Reference# This contains details of the Python API as well as a reference to the command line interface. OpenFE API Reference Alchemical Data Objects Chemical Systems SmallMoleculeComponent ProteinComponent SolventComponent ChemicalSystem ChemicalSystem.components ChemicalSystem.name Atom Mappings LigandAtomMapper LigandAtomMapper.suggest_mappings() LigandAtomMapping LigandAtomMapping.componentA_to_componentB LigandAtomMapping.componentA_unique LigandAtomMapping.componentB_to_componentA LigandAtomMapping.componentB_unique LigandAtomMapping.draw_to_file() LigandAtomMapping.get_distances() LigandAtomMapping.with_annotations() Alchemical Simulations Transformation Transformation.stateA Transformation.stateB Transformation.protocol Transformation.mapping Transformation.name AlchemicalNetwork AlchemicalNetwork.edges AlchemicalNetwork.nodes AlchemicalNetwork.name Ligand Network Tools Atom Mappers LomapAtomMapper PersesAtomMapper Scorers LOMAP Scorers default_lomap_score() ecr_score() mcsr_score() mncar_score() tmcsr_score() atomic_number_score() hybridization_score() sulfonamides_score() heterocycles_score() transmuting_methyl_into_ring_score() transmuting_ring_sizes_score() PersesScorers default_perses_scorer() Network Planners generate_radial_network() generate_maximal_network() generate_minimal_spanning_network() Alchemical Network Planning Alchemical Network Planners RBFEAlchemicalNetworkPlanner RHFEAlchemicalNetworkPlanner Chemical System Generators EasyChemicalSystemGenerator CLI Reference quickrun command openfe quickrun plan-rhfe-network command openfe plan-rhfe-network plan-rbfe-network command openfe plan-rbfe-network