polymerist.rdutils.bonding.portlib

Specification for representing, defining, and characterizing selective intermolecular bond placeholders (“ports”)

Attributes

`PORT_SCHEMA`
`PORT_QUERY`

Raised when port-related errors as encountered

Class for encapsulating the components of a "port" bonding site (linker-bond-bridgehead)

`is_linker`(→ bool)	Indicate whether an atom is a linker (intermonomer "*" type atom)
`get_num_linkers`(→ int)	Count how many wild-type inter-molecule linker atoms are in a Mol
`get_port_ids`(→ Generator[tuple[int, int], None, None])	Get the linker and bridgehead indices of all ports found in an RDKit Mol
`get_linker_ids`(→ Generator[int, None, None])	Get indices of all atoms which are ports
`get_ports`(→ Generator[Port, None, None])	Find and generate all ports in a molecule. Can optioanlly narrow scope to port whose bridegehead is a particular atom and/or whose linker has a particular flavor
`get_num_ports`(→ int)	Counts the number of port atoms present in a Mol
`get_single_port`(→ Port)	Get the singular port of a Mol which contains only 1 port

exception polymerist.rdutils.bonding.portlib.MolPortError[source]

Bases: Exception

Raised when port-related errors as encountered

polymerist.rdutils.bonding.portlib.is_linker(rdatom: rdkit.Chem.rdchem.Atom) → bool[source]: Indicate whether an atom is a linker (intermonomer “*” type atom)

polymerist.rdutils.bonding.portlib.get_num_linkers(rdmol: rdkit.Chem.rdchem.Mol) → int[source]: Count how many wild-type inter-molecule linker atoms are in a Mol

class polymerist.rdutils.bonding.portlib.Port[source]

Class for encapsulating the components of a “port” bonding site (linker-bond-bridgehead)

bondable_flavors: ClassVar[polymerist.genutils.containers.UnorderedRegistry]

static are_bondable(port_1: Port, port_2: Port) → bool[source]: Determine if two port atoms can be combined into a new bond

matches_flavor(target_flavor: int | None) → bool[source]: Returns whether a port has a particular flavor

polymerist.rdutils.bonding.portlib.get_port_ids(rdmol: rdkit.Chem.rdchem.Mol) → Generator[tuple[int, int], None, None][source]: Get the linker and bridgehead indices of all ports found in an RDKit Mol

polymerist.rdutils.bonding.portlib.get_linker_ids(rdmol: rdkit.Chem.rdchem.Mol) → Generator[int, None, None][source]: Get indices of all atoms which are ports

polymerist.rdutils.bonding.portlib.get_ports(rdmol: rdkit.Chem.rdchem.Mol, target_atom_id: int | None = None, target_flavor: int | None = None) → Generator[Port, None, None][source]: Find and generate all ports in a molecule. Can optioanlly narrow scope to port whose bridegehead is a particular atom and/or whose linker has a particular flavor

polymerist.rdutils.bonding.portlib.get_num_ports(rdmol: rdkit.Chem.rdchem.Mol, target_atom_id: int | None = None, target_flavor: int | None = None) → int[source]: Counts the number of port atoms present in a Mol

polymerist.rdutils.bonding.portlib.get_single_port(rdmol: rdkit.Chem.rdchem.Mol) → Port[source]: Get the singular port of a Mol which contains only 1 port