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 LigandAtomMapping 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