qp.protonate.get_protoss.repair_ligands

qp.protonate.get_protoss.repair_ligands(path, orig)[source]

Repair ligands that Protoss renamed to MOL.

Protoss sometimes replaces unrecognized ligand residues with a generic MOL label. This function restores the original residue names and structures by matching them back from the pre-Protoss PDB, then reassigns hydrogen atoms to the closest heavy atoms.

Parameters:

  • path (str) – Path to the Protoss output PDB file (modified in place).

  • orig (str) – Path to the original (pre-Protoss) PDB file.