Interaction analysis for molecular structures and ensembles

Performing simulation time-segmentation using TICC

The following steps will generate a contacts for a simulation, use them as input to TICC clustered time-segmentation, and finally generate a clustermap and flareplot illustrating the differences between each cluster.

Assume you have a simulation represented with a topology file, top.pdb, and trajectory file, trj.dcd. We first generate a contact list (contacts.tsv) and a residue contact frequency for each cluster: --topology top.pdb --trajectory trj.dcd --itypes hb --output contacts.tsv --input_contacts contacts.tsv \
                        --clusters 3
                        --tab_output ticc.tsv
                        --frequency_output segments

The --frequency_output argument is used as a prefix for cluster-specific residue contact frequency files:

Finally, the residue contact frequencies are combined into clustermap and flareplot comparison files: --input_frequencies segments_resfreq_cluster*.tsv \
                              --column_headers Cluster0 Cluster1 Cluster2 \
                              --plot_output fingerprint.png \
                              --flare_output compareflare.json \