.. 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.
Development Setup for conda
---------------------------
Following steps are for development setup. However, these steps can be used for installation using conda
# 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
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"description": "\n.. image:: https://travis-ci.org/rjdkmr/gmx_clusterByFeatures.svg?branch=master\n :target: https://travis-ci.org/rjdkmr/gmx_clusterByFeatures\n\n.. image:: https://readthedocs.org/projects/gmx-clusterbyfeatures/badge/?version=latest\n :target: https://gmx-clusterbyfeatures.readthedocs.io/en/latest/?badge=latest\n :alt: Documentation Status\n\ngmx_clusterByFeatures\n=====================\nIt can be used to cluster the conformations of a molecule in a molecular dynamics\ntrajectory using collection of features. The features could be any quantity as a\nfunction of time such as Projections of eigenvector from PCA or dihedral-PCA,\ndistances, angles, channel radius etc.\n\n**See details at:** `gmx_clusterByFeatures homepage <https://gmx-clusterbyfeatures.readthedocs.io>`_\n\n.. note:: It is developed for **GROMACS MD trajectory.** However, it can be used with\n any other trajectory format after converting it to GROMACS format trajectory.\n\nInstallation on Linux and MacOS\n-------------------------------\n\n.. code-block:: bash\n\n sudo pip3 install gmx-clusterByFeatures\n\nNo dependency on GROMACS. Install and use it.\n\nFor more details, visit `download and installation <https://gmx-clusterbyfeatures.readthedocs.io/en/latest/install.html>`_ section. \n\nUsage\n-----------\n\n.. list-table:: List of sub-commands available in gmx_clusterByFeatures\n :widths: 1, 4\n :header-rows: 1\n :name: commands-table\n\n * - Command\n - Function\n\n * - `cluster <https://gmx-clusterbyfeatures.readthedocs.io/en/latest/commands/cluster.html>`_\n - Main module to perform clustering\n\n * - `featuresplot <https://gmx-clusterbyfeatures.readthedocs.io/en/latest/commands/featuresplot.html>`_\n - Feature vs Feature plot to check quality of clustering\n\n * - `distmat <https://gmx-clusterbyfeatures.readthedocs.io/en/latest/commands/distmat.html>`_\n - Distance-matrix related calculations\n\n * - `matplot <https://gmx-clusterbyfeatures.readthedocs.io/en/latest/commands/matplot.html>`_\n - To visulaize/plot matrix obtained from ``distmat``\n \n * - `hole <https://gmx-clusterbyfeatures.readthedocs.io/en/latest/commands/hole.html>`_\n - To calculate cavity/channel radius using HOLE program\n \n * - `holeplot <https://gmx-clusterbyfeatures.readthedocs.io/en/latest/commands/holeplot.html>`_\n - To calculate average and plot hole output radius file\n \n * - `holefeatures <https://gmx-clusterbyfeatures.readthedocs.io/en/latest/commands/holefeatures.html>`_\n - To write radius as a features for clustering\n \n * - `holeclustersplot <https://gmx-clusterbyfeatures.readthedocs.io/en/latest/commands/holeclustersplot.html>`_\n - To plot or write radius for clusters separately\n\nFor more details, visit `usage <https://gmx-clusterbyfeatures.readthedocs.io/en/latest/usage.html>`_ section. \n\n\nDevelopment Setup for conda\n---------------------------\nFollowing steps are for development setup. However, these steps can be used for installation using conda\n\n # Clone the repository and setup development environment\n git clone --recursive https://github.com/rjdkmr/gmx_clusterByFeatures.git\n cd gmx_clusterByFeatures\n conda env create -y --prefix ./venv --file environment.yaml # Create development conda environment\n conda activate ./venv # Activate the environment\n bash -i scripts/build_dev_setup_conda.sh # all build and setup steps are in this script\n",
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