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Features Based Conformational Clustering of Molecular Dynamics trajectories.

Project description

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

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

sudo pip3 install gmx-clusterByFeatures

No dependency on GROMACS. Install and use it.

For more details, visit download and installation section.

Usage

List of sub-commands available in gmx_clusterByFeatures
Command Function
cluster Main module to perform clustering
featuresplot Feature vs Feature plot to check quality of clustering
distmat Distance-matrix related calculations
matplot To visulaize/plot matrix obtained from distmat
hole To calculate cavity/channel radius using HOLE program
holeplot To calculate average and plot hole output radius file
holefeatures To write radius as a features for clustering
holeclustersplot To plot or write radius for clusters separately

For more details, visit usage section.

Project details


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