drugforge.data.backend.openeye.combine_protein_ligand

drugforge.data.backend.openeye.combine_protein_ligand(prot: openeye.oechem.OEMol, lig: openeye.oechem.OEMol, lig_name: str = 'LIG', lig_chain: str | None = '', resid: int | None = None, start_atom_id: int | None = None) → openeye.oechem.OEMol[source]

Combine a protein OEMol and ligand OEMol into one, handling residue/atom numbering, and HetAtom status.

Parameters:

  • prot (oechem.OEMol) – OEMol with the protein atoms. This should have perceived resiudes

  • lig (oechem.OEMol) – OEMol with the ligand atoms

  • lig_name (str, default=”LIG”) – Residue name to give to the ligand atoms

  • resid (int, optional) – Which residue number to assign to the ligand. If not given, the largest existing residue number in prot will be found, and the ligand will be assigned the next number

  • start_atom_id (int, optional) – Which atom number to assign to the first atom in the ligand. If not given, the next available atom number will be calculated and assigned

Returns:

Combined molecule, with the appropriate biopolymer field set for the lig atoms

Return type:

oechem.OEMol