A simple python package for cluster analysis in molecular dynamics trajectories.
pip install git+https://github.com/exenGT/clusteranalysis
Create an example script main.py with the following content:
from cluster_analysis.cluster import analyze
analyze()
then run in command line prompt:
python main.py --help
to find out the available options.
To do a test, go to cluster_analysis/data/test, and run:
python test.py
The package separates a molecular dynamics image into individual images (*.cif files), each one containing a separate cluster.
Meanwhile, the package returns the information about the cluster size, distribution, etc.
If requested, the clusters' size are stored in clusters_size_hist.txt, and the clusters' radius of gyration are stored in clusters_rg_hist.txt.