gmx-clusterByFeatures 0.1.29

Features Based Conformational Clustering of Molecular Dynamics trajectories.

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 python3 -m pip 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.

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