openfe.setup.atom_mapping.perses_scorers.default_perses_scorer(mapping: LigandAtomMapping, use_positions: bool = False, normalize: bool = True) → float#

Score an atom mapping with the default Perses score function.

Parameters:

  • mapping (LigandAtomMapping) – is an OpenFE Ligand Mapping, that should be mapped

  • use_positions (bool, optional) – if the positions are used, perses takes the inverse eucledian distance of mapped atoms into account. else the number of mapped atoms is used for the score. default True

  • normalize (bool, optional) – if true, the scores get normalized, such that different molecule pairs can be compared for one scorer metric, default = True Warning does not work for use_positions right now!

Raises:

NotImplementedError – Normalization of the score using positions is not implemented right now.

Return type:

float