polymerist.rdutils.bonding.identification

Tools for determining how many and which bondable ports are in an RDKit Mol

Functions

get_total_port_degree_on_atom(rdmol, atom_id[, ...])	Get the maximum combined bond degree for all ports of a particular flavor on an atom (or of all flavors, if None is provided)
max_bondable_order_between_atoms(→ int)	Return the highest possible bond order which could be created between a pair of atoms
enumerate_bondable_port_pairs(...)	Generate all possible pairs of Ports between two molecules which could be bonded together
enumerate_bondable_port_pairs_internal(...)	Generate all possible pairs of Ports within a single molecule which could be bonded together
get_bondable_port_pairs(...)	Get every pair of ports within an RDKit Mol which could be bonded and match a specified flavor pair (could be partially or fully None for less specificity)
get_first_bondable_port_pair(...)	Get the first pair of ports between atoms at given indices which are bondable, raising Exception if none exists
get_num_bondable_port_pairs() → int)	Count how many bondable port pairs exist within a Mol

Module Contents

polymerist.rdutils.bonding.identification.get_total_port_degree_on_atom(rdmol: rdkit.Chem.rdchem.Mol, atom_id: int, target_flavor: int | None = None)

Get the maximum combined bond degree for all ports of a particular flavor on an atom (or of all flavors, if None is provided)

polymerist.rdutils.bonding.identification.max_bondable_order_between_atoms(rdmol: rdkit.Chem.rdchem.Mol, atom_id_1: int, atom_id_2: int, target_flavor: int) → int

Return the highest possible bond order which could be created between a pair of atoms

polymerist.rdutils.bonding.identification.enumerate_bondable_port_pairs(ports_1: Iterable[polymerist.rdutils.bonding.portlib.Port], ports_2: Iterable[polymerist.rdutils.bonding.portlib.Port]) → Generator[tuple[polymerist.rdutils.bonding.portlib.Port, polymerist.rdutils.bonding.portlib.Port], None, None]

Generate all possible pairs of Ports between two molecules which could be bonded together

polymerist.rdutils.bonding.identification.enumerate_bondable_port_pairs_internal(ports: Iterable[polymerist.rdutils.bonding.portlib.Port]) → Generator[tuple[polymerist.rdutils.bonding.portlib.Port, polymerist.rdutils.bonding.portlib.Port], None, None]

Generate all possible pairs of Ports within a single molecule which could be bonded together

polymerist.rdutils.bonding.identification.get_bondable_port_pairs(rdmol: rdkit.Chem.rdchem.Mol, atom_id_1: int | None = None, atom_id_2: int | None = None, flavor_pair: tuple[int | None, int | None] = (None, None)) → Generator[tuple[polymerist.rdutils.bonding.portlib.Port, polymerist.rdutils.bonding.portlib.Port], None, None]

Get every pair of ports within an RDKit Mol which could be bonded and match a specified flavor pair (could be partially or fully None for less specificity) Can optionally localize search to only have port bridegehead coinciding with atoms at particular indices Pairs are returned n descending order of linker atom index to simplify atom removal if modifying later

polymerist.rdutils.bonding.identification.get_first_bondable_port_pair(rdmol: rdkit.Chem.rdchem.Mol, atom_id_1: int | None = None, atom_id_2: int | None = None, flavor_pair: tuple[int | None, int | None] = (None, None)) → tuple[polymerist.rdutils.bonding.portlib.Port, polymerist.rdutils.bonding.portlib.Port]

Get the first pair of ports between atoms at given indices which are bondable, raising Exception if none exists

polymerist.rdutils.bonding.identification.get_num_bondable_port_pairs(rdmol: rdkit.Chem.rdchem.Mol, atom_id_1: int | None = None, atom_id_2: int | None = None, flavor_pair: tuple[int | None, int | None] = (None, None)) → int

Count how many bondable port pairs exist within a Mol