Metadata-Version: 2.1
Name: gmx-clusterByFeatures
Version: 0.1.13
Summary: Features Based Conformational Clustering of Molecular Dynamics trajectories. 
Home-page: https://github.com/rjdkmr/gmx_clusterByFeatures
Author: Rajendra Kumar
Author-email: rjdkmr@gmail.com
License: GNU General Public License v3 (GPLv3)
Keywords: Molecular Modeling,Molecular Dynamics Simulations,Computational Chemistry,Computational Biophysics
Platform: UNKNOWN
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
Requires-Dist: pkgconfig (>=1.3)
Requires-Dist: pybind11 (>=2.2)
Requires-Dist: numpy (>=1.6)
Requires-Dist: scipy (>=0.9)
Requires-Dist: matplotlib (>=1.1.0)
Requires-Dist: scikit-learn (>=0.19.0)


.. image:: https://travis-ci.org/rjdkmr/gmx_clusterByFeatures.svg?branch=master
    :target: https://travis-ci.org/rjdkmr/gmx_clusterByFeatures

.. image:: https://readthedocs.org/projects/gmx-clusterbyfeatures/badge/?version=latest
    :target: https://gmx-clusterbyfeatures.readthedocs.io/en/latest/?badge=latest
    :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 pip3 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. 


