Index Symbols | A | C | D | E | G | H | L | M | N | O | P | R | S | T Symbols --mapper openfe-plan-rbfe-network command line option openfe-plan-rhfe-network command line option --mol-dir openfe-plan-rbfe-network command line option openfe-plan-rhfe-network command line option --output-dir openfe-plan-rbfe-network command line option openfe-plan-rhfe-network command line option --protein openfe-plan-rbfe-network command line option --work-dir openfe-quickrun command line option -d openfe-quickrun command line option -M openfe-plan-rbfe-network command line option openfe-plan-rhfe-network command line option -o openfe-plan-rbfe-network command line option openfe-plan-rhfe-network command line option openfe-quickrun command line option -p openfe-plan-rbfe-network command line option A AlchemicalNetwork (class in openfe) atomic_number_score() (in module openfe.setup.atom_mapping.lomap_scorers) C ChemicalSystem (class in openfe) components (openfe.ChemicalSystem attribute) D default_lomap_score() (in module openfe.setup.atom_mapping.lomap_scorers) default_perses_scorer() (in module openfe.setup.atom_mapping.perses_scorers) E EasyChemicalSystemGenerator (class in openfe.setup.chemicalsystem_generator) ecr_score() (in module openfe.setup.atom_mapping.lomap_scorers) edges (openfe.AlchemicalNetwork attribute) G generate_maximal_network() (in module openfe.setup.ligand_network_planning) generate_minimal_spanning_network() (in module openfe.setup.ligand_network_planning) generate_radial_network() (in module openfe.setup.ligand_network_planning) H heterocycles_score() (in module openfe.setup.atom_mapping.lomap_scorers) hybridization_score() (in module openfe.setup.atom_mapping.lomap_scorers) L LigandAtomMapping (class in openfe) LomapAtomMapper (class in openfe.setup) M mapping (openfe.Transformation attribute) mcsr_score() (in module openfe.setup.atom_mapping.lomap_scorers) mncar_score() (in module openfe.setup.atom_mapping.lomap_scorers) N name (openfe.AlchemicalNetwork attribute) (openfe.ChemicalSystem attribute) (openfe.Transformation attribute) nodes (openfe.AlchemicalNetwork attribute) O openfe-plan-rbfe-network command line option --mapper --mol-dir --output-dir --protein -M -o -p openfe-plan-rhfe-network command line option --mapper --mol-dir --output-dir -M -o openfe-quickrun command line option --work-dir -d -o TRANSFORMATION P PersesAtomMapper (class in openfe.setup) ProteinComponent (class in openfe) protocol (openfe.Transformation attribute) R RBFEAlchemicalNetworkPlanner (class in openfe.setup) RHFEAlchemicalNetworkPlanner (class in openfe.setup) S SmallMoleculeComponent (class in openfe) SolventComponent (class in openfe) stateA (openfe.Transformation attribute) stateB (openfe.Transformation attribute) sulfonamides_score() (in module openfe.setup.atom_mapping.lomap_scorers) T tmcsr_score() (in module openfe.setup.atom_mapping.lomap_scorers) TRANSFORMATION openfe-quickrun command line option Transformation (class in openfe) transmuting_methyl_into_ring_score() (in module openfe.setup.atom_mapping.lomap_scorers) transmuting_ring_sizes_score() (in module openfe.setup.atom_mapping.lomap_scorers)