Features Based Conformational Clustering of Molecular Dynamics trajectories.
Project description
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
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
Command |
Function |
---|---|
Main module to perform clustering |
|
Feature vs Feature plot to check quality of clustering |
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Distance-matrix related calculations |
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To visulaize/plot matrix obtained from distmat |
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To calculate cavity/channel radius using HOLE program |
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To calculate average and plot hole output radius file |
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To write radius as a features for clustering |
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To plot or write radius for clusters separately |
For more details, visit usage section.
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