Index Symbols | _ | A | B | C | D | E | F | G | H | I | L | M | N | O | P | R | S | T | U | V | W Symbols --allow-partial openfe-gather command line option --cofactors openfe-plan-rbfe-network command line option --molecules openfe-charge-molecules command line option openfe-plan-rbfe-network command line option openfe-plan-rhfe-network command line option --n-cores openfe-charge-molecules command line option openfe-plan-rbfe-network command line option openfe-plan-rhfe-network command line option --n-protocol-repeats openfe-plan-rbfe-network command line option openfe-plan-rhfe-network command line option --output openfe-charge-molecules command line option --output-dir openfe-plan-rbfe-network command line option openfe-plan-rhfe-network command line option --overwrite-charges openfe-charge-molecules command line option openfe-plan-rbfe-network command line option openfe-plan-rhfe-network command line option --protein openfe-plan-rbfe-network command line option --report openfe-gather command line option --settings openfe-charge-molecules command line option openfe-plan-rbfe-network command line option openfe-plan-rhfe-network command line option --tsv openfe-gather command line option --work-dir openfe-quickrun command line option -C openfe-plan-rbfe-network command line option -d openfe-quickrun command line option -M openfe-charge-molecules command line option openfe-plan-rbfe-network command line option openfe-plan-rhfe-network command line option -n openfe-charge-molecules command line option openfe-plan-rbfe-network command line option openfe-plan-rhfe-network command line option -o openfe-charge-molecules command line option openfe-gather command line option 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 -s openfe-charge-molecules command line option openfe-plan-rbfe-network command line option openfe-plan-rhfe-network command line option _ __call__() (openfe.setup.chemicalsystem_generator.EasyChemicalSystemGenerator method) (openfe.setup.RBFEAlchemicalNetworkPlanner method) (openfe.setup.RHFEAlchemicalNetworkPlanner method) A AbsoluteBindingComplexUnit (class in openfe.protocols.openmm_afe.equil_binding_afe_method) AbsoluteBindingProtocol (class in openfe.protocols.openmm_afe.equil_binding_afe_method) AbsoluteBindingProtocolResult (class in openfe.protocols.openmm_afe.equil_binding_afe_method) AbsoluteBindingSolventUnit (class in openfe.protocols.openmm_afe.equil_binding_afe_method) AbsoluteSolvationProtocol (class in openfe.protocols.openmm_afe.equil_solvation_afe_method) AbsoluteSolvationProtocolResult (class in openfe.protocols.openmm_afe.equil_solvation_afe_method) AbsoluteSolvationSolventUnit (class in openfe.protocols.openmm_afe.equil_solvation_afe_method) AbsoluteSolvationVacuumUnit (class in openfe.protocols.openmm_afe.equil_solvation_afe_method) alchemical_settings (openfe.protocols.openmm_afe.equil_afe_settings.AbsoluteBindingSettings attribute) (openfe.protocols.openmm_afe.equil_afe_settings.AbsoluteSolvationSettings attribute) (openfe.protocols.openmm_rfe.equil_rfe_settings.RelativeHybridTopologyProtocolSettings attribute) (openfe.protocols.openmm_septop.equil_septop_settings.SepTopSettings attribute) AlchemicalNetwork (class in openfe) allow_ring_breaking (openfe.setup.atom_mapping.PersesAtomMapper attribute) annotations (openfe.setup.atom_mapping.LigandAtomMapping property) atomic_number_score() (in module openfe.setup.atom_mapping.lomap_scorers) B barostat_frequency (openfe.protocols.openmm_utils.omm_settings.IntegratorSettings attribute) box_shape (openfe.protocols.openmm_utils.omm_settings.OpenMMSolvationSettings attribute) box_size (openfe.protocols.openmm_utils.omm_settings.OpenMMSolvationSettings attribute) box_vectors (openfe.protocols.openmm_utils.omm_settings.OpenMMSolvationSettings attribute) C check_assign_velocities_with_virtual_site() (openfe.protocols.openmm_septop.equil_septop_method.SepTopComplexSetupUnit static method) (openfe.protocols.openmm_septop.equil_septop_method.SepTopSolventSetupUnit static method) checkpoint_interval (openfe.protocols.openmm_septop.equil_septop_settings.SepTopEquilOutputSettings attribute) (openfe.protocols.openmm_utils.omm_settings.MDOutputSettings attribute) (openfe.protocols.openmm_utils.omm_settings.MultiStateOutputSettings attribute) checkpoint_storage_filename (openfe.protocols.openmm_septop.equil_septop_settings.SepTopEquilOutputSettings attribute) (openfe.protocols.openmm_utils.omm_settings.MDOutputSettings attribute) (openfe.protocols.openmm_utils.omm_settings.MultiStateOutputSettings attribute) chemical_system_generator_type (openfe.setup.RBFEAlchemicalNetworkPlanner property) (openfe.setup.RHFEAlchemicalNetworkPlanner property) ChemicalSystem (class in openfe) complex_equil_output_settings (openfe.protocols.openmm_afe.equil_afe_settings.AbsoluteBindingSettings attribute) (openfe.protocols.openmm_septop.equil_septop_settings.SepTopSettings attribute) complex_equil_simulation_settings (openfe.protocols.openmm_afe.equil_afe_settings.AbsoluteBindingSettings attribute) (openfe.protocols.openmm_septop.equil_septop_settings.SepTopSettings attribute) complex_lambda_settings (openfe.protocols.openmm_afe.equil_afe_settings.AbsoluteBindingSettings attribute) (openfe.protocols.openmm_septop.equil_septop_settings.SepTopSettings attribute) complex_output_settings (openfe.protocols.openmm_afe.equil_afe_settings.AbsoluteBindingSettings attribute) (openfe.protocols.openmm_septop.equil_septop_settings.SepTopSettings attribute) complex_restraint_settings (openfe.protocols.openmm_septop.equil_septop_settings.SepTopSettings attribute) complex_simulation_settings (openfe.protocols.openmm_afe.equil_afe_settings.AbsoluteBindingSettings attribute) (openfe.protocols.openmm_septop.equil_septop_settings.SepTopSettings attribute) complex_solvation_settings (openfe.protocols.openmm_afe.equil_afe_settings.AbsoluteBindingSettings attribute) (openfe.protocols.openmm_septop.equil_septop_settings.SepTopSettings attribute) component_diff() (openfe.ChemicalSystem method) componentA (openfe.setup.atom_mapping.LigandAtomMapping property) componentA_to_componentB (openfe.setup.atom_mapping.LigandAtomMapping property) componentA_unique (openfe.setup.atom_mapping.LigandAtomMapping property) componentB (openfe.setup.atom_mapping.LigandAtomMapping property) componentB_to_componentA (openfe.setup.atom_mapping.LigandAtomMapping property) componentB_unique (openfe.setup.atom_mapping.LigandAtomMapping property) components (openfe.ChemicalSystem property) compute_mean_estimate() (openfe.protocols.openmm_rfe.equil_rfe_methods.RelativeHybridTopologyProtocolResult static method) compute_platform (openfe.protocols.openmm_utils.omm_settings.OpenMMEngineSettings attribute) compute_uncertainty() (openfe.protocols.openmm_rfe.equil_rfe_methods.RelativeHybridTopologyProtocolResult static method) connected_subgraphs() (openfe.AlchemicalNetwork method) constraint_tolerance (openfe.protocols.openmm_utils.omm_settings.IntegratorSettings attribute) constraints (openfe.protocols.openmm_utils.omm_settings.OpenMMSystemGeneratorFFSettings attribute) contains() (openfe.ChemicalSystem method) coordinate_tolerance (openfe.setup.atom_mapping.PersesAtomMapper attribute) copy_with_replacements() (openfe.SmallMoleculeComponent method) create() (openfe.Protocol method) (openfe.protocols.openmm_afe.equil_binding_afe_method.AbsoluteBindingProtocol method) (openfe.protocols.openmm_afe.equil_solvation_afe_method.AbsoluteSolvationProtocol method) (openfe.protocols.openmm_md.PlainMDProtocol method) (openfe.protocols.openmm_rfe.equil_rfe_methods.RelativeHybridTopologyProtocol method) (openfe.protocols.openmm_septop.equil_septop_method.SepTopProtocol method) (openfe.Transformation method) D data (openfe.ProtocolResult property) (openfe.protocols.openmm_afe.equil_binding_afe_method.AbsoluteBindingProtocolResult property) (openfe.protocols.openmm_afe.equil_solvation_afe_method.AbsoluteSolvationProtocolResult property) (openfe.protocols.openmm_md.PlainMDProtocolResult property) (openfe.protocols.openmm_rfe.equil_rfe_methods.RelativeHybridTopologyProtocolResult property) (openfe.protocols.openmm_septop.equil_septop_method.SepTopProtocolResult property) default_lomap_score() (in module openfe.setup.atom_mapping.lomap_scorers) default_perses_scorer() (in module openfe.setup.atom_mapping.perses_scorers) default_settings() (openfe.Protocol class method) (openfe.protocols.openmm_afe.equil_binding_afe_method.AbsoluteBindingProtocol class method) (openfe.protocols.openmm_afe.equil_solvation_afe_method.AbsoluteSolvationProtocol class method) (openfe.protocols.openmm_md.PlainMDProtocol class method) (openfe.protocols.openmm_rfe.equil_rfe_methods.RelativeHybridTopologyProtocol class method) (openfe.protocols.openmm_septop.equil_septop_method.SepTopProtocol class method) dependencies (openfe.protocols.openmm_afe.equil_binding_afe_method.AbsoluteBindingComplexUnit property) (openfe.protocols.openmm_afe.equil_binding_afe_method.AbsoluteBindingSolventUnit property) (openfe.protocols.openmm_afe.equil_solvation_afe_method.AbsoluteSolvationSolventUnit property) (openfe.protocols.openmm_afe.equil_solvation_afe_method.AbsoluteSolvationVacuumUnit property) (openfe.protocols.openmm_md.PlainMDProtocolUnit property) (openfe.protocols.openmm_rfe.equil_rfe_methods.RelativeHybridTopologyProtocolUnit property) (openfe.protocols.openmm_septop.equil_septop_method.SepTopComplexRunUnit property) (openfe.protocols.openmm_septop.equil_septop_method.SepTopComplexSetupUnit property) (openfe.protocols.openmm_septop.equil_septop_method.SepTopSolventRunUnit property) (openfe.protocols.openmm_septop.equil_septop_method.SepTopSolventSetupUnit property) (openfe.ProtocolUnit property) (openfe.ProtocolUnitFailure property) (openfe.ProtocolUnitResult property) draw_to_file() (openfe.setup.atom_mapping.LigandAtomMapping method) dump() (openfe.Transformation method) E early_termination_target_error (openfe.protocols.openmm_utils.omm_settings.MultiStateSimulationSettings attribute) EasyChemicalSystemGenerator (class in openfe.setup.chemicalsystem_generator) ecr_score() (in module openfe.setup.atom_mapping.lomap_scorers) edges (openfe.AlchemicalNetwork property) (openfe.setup.LigandNetwork property) element_change (openfe.setup.atom_mapping.LomapAtomMapper attribute) end_time (openfe.ProtocolUnitFailure property) (openfe.ProtocolUnitResult property) endstate_dispersion_correction (openfe.protocols.openmm_rfe.equil_rfe_settings.AlchemicalSettings attribute) engine_settings (openfe.protocols.openmm_afe.equil_afe_settings.AbsoluteBindingSettings attribute) (openfe.protocols.openmm_md.plain_md_settings.PlainMDProtocolSettings attribute) (openfe.protocols.openmm_rfe.equil_rfe_settings.RelativeHybridTopologyProtocolSettings attribute) (openfe.protocols.openmm_septop.equil_septop_settings.SepTopSettings attribute) enlarge_graph() (openfe.setup.LigandNetwork method) equil_npt_structure (openfe.protocols.openmm_septop.equil_septop_settings.SepTopEquilOutputSettings attribute) (openfe.protocols.openmm_utils.omm_settings.MDOutputSettings attribute) equil_nvt_structure (openfe.protocols.openmm_septop.equil_septop_settings.SepTopEquilOutputSettings attribute) (openfe.protocols.openmm_utils.omm_settings.MDOutputSettings attribute) equilibration_iterations() (openfe.protocols.openmm_afe.equil_binding_afe_method.AbsoluteBindingProtocolResult method) (openfe.protocols.openmm_afe.equil_solvation_afe_method.AbsoluteSolvationProtocolResult method) (openfe.protocols.openmm_rfe.equil_rfe_methods.RelativeHybridTopologyProtocolResult method) (openfe.protocols.openmm_septop.equil_septop_method.SepTopProtocolResult method) equilibration_length (openfe.protocols.openmm_utils.omm_settings.MDSimulationSettings attribute) (openfe.protocols.openmm_utils.omm_settings.MultiStateSimulationSettings attribute) equilibration_length_nvt (openfe.protocols.openmm_utils.omm_settings.MDSimulationSettings attribute) exception (openfe.ProtocolUnitFailure property) execute() (openfe.protocols.openmm_afe.equil_binding_afe_method.AbsoluteBindingComplexUnit method) (openfe.protocols.openmm_afe.equil_binding_afe_method.AbsoluteBindingSolventUnit method) (openfe.protocols.openmm_afe.equil_solvation_afe_method.AbsoluteSolvationSolventUnit method) (openfe.protocols.openmm_afe.equil_solvation_afe_method.AbsoluteSolvationVacuumUnit method) (openfe.protocols.openmm_md.PlainMDProtocolUnit method) (openfe.protocols.openmm_rfe.equil_rfe_methods.RelativeHybridTopologyProtocolUnit method) (openfe.protocols.openmm_septop.equil_septop_method.SepTopComplexRunUnit method) (openfe.protocols.openmm_septop.equil_septop_method.SepTopComplexSetupUnit method) (openfe.protocols.openmm_septop.equil_septop_method.SepTopSolventRunUnit method) (openfe.protocols.openmm_septop.equil_septop_method.SepTopSolventSetupUnit method) (openfe.ProtocolUnit method) execute_DAG() (in module openfe) explicit_charge_correction (openfe.protocols.openmm_rfe.equil_rfe_settings.AlchemicalSettings attribute) explicit_charge_correction_cutoff (openfe.protocols.openmm_rfe.equil_rfe_settings.AlchemicalSettings attribute) F forcefield_cache (openfe.protocols.openmm_septop.equil_septop_settings.SepTopEquilOutputSettings attribute) (openfe.protocols.openmm_utils.omm_settings.MDOutputSettings attribute) (openfe.protocols.openmm_utils.omm_settings.MultiStateOutputSettings attribute) forcefield_settings (openfe.protocols.openmm_afe.equil_afe_settings.AbsoluteBindingSettings attribute) (openfe.protocols.openmm_md.plain_md_settings.PlainMDProtocolSettings attribute) (openfe.protocols.openmm_rfe.equil_rfe_settings.RelativeHybridTopologyProtocolSettings attribute) (openfe.protocols.openmm_septop.equil_septop_settings.SepTopSettings attribute) forcefields (openfe.protocols.openmm_utils.omm_settings.OpenMMSystemGeneratorFFSettings attribute) from_graphml() (openfe.AlchemicalNetwork class method) (openfe.setup.LigandNetwork class method) from_openff() (openfe.SmallMoleculeComponent class method) from_pdb_file() (openfe.ProteinComponent class method) from_pdbx_file() (openfe.ProteinComponent class method) from_rdkit() (openfe.ProteinComponent class method) (openfe.SmallMoleculeComponent class method) from_sdf_file() (openfe.SmallMoleculeComponent class method) from_sdf_string() (openfe.SmallMoleculeComponent class method) G gather() (openfe.Protocol method) (openfe.protocols.openmm_afe.equil_binding_afe_method.AbsoluteBindingProtocol method) (openfe.protocols.openmm_afe.equil_solvation_afe_method.AbsoluteSolvationProtocol method) (openfe.protocols.openmm_md.PlainMDProtocol method) (openfe.protocols.openmm_rfe.equil_rfe_methods.RelativeHybridTopologyProtocol method) (openfe.protocols.openmm_septop.equil_septop_method.SepTopProtocol method) (openfe.Transformation method) generate_lomap_network() (in module openfe.setup.ligand_network_planning) generate_maximal_network() (in module openfe.setup.ligand_network_planning) generate_minimal_redundant_network() (in module openfe.setup.ligand_network_planning) generate_minimal_spanning_network() (in module openfe.setup.ligand_network_planning) generate_network_from_indices() (in module openfe.setup.ligand_network_planning) generate_network_from_names() (in module openfe.setup.ligand_network_planning) generate_radial_network() (in module openfe.setup.ligand_network_planning) get_alchemical_charge_difference() (openfe.setup.atom_mapping.LigandAtomMapping method) get_components_of_type() (openfe.ChemicalSystem method) get_distances() (openfe.setup.atom_mapping.LigandAtomMapping method) get_estimate() (openfe.ProtocolResult method) (openfe.protocols.openmm_afe.equil_binding_afe_method.AbsoluteBindingProtocolResult method) (openfe.protocols.openmm_afe.equil_solvation_afe_method.AbsoluteSolvationProtocolResult method) (openfe.protocols.openmm_md.PlainMDProtocolResult method) (openfe.protocols.openmm_rfe.equil_rfe_methods.RelativeHybridTopologyProtocolResult method) (openfe.protocols.openmm_septop.equil_septop_method.SepTopProtocolResult method) get_forward_and_reverse_energy_analysis() (openfe.protocols.openmm_afe.equil_binding_afe_method.AbsoluteBindingProtocolResult method) (openfe.protocols.openmm_afe.equil_solvation_afe_method.AbsoluteSolvationProtocolResult method) (openfe.protocols.openmm_rfe.equil_rfe_methods.RelativeHybridTopologyProtocolResult method) (openfe.protocols.openmm_septop.equil_septop_method.SepTopProtocolResult method) get_individual_estimates() (openfe.protocols.openmm_afe.equil_binding_afe_method.AbsoluteBindingProtocolResult method) (openfe.protocols.openmm_afe.equil_solvation_afe_method.AbsoluteSolvationProtocolResult method) (openfe.protocols.openmm_rfe.equil_rfe_methods.RelativeHybridTopologyProtocolResult method) (openfe.protocols.openmm_septop.equil_septop_method.SepTopProtocolResult method) get_overlap_matrices() (openfe.protocols.openmm_afe.equil_binding_afe_method.AbsoluteBindingProtocolResult method) (openfe.protocols.openmm_afe.equil_solvation_afe_method.AbsoluteSolvationProtocolResult method) (openfe.protocols.openmm_rfe.equil_rfe_methods.RelativeHybridTopologyProtocolResult method) (openfe.protocols.openmm_septop.equil_septop_method.SepTopProtocolResult method) get_pdb_filename() (openfe.protocols.openmm_md.PlainMDProtocolResult method) get_replica_states() (openfe.protocols.openmm_afe.equil_binding_afe_method.AbsoluteBindingProtocolResult method) (openfe.protocols.openmm_afe.equil_solvation_afe_method.AbsoluteSolvationProtocolResult method) (openfe.protocols.openmm_rfe.equil_rfe_methods.RelativeHybridTopologyProtocolResult method) (openfe.protocols.openmm_septop.equil_septop_method.SepTopProtocolResult method) get_replica_transition_statistics() (openfe.protocols.openmm_afe.equil_binding_afe_method.AbsoluteBindingProtocolResult method) (openfe.protocols.openmm_afe.equil_solvation_afe_method.AbsoluteSolvationProtocolResult method) (openfe.protocols.openmm_rfe.equil_rfe_methods.RelativeHybridTopologyProtocolResult method) (openfe.protocols.openmm_septop.equil_septop_method.SepTopProtocolResult method) get_smc_comps() (openfe.protocols.openmm_septop.equil_septop_method.SepTopComplexSetupUnit static method) (openfe.protocols.openmm_septop.equil_septop_method.SepTopSolventSetupUnit static method) get_system() (openfe.protocols.openmm_septop.equil_septop_method.SepTopComplexSetupUnit method) (openfe.protocols.openmm_septop.equil_septop_method.SepTopSolventSetupUnit method) get_system_AB() (openfe.protocols.openmm_septop.equil_septop_method.SepTopComplexSetupUnit method) get_traj_filename() (openfe.protocols.openmm_md.PlainMDProtocolResult method) get_uncertainty() (openfe.ProtocolResult method) (openfe.protocols.openmm_afe.equil_binding_afe_method.AbsoluteBindingProtocolResult method) (openfe.protocols.openmm_afe.equil_solvation_afe_method.AbsoluteSolvationProtocolResult method) (openfe.protocols.openmm_md.PlainMDProtocolResult method) (openfe.protocols.openmm_rfe.equil_rfe_methods.RelativeHybridTopologyProtocolResult method) (openfe.protocols.openmm_septop.equil_septop_method.SepTopProtocolResult method) gpu_device_index (openfe.protocols.openmm_utils.omm_settings.OpenMMEngineSettings attribute) graph (openfe.AlchemicalNetwork property) (openfe.setup.LigandNetwork property) H heterocycles_score() (in module openfe.setup.atom_mapping.lomap_scorers) hybridization_score() (in module openfe.setup.atom_mapping.lomap_scorers) hydrogen_mass (openfe.protocols.openmm_utils.omm_settings.OpenMMSystemGeneratorFFSettings attribute) I inputs (openfe.protocols.openmm_afe.equil_binding_afe_method.AbsoluteBindingComplexUnit property) (openfe.protocols.openmm_afe.equil_binding_afe_method.AbsoluteBindingSolventUnit property) (openfe.protocols.openmm_afe.equil_solvation_afe_method.AbsoluteSolvationSolventUnit property) (openfe.protocols.openmm_afe.equil_solvation_afe_method.AbsoluteSolvationVacuumUnit property) (openfe.protocols.openmm_md.PlainMDProtocolUnit property) (openfe.protocols.openmm_rfe.equil_rfe_methods.RelativeHybridTopologyProtocolUnit property) (openfe.protocols.openmm_septop.equil_septop_method.SepTopComplexRunUnit property) (openfe.protocols.openmm_septop.equil_septop_method.SepTopComplexSetupUnit property) (openfe.protocols.openmm_septop.equil_septop_method.SepTopSolventRunUnit property) (openfe.protocols.openmm_septop.equil_septop_method.SepTopSolventSetupUnit property) (openfe.ProtocolUnit property) (openfe.ProtocolUnitFailure property) (openfe.ProtocolUnitResult property) integrator_settings (openfe.protocols.openmm_afe.equil_afe_settings.AbsoluteBindingSettings attribute) (openfe.protocols.openmm_afe.equil_afe_settings.AbsoluteSolvationSettings attribute) (openfe.protocols.openmm_md.plain_md_settings.PlainMDProtocolSettings attribute) (openfe.protocols.openmm_rfe.equil_rfe_settings.RelativeHybridTopologyProtocolSettings attribute) (openfe.protocols.openmm_septop.equil_septop_settings.SepTopSettings attribute) ion_concentration (openfe.SolventComponent property) is_connected() (openfe.setup.LigandNetwork method) L lambda_elec (openfe.protocols.openmm_afe.equil_afe_settings.LambdaSettings attribute) lambda_elec_A (openfe.protocols.openmm_septop.equil_septop_settings.LambdaSettings attribute) lambda_elec_B (openfe.protocols.openmm_septop.equil_septop_settings.LambdaSettings attribute) lambda_functions (openfe.protocols.openmm_rfe.equil_rfe_settings.LambdaSettings attribute) lambda_restraints (openfe.protocols.openmm_afe.equil_afe_settings.LambdaSettings attribute) lambda_restraints_A (openfe.protocols.openmm_septop.equil_septop_settings.LambdaSettings attribute) lambda_restraints_B (openfe.protocols.openmm_septop.equil_septop_settings.LambdaSettings attribute) lambda_settings (openfe.protocols.openmm_afe.equil_afe_settings.AbsoluteSolvationSettings attribute) (openfe.protocols.openmm_rfe.equil_rfe_settings.RelativeHybridTopologyProtocolSettings attribute) lambda_vdw (openfe.protocols.openmm_afe.equil_afe_settings.LambdaSettings attribute) lambda_vdw_A (openfe.protocols.openmm_septop.equil_septop_settings.LambdaSettings attribute) lambda_vdw_B (openfe.protocols.openmm_septop.equil_septop_settings.LambdaSettings attribute) lambda_windows (openfe.protocols.openmm_rfe.equil_rfe_settings.LambdaSettings attribute) langevin_collision_rate (openfe.protocols.openmm_utils.omm_settings.IntegratorSettings attribute) ligand_network_planner (openfe.setup.RBFEAlchemicalNetworkPlanner property) (openfe.setup.RHFEAlchemicalNetworkPlanner property) LigandAtomMapper (class in openfe.setup.atom_mapping) LigandAtomMapping (class in openfe.setup.atom_mapping) LigandNetwork (class in openfe.setup) load() (openfe.Transformation class method) load_fepplus_network() (in module openfe.setup.ligand_network_planning) load_orion_network() (in module openfe.setup.ligand_network_planning) log_output (openfe.protocols.openmm_septop.equil_septop_settings.SepTopEquilOutputSettings attribute) (openfe.protocols.openmm_utils.omm_settings.MDOutputSettings attribute) LomapAtomMapper (class in openfe.setup.atom_mapping) M mappers (openfe.setup.RBFEAlchemicalNetworkPlanner property) (openfe.setup.RHFEAlchemicalNetworkPlanner property) mapping (openfe.Transformation property) mapping_scorer (openfe.setup.RBFEAlchemicalNetworkPlanner property) (openfe.setup.RHFEAlchemicalNetworkPlanner property) max3d (openfe.setup.atom_mapping.LomapAtomMapper attribute) mcsr_score() (in module openfe.setup.atom_mapping.lomap_scorers) minimization_steps (openfe.protocols.openmm_utils.omm_settings.MDSimulationSettings attribute) (openfe.protocols.openmm_utils.omm_settings.MultiStateSimulationSettings attribute) minimized_structure (openfe.protocols.openmm_septop.equil_septop_settings.SepTopEquilOutputSettings attribute) (openfe.protocols.openmm_utils.omm_settings.MDOutputSettings attribute) mncar_score() (in module openfe.setup.atom_mapping.lomap_scorers) module openfe openfe.protocols.openmm_afe.equil_afe_settings openfe.protocols.openmm_afe.equil_binding_afe_method openfe.protocols.openmm_afe.equil_solvation_afe_method openfe.protocols.openmm_md openfe.protocols.openmm_md.plain_md_settings openfe.protocols.openmm_rfe.equil_rfe_methods openfe.protocols.openmm_septop.equil_septop_method openfe.protocols.openmm_septop.equil_septop_settings openfe.protocols.openmm_utils.omm_settings openfe.setup.atom_mapping openfe.setup.atom_mapping.lomap_scorers openfe.setup.atom_mapping.perses_scorers openfe.setup.chemicalsystem_generator openfe.setup.ligand_network_planning N n_protocol_dag_results (openfe.ProtocolResult property) (openfe.protocols.openmm_afe.equil_binding_afe_method.AbsoluteBindingProtocolResult property) (openfe.protocols.openmm_afe.equil_solvation_afe_method.AbsoluteSolvationProtocolResult property) (openfe.protocols.openmm_md.PlainMDProtocolResult property) (openfe.protocols.openmm_rfe.equil_rfe_methods.RelativeHybridTopologyProtocolResult property) (openfe.protocols.openmm_septop.equil_septop_method.SepTopProtocolResult property) n_replicas (openfe.protocols.openmm_utils.omm_settings.MultiStateSimulationSettings attribute) n_restart_attempts (openfe.protocols.openmm_utils.omm_settings.IntegratorSettings attribute) nagl_model (openfe.protocols.openmm_utils.omm_settings.OpenFFPartialChargeSettings attribute) name (openfe.AlchemicalNetwork property) (openfe.ChemicalSystem property) (openfe.ProteinComponent property) (openfe.protocols.openmm_afe.equil_binding_afe_method.AbsoluteBindingComplexUnit property) (openfe.protocols.openmm_afe.equil_binding_afe_method.AbsoluteBindingSolventUnit property) (openfe.protocols.openmm_afe.equil_solvation_afe_method.AbsoluteSolvationSolventUnit property) (openfe.protocols.openmm_afe.equil_solvation_afe_method.AbsoluteSolvationVacuumUnit property) (openfe.protocols.openmm_md.PlainMDProtocolUnit property) (openfe.protocols.openmm_rfe.equil_rfe_methods.RelativeHybridTopologyProtocolUnit property) (openfe.protocols.openmm_septop.equil_septop_method.SepTopComplexRunUnit property) (openfe.protocols.openmm_septop.equil_septop_method.SepTopComplexSetupUnit property) (openfe.protocols.openmm_septop.equil_septop_method.SepTopSolventRunUnit property) (openfe.protocols.openmm_septop.equil_septop_method.SepTopSolventSetupUnit property) (openfe.ProtocolUnit property) (openfe.ProtocolUnitFailure property) (openfe.ProtocolUnitResult property) (openfe.SmallMoleculeComponent property) (openfe.SolventComponent property) (openfe.Transformation property) negative_ion (openfe.SolventComponent property) neutralize (openfe.SolventComponent property) nodes (openfe.AlchemicalNetwork property) (openfe.setup.LigandNetwork property) nonbonded_cutoff (openfe.protocols.openmm_utils.omm_settings.OpenMMSystemGeneratorFFSettings attribute) nonbonded_method (openfe.protocols.openmm_utils.omm_settings.OpenMMSystemGeneratorFFSettings attribute) number_of_conformers (openfe.protocols.openmm_utils.omm_settings.OpenFFPartialChargeSettings attribute) number_of_solvent_molecules (openfe.protocols.openmm_utils.omm_settings.OpenMMSolvationSettings attribute) O off_toolkit_backend (openfe.protocols.openmm_utils.omm_settings.OpenFFPartialChargeSettings attribute) ok() (openfe.ProtocolDAGResult method) (openfe.ProtocolUnitFailure static method) (openfe.ProtocolUnitResult static method) openfe module openfe-charge-molecules command line option --molecules --n-cores --output --overwrite-charges --settings -M -n -o -s openfe-gather command line option --allow-partial --report --tsv -o RESULTS openfe-plan-rbfe-network command line option --cofactors --molecules --n-cores --n-protocol-repeats --output-dir --overwrite-charges --protein --settings -C -M -n -o -p -s openfe-plan-rhfe-network command line option --molecules --n-cores --n-protocol-repeats --output-dir --overwrite-charges --settings -M -n -o -s openfe-quickrun command line option --work-dir -d -o TRANSFORMATION openfe.protocols.openmm_afe.equil_afe_settings module openfe.protocols.openmm_afe.equil_binding_afe_method module openfe.protocols.openmm_afe.equil_solvation_afe_method module openfe.protocols.openmm_md module openfe.protocols.openmm_md.plain_md_settings module openfe.protocols.openmm_rfe.equil_rfe_methods module openfe.protocols.openmm_septop.equil_septop_method module openfe.protocols.openmm_septop.equil_septop_settings module openfe.protocols.openmm_utils.omm_settings module openfe.setup.atom_mapping module openfe.setup.atom_mapping.lomap_scorers module openfe.setup.atom_mapping.perses_scorers module openfe.setup.chemicalsystem_generator module openfe.setup.ligand_network_planning module output_filename (openfe.protocols.openmm_utils.omm_settings.MultiStateOutputSettings attribute) output_indices (openfe.protocols.openmm_septop.equil_septop_settings.SepTopEquilOutputSettings attribute) (openfe.protocols.openmm_utils.omm_settings.MDOutputSettings attribute) (openfe.protocols.openmm_utils.omm_settings.MultiStateOutputSettings attribute) output_settings (openfe.protocols.openmm_md.plain_md_settings.PlainMDProtocolSettings attribute) (openfe.protocols.openmm_rfe.equil_rfe_settings.RelativeHybridTopologyProtocolSettings attribute) output_structure (openfe.protocols.openmm_utils.omm_settings.MultiStateOutputSettings attribute) outputs (openfe.ProtocolUnitFailure property) (openfe.ProtocolUnitResult property) P partial_charge_method (openfe.protocols.openmm_utils.omm_settings.OpenFFPartialChargeSettings attribute) partial_charge_settings (openfe.protocols.openmm_afe.equil_afe_settings.AbsoluteBindingSettings attribute) (openfe.protocols.openmm_afe.equil_afe_settings.AbsoluteSolvationSettings attribute) (openfe.protocols.openmm_md.plain_md_settings.PlainMDProtocolSettings attribute) (openfe.protocols.openmm_rfe.equil_rfe_settings.RelativeHybridTopologyProtocolSettings attribute) (openfe.protocols.openmm_septop.equil_septop_settings.SepTopSettings attribute) PersesAtomMapper (class in openfe.setup.atom_mapping) ph (openfe.protocols.openmm_utils.omm_settings.ThermoSettings attribute) PlainMDProtocol (class in openfe.protocols.openmm_md) PlainMDProtocolResult (class in openfe.protocols.openmm_md) PlainMDProtocolUnit (class in openfe.protocols.openmm_md) positions_write_frequency (openfe.protocols.openmm_utils.omm_settings.MultiStateOutputSettings attribute) positive_ion (openfe.SolventComponent property) preminimized_structure (openfe.protocols.openmm_septop.equil_septop_settings.SepTopEquilOutputSettings attribute) (openfe.protocols.openmm_utils.omm_settings.MDOutputSettings attribute) preserve_chirality (openfe.setup.atom_mapping.PersesAtomMapper attribute) pressure (openfe.protocols.openmm_utils.omm_settings.ThermoSettings attribute) production_iterations() (openfe.protocols.openmm_afe.equil_binding_afe_method.AbsoluteBindingProtocolResult method) (openfe.protocols.openmm_afe.equil_solvation_afe_method.AbsoluteSolvationProtocolResult method) (openfe.protocols.openmm_rfe.equil_rfe_methods.RelativeHybridTopologyProtocolResult method) (openfe.protocols.openmm_septop.equil_septop_method.SepTopProtocolResult method) production_length (openfe.protocols.openmm_utils.omm_settings.MDSimulationSettings attribute) (openfe.protocols.openmm_utils.omm_settings.MultiStateSimulationSettings attribute) production_trajectory_filename (openfe.protocols.openmm_septop.equil_septop_settings.SepTopEquilOutputSettings attribute) (openfe.protocols.openmm_utils.omm_settings.MDOutputSettings attribute) ProteinComponent (class in openfe) Protocol (class in openfe) protocol (openfe.Transformation property) protocol_repeats (openfe.protocols.openmm_afe.equil_afe_settings.AbsoluteBindingSettings attribute) (openfe.protocols.openmm_afe.equil_afe_settings.AbsoluteSolvationSettings attribute) (openfe.protocols.openmm_md.plain_md_settings.PlainMDProtocolSettings attribute) (openfe.protocols.openmm_rfe.equil_rfe_settings.RelativeHybridTopologyProtocolSettings attribute) (openfe.protocols.openmm_septop.equil_septop_settings.SepTopSettings attribute) protocol_unit_failures (openfe.ProtocolDAGResult property) protocol_unit_results (openfe.ProtocolDAGResult property) protocol_unit_successes (openfe.ProtocolDAGResult property) ProtocolDAG (class in openfe) ProtocolDAGResult (class in openfe) ProtocolResult (class in openfe) ProtocolUnit (class in openfe) ProtocolUnitFailure (class in openfe) ProtocolUnitResult (class in openfe) R RBFEAlchemicalNetworkPlanner (class in openfe.setup) real_time_analysis_interval (openfe.protocols.openmm_utils.omm_settings.MultiStateSimulationSettings attribute) real_time_analysis_minimum_time (openfe.protocols.openmm_utils.omm_settings.MultiStateSimulationSettings attribute) reassign_velocities (openfe.protocols.openmm_utils.omm_settings.IntegratorSettings attribute) redox_potential (openfe.protocols.openmm_utils.omm_settings.ThermoSettings attribute) RelativeHybridTopologyProtocol (class in openfe.protocols.openmm_rfe.equil_rfe_methods) RelativeHybridTopologyProtocolResult (class in openfe.protocols.openmm_rfe.equil_rfe_methods) RelativeHybridTopologyProtocolUnit (class in openfe.protocols.openmm_rfe.equil_rfe_methods) remove_com (openfe.protocols.openmm_utils.omm_settings.IntegratorSettings attribute) restraint_geometries() (openfe.protocols.openmm_afe.equil_binding_afe_method.AbsoluteBindingProtocolResult method) (openfe.protocols.openmm_septop.equil_septop_method.SepTopProtocolResult method) restraint_settings (openfe.protocols.openmm_afe.equil_afe_settings.AbsoluteBindingSettings attribute) result_cls (openfe.Protocol attribute) (openfe.protocols.openmm_afe.equil_binding_afe_method.AbsoluteBindingProtocol attribute) (openfe.protocols.openmm_afe.equil_solvation_afe_method.AbsoluteSolvationProtocol attribute) (openfe.protocols.openmm_md.PlainMDProtocol attribute) (openfe.protocols.openmm_rfe.equil_rfe_methods.RelativeHybridTopologyProtocol attribute) (openfe.protocols.openmm_septop.equil_septop_method.SepTopProtocol attribute) result_graph (openfe.ProtocolDAGResult property) result_to_unit() (openfe.ProtocolDAGResult method) RESULTS openfe-gather command line option RHFEAlchemicalNetworkPlanner (class in openfe.setup) rigid_water (openfe.protocols.openmm_utils.omm_settings.OpenMMSystemGeneratorFFSettings attribute) run() (openfe.protocols.openmm_afe.equil_binding_afe_method.AbsoluteBindingComplexUnit method) (openfe.protocols.openmm_afe.equil_binding_afe_method.AbsoluteBindingSolventUnit method) (openfe.protocols.openmm_afe.equil_solvation_afe_method.AbsoluteSolvationSolventUnit method) (openfe.protocols.openmm_afe.equil_solvation_afe_method.AbsoluteSolvationVacuumUnit method) (openfe.protocols.openmm_md.PlainMDProtocolUnit method) (openfe.protocols.openmm_rfe.equil_rfe_methods.RelativeHybridTopologyProtocolUnit method) (openfe.protocols.openmm_septop.equil_septop_method.SepTopComplexRunUnit method) (openfe.protocols.openmm_septop.equil_septop_method.SepTopComplexSetupUnit method) (openfe.protocols.openmm_septop.equil_septop_method.SepTopSolventRunUnit method) (openfe.protocols.openmm_septop.equil_septop_method.SepTopSolventSetupUnit method) S sampler_method (openfe.protocols.openmm_utils.omm_settings.MultiStateSimulationSettings attribute) sams_flatness_criteria (openfe.protocols.openmm_utils.omm_settings.MultiStateSimulationSettings attribute) sams_gamma0 (openfe.protocols.openmm_utils.omm_settings.MultiStateSimulationSettings attribute) seed (openfe.setup.atom_mapping.LomapAtomMapper attribute) selection_indices() (openfe.protocols.openmm_afe.equil_binding_afe_method.AbsoluteBindingProtocolResult method) (openfe.protocols.openmm_septop.equil_septop_method.SepTopProtocolResult method) SepTopComplexRunUnit (class in openfe.protocols.openmm_septop.equil_septop_method) SepTopComplexSetupUnit (class in openfe.protocols.openmm_septop.equil_septop_method) SepTopProtocol (class in openfe.protocols.openmm_septop.equil_septop_method) SepTopProtocolResult (class in openfe.protocols.openmm_septop.equil_septop_method) SepTopSolventRunUnit (class in openfe.protocols.openmm_septop.equil_septop_method) SepTopSolventSetupUnit (class in openfe.protocols.openmm_septop.equil_septop_method) settings (openfe.Protocol property) (openfe.protocols.openmm_afe.equil_binding_afe_method.AbsoluteBindingProtocol property) (openfe.protocols.openmm_afe.equil_solvation_afe_method.AbsoluteSolvationProtocol property) (openfe.protocols.openmm_md.PlainMDProtocol property) (openfe.protocols.openmm_rfe.equil_rfe_methods.RelativeHybridTopologyProtocol property) (openfe.protocols.openmm_septop.equil_septop_method.SepTopProtocol property) shift (openfe.setup.atom_mapping.LomapAtomMapper attribute) simtype (openfe.protocols.openmm_afe.equil_binding_afe_method.AbsoluteBindingComplexUnit attribute) (openfe.protocols.openmm_afe.equil_binding_afe_method.AbsoluteBindingSolventUnit attribute) (openfe.protocols.openmm_afe.equil_solvation_afe_method.AbsoluteSolvationSolventUnit attribute) (openfe.protocols.openmm_afe.equil_solvation_afe_method.AbsoluteSolvationVacuumUnit attribute) simulation_settings (openfe.protocols.openmm_md.plain_md_settings.PlainMDProtocolSettings attribute) (openfe.protocols.openmm_rfe.equil_rfe_settings.RelativeHybridTopologyProtocolSettings attribute) small_molecule_forcefield (openfe.protocols.openmm_utils.omm_settings.OpenMMSystemGeneratorFFSettings attribute) SmallMoleculeComponent (class in openfe) smiles (openfe.ProteinComponent property) (openfe.SmallMoleculeComponent property) (openfe.SolventComponent property) softcore_alpha (openfe.protocols.openmm_rfe.equil_rfe_settings.AlchemicalSettings attribute) softcore_LJ (openfe.protocols.openmm_rfe.equil_rfe_settings.AlchemicalSettings attribute) solvation_settings (openfe.protocols.openmm_afe.equil_afe_settings.AbsoluteSolvationSettings attribute) (openfe.protocols.openmm_md.plain_md_settings.PlainMDProtocolSettings attribute) (openfe.protocols.openmm_rfe.equil_rfe_settings.RelativeHybridTopologyProtocolSettings attribute) solvent_engine_settings (openfe.protocols.openmm_afe.equil_afe_settings.AbsoluteSolvationSettings attribute) solvent_equil_output_settings (openfe.protocols.openmm_afe.equil_afe_settings.AbsoluteBindingSettings attribute) (openfe.protocols.openmm_afe.equil_afe_settings.AbsoluteSolvationSettings attribute) (openfe.protocols.openmm_septop.equil_septop_settings.SepTopSettings attribute) solvent_equil_simulation_settings (openfe.protocols.openmm_afe.equil_afe_settings.AbsoluteBindingSettings attribute) (openfe.protocols.openmm_afe.equil_afe_settings.AbsoluteSolvationSettings attribute) (openfe.protocols.openmm_septop.equil_septop_settings.SepTopSettings attribute) solvent_forcefield_settings (openfe.protocols.openmm_afe.equil_afe_settings.AbsoluteSolvationSettings attribute) solvent_lambda_settings (openfe.protocols.openmm_afe.equil_afe_settings.AbsoluteBindingSettings attribute) (openfe.protocols.openmm_septop.equil_septop_settings.SepTopSettings attribute) solvent_model (openfe.protocols.openmm_utils.omm_settings.OpenMMSolvationSettings attribute) solvent_output_settings (openfe.protocols.openmm_afe.equil_afe_settings.AbsoluteBindingSettings attribute) (openfe.protocols.openmm_afe.equil_afe_settings.AbsoluteSolvationSettings attribute) (openfe.protocols.openmm_septop.equil_septop_settings.SepTopSettings attribute) solvent_padding (openfe.protocols.openmm_utils.omm_settings.OpenMMSolvationSettings attribute) solvent_restraint_settings (openfe.protocols.openmm_septop.equil_septop_settings.SepTopSettings attribute) solvent_simulation_settings (openfe.protocols.openmm_afe.equil_afe_settings.AbsoluteBindingSettings attribute) (openfe.protocols.openmm_afe.equil_afe_settings.AbsoluteSolvationSettings attribute) (openfe.protocols.openmm_septop.equil_septop_settings.SepTopSettings attribute) solvent_solvation_settings (openfe.protocols.openmm_afe.equil_afe_settings.AbsoluteBindingSettings attribute) (openfe.protocols.openmm_septop.equil_septop_settings.SepTopSettings attribute) SolventComponent (class in openfe) source_key (openfe.ProtocolUnitFailure property) (openfe.ProtocolUnitResult property) start_time (openfe.ProtocolUnitFailure property) (openfe.ProtocolUnitResult property) stateA (openfe.Transformation property) stateB (openfe.Transformation property) stderr (openfe.ProtocolUnitFailure property) (openfe.ProtocolUnitResult property) stdout (openfe.ProtocolUnitFailure property) (openfe.ProtocolUnitResult property) structural_analysis() (openfe.protocols.openmm_rfe.equil_rfe_methods.RelativeHybridTopologyProtocolUnit static method) suggest_mappings() (openfe.setup.atom_mapping.LigandAtomMapper method) (openfe.setup.atom_mapping.LomapAtomMapper method) (openfe.setup.atom_mapping.PersesAtomMapper method) sulfonamides_score() (in module openfe.setup.atom_mapping.lomap_scorers) T temperature (openfe.protocols.openmm_utils.omm_settings.ThermoSettings attribute) terminal_protocol_unit_results (openfe.ProtocolDAGResult property) thermo_settings (openfe.protocols.openmm_afe.equil_afe_settings.AbsoluteBindingSettings attribute) (openfe.protocols.openmm_afe.equil_afe_settings.AbsoluteSolvationSettings attribute) (openfe.protocols.openmm_md.plain_md_settings.PlainMDProtocolSettings attribute) (openfe.protocols.openmm_rfe.equil_rfe_settings.RelativeHybridTopologyProtocolSettings attribute) (openfe.protocols.openmm_septop.equil_septop_settings.SepTopSettings attribute) threed (openfe.setup.atom_mapping.LomapAtomMapper attribute) time (openfe.setup.atom_mapping.LomapAtomMapper attribute) time_per_iteration (openfe.protocols.openmm_utils.omm_settings.MultiStateSimulationSettings attribute) timestep (openfe.protocols.openmm_utils.omm_settings.IntegratorSettings attribute) to_graphml() (openfe.AlchemicalNetwork method) (openfe.setup.LigandNetwork method) to_openff() (openfe.SmallMoleculeComponent method) to_openmm_positions() (openfe.ProteinComponent method) to_openmm_topology() (openfe.ProteinComponent method) to_pdb_file() (openfe.ProteinComponent method) to_pdbx_file() (openfe.ProteinComponent method) to_rbfe_alchemical_network() (openfe.setup.LigandNetwork method) to_rdkit() (openfe.ProteinComponent method) (openfe.SmallMoleculeComponent method) to_sdf() (openfe.SmallMoleculeComponent method) total_charge (openfe.ChemicalSystem property) (openfe.ProteinComponent property) (openfe.SmallMoleculeComponent property) (openfe.SolventComponent property) traceback (openfe.ProtocolUnitFailure property) trajectory_write_interval (openfe.protocols.openmm_septop.equil_septop_settings.SepTopEquilOutputSettings attribute) (openfe.protocols.openmm_utils.omm_settings.MDOutputSettings attribute) TRANSFORMATION openfe-quickrun command line option Transformation (class in openfe) transformation_protocol (openfe.setup.RBFEAlchemicalNetworkPlanner property) (openfe.setup.RHFEAlchemicalNetworkPlanner property) 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) trim_graph() (openfe.setup.LigandNetwork method) turn_off_core_unique_exceptions (openfe.protocols.openmm_rfe.equil_rfe_settings.AlchemicalSettings attribute) U unit_to_all_results() (openfe.ProtocolDAGResult method) unit_to_result() (openfe.ProtocolDAGResult method) use_dispersion_correction (openfe.protocols.openmm_rfe.equil_rfe_settings.AlchemicalSettings attribute) use_positions (openfe.setup.atom_mapping.PersesAtomMapper attribute) V vacuum_engine_settings (openfe.protocols.openmm_afe.equil_afe_settings.AbsoluteSolvationSettings attribute) vacuum_equil_output_settings (openfe.protocols.openmm_afe.equil_afe_settings.AbsoluteSolvationSettings attribute) vacuum_equil_simulation_settings (openfe.protocols.openmm_afe.equil_afe_settings.AbsoluteSolvationSettings attribute) vacuum_forcefield_settings (openfe.protocols.openmm_afe.equil_afe_settings.AbsoluteSolvationSettings attribute) vacuum_output_settings (openfe.protocols.openmm_afe.equil_afe_settings.AbsoluteSolvationSettings attribute) vacuum_simulation_settings (openfe.protocols.openmm_afe.equil_afe_settings.AbsoluteSolvationSettings attribute) validate() (openfe.Protocol method) (openfe.protocols.openmm_afe.equil_binding_afe_method.AbsoluteBindingProtocol method) (openfe.protocols.openmm_afe.equil_solvation_afe_method.AbsoluteSolvationProtocol method) (openfe.protocols.openmm_md.PlainMDProtocol method) (openfe.protocols.openmm_rfe.equil_rfe_methods.RelativeHybridTopologyProtocol method) (openfe.protocols.openmm_septop.equil_septop_method.SepTopProtocol method) velocities_write_frequency (openfe.protocols.openmm_utils.omm_settings.MultiStateOutputSettings attribute) view_3d() (openfe.setup.atom_mapping.LigandAtomMapping method) W with_annotations() (openfe.setup.atom_mapping.LigandAtomMapping method)
