Metadata-Version: 2.4
Name: gmx_clusterByFeatures
Version: 0.1.29
Summary: Features Based Conformational Clustering of Molecular Dynamics trajectories.
Author-email: Rajendra Kumar <rjdkmr@gmail.com>
License: GNU General Public License v3 (GPLv3)
Project-URL: homepage, https://gmx-clusterbyfeatures.readthedocs.io/
Project-URL: repository, https://github.com/rjdkmr/gmx_clusterByFeatures
Keywords: Molecular Modeling,Molecular Dynamics Simulations,Computational Chemistry,Computational Biophysics,Clustering
Classifier: Environment :: Console
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: End Users/Desktop
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
Classifier: Natural Language :: English
Classifier: Operating System :: MacOS
Classifier: Operating System :: POSIX :: Linux
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Description-Content-Type: text/x-rst
License-File: LICENSE
Requires-Dist: numpy>=1.6
Requires-Dist: scipy>=0.9
Requires-Dist: matplotlib>=1.1.0
Requires-Dist: scikit-learn>=0.19.0
Dynamic: license-file

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    :target: https://github.com/rjdkmr/gmx_clusterByFeatures/actions/workflows/linux-wheels.yml
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    :target: https://github.com/rjdkmr/gmx_clusterByFeatures/actions/workflows/macos-wheels.yml
    :alt: MacOS-Wheels-Build

.. image:: https://readthedocs.org/projects/gmx-clusterbyfeatures/badge/?version=latest
    :target: https://gmx-clusterbyfeatures.readthedocs.io/
    :alt: Documentation Status

gmx_clusterByFeatures
=====================
It can be used to cluster the conformations of a molecule in a molecular dynamics
trajectory using collection of features. The features could be any quantity as a
function of time such as Projections of eigenvector from PCA or dihedral-PCA,
distances, angles, channel radius etc.

**See details at:** `gmx_clusterByFeatures homepage <https://gmx-clusterbyfeatures.readthedocs.io>`_



.. note:: It is developed for **GROMACS MD trajectory.** However, it can be used with
  any other trajectory format after converting it to GROMACS format trajectory.

Installation on Linux and MacOS
-------------------------------

.. code-block:: bash

    sudo python3 -m pip install gmx-clusterByFeatures

No dependency on GROMACS. Install and use it.

For more details, visit `download and installation <https://gmx-clusterbyfeatures.readthedocs.io/en/latest/install.html>`_ section. 

Usage
-----------

.. list-table:: List of sub-commands available in gmx_clusterByFeatures
    :widths: 1, 4
    :header-rows: 1
    :name: commands-table

    * - Command
      - Function

    * - `cluster <https://gmx-clusterbyfeatures.readthedocs.io/en/latest/commands/cluster.html>`_
      - Main module to perform clustering

    * - `featuresplot <https://gmx-clusterbyfeatures.readthedocs.io/en/latest/commands/featuresplot.html>`_
      - Feature vs Feature plot to check quality of clustering

    * - `distmat <https://gmx-clusterbyfeatures.readthedocs.io/en/latest/commands/distmat.html>`_
      - Distance-matrix related calculations

    * - `matplot <https://gmx-clusterbyfeatures.readthedocs.io/en/latest/commands/matplot.html>`_
      - To visulaize/plot matrix obtained from ``distmat``
      
    * - `hole <https://gmx-clusterbyfeatures.readthedocs.io/en/latest/commands/hole.html>`_
      - To calculate cavity/channel radius using HOLE program
      
    * - `holeplot <https://gmx-clusterbyfeatures.readthedocs.io/en/latest/commands/holeplot.html>`_
      - To calculate average and plot hole output radius file
    
    * - `holefeatures <https://gmx-clusterbyfeatures.readthedocs.io/en/latest/commands/holefeatures.html>`_
      - To write radius as a features for clustering
      
    * - `holeclustersplot <https://gmx-clusterbyfeatures.readthedocs.io/en/latest/commands/holeclustersplot.html>`_
      - To plot or write radius for clusters separately

For more details, visit `usage <https://gmx-clusterbyfeatures.readthedocs.io/en/latest/usage.html>`_ section. 


Development Setup for conda
---------------------------
Following steps are for development setup. However, these steps can be used for installation using conda

.. code-block:: bash

  # Clone the repository and setup development environment
  git clone --recursive https://github.com/rjdkmr/gmx_clusterByFeatures.git
  cd gmx_clusterByFeatures
  conda env create -y --prefix ./venv --file environment.yaml # Create development conda environment
  conda activate ./venv # Activate the environment
  bash -i scripts/build_dev_setup_conda.sh # all build and setup steps are in this script
