Index Symbols | _ | A | B | C | D | E | F | G | H | I | K | L | M | N | O | P | R | S | T | U | W Symbols --allow-partial openfe-gather command line option --cofactors openfe-plan-rbfe-network command line option --molecules 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 --report 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-plan-rbfe-network command line option openfe-plan-rhfe-network command line option -o 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 _ __call__() (openfe.setup.chemicalsystem_generator.EasyChemicalSystemGenerator method) (openfe.setup.RBFEAlchemicalNetworkPlanner method) (openfe.setup.RHFEAlchemicalNetworkPlanner method) A AbsoluteSolvationProtocol (class in openfe.protocols.openmm_afe.equil_solvation_afe_method) AbsoluteSolvationProtocolResult (class in openfe.protocols.openmm_afe.equil_solvation_afe_method) alchemical_sampler_settings (openfe.protocols.openmm_rfe.RelativeHybridTopologyProtocolSettings attribute) alchemical_settings (openfe.protocols.openmm_rfe.RelativeHybridTopologyProtocolSettings attribute) AlchemicalNetwork (class in openfe) allow_ring_breaking (openfe.setup.atom_mapping.PersesAtomMapper attribute) annotations (openfe.setup.atom_mapping.LigandAtomMapping property) as_protein_smallmolecule_solvent() (openfe.ChemicalSystem class method) as_smallmolecule_solvent() (openfe.ChemicalSystem class method) atomic_number_score() (in module openfe.setup.atom_mapping.lomap_scorers) B barostat_frequency (openfe.protocols.openmm_rfe.equil_rfe_settings.IntegratorSettings attribute) C checkpoint_interval (openfe.protocols.openmm_rfe.equil_rfe_settings.SimulationSettings attribute) checkpoint_storage (openfe.protocols.openmm_rfe.equil_rfe_settings.SimulationSettings attribute) chemical_system_generator_type (openfe.setup.RBFEAlchemicalNetworkPlanner property) (openfe.setup.RHFEAlchemicalNetworkPlanner property) ChemicalSystem (class in openfe) collision_rate (openfe.protocols.openmm_rfe.equil_rfe_settings.IntegratorSettings attribute) Component (class in openfe) 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_platform (openfe.protocols.openmm_rfe.equil_rfe_settings.OpenMMEngineSettings attribute) constraint_tolerance (openfe.protocols.openmm_rfe.equil_rfe_settings.IntegratorSettings attribute) constraints (openfe.protocols.openmm_rfe.equil_rfe_settings.OpenMMSystemGeneratorFFSettings attribute) copy_with_replacements() (gufe.tokenization.GufeTokenizable method) create() (openfe.Protocol method) (openfe.protocols.openmm_afe.equil_solvation_afe_method.AbsoluteSolvationProtocol method) (openfe.protocols.openmm_rfe.RelativeHybridTopologyProtocol method) (openfe.Transformation method) D data (openfe.ProtocolResult property) (openfe.protocols.openmm_afe.equil_solvation_afe_method.AbsoluteSolvationProtocolResult property) (openfe.protocols.openmm_rfe.RelativeHybridTopologyProtocolResult 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_solvation_afe_method.AbsoluteSolvationProtocol class method) (openfe.protocols.openmm_rfe.RelativeHybridTopologyProtocol class method) defaults() (gufe.tokenization.GufeTokenizable class method) dependencies (openfe.ProtocolUnit property) (openfe.ProtocolUnitFailure property) (openfe.ProtocolUnitResult property) draw_to_file() (openfe.setup.atom_mapping.LigandAtomMapping method) dump() (openfe.Transformation method) E 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) engine_settings (openfe.protocols.openmm_rfe.RelativeHybridTopologyProtocolSettings attribute) enlarge_graph() (openfe.setup.LigandNetwork method) equilibration_iterations() (openfe.protocols.openmm_afe.equil_solvation_afe_method.AbsoluteSolvationProtocolResult method) (openfe.protocols.openmm_rfe.RelativeHybridTopologyProtocolResult method) equilibration_length (openfe.protocols.openmm_rfe.equil_rfe_settings.SimulationSettings attribute) exception (openfe.ProtocolUnitFailure property) execute() (openfe.ProtocolUnit method) execute_DAG() (in module openfe) extends_key (openfe.ProtocolDAG attribute) F flatness_criteria (openfe.protocols.openmm_rfe.equil_rfe_settings.AlchemicalSamplerSettings attribute) flatten_torsions (openfe.protocols.openmm_rfe.equil_rfe_settings.AlchemicalSettings attribute) forcefield_cache (openfe.protocols.openmm_rfe.equil_rfe_settings.SimulationSettings attribute) forcefield_settings (openfe.protocols.openmm_rfe.RelativeHybridTopologyProtocolSettings attribute) forcefields (openfe.protocols.openmm_rfe.equil_rfe_settings.OpenMMSystemGeneratorFFSettings attribute) from_dict() (gufe.tokenization.GufeTokenizable class method) from_graphml() (openfe.AlchemicalNetwork class method) (openfe.setup.LigandNetwork class method) from_json() (openfe.ProteinComponent class method) (openfe.SmallMoleculeComponent class method) from_keyed_dict() (gufe.tokenization.GufeTokenizable 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) from_shallow_dict() (gufe.tokenization.GufeTokenizable class method) G gamma0 (openfe.protocols.openmm_rfe.equil_rfe_settings.AlchemicalSamplerSettings attribute) gather() (openfe.Protocol method) (openfe.protocols.openmm_afe.equil_solvation_afe_method.AbsoluteSolvationProtocol method) (openfe.protocols.openmm_rfe.RelativeHybridTopologyProtocol method) (openfe.Transformation method) generate_maximal_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_distances() (openfe.setup.atom_mapping.LigandAtomMapping method) get_estimate() (openfe.ProtocolResult method) (openfe.protocols.openmm_afe.equil_solvation_afe_method.AbsoluteSolvationProtocolResult method) (openfe.protocols.openmm_rfe.RelativeHybridTopologyProtocolResult method) get_forward_and_reverse_energy_analysis() (openfe.protocols.openmm_afe.equil_solvation_afe_method.AbsoluteSolvationProtocolResult method) (openfe.protocols.openmm_rfe.RelativeHybridTopologyProtocolResult method) get_individual_estimates() (openfe.protocols.openmm_afe.equil_solvation_afe_method.AbsoluteSolvationProtocolResult method) (openfe.protocols.openmm_rfe.RelativeHybridTopologyProtocolResult method) get_overlap_matrices() (openfe.protocols.openmm_afe.equil_solvation_afe_method.AbsoluteSolvationProtocolResult method) (openfe.protocols.openmm_rfe.RelativeHybridTopologyProtocolResult method) get_replica_states() (openfe.protocols.openmm_afe.equil_solvation_afe_method.AbsoluteSolvationProtocolResult method) (openfe.protocols.openmm_rfe.RelativeHybridTopologyProtocolResult method) get_replica_transition_statistics() (openfe.protocols.openmm_afe.equil_solvation_afe_method.AbsoluteSolvationProtocolResult method) (openfe.protocols.openmm_rfe.RelativeHybridTopologyProtocolResult method) get_uncertainty() (openfe.ProtocolResult method) (openfe.protocols.openmm_afe.equil_solvation_afe_method.AbsoluteSolvationProtocolResult method) (openfe.protocols.openmm_rfe.RelativeHybridTopologyProtocolResult method) graph (openfe.AlchemicalNetwork property) (openfe.ProtocolDAG attribute) (openfe.setup.LigandNetwork property) gufe.tokenization module GufeTokenizable (class in gufe.tokenization) 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_rfe.equil_rfe_settings.OpenMMSystemGeneratorFFSettings attribute) I inputs (openfe.ProtocolUnit property) (openfe.ProtocolUnitFailure property) (openfe.ProtocolUnitResult property) integrator_settings (openfe.protocols.openmm_rfe.RelativeHybridTopologyProtocolSettings attribute) interpolate_old_and_new_14s (openfe.protocols.openmm_rfe.equil_rfe_settings.AlchemicalSettings attribute) ion_concentration (openfe.SolventComponent property) is_connected() (openfe.setup.LigandNetwork method) K key (gufe.tokenization.GufeTokenizable property) L lambda_functions (openfe.protocols.openmm_rfe.equil_rfe_settings.AlchemicalSettings attribute) lambda_windows (openfe.protocols.openmm_rfe.equil_rfe_settings.AlchemicalSettings 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) logger (gufe.tokenization.GufeTokenizable property) 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_rfe.equil_rfe_settings.SimulationSettings attribute) mncar_score() (in module openfe.setup.atom_mapping.lomap_scorers) module gufe.tokenization openfe openfe.protocols.openmm_afe.equil_afe_settings openfe.protocols.openmm_afe.equil_solvation_afe_method openfe.protocols.openmm_rfe openfe.protocols.openmm_rfe.equil_rfe_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_repeats (openfe.protocols.openmm_rfe.equil_rfe_settings.AlchemicalSamplerSettings attribute) n_replicas (openfe.protocols.openmm_rfe.equil_rfe_settings.AlchemicalSamplerSettings attribute) n_restart_attempts (openfe.protocols.openmm_rfe.equil_rfe_settings.IntegratorSettings attribute) n_steps (openfe.protocols.openmm_rfe.equil_rfe_settings.IntegratorSettings attribute) name (openfe.AlchemicalNetwork property) (openfe.ChemicalSystem property) (openfe.Component property) (openfe.ProteinComponent property) (openfe.ProtocolDAG attribute) (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_rfe.equil_rfe_settings.SystemSettings attribute) nonbonded_method (openfe.protocols.openmm_rfe.equil_rfe_settings.SystemSettings attribute) O ok() (openfe.ProtocolDAGResult method) (openfe.ProtocolUnitFailure static method) (openfe.ProtocolUnitResult static method) online_analysis_interval (openfe.protocols.openmm_rfe.equil_rfe_settings.AlchemicalSamplerSettings attribute) online_analysis_minimum_iterations (openfe.protocols.openmm_rfe.equil_rfe_settings.AlchemicalSamplerSettings attribute) online_analysis_target_error (openfe.protocols.openmm_rfe.equil_rfe_settings.AlchemicalSamplerSettings attribute) openfe module openfe-gather command line option --allow-partial --report -o ROOTDIR openfe-plan-rbfe-network command line option --cofactors --molecules --output-dir --protein -C -M -o -p openfe-plan-rhfe-network command line option --molecules --output-dir -M -o openfe-quickrun command line option --work-dir -d -o TRANSFORMATION openfe.protocols.openmm_afe.equil_afe_settings module openfe.protocols.openmm_afe.equil_solvation_afe_method module openfe.protocols.openmm_rfe module openfe.protocols.openmm_rfe.equil_rfe_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_rfe.equil_rfe_settings.SimulationSettings attribute) output_indices (openfe.protocols.openmm_rfe.equil_rfe_settings.SimulationSettings attribute) output_structure (openfe.protocols.openmm_rfe.equil_rfe_settings.SimulationSettings attribute) outputs (openfe.ProtocolUnitFailure property) (openfe.ProtocolUnitResult property) P PersesAtomMapper (class in openfe.setup.atom_mapping) ph (openfe.protocols.openmm_rfe.equil_rfe_settings.ThermoSettings attribute) positive_ion (openfe.SolventComponent property) preserve_chirality (openfe.setup.atom_mapping.PersesAtomMapper attribute) pressure (openfe.protocols.openmm_rfe.equil_rfe_settings.ThermoSettings attribute) production_iterations() (openfe.protocols.openmm_afe.equil_solvation_afe_method.AbsoluteSolvationProtocolResult method) (openfe.protocols.openmm_rfe.RelativeHybridTopologyProtocolResult method) production_length (openfe.protocols.openmm_rfe.equil_rfe_settings.SimulationSettings attribute) ProteinComponent (class in openfe) Protocol (class in openfe) protocol (openfe.Transformation property) protocol_unit_failures (openfe.ProtocolDAGResult property) protocol_unit_results (openfe.ProtocolDAGResult property) protocol_unit_successes (openfe.ProtocolDAGResult property) protocol_units (openfe.ProtocolDAG attribute) 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) reassign_velocities (openfe.protocols.openmm_rfe.equil_rfe_settings.IntegratorSettings attribute) redox_potential (openfe.protocols.openmm_rfe.equil_rfe_settings.ThermoSettings attribute) RelativeHybridTopologyProtocol (class in openfe.protocols.openmm_rfe) RelativeHybridTopologyProtocolResult (class in openfe.protocols.openmm_rfe) remove_com (openfe.protocols.openmm_rfe.equil_rfe_settings.OpenMMSystemGeneratorFFSettings attribute) result_cls (openfe.Protocol attribute) (openfe.protocols.openmm_afe.equil_solvation_afe_method.AbsoluteSolvationProtocol attribute) (openfe.protocols.openmm_rfe.RelativeHybridTopologyProtocol attribute) result_graph (openfe.ProtocolDAGResult property) result_to_unit() (openfe.ProtocolDAGResult method) RHFEAlchemicalNetworkPlanner (class in openfe.setup) rigid_water (openfe.protocols.openmm_rfe.equil_rfe_settings.OpenMMSystemGeneratorFFSettings attribute) ROOTDIR openfe-gather command line option S sampler_method (openfe.protocols.openmm_rfe.equil_rfe_settings.AlchemicalSamplerSettings attribute) seed (openfe.setup.atom_mapping.LomapAtomMapper attribute) settings (openfe.Protocol property) (openfe.protocols.openmm_afe.equil_solvation_afe_method.AbsoluteSolvationProtocol property) (openfe.protocols.openmm_rfe.RelativeHybridTopologyProtocol property) shift (openfe.setup.atom_mapping.LomapAtomMapper attribute) simulation_settings (openfe.protocols.openmm_rfe.RelativeHybridTopologyProtocolSettings attribute) small_molecule_forcefield (openfe.protocols.openmm_rfe.equil_rfe_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_v2 (openfe.protocols.openmm_rfe.equil_rfe_settings.AlchemicalSettings attribute) solvation_settings (openfe.protocols.openmm_rfe.RelativeHybridTopologyProtocolSettings attribute) solvent_model (openfe.protocols.openmm_rfe.equil_rfe_settings.SolvationSettings attribute) solvent_padding (openfe.protocols.openmm_rfe.equil_rfe_settings.SolvationSettings 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) 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) system_settings (openfe.protocols.openmm_rfe.RelativeHybridTopologyProtocolSettings attribute) T temperature (openfe.protocols.openmm_rfe.equil_rfe_settings.ThermoSettings attribute) terminal_protocol_unit_results (openfe.ProtocolDAGResult property) thermo_settings (openfe.protocols.openmm_rfe.RelativeHybridTopologyProtocolSettings attribute) threed (openfe.setup.atom_mapping.LomapAtomMapper attribute) time (openfe.setup.atom_mapping.LomapAtomMapper attribute) timestep (openfe.protocols.openmm_rfe.equil_rfe_settings.IntegratorSettings attribute) to_dict() (gufe.tokenization.GufeTokenizable method) to_graphml() (openfe.AlchemicalNetwork method) (openfe.setup.LigandNetwork method) to_json() (openfe.ProteinComponent method) (openfe.SmallMoleculeComponent method) to_keyed_dict() (gufe.tokenization.GufeTokenizable 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) to_shallow_dict() (gufe.tokenization.GufeTokenizable method) total_charge (openfe.ChemicalSystem property) (openfe.Component property) (openfe.ProteinComponent property) (openfe.SmallMoleculeComponent property) (openfe.SolventComponent property) traceback (openfe.ProtocolUnitFailure property) TRANSFORMATION openfe-quickrun command line option Transformation (class in openfe) transformation_key (openfe.ProtocolDAG attribute) 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) U unit_to_all_results() (openfe.ProtocolDAGResult method) unit_to_result() (openfe.ProtocolDAGResult method) unsampled_endstates (openfe.protocols.openmm_rfe.equil_rfe_settings.AlchemicalSettings attribute) use_dispersion_correction (openfe.protocols.openmm_rfe.equil_rfe_settings.AlchemicalSettings attribute) use_positions (openfe.setup.atom_mapping.PersesAtomMapper attribute) W with_annotations() (openfe.setup.atom_mapping.LigandAtomMapping method)