class openfe.setup.RBFEAlchemicalNetworkPlanner(name: str = 'easy_rbfe', mappers: ~typing.Iterable[~openfe.setup.atom_mapping.ligandatommapper.LigandAtomMapper] | None = None, mapping_scorer: ~typing.Callable[[~gufe.mapping.ligandatommapping.LigandAtomMapping], float] = <function default_lomap_score>, ligand_network_planner: ~typing.Callable = <function generate_minimal_spanning_network>, protocol: ~gufe.protocols.protocol.Protocol | None = None)

Plan alchemical networks for Relative Binding Free Energy calculations.

Create an instance of the class with a simulation protocol and ligand network planning scheme, then call it on a collection of ligands, protein, solvent, and co-factors to create the network.

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() )

__call__(ligands: Iterable[SmallMoleculeComponent], solvent: SolventComponent, protein: ProteinComponent, cofactors: Iterable[SmallMoleculeComponent] | None = None) → AlchemicalNetwork

plan the alchemical network for RBFE calculations with the given ligands, protein and solvent.

Parameters:

• ligands (Iterable[SmallMoleculeComponent]) – ligands that shall be used for the alchemical network.

• solvent (SolventComponent) – solvent for solvated and complex simulations

• protein (ProteinComponent) – protein for complex simulations

• cofactors (Iterable[SmallMoleculeComponent]) – any cofactors in the system, can be empty list

Returns:

RBFE network for the given ligands, protein and solvent.

Return type:

AlchemicalNetwork

property chemical_system_generator_type: Type[AbstractChemicalSystemGenerator]

property ligand_network_planner: Callable

property mappers: Iterable[LigandAtomMapper]

property mapping_scorer: Callable

property transformation_protocol: Protocol