vermouth.rcsu.contact_map module

class vermouth.rcsu.contact_map.GenerateContactMap(write_file)[source]

Bases: Processor

Processor to generate the contact rCSU contact map for a protein from an atomistic structure

run_molecule(molecule)[source]

Process system.

Parameters:

system (vermouth.system.System) – The system to process. Is modified in-place.

run_system(system)[source]
vermouth.rcsu.contact_map.atom2res(arrin, nresidues, atom_map, norm=False)[source]

take an array with atom level data and sum the entries over within the residue

vermouth.rcsu.contact_map.do_contacts(molecule, write_file)[source]

master function to calculate Go contacts

molecule: vermouth.Molecule

molecule to calculate contacts for

write_file: bool

write the file of the contacts out

vermouth.rcsu.contact_map.make_atom_map(res_serial)[source]
vermouth.rcsu.contact_map.read_go_map(system, file_path)[source]

Read a RCSU contact map from the c code as published in doi:10.5281/zenodo.3817447. The format requires all contacts to have 18 columns and the first column to be a capital R.

Parameters:
Returns:

contact as chain id, res id, chain id, res id

Return type:

list(tuple)