Index A | B | C | D | E | F | G | H | I | K | L | M | N | O | P | R | S | T | U A AlchemicalNetwork (class in gufe.network) arbitrary_types_allowed (gufe.settings.models.BaseForceFieldSettings.Config attribute) (gufe.settings.models.OpenMMSystemGeneratorFFSettings.Config attribute) (gufe.settings.models.Settings.Config attribute) (gufe.settings.models.SettingsBaseModel.Config attribute) (gufe.settings.models.ThermoSettings.Config attribute) as_protein_smallmolecule_solvent() (gufe.chemicalsystem.ChemicalSystem class method) as_smallmolecule_solvent() (gufe.chemicalsystem.ChemicalSystem class method) B BaseForceFieldSettings (class in gufe.settings.models) BaseForceFieldSettings.Config (class in gufe.settings.models) C ChemicalSystem (class in gufe.chemicalsystem) Component (class in gufe.components) components (gufe.chemicalsystem.ChemicalSystem property) constraint_check() (gufe.settings.models.OpenMMSystemGeneratorFFSettings class method) constraints (gufe.settings.models.OpenMMSystemGeneratorFFSettings attribute) copy_with_replacements() (gufe.components.SmallMoleculeComponent method) (gufe.tokenization.GufeTokenizable method) create() (gufe.protocols.Protocol method) (gufe.transformations.NonTransformation method) (gufe.transformations.Transformation method) D data (gufe.protocols.ProtocolResult property) default_settings() (gufe.protocols.Protocol class method) defaults() (gufe.tokenization.GufeTokenizable class method) dependencies (gufe.protocols.ProtocolUnit property) (gufe.protocols.ProtocolUnitFailure property) (gufe.protocols.ProtocolUnitResult property) dump() (gufe.transformations.NonTransformation method) (gufe.transformations.Transformation method) E edges (gufe.network.AlchemicalNetwork property) end_time (gufe.protocols.ProtocolUnitFailure property) (gufe.protocols.ProtocolUnitResult property) exception (gufe.protocols.ProtocolUnitFailure property) execute() (gufe.protocols.ProtocolUnit method) extends_key (gufe.protocols.ProtocolDAG attribute) extra (gufe.settings.models.BaseForceFieldSettings.Config attribute) (gufe.settings.models.OpenMMSystemGeneratorFFSettings.Config attribute) (gufe.settings.models.Settings.Config attribute) (gufe.settings.models.SettingsBaseModel.Config attribute) (gufe.settings.models.ThermoSettings.Config attribute) F forcefield_settings (gufe.settings.models.Settings attribute) forcefields (gufe.settings.models.OpenMMSystemGeneratorFFSettings attribute) from_dict() (gufe.tokenization.GufeTokenizable class method) from_graphml() (gufe.network.AlchemicalNetwork class method) from_json() (gufe.components.ProteinComponent class method) (gufe.components.SmallMoleculeComponent class method) from_keyed_dict() (gufe.tokenization.GufeTokenizable class method) from_openff() (gufe.components.SmallMoleculeComponent class method) from_pdb_file() (gufe.components.ProteinComponent class method) from_pdbx_file() (gufe.components.ProteinComponent class method) from_rdkit() (gufe.components.ProteinComponent class method) (gufe.components.SmallMoleculeComponent class method) from_sdf_file() (gufe.components.SmallMoleculeComponent class method) from_sdf_string() (gufe.components.SmallMoleculeComponent class method) from_shallow_dict() (gufe.tokenization.GufeTokenizable class method) G gather() (gufe.protocols.Protocol method) (gufe.transformations.NonTransformation method) (gufe.transformations.Transformation method) get_defaults() (gufe.settings.models.Settings class method) get_estimate() (gufe.protocols.ProtocolResult method) get_uncertainty() (gufe.protocols.ProtocolResult method) graph (gufe.network.AlchemicalNetwork property) (gufe.protocols.ProtocolDAG attribute) gufe.settings.models module GufeTokenizable (class in gufe.tokenization) H hydrogen_mass (gufe.settings.models.OpenMMSystemGeneratorFFSettings attribute) I inputs (gufe.protocols.ProtocolUnit property) (gufe.protocols.ProtocolUnitFailure property) (gufe.protocols.ProtocolUnitResult property) ion_concentration (gufe.components.SolventComponent property) K key (gufe.tokenization.GufeTokenizable property) key_renamed() (in module gufe.tokenization) L load() (gufe.transformations.NonTransformation class method) (gufe.transformations.Transformation class method) logger (gufe.tokenization.GufeTokenizable property) M mapping (gufe.transformations.NonTransformation property) (gufe.transformations.Transformation property) module gufe.settings.models N name (gufe.chemicalsystem.ChemicalSystem property) (gufe.components.Component property) (gufe.components.ProteinComponent property) (gufe.components.SmallMoleculeComponent property) (gufe.components.SolventComponent property) (gufe.network.AlchemicalNetwork property) (gufe.protocols.ProtocolDAG attribute) (gufe.protocols.ProtocolUnit property) (gufe.protocols.ProtocolUnitFailure property) (gufe.protocols.ProtocolUnitResult property) (gufe.transformations.NonTransformation property) (gufe.transformations.Transformation property) negative_ion (gufe.components.SolventComponent property) nested_key_moved() (in module gufe.tokenization) neutralize (gufe.components.SolventComponent property) new_key_added() (in module gufe.tokenization) nodes (gufe.network.AlchemicalNetwork property) NonTransformation (class in gufe.transformations) O ok() (gufe.protocols.ProtocolDAGResult method) (gufe.protocols.ProtocolUnitFailure static method) (gufe.protocols.ProtocolUnitResult static method) old_key_removed() (in module gufe.tokenization) OpenMMSystemGeneratorFFSettings (class in gufe.settings.models) OpenMMSystemGeneratorFFSettings.Config (class in gufe.settings.models) outputs (gufe.protocols.ProtocolUnitFailure property) (gufe.protocols.ProtocolUnitResult property) P ph (gufe.settings.models.ThermoSettings attribute) positive_ion (gufe.components.SolventComponent property) pressure (gufe.settings.models.ThermoSettings attribute) ProteinComponent (class in gufe.components) Protocol (class in gufe.protocols) protocol (gufe.transformations.NonTransformation property) (gufe.transformations.Transformation property) protocol_unit_failures (gufe.protocols.ProtocolDAGResult property) protocol_unit_results (gufe.protocols.ProtocolDAGResult property) protocol_unit_successes (gufe.protocols.ProtocolDAGResult property) protocol_units (gufe.protocols.ProtocolDAG attribute) ProtocolDAG (class in gufe.protocols) ProtocolDAGResult (class in gufe.protocols) ProtocolResult (class in gufe.protocols) ProtocolUnit (class in gufe.protocols) ProtocolUnitFailure (class in gufe.protocols) ProtocolUnitResult (class in gufe.protocols) R redox_potential (gufe.settings.models.ThermoSettings attribute) remove_com (gufe.settings.models.OpenMMSystemGeneratorFFSettings attribute) result_cls (gufe.protocols.Protocol attribute) result_graph (gufe.protocols.ProtocolDAGResult property) result_to_unit() (gufe.protocols.ProtocolDAGResult method) rigid_water (gufe.settings.models.OpenMMSystemGeneratorFFSettings attribute) S serialization_migration() (gufe.tokenization.GufeTokenizable class method) Settings (class in gufe.settings.models) settings (gufe.protocols.Protocol property) Settings.Config (class in gufe.settings.models) SettingsBaseModel (class in gufe.settings.models) SettingsBaseModel.Config (class in gufe.settings.models) small_molecule_forcefield (gufe.settings.models.OpenMMSystemGeneratorFFSettings attribute) SmallMoleculeComponent (class in gufe.components) smart_union (gufe.settings.models.BaseForceFieldSettings.Config attribute) (gufe.settings.models.OpenMMSystemGeneratorFFSettings.Config attribute) (gufe.settings.models.Settings.Config attribute) (gufe.settings.models.SettingsBaseModel.Config attribute) (gufe.settings.models.ThermoSettings.Config attribute) smiles (gufe.components.ProteinComponent property) (gufe.components.SmallMoleculeComponent property) (gufe.components.SolventComponent property) SolventComponent (class in gufe.components) source_key (gufe.protocols.ProtocolUnitFailure property) (gufe.protocols.ProtocolUnitResult property) start_time (gufe.protocols.ProtocolUnitFailure property) (gufe.protocols.ProtocolUnitResult property) stateA (gufe.transformations.NonTransformation property) (gufe.transformations.Transformation property) stateB (gufe.transformations.NonTransformation property) (gufe.transformations.Transformation property) system (gufe.transformations.NonTransformation property) T temperature (gufe.settings.models.ThermoSettings attribute) terminal_protocol_unit_results (gufe.protocols.ProtocolDAGResult property) thermo_settings (gufe.settings.models.Settings attribute) ThermoSettings (class in gufe.settings.models) ThermoSettings.Config (class in gufe.settings.models) to_dict() (gufe.tokenization.GufeTokenizable method) to_graphml() (gufe.network.AlchemicalNetwork method) to_json() (gufe.components.ProteinComponent method) (gufe.components.SmallMoleculeComponent method) to_keyed_dict() (gufe.tokenization.GufeTokenizable method) to_openff() (gufe.components.SmallMoleculeComponent method) to_openmm_positions() (gufe.components.ProteinComponent method) to_openmm_topology() (gufe.components.ProteinComponent method) to_pdb_file() (gufe.components.ProteinComponent method) to_pdbx_file() (gufe.components.ProteinComponent method) to_rdkit() (gufe.components.ProteinComponent method) (gufe.components.SmallMoleculeComponent method) to_sdf() (gufe.components.SmallMoleculeComponent method) to_shallow_dict() (gufe.tokenization.GufeTokenizable method) total_charge (gufe.chemicalsystem.ChemicalSystem property) (gufe.components.Component property) (gufe.components.ProteinComponent property) (gufe.components.SmallMoleculeComponent property) (gufe.components.SolventComponent property) traceback (gufe.protocols.ProtocolUnitFailure property) Transformation (class in gufe.transformations) transformation_key (gufe.protocols.ProtocolDAG attribute) U unit_to_all_results() (gufe.protocols.ProtocolDAGResult method) unit_to_result() (gufe.protocols.ProtocolDAGResult method)