polymerist.rdutils.bonding.substitution

Tools for replacing Ports and functional groups

Functions

splice_atoms() → None)	Completely combine a single pair of ports on two target atoms to create a bond of desired order
saturate_ports(, flavor_to_saturate)	Takes an RDKit Mol and another "cap" molecule (by default just hydrogen) and caps all valid ports (with the specified flavor) on the target Mol with the cap group
hydrogenate_rdmol_ports(→ None)	Replace all port atoms with hydrogens

Module Contents

polymerist.rdutils.bonding.substitution.splice_atoms(rwmol: rdkit.Chem.RWMol, atom_id_1: int | None = None, atom_id_2: int | None = None, flavor_pair: tuple[int | None, int | None] = (None, None)) → None

Completely combine a single pair of ports on two target atoms to create a bond of desired order

polymerist.rdutils.bonding.substitution.saturate_ports(rdmol: rdkit.Chem.Mol, cap: rdkit.Chem.Mol = Chem.MolFromSmiles('[*]-[H]'), flavor_to_saturate: int = 0) → None

Takes an RDKit Mol and another “cap” molecule (by default just hydrogen) and caps all valid ports (with the specified flavor) on the target Mol with the cap group

polymerist.rdutils.bonding.substitution.hydrogenate_rdmol_ports(rdmol: rdkit.Chem.Mol) → None

Replace all port atoms with hydrogens