RelativeAlchemicalNetworkPlanner#

class openfe.setup.alchemical_network_planner.relative_alchemical_network_planner.RelativeAlchemicalNetworkPlanner(name: str = 'easy_rfe_calculation', mappers: Iterable[LigandAtomMapper] | None = None, mapping_scorer: Callable[[LigandAtomMapping], float] = default_lomap_score, ligand_network_planner: Callable = generate_minimal_spanning_network, protocol: Protocol | None = None)#

Bases: AbstractAlchemicalNetworkPlanner, ABC

A simple strategy for executing a given protocol with mapper, mapping_scorers and networks for relative FE approaches.

Parameters:

  • name (str, optional) – name of the approach/project the rfe, by default “easy_rfe_calculation”

  • mappers (Iterable[LigandAtomMapper], optional) – mappers used to connect the ligands, by default the LomapAtomMapper with sensible default settings

  • mapping_scorer (Callable, optional) – scorer evaluating the quality of the atom mappings, by default default_lomap_score

  • ligand_network_planner (Callable, optional) – network using mapper and mapping_scorer to build up an optimal network, by default generate_minimal_spanning_network

  • protocol (Protocol, optional) – FE-protocol for each transformation (edge of ligand network) that is required in order to calculate the FE graph, by default RelativeHybridTopologyProtocol( RelativeHybridTopologyProtocol._default_settings() )

Attributes

chemical_system_generator_type

ligand_network_planner

mappers

mapping_scorer

transformation_protocol

abstract __call__(*args, **kwargs) → AlchemicalNetwork#

Call self as a function.

property chemical_system_generator_type: Type[AbstractChemicalSystemGenerator]#
property ligand_network_planner: Callable#
property mappers: Iterable[LigandAtomMapper]#
property mapping_scorer: Callable#
property transformation_protocol: Protocol#