pyqmmm.md.cluster_frame_indexer

This script will find all frames in the main cluster and condense them.

Module Contents

Functions

get_clusters(file)	Opens the CPPTraj cnumvtime.dat file,
condense_numbering(cluster_list)
main()	Condenses the frame indices of a clustered MD run into a single string.

pyqmmm.md.cluster_frame_indexer.get_clusters(file)

Opens the CPPTraj cnumvtime.dat file, which contains every frame and its assigned cluster. Creates a list containing the indices of all frames in cluster 0, which will always be the predominant cluster.

Parameters:

file (str) – The file containing the cluster assignments for every frame.

Returns:

cluster_list – A list of all the frame indices from cluster 0.

Return type:

list

pyqmmm.md.cluster_frame_indexer.condense_numbering(cluster_list)

pyqmmm.md.cluster_frame_indexer.main()

Condenses the frame indices of a clustered MD run into a single string.

Examples

Run the following to generate the CPPTraj output first

>> parm welo5_solv.prmtop >> trajin constP_prod.mdcrd >> trajout output.mdcrd onlyframes 2,5-200,202-400