LomapAtomMapper

class openfe.setup.atom_mapping.LomapAtomMapper(*, time: int = 20, threed: bool = True, max3d: float = 1000.0, element_change: bool = True, seed: str = '', shift: bool = True)

Bases: LigandAtomMapper

Suggest atom mappings with the MCS atom mapper from Lomap.

Keyword arguments are passed directly to the MCS class from Lomap for each mapping created.

Parameters:

• time (int, optional) – timeout of MCS algorithm, passed to RDKit default 20

• threed (bool, optional) – if true, positional info is used to choose between symmetrically equivalent mappings and prune the mapping, default True

• max3d (float, optional) – maximum discrepancy in Angstroms between atoms before mapping is not allowed, default 1000.0, which effectively trims no atoms

• element_change (bool, optional) – whether to allow element changes in the mappings, default True

• seed (str, optional) – SMARTS string to use as seed for MCS searches. When used across an entire set of ligands, this can create

• shift (bool, optional) – when determining 3D overlap, if to translate the two molecules MCS to minimise RMSD to boost potential alignment.

Attributes

time
threed
max3d
element_change
seed
shift

element_change: bool

max3d: float

seed: str

shift: bool

suggest_mappings(componentA: SmallMoleculeComponent, componentB: SmallMoleculeComponent) → Iterable[LigandAtomMapping]

Suggest LigandAtomMapping options for the input molecules.

Parameters:

• componentA (SmallMoleculeComponent) – the two molecules to create a mapping for

• componentB (SmallMoleculeComponent) – the two molecules to create a mapping for

Returns:

an iterable over proposed mappings

Return type:

Iterable[LigandAtomMapping]

threed: bool

time: int