
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If you have conda installed, you can also type the following instead::
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conda install ProDy
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Download & Install
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------------------
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After installing the required packages, you will need to download a suitable
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ProDy source or installation file from http://python.org/pypi/ProDy.
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For changes and list of new features see :ref:`changes`.
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Installing From Source (not recommended)
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----------------------------------------
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**Linux**
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For installing ProDy, please follow the Linux installation instructions.
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**Windows**
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Remove previously installed ProDy release from :program:`Uninstall a program`
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in :guilabel:`Control Panel`.
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Download :file:`ProDy-1.{x}.{y}.win32-py2.{z}.exe` and run to install ProDy.
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To be able use :ref:`prody-apps` and :ref:`evol-apps` in command prompt
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(:program:`cmd.exe`), append Python and scripts folders (e.g.
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:file:`C:\\Python27` and :file:`C:\\Python27\\Scripts`) to :envvar:`PATH`
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environment variable.
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Recommended Software
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--------------------
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* `Scipy`_, when installed, replaces linear algebra module of Numpy.
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Scipy linear algebra module is more flexible and can be faster.
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* `IPython`_ is a must have for interactive ProDy sessions.
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* `PyReadline`_ for colorful IPython sessions on Windows.
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* `MDAnalysis`_ or `MDTraj`_ for reading molecular dynamics trajectories.
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* `argparse`_ is used to implement applications and provided for
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compatibility with Python 2.6.
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* `Scipy`_, when installed, replaces linear algebra module of Numpy.
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Scipy linear algebra module is more flexible and can be faster.
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.. _argparse: http://code.google.com/p/argparse/
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‎PKG-INFO‎

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Metadata-Version: 1.1
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Name: ProDy
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Version: 2.5.0
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Version: 2.6.1
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Summary: A Python Package for Protein Dynamics Analysis
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Home-page: http://www.csb.pitt.edu/ProDy
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Author: James Krieger, She Zhang, Hongchun Li, Cihan Kaya, Ahmet Bakan, and others
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Classifier: Intended Audience :: Science/Research
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Classifier: License :: OSI Approved :: MIT License
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Classifier: Operating System :: MacOS
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Classifier: Operating System :: Microsoft :: Windows
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Classifier: Operating System :: POSIX
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Classifier: Programming Language :: Python
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Classifier: Programming Language :: Python :: 2
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Classifier: Programming Language :: Python :: 3
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Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
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Classifier: Topic :: Scientific/Engineering :: Chemistry

‎README.md‎

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[![ProDy workflow status](https://img.shields.io/github/actions/workflow/status/prody/prody/main.yml)](https://github.com/prody/ProDy/actions/workflows/main.yml)
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[![ProDy conda-forge page](https://anaconda.org/conda-forge/prody/badges/version.svg)](https://anaconda.org/conda-forge/prody)
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[![ProDy pypi page](https://img.shields.io/pypi/v/ProDy.svg)](https://pypi.org/project/ProDy/)
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## **SYNOPSIS**
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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.
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Further details are described in the ProDy papers:
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Bakan A, Meireles LM, Bahar I.
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ProDy: Protein Dynamics Inferred from Theory and Experiments.
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Bioinformatics 2011 27(11):1575-1577.
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Bakan A, Dutta A, Mao W, Liu Y, Chennubhotla C, Lezon TR, Bahar I.
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Evol and ProDy for Bridging Protein Sequence Evolution and Structural Dynamics.
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Bioinformatics 2014 30(18):2681-2683.
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Zhang S, Krieger JM, Zhang Y, Kaya C, Kaynak B, Mikulska-Ruminska K, Doruker P, Li H, Bahar I.
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ProDy 2.0: Increased Scale and Scope after 10 Years of Protein Dynamics Modelling with Python.
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Bioinformatics 2021 37(20):3657-3659.
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## **INSTALLING PRODY**
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We recommend downloading and installing the Anaconda package manager to handle dependencies in controlled environments. ProDy can be installed with the following command:
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conda install \-c conda-forge ProDy
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ProDy is under active development. Install it from the source on GitHub if you want the most recent fixes.
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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:
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git clone https://github.com/prody/ProDy.git
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Then, change into the ProDy directory and install it by running the following commands:
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cd ProDy
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python setup.py build\_ext \--inplace \--force
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pip install \-Ue .
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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).
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## **MODULES**
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ProDy has a modular structure with modules inside various subpackages.
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The main ones are:
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* **prody.atomic**: handles all Atomic objects including AtomGroup and Selection
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* **prody.database**: interfaces with databases such as CATH, DALI, UniProt and Pfam
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* **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.
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* **prody.ensemble**: enables construction of heterogeneous structural ensembles for exploring dynamics from experiments and simulations
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* **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).
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* **prody.sequence**: has all the sequence alignment and evolutionary analysis tools of Evol
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Smaller ones include:
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* **prody.chromatin**: specific to chromatin dynamics (ChromDy) including prody.chromatin.hic and prody.chromatin.cluster
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* **prody.compounds**: for parsing small molecule compounds/ligands from the PDB and related databases
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* **prody.domain\_decomposition**: for Spectrus dynamical domain decomposition
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* **prody.trajectory**: for trajectories in DCD format
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* **prody.utilities**
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## **GETTING PRODY**
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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/)
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## **DOCUMENTATION**
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* **Homepage**: [http://www.bahargroup.org/prody/](http://www.bahargroup.org/prody/)
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* **Tutorials**: [http://www.bahargroup.org/prody/tutorials](http://www.bahargroup.org/prody/tutorials)
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* **Reference**: [http://www.bahargroup.org/prody/manual](http://www.bahargroup.org/prody/manual)
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* **Applications**: [http://www.bahargroup.org/prody/manual/apps](http://www.bahargroup.org/prody/manual/apps)
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* **NMWiz GUI**: [http://www.bahargroup.org/prody/nmwiz](http://www.bahargroup.org/prody/nmwiz)
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* **Changes**: [http://www.bahargroup.org/prody/manual/release](http://www.bahargroup.org/prody/manual/release)
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* See also [https://github.com/prody/ProDy-website](https://github.com/prody/ProDy-website) for latest versions.
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## **SOURCE CODE**
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* **Source code**: [https://github.com/prody/ProDy](https://github.com/prody/ProDy)
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* **Issue tracker**: [https://github.com/prody/ProDy/issues](https://github.com/prody/ProDy/issues)
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## **LICENSE**
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ProDy is available under the MIT License. See LICENSE.txt for more details.
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* **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)).
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* **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)).
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* **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.
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* **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)).

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