GetContacts

Computing contact fingerprints from multiple MD simulations

The following steps will generate a contact fingerprint for a set of static structures (e.g. PDB-files solved with X-ray crystallography).

• The first step extracts atomic-level interactions.
• The second step computes residue-level frequencies and renames residues according to a residue-label file
• The third step combines the frequency files into a fingerprint heatmap.

Assume you have two simulations of different molecules represented with the following topology and trajectory files:

• top_1.pdb and trj_1.dcd
• top_2.pdb and trj_2.dcd

For each trajectory we first generate a contact list and then set of residue contact frequencies:

  get_dynamic_contacts.py --topology top_1.pdb --trajectory trj_1.dcd --itypes hb --output contacts_1.tsv
  get_dynamic_contacts.py --topology top_2.pdb --trajectory trj_2.dcd --itypes hb --output contacts_2.tsv

  get_contact_frequencies.py --input_files contacts_1.tsv --output_file resfrequencies_1.tsv
  get_contact_frequencies.py --input_files contacts_2.tsv --output_file resfrequencies_2.tsv
        

Next, the residue contact frequencies are combined a plot is written to a png file:

  get_contact_fingerprints.py --input_frequencies resfrequencies_1.tsv resfrequencies_2.tsv \
                              --column_headers Sim1 Sim2 \
                              --frequency_cutoff 0.6 \
                              --plot_output fingerprint.png
        

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