qp.protonate.parse_output.parse_log¶

qp.protonate.parse_output.parse_log(log_path, pdb_path, AA)[source]¶

Parse the Protoss log file to identify residues with clashes and their chain indices.

Parameters:

log_path (str) – Path to the Protoss log file.
pdb_path (str) – Path to the PDB file.
AA (dict) – Dictionary mapping three-letter codes to one-letter codes.

Returns:

residues_with_clashes – Set of residues with clashes in the format compatible with residues. Each tuple contains ((res_id, ‘ ‘), one_letter_code, ‘R’) and the chain index.

Return type:

set of tuples