polymerist.rdutils.reactions.fragment

For fragmenting molecules by reaction and residue information

Attributes

LOGGER
P
HEAVY_FORMER_LINKER_QUERY_ATOM
bond_adjoins_linker
IBIS

Classes

IntermonomerBondIdentificationStrategy	Abstract base for Intermonomer Bond Identification Strategies for fragmentation during in-silico polymerization
ReseparateRGroups	IBIS which cleaves any new bonds formed between atoms that were formerly the start of an R-group in the reaction template
CutMinimumCostBondsStrategy	Subtype of IBIS which chooses bonds as solutions to minimum graph cut problem

Functions

bridgehead_atom_ids(→ Generator[int, None, None])	Generates the indices of all atoms in a reaction product which were tagged
get_shortest_path_bonds(→ list[int])	Returns bond indices along shortest path between two atoms in a Mol
bond_is_newly_formed(→ bool)	Bond condition checking if a bond was newly formed in a reaction

Module Contents

polymerist.rdutils.reactions.fragment.LOGGER

polymerist.rdutils.reactions.fragment.P

polymerist.rdutils.reactions.fragment.HEAVY_FORMER_LINKER_QUERY_ATOM: rdkit.Chem.QueryAtom

polymerist.rdutils.reactions.fragment.bridgehead_atom_ids(product: rdkit.Chem.Mol) → Generator[int, None, None]

Generates the indices of all atoms in a reaction product which were tagged as R-group bridgehead (i.e. wild) atoms in the reaction template definition

polymerist.rdutils.reactions.fragment.get_shortest_path_bonds(rdmol: rdkit.Chem.Mol, start_atom_idx: int, end_atom_idx: int) → list[int]

Returns bond indices along shortest path between two atoms in a Mol

polymerist.rdutils.reactions.fragment.bond_is_newly_formed(bond: rdkit.Chem.Bond) → bool

Bond condition checking if a bond was newly formed in a reaction (i.e. present in the product(s) but not the reactant(s))

polymerist.rdutils.reactions.fragment.bond_adjoins_linker: polymerist.rdutils.selection.BondCondition

class polymerist.rdutils.reactions.fragment.IntermonomerBondIdentificationStrategy

Bases: abc.ABC

Abstract base for Intermonomer Bond Identification Strategies for fragmentation during in-silico polymerization

locate_intermonomer_bonds(product: rdkit.Chem.Mol) → Generator[int, None, None]

Generates the indices of all identified inter-monomer bonds by molecule, no more than once each

produce_fragments(product: rdkit.Chem.Mol, separate: bool = True) → rdkit.Chem.Mol | tuple[rdkit.Chem.Mol]

Apply break all bonds identified by this IBIS algorithm and return the resulting fragments

polymerist.rdutils.reactions.fragment.IBIS

class polymerist.rdutils.reactions.fragment.ReseparateRGroups

Bases: IntermonomerBondIdentificationStrategy

IBIS which cleaves any new bonds formed between atoms that were formerly the start of an R-group in the reaction template

class polymerist.rdutils.reactions.fragment.CutMinimumCostBondsStrategy(base_bond_cost: float | None = None, bond_discounts: dict[str, tuple[int, Callable[[rdkit.Chem.Mol], tuple[int, int]]]] | None = None, bond_cost_keyword: str | None = 'cost_to_cut', max_bonds_per_cut: int = 1, *args: P, **kwargs: P)

Bases: IntermonomerBondIdentificationStrategy

Subtype of IBIS which chooses bonds as solutions to minimum graph cut problem All bonds in a molecule are given some base cost to cut, then a discount is applied to some bonds by specified conditions

Cuts are then made (no more than once) on the lowest cost bond(s) separating each pair of R-groups

base_bond_cost = None

bond_discounts = None

bond_cost_keyword = 'cost_to_cut'

max_bonds_per_cut = 1