Index Symbols | _ | A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | R | S | T | U | V | W Symbols --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.alchemical_network_planner.abstract_alchemical_network_planner.AbstractAlchemicalNetworkPlanner method) (openfe.setup.alchemical_network_planner.relative_alchemical_network_planner.RBFEAlchemicalNetworkPlanner method) (openfe.setup.alchemical_network_planner.relative_alchemical_network_planner.RelativeAlchemicalNetworkPlanner method) (openfe.setup.alchemical_network_planner.relative_alchemical_network_planner.RHFEAlchemicalNetworkPlanner method) A AbstractAlchemicalNetworkPlanner (class in openfe.setup.alchemical_network_planner.abstract_alchemical_network_planner) alchemical_sampler_settings (openfe.protocols.openmm_rfe.RelativeHybridTopologyProtocolSettings attribute) alchemical_settings (openfe.protocols.openmm_rfe.RelativeHybridTopologyProtocolSettings attribute) AlchemicalNetwork (class in openfe.setup) allow_ring_breaking (openfe.setup.atom_mapping.PersesAtomMapper attribute) annotations (openfe.setup.atom_mapping.LigandAtomMapping property) as_protein_smallmolecule_solvent() (openfe.setup.system.ChemicalSystem class method) as_smallmolecule_solvent() (openfe.setup.system.ChemicalSystem class method) atomic_number_score() (in module openfe.setup.atom_mapping.lomap_scorers) B barostat_frequency (openfe.protocols.settings.IntegratorSettings attribute) C checkpoint_interval (openfe.protocols.settings.SimulationSettings attribute) checkpoint_storage (openfe.protocols.settings.SimulationSettings attribute) chemical_system_generator_type (openfe.setup.alchemical_network_planner.relative_alchemical_network_planner.RBFEAlchemicalNetworkPlanner property) (openfe.setup.alchemical_network_planner.relative_alchemical_network_planner.RelativeAlchemicalNetworkPlanner property) (openfe.setup.alchemical_network_planner.relative_alchemical_network_planner.RHFEAlchemicalNetworkPlanner property) ChemicalSystem (class in openfe.setup.system) CloneResult (class in openfe.storage.resultclient) collision_rate (openfe.protocols.settings.IntegratorSettings attribute) Component (class in openfe.setup.system) 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.setup.system.ChemicalSystem property) compute_platform (openfe.protocols.settings.OpenMMEngineSettings attribute) constraint_tolerance (openfe.protocols.settings.IntegratorSettings attribute) constraints (openfe.protocols.settings.OpenMMSystemGeneratorFFSettings attribute) copy_with_replacements() (openfe.utils.GufeTokenizable method) create() (openfe.protocols.openmm_rfe.RelativeHybridTopologyProtocol method) (openfe.protocols.Protocol method) (openfe.setup.Transformation method) D data (openfe.protocols.openmm_rfe.RelativeHybridTopologyProtocolResult property) (openfe.protocols.ProtocolResult property) DEFAULT_ANS_DIFFICULTY (in module openfe.setup.atom_mapping.lomap_scorers) 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.protocols.openmm_rfe.RelativeHybridTopologyProtocol class method) (openfe.protocols.Protocol class method) defaults() (openfe.utils.GufeTokenizable class method) delete() (openfe.storage.resultclient.ResultClient method) (openfe.storage.resultserver.ResultServer method) dependencies (openfe.protocols.openmm_rfe.RelativeHybridTopologyProtocolUnit property) (openfe.protocols.ProtocolUnit property) (openfe.protocols.ProtocolUnitFailure property) (openfe.protocols.ProtocolUnitResult property) draw_to_file() (openfe.setup.atom_mapping.LigandAtomMapping method) dump() (openfe.setup.Transformation method) E ecr_score() (in module openfe.setup.atom_mapping.lomap_scorers) edges (openfe.setup.AlchemicalNetwork property) (openfe.setup.LigandNetwork property) element_change (openfe.setup.atom_mapping.LomapAtomMapper attribute) end_time (openfe.protocols.ProtocolUnitFailure property) (openfe.protocols.ProtocolUnitResult property) engine_settings (openfe.protocols.openmm_rfe.RelativeHybridTopologyProtocolSettings attribute) enlarge_graph() (openfe.setup.LigandNetwork method) equilibration_iterations() (openfe.protocols.openmm_rfe.RelativeHybridTopologyProtocolResult method) equilibration_length (openfe.protocols.settings.SimulationSettings attribute) exception (openfe.protocols.ProtocolUnitFailure property) execute() (openfe.protocols.openmm_rfe.RelativeHybridTopologyProtocolUnit method) (openfe.protocols.ProtocolUnit method) execute_DAG() (in module openfe.orchestration) extends_key (openfe.protocols.ProtocolDAG attribute) ExtensionResult (class in openfe.storage.resultclient) F find_missing_files() (openfe.storage.resultserver.ResultServer method) flatness_criteria (openfe.protocols.settings.AlchemicalSamplerSettings attribute) flatten_torsions (openfe.protocols.settings.AlchemicalSettings attribute) forcefield_cache (openfe.protocols.settings.SimulationSettings attribute) forcefield_settings (openfe.protocols.openmm_rfe.RelativeHybridTopologyProtocolSettings attribute) (openfe.protocols.settings.Settings attribute) forcefields (openfe.protocols.settings.OpenMMSystemGeneratorFFSettings attribute) from_dict() (openfe.utils.GufeTokenizable class method) from_graphml() (openfe.setup.AlchemicalNetwork class method) (openfe.setup.LigandNetwork class method) from_json() (openfe.setup.system.ProteinComponent class method) (openfe.setup.system.SmallMoleculeComponent class method) from_keyed_dict() (openfe.utils.GufeTokenizable class method) from_openff() (openfe.setup.system.SmallMoleculeComponent class method) from_pdb_file() (openfe.setup.system.ProteinComponent class method) from_pdbx_file() (openfe.setup.system.ProteinComponent class method) from_rdkit() (openfe.setup.system.ProteinComponent class method) (openfe.setup.system.SmallMoleculeComponent class method) from_sdf_file() (openfe.setup.system.SmallMoleculeComponent class method) from_sdf_string() (openfe.setup.system.SmallMoleculeComponent class method) from_shallow_dict() (openfe.utils.GufeTokenizable class method) G gamma0 (openfe.protocols.settings.AlchemicalSamplerSettings attribute) gather() (openfe.protocols.openmm_rfe.RelativeHybridTopologyProtocol method) (openfe.protocols.Protocol method) (openfe.setup.Transformation method) 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() (openfe.storage.metadatastore.JSONMetadataStore method) (openfe.storage.metadatastore.MetadataStore method) (openfe.storage.metadatastore.PerFileJSONMetadataStore method) get_distances() (openfe.setup.atom_mapping.LigandAtomMapping method) get_estimate() (openfe.protocols.openmm_rfe.RelativeHybridTopologyProtocolResult method) (openfe.protocols.ProtocolResult method) get_forward_and_reverse_energy_analysis() (openfe.protocols.openmm_rfe.RelativeHybridTopologyProtocolResult method) get_individual_estimates() (openfe.protocols.openmm_rfe.RelativeHybridTopologyProtocolResult method) get_overlap_matrices() (openfe.protocols.openmm_rfe.RelativeHybridTopologyProtocolResult method) get_replica_states() (openfe.protocols.openmm_rfe.RelativeHybridTopologyProtocolResult method) get_replica_transition_statistics() (openfe.protocols.openmm_rfe.RelativeHybridTopologyProtocolResult method) get_uncertainty() (openfe.protocols.openmm_rfe.RelativeHybridTopologyProtocolResult method) (openfe.protocols.ProtocolResult method) graph (openfe.protocols.ProtocolDAG attribute) (openfe.setup.AlchemicalNetwork property) (openfe.setup.LigandNetwork property) GufeTokenizable (class in openfe.utils) 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.settings.OpenMMSystemGeneratorFFSettings attribute) I inputs (openfe.protocols.openmm_rfe.RelativeHybridTopologyProtocolUnit property) (openfe.protocols.ProtocolUnit property) (openfe.protocols.ProtocolUnitFailure property) (openfe.protocols.ProtocolUnitResult property) integrator_settings (openfe.protocols.openmm_rfe.RelativeHybridTopologyProtocolSettings attribute) interpolate_old_and_new_14s (openfe.protocols.settings.AlchemicalSettings attribute) ion_concentration (openfe.setup.system.SolventComponent property) is_connected() (openfe.setup.LigandNetwork method) items() (openfe.storage.metadatastore.JSONMetadataStore method) (openfe.storage.metadatastore.MetadataStore method) (openfe.storage.metadatastore.PerFileJSONMetadataStore method) J JSONMetadataStore (class in openfe.storage.metadatastore) K key (openfe.utils.GufeTokenizable property) keys() (openfe.storage.metadatastore.JSONMetadataStore method) (openfe.storage.metadatastore.MetadataStore method) (openfe.storage.metadatastore.PerFileJSONMetadataStore method) L lambda_functions (openfe.protocols.settings.AlchemicalSettings attribute) lambda_windows (openfe.protocols.settings.AlchemicalSettings attribute) ligand_network_planner (openfe.setup.alchemical_network_planner.relative_alchemical_network_planner.RBFEAlchemicalNetworkPlanner property) (openfe.setup.alchemical_network_planner.relative_alchemical_network_planner.RelativeAlchemicalNetworkPlanner property) (openfe.setup.alchemical_network_planner.relative_alchemical_network_planner.RHFEAlchemicalNetworkPlanner property) LigandAtomMapper (class in openfe.setup.atom_mapping) LigandAtomMapping (class in openfe.setup.atom_mapping) LigandNetwork (class in openfe.setup) load() (openfe.setup.Transformation class method) load_all_metadata() (openfe.storage.metadatastore.JSONMetadataStore method) (openfe.storage.metadatastore.MetadataStore method) (openfe.storage.metadatastore.PerFileJSONMetadataStore method) load_bytes() (openfe.storage.resultclient.CloneResult method) (openfe.storage.resultclient.ExtensionResult method) (openfe.storage.resultclient.ResultClient method) (openfe.storage.resultclient.TransformationResult method) load_fepplus_network() (in module openfe.setup.ligand_network_planning) load_network() (openfe.storage.resultclient.ResultClient method) load_orion_network() (in module openfe.setup.ligand_network_planning) load_stream() (openfe.storage.resultclient.CloneResult method) (openfe.storage.resultclient.ExtensionResult method) (openfe.storage.resultclient.ResultClient method) (openfe.storage.resultclient.TransformationResult method) (openfe.storage.resultserver.ResultServer method) load_transformation() (openfe.storage.resultclient.ResultClient method) log_system_probe() (in module openfe.utils) logger (openfe.utils.GufeTokenizable property) LomapAtomMapper (class in openfe.setup.atom_mapping) M mappers (openfe.setup.alchemical_network_planner.relative_alchemical_network_planner.RBFEAlchemicalNetworkPlanner property) (openfe.setup.alchemical_network_planner.relative_alchemical_network_planner.RelativeAlchemicalNetworkPlanner property) (openfe.setup.alchemical_network_planner.relative_alchemical_network_planner.RHFEAlchemicalNetworkPlanner property) mapping (openfe.setup.Transformation property) mapping_scorer (openfe.setup.alchemical_network_planner.relative_alchemical_network_planner.RBFEAlchemicalNetworkPlanner property) (openfe.setup.alchemical_network_planner.relative_alchemical_network_planner.RelativeAlchemicalNetworkPlanner property) (openfe.setup.alchemical_network_planner.relative_alchemical_network_planner.RHFEAlchemicalNetworkPlanner property) max3d (openfe.setup.atom_mapping.LomapAtomMapper attribute) mcsr_score() (in module openfe.setup.atom_mapping.lomap_scorers) MetadataStore (class in openfe.storage.metadatastore) minimization_steps (openfe.protocols.settings.SimulationSettings attribute) mncar_score() (in module openfe.setup.atom_mapping.lomap_scorers) module openfe openfe.analysis openfe.analysis.plotting openfe.orchestration openfe.protocols openfe.protocols.openmm_rfe openfe.protocols.settings openfe.setup openfe.setup.alchemical_network_planner openfe.setup.alchemical_network_planner.abstract_alchemical_network_planner openfe.setup.alchemical_network_planner.relative_alchemical_network_planner openfe.setup.atom_mapping openfe.setup.atom_mapping.lomap_scorers openfe.setup.atom_mapping.perses_scorers openfe.setup.ligand_network_planning openfe.setup.system openfe.storage openfe.storage.metadatastore openfe.storage.resultclient openfe.storage.resultserver openfe.utils openfe.utils.custom_typing N n_repeats (openfe.protocols.settings.AlchemicalSamplerSettings attribute) n_replicas (openfe.protocols.settings.AlchemicalSamplerSettings attribute) n_restart_attempts (openfe.protocols.settings.IntegratorSettings attribute) n_steps (openfe.protocols.settings.IntegratorSettings attribute) name (openfe.protocols.openmm_rfe.RelativeHybridTopologyProtocolUnit property) (openfe.protocols.ProtocolDAG attribute) (openfe.protocols.ProtocolUnit property) (openfe.protocols.ProtocolUnitFailure property) (openfe.protocols.ProtocolUnitResult property) (openfe.setup.AlchemicalNetwork property) (openfe.setup.system.ChemicalSystem property) (openfe.setup.system.Component property) (openfe.setup.system.ProteinComponent property) (openfe.setup.system.SmallMoleculeComponent property) (openfe.setup.system.SolventComponent property) (openfe.setup.Transformation property) negative_ion (openfe.setup.system.SolventComponent property) neutralize (openfe.setup.system.SolventComponent property) nodes (openfe.setup.AlchemicalNetwork property) (openfe.setup.LigandNetwork property) nonbonded_cutoff (openfe.protocols.settings.SystemSettings attribute) nonbonded_method (openfe.protocols.settings.SystemSettings attribute) O OEMol (in module openfe.utils.custom_typing) ok() (openfe.protocols.ProtocolDAGResult method) (openfe.protocols.ProtocolUnitFailure static method) (openfe.protocols.ProtocolUnitResult static method) online_analysis_interval (openfe.protocols.settings.AlchemicalSamplerSettings attribute) online_analysis_minimum_iterations (openfe.protocols.settings.AlchemicalSamplerSettings attribute) online_analysis_target_error (openfe.protocols.settings.AlchemicalSamplerSettings attribute) openfe module openfe-gather command line option --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.analysis module openfe.analysis.plotting module openfe.orchestration module openfe.protocols module openfe.protocols.openmm_rfe module openfe.protocols.settings module openfe.setup module openfe.setup.alchemical_network_planner module openfe.setup.alchemical_network_planner.abstract_alchemical_network_planner module openfe.setup.alchemical_network_planner.relative_alchemical_network_planner module openfe.setup.atom_mapping module openfe.setup.atom_mapping.lomap_scorers module openfe.setup.atom_mapping.perses_scorers module openfe.setup.ligand_network_planning module openfe.setup.system module openfe.storage module openfe.storage.metadatastore module openfe.storage.resultclient module openfe.storage.resultserver module openfe.utils module openfe.utils.custom_typing module output_filename (openfe.protocols.settings.SimulationSettings attribute) output_indices (openfe.protocols.settings.SimulationSettings attribute) output_structure (openfe.protocols.settings.SimulationSettings attribute) outputs (openfe.protocols.ProtocolUnitFailure property) (openfe.protocols.ProtocolUnitResult property) P path (openfe.storage.resultclient.CloneResult property) (openfe.storage.resultclient.ExtensionResult property) (openfe.storage.resultclient.ResultClient property) (openfe.storage.resultclient.TransformationResult property) PerFileJSONMetadataStore (class in openfe.storage.metadatastore) PersesAtomMapper (class in openfe.setup.atom_mapping) ph (openfe.protocols.settings.ThermoSettings attribute) plot_convergence() (in module openfe.analysis.plotting) plot_lambda_transition_matrix() (in module openfe.analysis.plotting) plot_replica_timeseries() (in module openfe.analysis.plotting) positive_ion (openfe.setup.system.SolventComponent property) preserve_chirality (openfe.setup.atom_mapping.PersesAtomMapper attribute) pressure (openfe.protocols.settings.ThermoSettings attribute) production_iterations() (openfe.protocols.openmm_rfe.RelativeHybridTopologyProtocolResult method) production_length (openfe.protocols.settings.SimulationSettings attribute) ProteinComponent (class in openfe.setup.system) Protocol (class in openfe.protocols) protocol (openfe.setup.Transformation property) PROTOCOL_GENERATOR (in module openfe.setup.alchemical_network_planner.relative_alchemical_network_planner) protocol_unit_failures (openfe.protocols.ProtocolDAGResult property) protocol_unit_results (openfe.protocols.ProtocolDAGResult property) protocol_unit_successes (openfe.protocols.ProtocolDAGResult property) protocol_units (openfe.protocols.ProtocolDAG attribute) ProtocolDAG (class in openfe.protocols) ProtocolDAGResult (class in openfe.protocols) ProtocolResult (class in openfe.protocols) ProtocolUnit (class in openfe.protocols) ProtocolUnitFailure (class in openfe.protocols) ProtocolUnitResult (class in openfe.protocols) R RBFEAlchemicalNetworkPlanner (class in openfe.setup.alchemical_network_planner.relative_alchemical_network_planner) reassign_velocities (openfe.protocols.settings.IntegratorSettings attribute) redox_potential (openfe.protocols.settings.ThermoSettings attribute) RelativeAlchemicalNetworkPlanner (class in openfe.setup.alchemical_network_planner.relative_alchemical_network_planner) RelativeHybridTopologyProtocol (class in openfe.protocols.openmm_rfe) RelativeHybridTopologyProtocolResult (class in openfe.protocols.openmm_rfe) RelativeHybridTopologyProtocolUnit (class in openfe.protocols.openmm_rfe) remove_com (openfe.protocols.settings.OpenMMSystemGeneratorFFSettings attribute) requires_package() (in module openfe.utils) result_cls (openfe.protocols.openmm_rfe.RelativeHybridTopologyProtocol attribute) (openfe.protocols.Protocol attribute) result_graph (openfe.protocols.ProtocolDAGResult property) result_server (openfe.storage.resultclient.CloneResult property) (openfe.storage.resultclient.ExtensionResult property) (openfe.storage.resultclient.ResultClient property) (openfe.storage.resultclient.TransformationResult property) result_to_unit() (openfe.protocols.ProtocolDAGResult method) ResultClient (class in openfe.storage.resultclient) ResultServer (class in openfe.storage.resultserver) RHFEAlchemicalNetworkPlanner (class in openfe.setup.alchemical_network_planner.relative_alchemical_network_planner) rigid_water (openfe.protocols.settings.OpenMMSystemGeneratorFFSettings attribute) ROOTDIR openfe-gather command line option run() (openfe.protocols.openmm_rfe.RelativeHybridTopologyProtocolUnit method) S sampler_method (openfe.protocols.settings.AlchemicalSamplerSettings attribute) seed (openfe.setup.atom_mapping.LomapAtomMapper attribute) settings (openfe.protocols.openmm_rfe.RelativeHybridTopologyProtocol property) (openfe.protocols.Protocol property) shift (openfe.setup.atom_mapping.LomapAtomMapper attribute) simulation_settings (openfe.protocols.openmm_rfe.RelativeHybridTopologyProtocolSettings attribute) small_molecule_forcefield (openfe.protocols.settings.OpenMMSystemGeneratorFFSettings attribute) SmallMoleculeComponent (class in openfe.setup.system) smiles (openfe.setup.system.ProteinComponent property) (openfe.setup.system.SmallMoleculeComponent property) (openfe.setup.system.SolventComponent property) softcore_alpha (openfe.protocols.settings.AlchemicalSettings attribute) softcore_LJ_v2 (openfe.protocols.settings.AlchemicalSettings attribute) solvation_settings (openfe.protocols.openmm_rfe.RelativeHybridTopologyProtocolSettings attribute) solvent_model (openfe.protocols.settings.SolvationSettings attribute) solvent_padding (openfe.protocols.settings.SolvationSettings attribute) SolventComponent (class in openfe.setup.system) source_key (openfe.protocols.ProtocolUnitFailure property) (openfe.protocols.ProtocolUnitResult property) start_time (openfe.protocols.ProtocolUnitFailure property) (openfe.protocols.ProtocolUnitResult property) stateA (openfe.setup.Transformation property) stateB (openfe.setup.Transformation property) store_bytes() (openfe.storage.resultserver.ResultServer method) store_metadata() (openfe.storage.metadatastore.JSONMetadataStore method) (openfe.storage.metadatastore.MetadataStore method) (openfe.storage.metadatastore.PerFileJSONMetadataStore method) store_network() (openfe.storage.resultclient.ResultClient method) store_path() (openfe.storage.resultserver.ResultServer method) store_transformation() (openfe.storage.resultclient.ResultClient 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) system_settings (openfe.protocols.openmm_rfe.RelativeHybridTopologyProtocolSettings attribute) T temperature (openfe.protocols.settings.ThermoSettings attribute) terminal_protocol_unit_results (openfe.protocols.ProtocolDAGResult property) thermo_settings (openfe.protocols.openmm_rfe.RelativeHybridTopologyProtocolSettings attribute) (openfe.protocols.settings.Settings attribute) threed (openfe.setup.atom_mapping.LomapAtomMapper attribute) time (openfe.setup.atom_mapping.LomapAtomMapper attribute) timestep (openfe.protocols.settings.IntegratorSettings attribute) tmcsr_score() (in module openfe.setup.atom_mapping.lomap_scorers) to_dict() (openfe.utils.GufeTokenizable method) to_graphml() (openfe.setup.AlchemicalNetwork method) (openfe.setup.LigandNetwork method) to_json() (openfe.setup.system.ProteinComponent method) (openfe.setup.system.SmallMoleculeComponent method) to_keyed_dict() (openfe.utils.GufeTokenizable method) to_openff() (openfe.setup.system.SmallMoleculeComponent method) to_openmm_positions() (openfe.setup.system.ProteinComponent method) to_openmm_topology() (openfe.setup.system.ProteinComponent method) to_pdb_file() (openfe.setup.system.ProteinComponent method) to_pdbx_file() (openfe.setup.system.ProteinComponent method) to_rbfe_alchemical_network() (openfe.setup.LigandNetwork method) to_rdkit() (openfe.setup.system.ProteinComponent method) (openfe.setup.system.SmallMoleculeComponent method) to_sdf() (openfe.setup.system.SmallMoleculeComponent method) to_shallow_dict() (openfe.utils.GufeTokenizable method) total_charge (openfe.setup.system.ChemicalSystem property) (openfe.setup.system.Component property) (openfe.setup.system.ProteinComponent property) (openfe.setup.system.SmallMoleculeComponent property) (openfe.setup.system.SolventComponent property) traceback (openfe.protocols.ProtocolUnitFailure property) TRANSFORMATION openfe-quickrun command line option Transformation (class in openfe.setup) transformation_key (openfe.protocols.ProtocolDAG attribute) transformation_protocol (openfe.setup.alchemical_network_planner.relative_alchemical_network_planner.RBFEAlchemicalNetworkPlanner property) (openfe.setup.alchemical_network_planner.relative_alchemical_network_planner.RelativeAlchemicalNetworkPlanner property) (openfe.setup.alchemical_network_planner.relative_alchemical_network_planner.RHFEAlchemicalNetworkPlanner property) TransformationResult (class in openfe.storage.resultclient) 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.protocols.ProtocolDAGResult method) unit_to_result() (openfe.protocols.ProtocolDAGResult method) unsampled_endstates (openfe.protocols.settings.AlchemicalSettings attribute) use_dispersion_correction (openfe.protocols.settings.AlchemicalSettings attribute) use_positions (openfe.setup.atom_mapping.PersesAtomMapper attribute) V validate() (openfe.storage.resultserver.ResultServer method) values() (openfe.storage.metadatastore.JSONMetadataStore method) (openfe.storage.metadatastore.MetadataStore method) (openfe.storage.metadatastore.PerFileJSONMetadataStore method) W with_annotations() (openfe.setup.atom_mapping.LigandAtomMapping method) without_oechem_backend() (in module openfe.utils)