class openfe.setup.atom_mapping.PersesAtomMapper(allow_ring_breaking: bool = True, preserve_chirality: bool = True, use_positions: bool = True, coordinate_tolerance: float = Quantity(value=0.25, unit=angstrom))

Suggest atom mappings with the Perses atom mapper.

Parameters:

• allow_ring_breaking (bool, optional) – this option checks if on only full cycles of the molecules shall be mapped, default: False

• preserve_chirality (bool, optional) – if mappings must strictly preserve chirality, default: True

• use_positions (bool, optional) – this option defines, if the

• coordinate_tolerance (float, optional) – tolerance on how close coordinates need to be, such they can be mapped, default: 0.25*unit.angstrom

allow_ring_breaking: bool

preserve_chirality: 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]

use_positions: bool