Index Symbols | A | B | C | D | E | F | G | H | I | L | M | N | O | P | R | S | T | U | W Symbols --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 --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-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 A alchemical_sampler_settings (openfe.protocols.openmm_rfe.equil_rfe_settings.RelativeHybridTopologyProtocolSettings attribute) alchemical_settings (openfe.protocols.openmm_rfe.equil_rfe_settings.RelativeHybridTopologyProtocolSettings attribute) AlchemicalNetwork (class in openfe) 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) ChemicalSystem (class in openfe) collision_rate (openfe.protocols.openmm_rfe.equil_rfe_settings.IntegratorSettings attribute) componentA_to_componentB (openfe.LigandAtomMapping property) componentA_unique (openfe.LigandAtomMapping property) componentB_to_componentA (openfe.LigandAtomMapping property) componentB_unique (openfe.LigandAtomMapping property) components (openfe.ChemicalSystem attribute) 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) create() (openfe.Protocol method) D data (openfe.ProtocolResult attribute) 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) dependencies (openfe.ProtocolUnit property) (openfe.ProtocolUnitResult property) draw_to_file() (openfe.LigandAtomMapping method) E EasyChemicalSystemGenerator (class in openfe.setup.chemicalsystem_generator) ecr_score() (in module openfe.setup.atom_mapping.lomap_scorers) edges (openfe.AlchemicalNetwork attribute) end_time (openfe.ProtocolUnitResult property) engine_settings (openfe.protocols.openmm_rfe.equil_rfe_settings.RelativeHybridTopologyProtocolSettings attribute) equilibration_length (openfe.protocols.openmm_rfe.equil_rfe_settings.SimulationSettings attribute) execute() (openfe.ProtocolUnit method) execute_DAG() (in module openfe) extends_key (openfe.ProtocolDAG attribute) (openfe.ProtocolDAGResult 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) forcefields (openfe.protocols.openmm_rfe.equil_rfe_settings.OpenMMSystemGeneratorFFSettings attribute) G gamma0 (openfe.protocols.openmm_rfe.equil_rfe_settings.AlchemicalSamplerSettings attribute) gather() (openfe.Protocol method) 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) get_distances() (openfe.LigandAtomMapping method) graph (openfe.ProtocolDAG attribute) (openfe.ProtocolDAGResult attribute) 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 attribute) integrator_settings (openfe.protocols.openmm_rfe.equil_rfe_settings.RelativeHybridTopologyProtocolSettings attribute) interpolate_old_and_new_14s (openfe.protocols.openmm_rfe.equil_rfe_settings.AlchemicalSettings attribute) L lambda_functions (openfe.protocols.openmm_rfe.equil_rfe_settings.AlchemicalSettings attribute) lambda_windows (openfe.protocols.openmm_rfe.equil_rfe_settings.AlchemicalSettings attribute) LigandAtomMapper (class in openfe) LigandAtomMapping (class in openfe) LomapAtomMapper (class in openfe.setup) M mapping (openfe.Transformation 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 openfe 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 attribute) (openfe.ChemicalSystem attribute) (openfe.ProtocolDAG attribute) (openfe.ProtocolDAGResult attribute) (openfe.ProtocolUnit attribute) (openfe.Transformation attribute) nodes (openfe.AlchemicalNetwork attribute) nonbonded_cutoff (openfe.protocols.openmm_rfe.equil_rfe_settings.SystemSettings attribute) nonbonded_method (openfe.protocols.openmm_rfe.equil_rfe_settings.SystemSettings attribute) O 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 -o ROOTDIR openfe-plan-rbfe-network command line option --molecules --output-dir --protein -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 output_filename (openfe.protocols.openmm_rfe.equil_rfe_settings.SimulationSettings attribute) output_indices (openfe.protocols.openmm_rfe.equil_rfe_settings.SimulationSettings attribute) P PersesAtomMapper (class in openfe.setup) ph (openfe.protocols.openmm_rfe.equil_rfe_settings.ThermoSettings attribute) pressure (openfe.protocols.openmm_rfe.equil_rfe_settings.ThermoSettings attribute) production_length (openfe.protocols.openmm_rfe.equil_rfe_settings.SimulationSettings attribute) ProteinComponent (class in openfe) Protocol (class in openfe) protocol (openfe.Transformation attribute) protocol_unit_failures (openfe.ProtocolDAGResult property) protocol_unit_results (openfe.ProtocolDAGResult attribute) protocol_unit_successes (openfe.ProtocolDAGResult property) protocol_units (openfe.ProtocolDAG attribute) (openfe.ProtocolDAGResult 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) remove_com (openfe.protocols.openmm_rfe.equil_rfe_settings.OpenMMSystemGeneratorFFSettings attribute) result_cls (openfe.Protocol attribute) (openfe.protocols.openmm_rfe.RelativeHybridTopologyProtocol attribute) result_graph (openfe.ProtocolDAGResult attribute) 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) settings (openfe.Protocol property) simulation_settings (openfe.protocols.openmm_rfe.equil_rfe_settings.RelativeHybridTopologyProtocolSettings attribute) small_molecule_forcefield (openfe.protocols.openmm_rfe.equil_rfe_settings.OpenMMSystemGeneratorFFSettings attribute) SmallMoleculeComponent (class in openfe) softcore_alpha (openfe.protocols.openmm_rfe.equil_rfe_settings.AlchemicalSettings attribute) softcore_electrostatics (openfe.protocols.openmm_rfe.equil_rfe_settings.AlchemicalSettings attribute) softcore_electrostatics_alpha (openfe.protocols.openmm_rfe.equil_rfe_settings.AlchemicalSettings attribute) softcore_LJ_v2 (openfe.protocols.openmm_rfe.equil_rfe_settings.AlchemicalSettings attribute) softcore_sigma_Q (openfe.protocols.openmm_rfe.equil_rfe_settings.AlchemicalSettings attribute) solvation_settings (openfe.protocols.openmm_rfe.equil_rfe_settings.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) start_time (openfe.ProtocolUnitResult property) stateA (openfe.Transformation attribute) stateB (openfe.Transformation attribute) suggest_mappings() (openfe.LigandAtomMapper method) sulfonamides_score() (in module openfe.setup.atom_mapping.lomap_scorers) system_settings (openfe.protocols.openmm_rfe.equil_rfe_settings.RelativeHybridTopologyProtocolSettings attribute) T temperature (openfe.protocols.openmm_rfe.equil_rfe_settings.ThermoSettings attribute) terminal_protocol_unit_results (openfe.ProtocolDAGResult property) timestep (openfe.protocols.openmm_rfe.equil_rfe_settings.IntegratorSettings attribute) tmcsr_score() (in module openfe.setup.atom_mapping.lomap_scorers) TRANSFORMATION openfe-quickrun command line option Transformation (class in openfe) transformation_key (openfe.ProtocolDAG attribute) (openfe.ProtocolDAGResult attribute) 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) W with_annotations() (openfe.LigandAtomMapping method)