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.
- 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.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:
system (vermouth.system.System) – The system to process. Is modified in-place.
file_path (
pathlib.Path
) – path to the contact map file
- Returns:
contact as chain id, res id, chain id, res id
- Return type: