schrodinger.livedesign.biologics.rdmol_hierarchy module

schrodinger.livedesign.biologics.rdmol_hierarchy.add_substance_group(mol: Mol, atoms: list[rdkit.Chem.rdchem.Atom] = None)

Add a substance group to the RDMol. The RDMol is a mol consisting of atoms. The substance group groups these atoms within the mol creating relationships within the mol that denote the heirarchy.

Parameters:

• mol – RDMol object

• atoms – A list of atoms to include in the substance group. If not supplied, the substance group will contain all the atoms in the mol. If supplied, these atoms must be part of the mol.

schrodinger.livedesign.biologics.rdmol_hierarchy.get_chain_atoms(mol: Mol, chain_names: list[str]) → list[rdkit.Chem.rdchem.Atom]

Get all atoms in the RDMol that belong to a specific chain.

Parameters:

• mol – RDMol object

• chain_names – Chain IDs to filter atoms by

Returns:

List of atoms in the specified chain