Index _ | A | B | C | D | E | F | G | H | I | K | L | M | N | O | P | R | S | T | U | V | W | X _ __init__() (openff.toolkit.topology.Atom method) (openff.toolkit.topology.Bond method) (openff.toolkit.topology.FrozenMolecule method) (openff.toolkit.topology.HierarchyElement method) (openff.toolkit.topology.HierarchyScheme method) (openff.toolkit.topology.ImproperDict method) (openff.toolkit.topology.Molecule method) (openff.toolkit.topology.Particle method) (openff.toolkit.topology.Topology method) (openff.toolkit.topology.ValenceDict method) (openff.toolkit.typing.engines.smirnoff.ForceField method) (openff.toolkit.typing.engines.smirnoff.io.ParameterIOHandler method) (openff.toolkit.typing.engines.smirnoff.io.XMLParameterIOHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.AngleHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.AngleType method) (openff.toolkit.typing.engines.smirnoff.parameters.BondHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.BondType method) (openff.toolkit.typing.engines.smirnoff.parameters.ChargeIncrementModelHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.ChargeIncrementType method) (openff.toolkit.typing.engines.smirnoff.parameters.ConstraintHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.ConstraintType method) (openff.toolkit.typing.engines.smirnoff.parameters.ElectrostaticsHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.GBSAHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.GBSAType method) (openff.toolkit.typing.engines.smirnoff.parameters.ImproperTorsionHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.ImproperTorsionType method) (openff.toolkit.typing.engines.smirnoff.parameters.IndexedMappedParameterAttribute method) (openff.toolkit.typing.engines.smirnoff.parameters.IndexedParameterAttribute method) (openff.toolkit.typing.engines.smirnoff.parameters.LibraryChargeHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.LibraryChargeType method) (openff.toolkit.typing.engines.smirnoff.parameters.MappedParameterAttribute method) (openff.toolkit.typing.engines.smirnoff.parameters.ParameterAttribute method) (openff.toolkit.typing.engines.smirnoff.parameters.ParameterHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.ParameterList method) (openff.toolkit.typing.engines.smirnoff.parameters.ParameterType method) (openff.toolkit.typing.engines.smirnoff.parameters.ProperTorsionHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.ProperTorsionType method) (openff.toolkit.typing.engines.smirnoff.parameters.ToolkitAM1BCCHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.vdWHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.vdWType method) (openff.toolkit.typing.engines.smirnoff.parameters.VirtualSiteHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.VirtualSiteType method) (openff.toolkit.utils.collections.ValidatedDict method) (openff.toolkit.utils.collections.ValidatedList method) (openff.toolkit.utils.serialization.Serializable method) (openff.toolkit.utils.toolkits.AmberToolsToolkitWrapper method) (openff.toolkit.utils.toolkits.BuiltInToolkitWrapper method) (openff.toolkit.utils.toolkits.NAGLToolkitWrapper method) (openff.toolkit.utils.toolkits.OpenEyeToolkitWrapper method) (openff.toolkit.utils.toolkits.RDKitToolkitWrapper method) (openff.toolkit.utils.toolkits.ToolkitRegistry method) (openff.toolkit.utils.toolkits.ToolkitWrapper method) A add_atom() (openff.toolkit.topology.Molecule method) add_bond() (openff.toolkit.topology.Atom method) (openff.toolkit.topology.Molecule method) add_conformer() (openff.toolkit.topology.Molecule method) add_constraint() (openff.toolkit.topology.Topology method) add_cosmetic_attribute() (openff.toolkit.typing.engines.smirnoff.parameters.AngleHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.AngleHandler.AngleType method) (openff.toolkit.typing.engines.smirnoff.parameters.AngleType method) (openff.toolkit.typing.engines.smirnoff.parameters.BondHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.BondHandler.BondType method) (openff.toolkit.typing.engines.smirnoff.parameters.BondType method) (openff.toolkit.typing.engines.smirnoff.parameters.ChargeIncrementModelHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.ChargeIncrementModelHandler.ChargeIncrementType method) (openff.toolkit.typing.engines.smirnoff.parameters.ChargeIncrementType method) (openff.toolkit.typing.engines.smirnoff.parameters.ConstraintHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.ConstraintHandler.ConstraintType method) (openff.toolkit.typing.engines.smirnoff.parameters.ConstraintType method) (openff.toolkit.typing.engines.smirnoff.parameters.ElectrostaticsHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.GBSAHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.GBSAHandler.GBSAType method) (openff.toolkit.typing.engines.smirnoff.parameters.GBSAType method) (openff.toolkit.typing.engines.smirnoff.parameters.ImproperTorsionHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.ImproperTorsionHandler.ImproperTorsionType method) (openff.toolkit.typing.engines.smirnoff.parameters.ImproperTorsionType method) (openff.toolkit.typing.engines.smirnoff.parameters.LibraryChargeHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.LibraryChargeHandler.LibraryChargeType method) (openff.toolkit.typing.engines.smirnoff.parameters.LibraryChargeType method) (openff.toolkit.typing.engines.smirnoff.parameters.ParameterHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.ParameterType method) (openff.toolkit.typing.engines.smirnoff.parameters.ProperTorsionHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.ProperTorsionHandler.ProperTorsionType method) (openff.toolkit.typing.engines.smirnoff.parameters.ProperTorsionType method) (openff.toolkit.typing.engines.smirnoff.parameters.ToolkitAM1BCCHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.vdWHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.vdWHandler.vdWType method) (openff.toolkit.typing.engines.smirnoff.parameters.vdWType method) (openff.toolkit.typing.engines.smirnoff.parameters.VirtualSiteHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.VirtualSiteHandler.VirtualSiteType method) (openff.toolkit.typing.engines.smirnoff.parameters.VirtualSiteType method) add_default_hierarchy_schemes() (openff.toolkit.topology.FrozenMolecule method) (openff.toolkit.topology.Molecule method) add_hierarchy_element() (openff.toolkit.topology.HierarchyScheme method) add_hierarchy_scheme() (openff.toolkit.topology.FrozenMolecule method) (openff.toolkit.topology.Molecule method) add_molecule() (openff.toolkit.topology.Topology method) add_parameter() (openff.toolkit.typing.engines.smirnoff.parameters.AngleHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.BondHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.ChargeIncrementModelHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.ConstraintHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.ElectrostaticsHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.GBSAHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.ImproperTorsionHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.LibraryChargeHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.ParameterHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.ProperTorsionHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.ToolkitAM1BCCHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.vdWHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.VirtualSiteHandler method) add_toolkit() (openff.toolkit.utils.toolkits.ToolkitRegistry method) all_subclasses() (in module openff.toolkit.utils.utils) amber_impropers (openff.toolkit.topology.FrozenMolecule property) (openff.toolkit.topology.Molecule property) (openff.toolkit.topology.Topology property) AmberToolsToolkitWrapper (class in openff.toolkit.utils.toolkits) AmbiguousAtomChemicalAssignment AmbiguousBondChemicalAssignment AngleHandler (class in openff.toolkit.typing.engines.smirnoff.parameters) AngleHandler.AngleType (class in openff.toolkit.typing.engines.smirnoff.parameters) angles (openff.toolkit.topology.FrozenMolecule property) (openff.toolkit.topology.Molecule property) (openff.toolkit.topology.Topology property) AngleType (class in openff.toolkit.typing.engines.smirnoff.parameters) AntechamberNotFoundError append() (openff.toolkit.typing.engines.smirnoff.parameters.ParameterList method) (openff.toolkit.utils.collections.ValidatedList method) apply_elf_conformer_selection() (openff.toolkit.topology.FrozenMolecule method) (openff.toolkit.topology.Molecule method) (openff.toolkit.utils.toolkits.OpenEyeToolkitWrapper method) (openff.toolkit.utils.toolkits.RDKitToolkitWrapper method) are_isomorphic() (openff.toolkit.topology.FrozenMolecule static method) (openff.toolkit.topology.Molecule static method) aromaticity_model (openff.toolkit.topology.Topology property) (openff.toolkit.typing.engines.smirnoff.ForceField property) assert_bonded() (openff.toolkit.topology.Topology method) assign_fractional_bond_orders() (openff.toolkit.topology.FrozenMolecule method) (openff.toolkit.topology.Molecule method) (openff.toolkit.utils.toolkits.AmberToolsToolkitWrapper method) (openff.toolkit.utils.toolkits.OpenEyeToolkitWrapper method) assign_partial_charges() (openff.toolkit.topology.FrozenMolecule method) (openff.toolkit.topology.Molecule method) (openff.toolkit.utils.toolkits.AmberToolsToolkitWrapper method) (openff.toolkit.utils.toolkits.BuiltInToolkitWrapper method) (openff.toolkit.utils.toolkits.NAGLToolkitWrapper method) (openff.toolkit.utils.toolkits.OpenEyeToolkitWrapper method) (openff.toolkit.utils.toolkits.RDKitToolkitWrapper method) Atom (class in openff.toolkit.topology) atom() (openff.toolkit.topology.FrozenMolecule method) (openff.toolkit.topology.HierarchyElement method) (openff.toolkit.topology.Molecule method) (openff.toolkit.topology.Topology method) atom_index() (openff.toolkit.topology.FrozenMolecule method) (openff.toolkit.topology.Molecule method) (openff.toolkit.topology.Topology method) atom_is_in_ring() (openff.toolkit.utils.toolkits.OpenEyeToolkitWrapper method) (openff.toolkit.utils.toolkits.RDKitToolkitWrapper method) atomic_number (openff.toolkit.topology.Atom property) AtomMappingWarning AtomNotInTopologyError atoms (openff.toolkit.topology.FrozenMolecule property) (openff.toolkit.topology.HierarchyElement property) (openff.toolkit.topology.Molecule property) (openff.toolkit.topology.Topology property) attribute_is_cosmetic() (openff.toolkit.typing.engines.smirnoff.parameters.AngleHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.AngleHandler.AngleType method) (openff.toolkit.typing.engines.smirnoff.parameters.AngleType method) (openff.toolkit.typing.engines.smirnoff.parameters.BondHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.BondHandler.BondType method) (openff.toolkit.typing.engines.smirnoff.parameters.BondType method) (openff.toolkit.typing.engines.smirnoff.parameters.ChargeIncrementModelHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.ChargeIncrementModelHandler.ChargeIncrementType method) (openff.toolkit.typing.engines.smirnoff.parameters.ChargeIncrementType method) (openff.toolkit.typing.engines.smirnoff.parameters.ConstraintHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.ConstraintHandler.ConstraintType method) (openff.toolkit.typing.engines.smirnoff.parameters.ConstraintType method) (openff.toolkit.typing.engines.smirnoff.parameters.ElectrostaticsHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.GBSAHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.GBSAHandler.GBSAType method) (openff.toolkit.typing.engines.smirnoff.parameters.GBSAType method) (openff.toolkit.typing.engines.smirnoff.parameters.ImproperTorsionHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.ImproperTorsionHandler.ImproperTorsionType method) (openff.toolkit.typing.engines.smirnoff.parameters.ImproperTorsionType method) (openff.toolkit.typing.engines.smirnoff.parameters.LibraryChargeHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.LibraryChargeHandler.LibraryChargeType method) (openff.toolkit.typing.engines.smirnoff.parameters.LibraryChargeType method) (openff.toolkit.typing.engines.smirnoff.parameters.ParameterHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.ParameterType method) (openff.toolkit.typing.engines.smirnoff.parameters.ProperTorsionHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.ProperTorsionHandler.ProperTorsionType method) (openff.toolkit.typing.engines.smirnoff.parameters.ProperTorsionType method) (openff.toolkit.typing.engines.smirnoff.parameters.ToolkitAM1BCCHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.vdWHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.vdWHandler.vdWType method) (openff.toolkit.typing.engines.smirnoff.parameters.vdWType method) (openff.toolkit.typing.engines.smirnoff.parameters.VirtualSiteHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.VirtualSiteHandler.VirtualSiteType method) (openff.toolkit.typing.engines.smirnoff.parameters.VirtualSiteType method) author (openff.toolkit.typing.engines.smirnoff.ForceField property) B Bond (class in openff.toolkit.topology) bond() (openff.toolkit.topology.FrozenMolecule method) (openff.toolkit.topology.Molecule method) (openff.toolkit.topology.Topology method) bond_is_in_ring() (openff.toolkit.utils.toolkits.OpenEyeToolkitWrapper method) (openff.toolkit.utils.toolkits.RDKitToolkitWrapper method) bonded_atoms (openff.toolkit.topology.Atom property) BondExistsError BondHandler (class in openff.toolkit.typing.engines.smirnoff.parameters) BondHandler.BondType (class in openff.toolkit.typing.engines.smirnoff.parameters) BondNotInTopologyError bonds (openff.toolkit.topology.Atom property) (openff.toolkit.topology.FrozenMolecule property) (openff.toolkit.topology.Molecule property) (openff.toolkit.topology.Topology property) BondType (class in openff.toolkit.typing.engines.smirnoff.parameters) box_vectors (openff.toolkit.topology.Topology property) BuiltInToolkitWrapper (class in openff.toolkit.utils.toolkits) C call() (openff.toolkit.utils.toolkits.ToolkitRegistry method) CallbackRegistrationError canonical_order_atoms() (openff.toolkit.topology.FrozenMolecule method) (openff.toolkit.topology.Molecule method) (openff.toolkit.utils.toolkits.OpenEyeToolkitWrapper method) (openff.toolkit.utils.toolkits.RDKitToolkitWrapper method) ChargeCalculationError ChargeIncrementModelHandler (class in openff.toolkit.typing.engines.smirnoff.parameters) ChargeIncrementModelHandler.ChargeIncrementType (class in openff.toolkit.typing.engines.smirnoff.parameters) ChargeIncrementType (class in openff.toolkit.typing.engines.smirnoff.parameters) ChargeMethodUnavailableError check_handler_compatibility() (openff.toolkit.typing.engines.smirnoff.parameters.AngleHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.BondHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.ChargeIncrementModelHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.ConstraintHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.ElectrostaticsHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.GBSAHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.ImproperTorsionHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.LibraryChargeHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.ParameterHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.ProperTorsionHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.ToolkitAM1BCCHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.vdWHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.VirtualSiteHandler method) chemical_environment_matches() (openff.toolkit.topology.FrozenMolecule method) (openff.toolkit.topology.Molecule method) (openff.toolkit.topology.Topology method) ChemicalEnvironmentParsingError clear() (openff.toolkit.topology.ImproperDict method) (openff.toolkit.topology.ValenceDict method) (openff.toolkit.typing.engines.smirnoff.parameters.ParameterList method) (openff.toolkit.utils.collections.ValidatedDict method) (openff.toolkit.utils.collections.ValidatedList method) clear_positions() (openff.toolkit.topology.Topology method) ConformerGenerationError conformers (openff.toolkit.topology.FrozenMolecule property) (openff.toolkit.topology.Molecule property) constrained_atom_pairs (openff.toolkit.topology.Topology property) ConstraintExsistsError ConstraintHandler (class in openff.toolkit.typing.engines.smirnoff.parameters) ConstraintHandler.ConstraintType (class in openff.toolkit.typing.engines.smirnoff.parameters) ConstraintType (class in openff.toolkit.typing.engines.smirnoff.parameters) convert_0_1_smirnoff_to_0_2() (in module openff.toolkit.utils.utils) convert_0_2_smirnoff_to_0_3() (in module openff.toolkit.utils.utils) converter() (openff.toolkit.typing.engines.smirnoff.parameters.IndexedMappedParameterAttribute method) (openff.toolkit.typing.engines.smirnoff.parameters.IndexedParameterAttribute method) (openff.toolkit.typing.engines.smirnoff.parameters.MappedParameterAttribute method) (openff.toolkit.typing.engines.smirnoff.parameters.ParameterAttribute method) copy() (openff.toolkit.typing.engines.smirnoff.parameters.ParameterList method) (openff.toolkit.utils.collections.ValidatedDict method) (openff.toolkit.utils.collections.ValidatedList method) count() (openff.toolkit.typing.engines.smirnoff.parameters.ParameterList method) (openff.toolkit.utils.collections.ValidatedList method) create_force() (openff.toolkit.typing.engines.smirnoff.parameters.AngleHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.BondHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.ChargeIncrementModelHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.ConstraintHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.ElectrostaticsHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.GBSAHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.ImproperTorsionHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.LibraryChargeHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.ParameterHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.ProperTorsionHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.ToolkitAM1BCCHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.vdWHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.VirtualSiteHandler method) create_interchange() (openff.toolkit.typing.engines.smirnoff.ForceField method) create_openmm_system() (openff.toolkit.typing.engines.smirnoff.ForceField method) D date (openff.toolkit.typing.engines.smirnoff.ForceField property) delete_cosmetic_attribute() (openff.toolkit.typing.engines.smirnoff.parameters.AngleHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.AngleHandler.AngleType method) (openff.toolkit.typing.engines.smirnoff.parameters.AngleType method) (openff.toolkit.typing.engines.smirnoff.parameters.BondHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.BondHandler.BondType method) (openff.toolkit.typing.engines.smirnoff.parameters.BondType method) (openff.toolkit.typing.engines.smirnoff.parameters.ChargeIncrementModelHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.ChargeIncrementModelHandler.ChargeIncrementType method) (openff.toolkit.typing.engines.smirnoff.parameters.ChargeIncrementType method) (openff.toolkit.typing.engines.smirnoff.parameters.ConstraintHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.ConstraintHandler.ConstraintType method) (openff.toolkit.typing.engines.smirnoff.parameters.ConstraintType method) (openff.toolkit.typing.engines.smirnoff.parameters.ElectrostaticsHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.GBSAHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.GBSAHandler.GBSAType method) (openff.toolkit.typing.engines.smirnoff.parameters.GBSAType method) (openff.toolkit.typing.engines.smirnoff.parameters.ImproperTorsionHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.ImproperTorsionHandler.ImproperTorsionType method) (openff.toolkit.typing.engines.smirnoff.parameters.ImproperTorsionType method) (openff.toolkit.typing.engines.smirnoff.parameters.LibraryChargeHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.LibraryChargeHandler.LibraryChargeType method) (openff.toolkit.typing.engines.smirnoff.parameters.LibraryChargeType method) (openff.toolkit.typing.engines.smirnoff.parameters.ParameterHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.ParameterType method) (openff.toolkit.typing.engines.smirnoff.parameters.ProperTorsionHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.ProperTorsionHandler.ProperTorsionType method) (openff.toolkit.typing.engines.smirnoff.parameters.ProperTorsionType method) (openff.toolkit.typing.engines.smirnoff.parameters.ToolkitAM1BCCHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.vdWHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.vdWHandler.vdWType method) (openff.toolkit.typing.engines.smirnoff.parameters.vdWType method) (openff.toolkit.typing.engines.smirnoff.parameters.VirtualSiteHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.VirtualSiteHandler.VirtualSiteType method) (openff.toolkit.typing.engines.smirnoff.parameters.VirtualSiteType method) delete_hierarchy_scheme() (openff.toolkit.topology.FrozenMolecule method) (openff.toolkit.topology.Molecule method) deregister_parameter_handler() (openff.toolkit.typing.engines.smirnoff.ForceField method) deregister_toolkit() (openff.toolkit.utils.toolkits.ToolkitRegistry method) DuplicateParameterError DuplicateUniqueMoleculeError DuplicateVirtualSiteTypeException E ElectrostaticsHandler (class in openff.toolkit.typing.engines.smirnoff.parameters) enumerate_protomers() (openff.toolkit.topology.FrozenMolecule method) (openff.toolkit.topology.Molecule method) (openff.toolkit.utils.toolkits.OpenEyeToolkitWrapper method) enumerate_stereoisomers() (openff.toolkit.topology.FrozenMolecule method) (openff.toolkit.topology.Molecule method) (openff.toolkit.utils.toolkits.OpenEyeToolkitWrapper method) (openff.toolkit.utils.toolkits.RDKitToolkitWrapper method) enumerate_tautomers() (openff.toolkit.topology.FrozenMolecule method) (openff.toolkit.topology.Molecule method) (openff.toolkit.utils.toolkits.OpenEyeToolkitWrapper method) (openff.toolkit.utils.toolkits.RDKitToolkitWrapper method) extend() (openff.toolkit.typing.engines.smirnoff.parameters.ParameterList method) (openff.toolkit.utils.collections.ValidatedList method) F find_matches() (openff.toolkit.typing.engines.smirnoff.parameters.AngleHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.BondHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.ChargeIncrementModelHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.ConstraintHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.ElectrostaticsHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.GBSAHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.ImproperTorsionHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.LibraryChargeHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.ParameterHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.ProperTorsionHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.ToolkitAM1BCCHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.vdWHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.VirtualSiteHandler method) find_rotatable_bonds() (openff.toolkit.topology.FrozenMolecule method) (openff.toolkit.topology.Molecule method) find_smarts_matches() (openff.toolkit.utils.toolkits.OpenEyeToolkitWrapper method) (openff.toolkit.utils.toolkits.RDKitToolkitWrapper method) ForceField (class in openff.toolkit.typing.engines.smirnoff) formal_charge (openff.toolkit.topology.Atom property) FractionalBondOrderInterpolationMethodUnsupportedError from_bson() (openff.toolkit.topology.Atom class method) (openff.toolkit.topology.Bond class method) (openff.toolkit.topology.FrozenMolecule class method) (openff.toolkit.topology.Molecule class method) (openff.toolkit.topology.Particle class method) (openff.toolkit.topology.Topology class method) (openff.toolkit.utils.serialization.Serializable class method) from_dict() (openff.toolkit.topology.Atom class method) (openff.toolkit.topology.Bond class method) (openff.toolkit.topology.FrozenMolecule class method) (openff.toolkit.topology.Molecule class method) (openff.toolkit.topology.Particle class method) (openff.toolkit.topology.Topology class method) from_file() (openff.toolkit.topology.FrozenMolecule class method) (openff.toolkit.topology.Molecule class method) (openff.toolkit.utils.toolkits.AmberToolsToolkitWrapper method) (openff.toolkit.utils.toolkits.BuiltInToolkitWrapper method) (openff.toolkit.utils.toolkits.NAGLToolkitWrapper method) (openff.toolkit.utils.toolkits.OpenEyeToolkitWrapper method) (openff.toolkit.utils.toolkits.RDKitToolkitWrapper method) (openff.toolkit.utils.toolkits.ToolkitWrapper method) from_file_obj() (openff.toolkit.utils.toolkits.AmberToolsToolkitWrapper method) (openff.toolkit.utils.toolkits.BuiltInToolkitWrapper method) (openff.toolkit.utils.toolkits.NAGLToolkitWrapper method) (openff.toolkit.utils.toolkits.OpenEyeToolkitWrapper method) (openff.toolkit.utils.toolkits.RDKitToolkitWrapper method) (openff.toolkit.utils.toolkits.ToolkitWrapper method) from_inchi() (openff.toolkit.topology.FrozenMolecule class method) (openff.toolkit.topology.Molecule class method) (openff.toolkit.utils.toolkits.OpenEyeToolkitWrapper method) (openff.toolkit.utils.toolkits.RDKitToolkitWrapper method) from_iupac() (openff.toolkit.topology.FrozenMolecule class method) (openff.toolkit.topology.Molecule class method) (openff.toolkit.utils.toolkits.OpenEyeToolkitWrapper method) from_json() (openff.toolkit.topology.Atom class method) (openff.toolkit.topology.Bond class method) (openff.toolkit.topology.FrozenMolecule class method) (openff.toolkit.topology.Molecule class method) (openff.toolkit.topology.Particle class method) (openff.toolkit.topology.Topology class method) (openff.toolkit.utils.serialization.Serializable class method) from_mapped_smiles() (openff.toolkit.topology.FrozenMolecule class method) (openff.toolkit.topology.Molecule class method) from_mdtraj() (openff.toolkit.topology.Topology class method) from_messagepack() (openff.toolkit.topology.Atom class method) (openff.toolkit.topology.Bond class method) (openff.toolkit.topology.FrozenMolecule class method) (openff.toolkit.topology.Molecule class method) (openff.toolkit.topology.Particle class method) (openff.toolkit.topology.Topology class method) (openff.toolkit.utils.serialization.Serializable class method) from_molecule() (openff.toolkit.typing.engines.smirnoff.parameters.LibraryChargeHandler.LibraryChargeType class method) (openff.toolkit.typing.engines.smirnoff.parameters.LibraryChargeType class method) from_molecules() (openff.toolkit.topology.Topology class method) from_object() (openff.toolkit.utils.toolkits.OpenEyeToolkitWrapper method) (openff.toolkit.utils.toolkits.RDKitToolkitWrapper method) from_openeye() (openff.toolkit.topology.FrozenMolecule class method) (openff.toolkit.topology.Molecule class method) (openff.toolkit.utils.toolkits.OpenEyeToolkitWrapper static method) from_openmm() (openff.toolkit.topology.Topology class method) from_pdb() (openff.toolkit.topology.Topology class method) from_pdb_and_smiles() (openff.toolkit.topology.FrozenMolecule class method) (openff.toolkit.topology.Molecule class method) (openff.toolkit.utils.toolkits.RDKitToolkitWrapper method) from_pickle() (openff.toolkit.topology.Atom class method) (openff.toolkit.topology.Bond class method) (openff.toolkit.topology.FrozenMolecule class method) (openff.toolkit.topology.Molecule class method) (openff.toolkit.topology.Particle class method) (openff.toolkit.topology.Topology class method) (openff.toolkit.utils.serialization.Serializable class method) from_polymer_pdb() (openff.toolkit.topology.FrozenMolecule class method) (openff.toolkit.topology.Molecule class method) from_qcschema() (openff.toolkit.topology.FrozenMolecule class method) (openff.toolkit.topology.Molecule class method) from_rdkit() (openff.toolkit.topology.FrozenMolecule class method) (openff.toolkit.topology.Molecule class method) (openff.toolkit.utils.toolkits.RDKitToolkitWrapper method) from_smiles() (openff.toolkit.topology.FrozenMolecule class method) (openff.toolkit.topology.Molecule class method) (openff.toolkit.utils.toolkits.OpenEyeToolkitWrapper method) (openff.toolkit.utils.toolkits.RDKitToolkitWrapper method) from_toml() (openff.toolkit.topology.Atom class method) (openff.toolkit.topology.Bond class method) (openff.toolkit.topology.FrozenMolecule class method) (openff.toolkit.topology.Molecule class method) (openff.toolkit.topology.Particle class method) (openff.toolkit.topology.Topology class method) (openff.toolkit.utils.serialization.Serializable class method) from_topology() (openff.toolkit.topology.FrozenMolecule class method) (openff.toolkit.topology.Molecule class method) from_xml() (openff.toolkit.topology.Atom class method) (openff.toolkit.topology.Bond class method) (openff.toolkit.topology.FrozenMolecule class method) (openff.toolkit.topology.Molecule class method) (openff.toolkit.topology.Particle class method) (openff.toolkit.topology.Topology class method) (openff.toolkit.utils.serialization.Serializable class method) from_yaml() (openff.toolkit.topology.Atom class method) (openff.toolkit.topology.Bond class method) (openff.toolkit.topology.FrozenMolecule class method) (openff.toolkit.topology.Molecule class method) (openff.toolkit.topology.Particle class method) (openff.toolkit.topology.Topology class method) (openff.toolkit.utils.serialization.Serializable class method) fromkeys() (openff.toolkit.utils.collections.ValidatedDict method) FrozenMolecule (class in openff.toolkit.topology) G GAFFAtomTypeWarning GBSAHandler (class in openff.toolkit.typing.engines.smirnoff.parameters) GBSAHandler.GBSAType (class in openff.toolkit.typing.engines.smirnoff.parameters) GBSAType (class in openff.toolkit.typing.engines.smirnoff.parameters) generate_conformers() (openff.toolkit.topology.FrozenMolecule method) (openff.toolkit.topology.Molecule method) (openff.toolkit.utils.toolkits.OpenEyeToolkitWrapper method) (openff.toolkit.utils.toolkits.RDKitToolkitWrapper method) generate_unique_atom_names() (openff.toolkit.topology.FrozenMolecule method) (openff.toolkit.topology.HierarchyElement method) (openff.toolkit.topology.Molecule method) get() (openff.toolkit.topology.ImproperDict method) (openff.toolkit.topology.ValenceDict method) (openff.toolkit.utils.collections.ValidatedDict method) get_available_charge_methods() (openff.toolkit.topology.FrozenMolecule method) (openff.toolkit.topology.Molecule method) get_available_force_fields() (in module openff.toolkit.typing.engines.smirnoff) get_bond_between() (openff.toolkit.topology.FrozenMolecule method) (openff.toolkit.topology.Molecule method) (openff.toolkit.topology.Topology method) get_data_file_path() (in module openff.toolkit.utils.utils) get_molecule_parameterIDs() (in module openff.toolkit.utils.utils) get_parameter() (openff.toolkit.typing.engines.smirnoff.parameters.AngleHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.BondHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.ChargeIncrementModelHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.ConstraintHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.ElectrostaticsHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.GBSAHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.ImproperTorsionHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.LibraryChargeHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.ParameterHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.ProperTorsionHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.ToolkitAM1BCCHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.vdWHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.VirtualSiteHandler method) get_parameter_handler() (openff.toolkit.typing.engines.smirnoff.ForceField method) get_parameter_io_handler() (openff.toolkit.typing.engines.smirnoff.ForceField method) get_partial_charges() (openff.toolkit.typing.engines.smirnoff.ForceField method) get_positions() (openff.toolkit.topology.Topology method) get_tagged_smarts_connectivity() (openff.toolkit.utils.toolkits.OpenEyeToolkitWrapper method) (openff.toolkit.utils.toolkits.RDKitToolkitWrapper method) H has_unique_atom_names (openff.toolkit.topology.FrozenMolecule property) (openff.toolkit.topology.HierarchyElement property) (openff.toolkit.topology.Molecule property) hierarchy_iterator() (openff.toolkit.topology.Topology method) hierarchy_schemes (openff.toolkit.topology.FrozenMolecule property) (openff.toolkit.topology.Molecule property) HierarchyElement (class in openff.toolkit.topology) HierarchyIteratorNameConflictError HierarchyScheme (class in openff.toolkit.topology) HierarchySchemeNotFoundException HierarchySchemeWithIteratorNameAlreadyRegisteredException hill_formula (openff.toolkit.topology.FrozenMolecule property) (openff.toolkit.topology.Molecule property) I identical_molecule_groups (openff.toolkit.topology.Topology property) ImproperDict (class in openff.toolkit.topology) impropers (openff.toolkit.topology.FrozenMolecule property) (openff.toolkit.topology.Molecule property) (openff.toolkit.topology.Topology property) ImproperTorsionHandler (class in openff.toolkit.typing.engines.smirnoff.parameters) ImproperTorsionHandler.ImproperTorsionType (class in openff.toolkit.typing.engines.smirnoff.parameters) ImproperTorsionType (class in openff.toolkit.typing.engines.smirnoff.parameters) InChIParseError IncompatibleParameterError IncompatibleShapeError IncompatibleTypeError IncompatibleUnitError InconsistentStereochemistryError IncorrectNumConformersError IncorrectNumConformersWarning index() (openff.toolkit.typing.engines.smirnoff.parameters.ParameterList method) (openff.toolkit.utils.collections.ValidatedList method) index_of() (openff.toolkit.topology.ImproperDict class method) (openff.toolkit.topology.ValenceDict class method) IndexedMappedParameterAttribute (class in openff.toolkit.typing.engines.smirnoff.parameters) IndexedParameterAttribute (class in openff.toolkit.typing.engines.smirnoff.parameters) inherit_docstrings() (in module openff.toolkit.utils.utils) insert() (openff.toolkit.typing.engines.smirnoff.parameters.ParameterList method) (openff.toolkit.utils.collections.ValidatedList method) InvalidAromaticityModelError InvalidAtomMetadataError InvalidBondOrderError InvalidBoxVectorsError InvalidConformerError InvalidIUPACNameError InvalidPeriodicityError InvalidQCInputError InvalidToolkitError InvalidToolkitRegistryError is_aromatic (openff.toolkit.topology.Atom property) is_available() (openff.toolkit.utils.toolkits.AmberToolsToolkitWrapper static method) (openff.toolkit.utils.toolkits.BuiltInToolkitWrapper class method) (openff.toolkit.utils.toolkits.NAGLToolkitWrapper class method) (openff.toolkit.utils.toolkits.OpenEyeToolkitWrapper class method) (openff.toolkit.utils.toolkits.RDKitToolkitWrapper class method) (openff.toolkit.utils.toolkits.ToolkitWrapper class method) is_bonded() (openff.toolkit.topology.Topology method) is_bonded_to() (openff.toolkit.topology.Atom method) is_constrained() (openff.toolkit.topology.Topology method) is_in_ring() (openff.toolkit.topology.Atom method) (openff.toolkit.topology.Bond method) is_isomorphic_with() (openff.toolkit.topology.FrozenMolecule method) (openff.toolkit.topology.Molecule method) is_periodic (openff.toolkit.topology.Topology property) items() (openff.toolkit.topology.ImproperDict method) (openff.toolkit.topology.ValenceDict method) (openff.toolkit.utils.collections.ValidatedDict method) K key_transform() (openff.toolkit.topology.ImproperDict static method) (openff.toolkit.topology.ValenceDict static method) keys() (openff.toolkit.topology.ImproperDict method) (openff.toolkit.topology.ValenceDict method) (openff.toolkit.utils.collections.ValidatedDict method) known_kwargs (openff.toolkit.typing.engines.smirnoff.parameters.AngleHandler property) (openff.toolkit.typing.engines.smirnoff.parameters.BondHandler property) (openff.toolkit.typing.engines.smirnoff.parameters.ChargeIncrementModelHandler property) (openff.toolkit.typing.engines.smirnoff.parameters.ConstraintHandler property) (openff.toolkit.typing.engines.smirnoff.parameters.ElectrostaticsHandler property) (openff.toolkit.typing.engines.smirnoff.parameters.GBSAHandler property) (openff.toolkit.typing.engines.smirnoff.parameters.ImproperTorsionHandler property) (openff.toolkit.typing.engines.smirnoff.parameters.LibraryChargeHandler property) (openff.toolkit.typing.engines.smirnoff.parameters.ParameterHandler property) (openff.toolkit.typing.engines.smirnoff.parameters.ProperTorsionHandler property) (openff.toolkit.typing.engines.smirnoff.parameters.ToolkitAM1BCCHandler property) (openff.toolkit.typing.engines.smirnoff.parameters.vdWHandler property) (openff.toolkit.typing.engines.smirnoff.parameters.VirtualSiteHandler property) L label_molecules() (openff.toolkit.typing.engines.smirnoff.ForceField method) LibraryChargeHandler (class in openff.toolkit.typing.engines.smirnoff.parameters) LibraryChargeHandler.LibraryChargeType (class in openff.toolkit.typing.engines.smirnoff.parameters) LibraryChargeType (class in openff.toolkit.typing.engines.smirnoff.parameters) LicenseError M MappedParameterAttribute (class in openff.toolkit.typing.engines.smirnoff.parameters) mass (openff.toolkit.topology.Atom property) metadata (openff.toolkit.topology.Atom property) MissingCMILESError MissingConformersError MissingIndexedAttributeError MissingPackageError MissingPartialChargesError MissingUniqueMoleculesError module openff.toolkit.utils.exceptions Molecule (class in openff.toolkit.topology) molecule (openff.toolkit.topology.Atom property) (openff.toolkit.topology.Particle property) molecule() (openff.toolkit.topology.Topology method) molecule_atom_index (openff.toolkit.topology.Atom property) molecule_atom_start_index() (openff.toolkit.topology.Topology method) molecule_bond_index (openff.toolkit.topology.Bond property) molecule_index() (openff.toolkit.topology.Topology method) molecule_particle_index (openff.toolkit.topology.Atom property) (openff.toolkit.topology.Particle property) MoleculeNotInTopologyError MoleculeParseError molecules (openff.toolkit.topology.Topology property) MultipleMoleculesInPDBError N n_angles (openff.toolkit.topology.FrozenMolecule property) (openff.toolkit.topology.Molecule property) (openff.toolkit.topology.Topology property) n_atoms (openff.toolkit.topology.FrozenMolecule property) (openff.toolkit.topology.HierarchyElement property) (openff.toolkit.topology.Molecule property) (openff.toolkit.topology.Topology property) n_bonds (openff.toolkit.topology.FrozenMolecule property) (openff.toolkit.topology.Molecule property) (openff.toolkit.topology.Topology property) n_conformers (openff.toolkit.topology.FrozenMolecule property) (openff.toolkit.topology.Molecule property) n_impropers (openff.toolkit.topology.FrozenMolecule property) (openff.toolkit.topology.Molecule property) (openff.toolkit.topology.Topology property) n_molecules (openff.toolkit.topology.Topology property) n_propers (openff.toolkit.topology.FrozenMolecule property) (openff.toolkit.topology.Molecule property) (openff.toolkit.topology.Topology property) n_unique_molecules (openff.toolkit.topology.Topology property) NAGLToolkitWrapper (class in openff.toolkit.utils.toolkits) name (openff.toolkit.topology.Atom property) (openff.toolkit.topology.FrozenMolecule property) (openff.toolkit.topology.Molecule property) (openff.toolkit.topology.Particle property) NonUniqueSubstructureName NotAttachedToMoleculeError NotBondedError NotEnoughPointsForInterpolationError NotInTopologyError nth_degree_neighbors() (openff.toolkit.topology.FrozenMolecule method) (openff.toolkit.topology.Molecule method) (openff.toolkit.topology.Topology method) O OpenEyeError OpenEyeImportError OpenEyeToolkitWrapper (class in openff.toolkit.utils.toolkits) openff.toolkit.utils.exceptions module OpenFFToolkitException ordered_connection_table_hash() (openff.toolkit.topology.FrozenMolecule method) (openff.toolkit.topology.Molecule method) P ParameterAttribute (class in openff.toolkit.typing.engines.smirnoff.parameters) ParameterHandler (class in openff.toolkit.typing.engines.smirnoff.parameters) ParameterHandlerRegistrationError ParameterIOHandler (class in openff.toolkit.typing.engines.smirnoff.io) ParameterList (class in openff.toolkit.typing.engines.smirnoff.parameters) ParameterLookupError parameters (openff.toolkit.typing.engines.smirnoff.parameters.AngleHandler property) (openff.toolkit.typing.engines.smirnoff.parameters.BondHandler property) (openff.toolkit.typing.engines.smirnoff.parameters.ChargeIncrementModelHandler property) (openff.toolkit.typing.engines.smirnoff.parameters.ConstraintHandler property) (openff.toolkit.typing.engines.smirnoff.parameters.ElectrostaticsHandler property) (openff.toolkit.typing.engines.smirnoff.parameters.GBSAHandler property) (openff.toolkit.typing.engines.smirnoff.parameters.ImproperTorsionHandler property) (openff.toolkit.typing.engines.smirnoff.parameters.LibraryChargeHandler property) (openff.toolkit.typing.engines.smirnoff.parameters.ParameterHandler property) (openff.toolkit.typing.engines.smirnoff.parameters.ProperTorsionHandler property) (openff.toolkit.typing.engines.smirnoff.parameters.ToolkitAM1BCCHandler property) (openff.toolkit.typing.engines.smirnoff.parameters.vdWHandler property) (openff.toolkit.typing.engines.smirnoff.parameters.VirtualSiteHandler property) ParameterType (class in openff.toolkit.typing.engines.smirnoff.parameters) parent (openff.toolkit.topology.HierarchyElement property) parent_index (openff.toolkit.typing.engines.smirnoff.parameters.VirtualSiteHandler.VirtualSiteType property) (openff.toolkit.typing.engines.smirnoff.parameters.VirtualSiteType property) parse_file() (openff.toolkit.typing.engines.smirnoff.io.ParameterIOHandler method) (openff.toolkit.typing.engines.smirnoff.io.XMLParameterIOHandler method) parse_smirnoff_from_source() (openff.toolkit.typing.engines.smirnoff.ForceField method) parse_sources() (openff.toolkit.typing.engines.smirnoff.ForceField method) parse_string() (openff.toolkit.typing.engines.smirnoff.io.ParameterIOHandler method) (openff.toolkit.typing.engines.smirnoff.io.XMLParameterIOHandler method) partial_charge (openff.toolkit.topology.Atom property) partial_charges (openff.toolkit.topology.FrozenMolecule property) (openff.toolkit.topology.Molecule property) PartialChargeVirtualSitesError Particle (class in openff.toolkit.topology) perceive_hierarchy() (openff.toolkit.topology.HierarchyScheme method) perceive_residues() (openff.toolkit.topology.Molecule method) pop() (openff.toolkit.topology.ImproperDict method) (openff.toolkit.topology.ValenceDict method) (openff.toolkit.typing.engines.smirnoff.parameters.ParameterList method) (openff.toolkit.utils.collections.ValidatedDict method) (openff.toolkit.utils.collections.ValidatedList method) popitem() (openff.toolkit.topology.ImproperDict method) (openff.toolkit.topology.ValenceDict method) (openff.toolkit.utils.collections.ValidatedDict method) propers (openff.toolkit.topology.FrozenMolecule property) (openff.toolkit.topology.Molecule property) (openff.toolkit.topology.Topology property) properties (openff.toolkit.topology.FrozenMolecule property) (openff.toolkit.topology.Molecule property) ProperTorsionHandler (class in openff.toolkit.typing.engines.smirnoff.parameters) ProperTorsionHandler.ProperTorsionType (class in openff.toolkit.typing.engines.smirnoff.parameters) ProperTorsionType (class in openff.toolkit.typing.engines.smirnoff.parameters) R RadicalsNotSupportedError RDKitToolkitWrapper (class in openff.toolkit.utils.toolkits) register_parameter_handler() (openff.toolkit.typing.engines.smirnoff.ForceField method) register_parameter_io_handler() (openff.toolkit.typing.engines.smirnoff.ForceField method) register_toolkit() (openff.toolkit.utils.toolkits.ToolkitRegistry method) registered_parameter_handlers (openff.toolkit.typing.engines.smirnoff.ForceField property) registered_toolkit_versions (openff.toolkit.utils.toolkits.ToolkitRegistry property) registered_toolkits (openff.toolkit.utils.toolkits.ToolkitRegistry property) remap() (openff.toolkit.topology.FrozenMolecule method) (openff.toolkit.topology.Molecule method) RemapIndexError remove() (openff.toolkit.typing.engines.smirnoff.parameters.ParameterList method) (openff.toolkit.utils.collections.ValidatedList method) resolve() (openff.toolkit.utils.toolkits.ToolkitRegistry method) reverse() (openff.toolkit.typing.engines.smirnoff.parameters.ParameterList method) (openff.toolkit.utils.collections.ValidatedList method) S Serializable (class in openff.toolkit.utils.serialization) set_positions() (openff.toolkit.topology.Topology method) setdefault() (openff.toolkit.topology.ImproperDict method) (openff.toolkit.topology.ValenceDict method) (openff.toolkit.utils.collections.ValidatedDict method) SMILESParseError SmilesParsingError SMIRKSMismatchError SMIRKSParsingError smirnoff_impropers (openff.toolkit.topology.FrozenMolecule property) (openff.toolkit.topology.Molecule property) (openff.toolkit.topology.Topology property) SMIRNOFFAromaticityError SMIRNOFFParseError SMIRNOFFSpecError SMIRNOFFSpecUnimplementedError SMIRNOFFVersionError sort() (openff.toolkit.typing.engines.smirnoff.parameters.ParameterList method) (openff.toolkit.utils.collections.ValidatedList method) sort_hierarchy_elements() (openff.toolkit.topology.HierarchyScheme method) stereochemistry (openff.toolkit.topology.Atom property) strip_atom_stereochemistry() (openff.toolkit.topology.FrozenMolecule method) (openff.toolkit.topology.Molecule method) SubstructureAtomSmartsInvalid SubstructureBondSmartsInvalid SubstructureImproperlySpecified symbol (openff.toolkit.topology.Atom property) T TAGNAME (openff.toolkit.typing.engines.smirnoff.parameters.AngleHandler property) (openff.toolkit.typing.engines.smirnoff.parameters.BondHandler property) (openff.toolkit.typing.engines.smirnoff.parameters.ChargeIncrementModelHandler property) (openff.toolkit.typing.engines.smirnoff.parameters.ConstraintHandler property) (openff.toolkit.typing.engines.smirnoff.parameters.ElectrostaticsHandler property) (openff.toolkit.typing.engines.smirnoff.parameters.GBSAHandler property) (openff.toolkit.typing.engines.smirnoff.parameters.ImproperTorsionHandler property) (openff.toolkit.typing.engines.smirnoff.parameters.LibraryChargeHandler property) (openff.toolkit.typing.engines.smirnoff.parameters.ParameterHandler property) (openff.toolkit.typing.engines.smirnoff.parameters.ProperTorsionHandler property) (openff.toolkit.typing.engines.smirnoff.parameters.ToolkitAM1BCCHandler property) (openff.toolkit.typing.engines.smirnoff.parameters.vdWHandler property) (openff.toolkit.typing.engines.smirnoff.parameters.VirtualSiteHandler property) temporary_cd() (in module openff.toolkit.utils.utils) to_bson() (openff.toolkit.topology.Atom method) (openff.toolkit.topology.Bond method) (openff.toolkit.topology.FrozenMolecule method) (openff.toolkit.topology.Molecule method) (openff.toolkit.topology.Particle method) (openff.toolkit.topology.Topology method) (openff.toolkit.utils.serialization.Serializable method) to_dict() (openff.toolkit.topology.Atom method) (openff.toolkit.topology.Bond method) (openff.toolkit.topology.FrozenMolecule method) (openff.toolkit.topology.HierarchyElement method) (openff.toolkit.topology.HierarchyScheme method) (openff.toolkit.topology.Molecule method) (openff.toolkit.topology.Particle method) (openff.toolkit.typing.engines.smirnoff.parameters.AngleHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.AngleHandler.AngleType method) (openff.toolkit.typing.engines.smirnoff.parameters.AngleType method) (openff.toolkit.typing.engines.smirnoff.parameters.BondHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.BondHandler.BondType method) (openff.toolkit.typing.engines.smirnoff.parameters.BondType method) (openff.toolkit.typing.engines.smirnoff.parameters.ChargeIncrementModelHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.ChargeIncrementModelHandler.ChargeIncrementType method) (openff.toolkit.typing.engines.smirnoff.parameters.ChargeIncrementType method) (openff.toolkit.typing.engines.smirnoff.parameters.ConstraintHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.ConstraintHandler.ConstraintType method) (openff.toolkit.typing.engines.smirnoff.parameters.ConstraintType method) (openff.toolkit.typing.engines.smirnoff.parameters.ElectrostaticsHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.GBSAHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.GBSAHandler.GBSAType method) (openff.toolkit.typing.engines.smirnoff.parameters.GBSAType method) (openff.toolkit.typing.engines.smirnoff.parameters.ImproperTorsionHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.ImproperTorsionHandler.ImproperTorsionType method) (openff.toolkit.typing.engines.smirnoff.parameters.ImproperTorsionType method) (openff.toolkit.typing.engines.smirnoff.parameters.LibraryChargeHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.LibraryChargeHandler.LibraryChargeType method) (openff.toolkit.typing.engines.smirnoff.parameters.LibraryChargeType method) (openff.toolkit.typing.engines.smirnoff.parameters.ParameterHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.ParameterType method) (openff.toolkit.typing.engines.smirnoff.parameters.ProperTorsionHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.ProperTorsionHandler.ProperTorsionType method) (openff.toolkit.typing.engines.smirnoff.parameters.ProperTorsionType method) (openff.toolkit.typing.engines.smirnoff.parameters.ToolkitAM1BCCHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.vdWHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.vdWHandler.vdWType method) (openff.toolkit.typing.engines.smirnoff.parameters.vdWType method) (openff.toolkit.typing.engines.smirnoff.parameters.VirtualSiteHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.VirtualSiteHandler.VirtualSiteType method) (openff.toolkit.typing.engines.smirnoff.parameters.VirtualSiteType method) to_file() (openff.toolkit.topology.FrozenMolecule method) (openff.toolkit.topology.Molecule method) (openff.toolkit.topology.Topology method) (openff.toolkit.typing.engines.smirnoff.ForceField method) (openff.toolkit.typing.engines.smirnoff.io.ParameterIOHandler method) (openff.toolkit.typing.engines.smirnoff.io.XMLParameterIOHandler method) (openff.toolkit.utils.toolkits.OpenEyeToolkitWrapper method) (openff.toolkit.utils.toolkits.RDKitToolkitWrapper method) to_file_obj() (openff.toolkit.utils.toolkits.OpenEyeToolkitWrapper method) (openff.toolkit.utils.toolkits.RDKitToolkitWrapper method) to_hill_formula() (openff.toolkit.topology.FrozenMolecule method) (openff.toolkit.topology.Molecule method) to_inchi() (openff.toolkit.topology.FrozenMolecule method) (openff.toolkit.topology.Molecule method) (openff.toolkit.utils.toolkits.OpenEyeToolkitWrapper method) (openff.toolkit.utils.toolkits.RDKitToolkitWrapper method) to_inchikey() (openff.toolkit.topology.FrozenMolecule method) (openff.toolkit.topology.Molecule method) (openff.toolkit.utils.toolkits.OpenEyeToolkitWrapper method) (openff.toolkit.utils.toolkits.RDKitToolkitWrapper method) to_iupac() (openff.toolkit.topology.FrozenMolecule method) (openff.toolkit.topology.Molecule method) (openff.toolkit.utils.toolkits.OpenEyeToolkitWrapper method) to_json() (openff.toolkit.topology.Atom method) (openff.toolkit.topology.Bond method) (openff.toolkit.topology.FrozenMolecule method) (openff.toolkit.topology.Molecule method) (openff.toolkit.topology.Particle method) (openff.toolkit.topology.Topology method) (openff.toolkit.utils.serialization.Serializable method) to_list() (openff.toolkit.typing.engines.smirnoff.parameters.ParameterList method) to_messagepack() (openff.toolkit.topology.Atom method) (openff.toolkit.topology.Bond method) (openff.toolkit.topology.FrozenMolecule method) (openff.toolkit.topology.Molecule method) (openff.toolkit.topology.Particle method) (openff.toolkit.topology.Topology method) (openff.toolkit.utils.serialization.Serializable method) to_networkx() (openff.toolkit.topology.FrozenMolecule method) (openff.toolkit.topology.Molecule method) to_openeye() (openff.toolkit.topology.FrozenMolecule method) (openff.toolkit.topology.Molecule method) (openff.toolkit.utils.toolkits.OpenEyeToolkitWrapper method) to_openmm() (openff.toolkit.topology.Topology method) to_pickle() (openff.toolkit.topology.Atom method) (openff.toolkit.topology.Bond method) (openff.toolkit.topology.FrozenMolecule method) (openff.toolkit.topology.Molecule method) (openff.toolkit.topology.Particle method) (openff.toolkit.topology.Topology method) (openff.toolkit.utils.serialization.Serializable method) to_qcschema() (openff.toolkit.topology.FrozenMolecule method) (openff.toolkit.topology.Molecule method) to_rdkit() (openff.toolkit.topology.FrozenMolecule method) (openff.toolkit.topology.Molecule method) (openff.toolkit.utils.toolkits.RDKitToolkitWrapper method) to_smiles() (openff.toolkit.topology.FrozenMolecule method) (openff.toolkit.topology.Molecule method) (openff.toolkit.utils.toolkits.OpenEyeToolkitWrapper method) (openff.toolkit.utils.toolkits.RDKitToolkitWrapper method) to_string() (openff.toolkit.typing.engines.smirnoff.ForceField method) (openff.toolkit.typing.engines.smirnoff.io.ParameterIOHandler method) (openff.toolkit.typing.engines.smirnoff.io.XMLParameterIOHandler method) to_toml() (openff.toolkit.topology.Atom method) (openff.toolkit.topology.Bond method) (openff.toolkit.topology.FrozenMolecule method) (openff.toolkit.topology.Molecule method) (openff.toolkit.topology.Particle method) (openff.toolkit.topology.Topology method) (openff.toolkit.utils.serialization.Serializable method) to_topology() (openff.toolkit.topology.FrozenMolecule method) (openff.toolkit.topology.Molecule method) to_xml() (openff.toolkit.topology.Atom method) (openff.toolkit.topology.Bond method) (openff.toolkit.topology.FrozenMolecule method) (openff.toolkit.topology.Molecule method) (openff.toolkit.topology.Particle method) (openff.toolkit.topology.Topology method) (openff.toolkit.utils.serialization.Serializable method) to_yaml() (openff.toolkit.topology.Atom method) (openff.toolkit.topology.Bond method) (openff.toolkit.topology.FrozenMolecule method) (openff.toolkit.topology.Molecule method) (openff.toolkit.topology.Particle method) (openff.toolkit.topology.Topology method) (openff.toolkit.utils.serialization.Serializable method) toolkit_file_read_formats (openff.toolkit.utils.toolkits.AmberToolsToolkitWrapper property) (openff.toolkit.utils.toolkits.BuiltInToolkitWrapper property) (openff.toolkit.utils.toolkits.NAGLToolkitWrapper property) (openff.toolkit.utils.toolkits.OpenEyeToolkitWrapper property) (openff.toolkit.utils.toolkits.RDKitToolkitWrapper property) (openff.toolkit.utils.toolkits.ToolkitWrapper property) toolkit_file_write_formats (openff.toolkit.utils.toolkits.AmberToolsToolkitWrapper property) (openff.toolkit.utils.toolkits.BuiltInToolkitWrapper property) (openff.toolkit.utils.toolkits.NAGLToolkitWrapper property) (openff.toolkit.utils.toolkits.OpenEyeToolkitWrapper property) (openff.toolkit.utils.toolkits.RDKitToolkitWrapper property) (openff.toolkit.utils.toolkits.ToolkitWrapper property) toolkit_installation_instructions (openff.toolkit.utils.toolkits.AmberToolsToolkitWrapper property) (openff.toolkit.utils.toolkits.BuiltInToolkitWrapper property) (openff.toolkit.utils.toolkits.NAGLToolkitWrapper property) (openff.toolkit.utils.toolkits.OpenEyeToolkitWrapper property) (openff.toolkit.utils.toolkits.RDKitToolkitWrapper property) (openff.toolkit.utils.toolkits.ToolkitWrapper property) toolkit_name (openff.toolkit.utils.toolkits.AmberToolsToolkitWrapper property) (openff.toolkit.utils.toolkits.BuiltInToolkitWrapper property) (openff.toolkit.utils.toolkits.NAGLToolkitWrapper property) (openff.toolkit.utils.toolkits.OpenEyeToolkitWrapper property) (openff.toolkit.utils.toolkits.RDKitToolkitWrapper property) (openff.toolkit.utils.toolkits.ToolkitWrapper property) toolkit_registry_manager() (in module openff.toolkit.utils.toolkit_registry) toolkit_version (openff.toolkit.utils.toolkits.AmberToolsToolkitWrapper property) (openff.toolkit.utils.toolkits.BuiltInToolkitWrapper property) (openff.toolkit.utils.toolkits.NAGLToolkitWrapper property) (openff.toolkit.utils.toolkits.OpenEyeToolkitWrapper property) (openff.toolkit.utils.toolkits.RDKitToolkitWrapper property) (openff.toolkit.utils.toolkits.ToolkitWrapper property) ToolkitAM1BCCHandler (class in openff.toolkit.typing.engines.smirnoff.parameters) ToolkitRegistry (class in openff.toolkit.utils.toolkits) ToolkitUnavailableException ToolkitWrapper (class in openff.toolkit.utils.toolkits) Topology (class in openff.toolkit.topology) torsions (openff.toolkit.topology.FrozenMolecule property) (openff.toolkit.topology.Molecule property) total_charge (openff.toolkit.topology.FrozenMolecule property) (openff.toolkit.topology.Molecule property) type_to_parent_index() (openff.toolkit.typing.engines.smirnoff.parameters.VirtualSiteHandler.VirtualSiteType class method) (openff.toolkit.typing.engines.smirnoff.parameters.VirtualSiteType class method) U UnassignedAngleParameterException UnassignedBondParameterException UnassignedChemistryInPDBError UnassignedMoleculeChargeException UnassignedProperTorsionParameterException UnassignedValenceParameterException UNDEFINED (openff.toolkit.typing.engines.smirnoff.parameters.IndexedMappedParameterAttribute attribute) (openff.toolkit.typing.engines.smirnoff.parameters.IndexedParameterAttribute attribute) (openff.toolkit.typing.engines.smirnoff.parameters.MappedParameterAttribute attribute) (openff.toolkit.typing.engines.smirnoff.parameters.ParameterAttribute attribute) UndefinedStereochemistryError unique_molecules (openff.toolkit.topology.Topology property) unit_to_string() (in module openff.toolkit.utils.utils) UnsupportedFileTypeError UnsupportedMoleculeConversionError update() (openff.toolkit.topology.ImproperDict method) (openff.toolkit.topology.ValenceDict method) (openff.toolkit.utils.collections.ValidatedDict method) update_hierarchy_schemes() (openff.toolkit.topology.FrozenMolecule method) (openff.toolkit.topology.Molecule method) V ValenceDict (class in openff.toolkit.topology) ValidatedDict (class in openff.toolkit.utils.collections) ValidatedList (class in openff.toolkit.utils.collections) values() (openff.toolkit.topology.ImproperDict method) (openff.toolkit.topology.ValenceDict method) (openff.toolkit.utils.collections.ValidatedDict method) vdWHandler (class in openff.toolkit.typing.engines.smirnoff.parameters) vdWHandler.vdWType (class in openff.toolkit.typing.engines.smirnoff.parameters) vdWType (class in openff.toolkit.typing.engines.smirnoff.parameters) VirtualSiteHandler (class in openff.toolkit.typing.engines.smirnoff.parameters) VirtualSiteHandler.VirtualSiteType (class in openff.toolkit.typing.engines.smirnoff.parameters) VirtualSitesUnsupportedError VirtualSiteType (class in openff.toolkit.typing.engines.smirnoff.parameters) visualize() (openff.toolkit.topology.Molecule method) (openff.toolkit.topology.Topology method) W with_traceback() (openff.toolkit.utils.exceptions.AmbiguousAtomChemicalAssignment method) (openff.toolkit.utils.exceptions.AmbiguousBondChemicalAssignment method) (openff.toolkit.utils.exceptions.AntechamberNotFoundError method) (openff.toolkit.utils.exceptions.AtomMappingWarning method) (openff.toolkit.utils.exceptions.AtomNotInTopologyError method) (openff.toolkit.utils.exceptions.BondExistsError method) (openff.toolkit.utils.exceptions.BondNotInTopologyError method) (openff.toolkit.utils.exceptions.CallbackRegistrationError method) (openff.toolkit.utils.exceptions.ChargeCalculationError method) (openff.toolkit.utils.exceptions.ChargeMethodUnavailableError method) (openff.toolkit.utils.exceptions.ChemicalEnvironmentParsingError method) (openff.toolkit.utils.exceptions.ConformerGenerationError method) (openff.toolkit.utils.exceptions.ConstraintExsistsError method) (openff.toolkit.utils.exceptions.DuplicateParameterError method) (openff.toolkit.utils.exceptions.DuplicateUniqueMoleculeError method) (openff.toolkit.utils.exceptions.DuplicateVirtualSiteTypeException method) (openff.toolkit.utils.exceptions.FractionalBondOrderInterpolationMethodUnsupportedError method) (openff.toolkit.utils.exceptions.GAFFAtomTypeWarning method) (openff.toolkit.utils.exceptions.HierarchyIteratorNameConflictError method) (openff.toolkit.utils.exceptions.HierarchySchemeNotFoundException method) (openff.toolkit.utils.exceptions.HierarchySchemeWithIteratorNameAlreadyRegisteredException method) (openff.toolkit.utils.exceptions.InChIParseError method) (openff.toolkit.utils.exceptions.IncompatibleParameterError method) (openff.toolkit.utils.exceptions.IncompatibleShapeError method) (openff.toolkit.utils.exceptions.IncompatibleTypeError method) (openff.toolkit.utils.exceptions.IncompatibleUnitError method) (openff.toolkit.utils.exceptions.InconsistentStereochemistryError method) (openff.toolkit.utils.exceptions.IncorrectNumConformersError method) (openff.toolkit.utils.exceptions.IncorrectNumConformersWarning method) (openff.toolkit.utils.exceptions.InvalidAromaticityModelError method) (openff.toolkit.utils.exceptions.InvalidAtomMetadataError method) (openff.toolkit.utils.exceptions.InvalidBondOrderError method) (openff.toolkit.utils.exceptions.InvalidBoxVectorsError method) (openff.toolkit.utils.exceptions.InvalidConformerError method) (openff.toolkit.utils.exceptions.InvalidIUPACNameError method) (openff.toolkit.utils.exceptions.InvalidPeriodicityError method) (openff.toolkit.utils.exceptions.InvalidQCInputError method) (openff.toolkit.utils.exceptions.InvalidToolkitError method) (openff.toolkit.utils.exceptions.InvalidToolkitRegistryError method) (openff.toolkit.utils.exceptions.LicenseError method) (openff.toolkit.utils.exceptions.MissingCMILESError method) (openff.toolkit.utils.exceptions.MissingConformersError method) (openff.toolkit.utils.exceptions.MissingIndexedAttributeError method) (openff.toolkit.utils.exceptions.MissingPackageError method) (openff.toolkit.utils.exceptions.MissingPartialChargesError method) (openff.toolkit.utils.exceptions.MissingUniqueMoleculesError method) (openff.toolkit.utils.exceptions.MoleculeNotInTopologyError method) (openff.toolkit.utils.exceptions.MoleculeParseError method) (openff.toolkit.utils.exceptions.MultipleMoleculesInPDBError method) (openff.toolkit.utils.exceptions.NonUniqueSubstructureName method) (openff.toolkit.utils.exceptions.NotAttachedToMoleculeError method) (openff.toolkit.utils.exceptions.NotBondedError method) (openff.toolkit.utils.exceptions.NotEnoughPointsForInterpolationError method) (openff.toolkit.utils.exceptions.NotInTopologyError method) (openff.toolkit.utils.exceptions.OpenEyeError method) (openff.toolkit.utils.exceptions.OpenEyeImportError method) (openff.toolkit.utils.exceptions.OpenFFToolkitException method) (openff.toolkit.utils.exceptions.ParameterHandlerRegistrationError method) (openff.toolkit.utils.exceptions.ParameterLookupError method) (openff.toolkit.utils.exceptions.PartialChargeVirtualSitesError method) (openff.toolkit.utils.exceptions.RadicalsNotSupportedError method) (openff.toolkit.utils.exceptions.RemapIndexError method) (openff.toolkit.utils.exceptions.SMILESParseError method) (openff.toolkit.utils.exceptions.SmilesParsingError method) (openff.toolkit.utils.exceptions.SMIRKSMismatchError method) (openff.toolkit.utils.exceptions.SMIRKSParsingError method) (openff.toolkit.utils.exceptions.SMIRNOFFAromaticityError method) (openff.toolkit.utils.exceptions.SMIRNOFFParseError method) (openff.toolkit.utils.exceptions.SMIRNOFFSpecError method) (openff.toolkit.utils.exceptions.SMIRNOFFSpecUnimplementedError method) (openff.toolkit.utils.exceptions.SMIRNOFFVersionError method) (openff.toolkit.utils.exceptions.SubstructureAtomSmartsInvalid method) (openff.toolkit.utils.exceptions.SubstructureBondSmartsInvalid method) (openff.toolkit.utils.exceptions.SubstructureImproperlySpecified method) (openff.toolkit.utils.exceptions.ToolkitUnavailableException method) (openff.toolkit.utils.exceptions.UnassignedAngleParameterException method) (openff.toolkit.utils.exceptions.UnassignedBondParameterException method) (openff.toolkit.utils.exceptions.UnassignedChemistryInPDBError method) (openff.toolkit.utils.exceptions.UnassignedMoleculeChargeException method) (openff.toolkit.utils.exceptions.UnassignedProperTorsionParameterException method) (openff.toolkit.utils.exceptions.UnassignedValenceParameterException method) (openff.toolkit.utils.exceptions.UndefinedStereochemistryError method) (openff.toolkit.utils.exceptions.UnsupportedFileTypeError method) (openff.toolkit.utils.exceptions.UnsupportedMoleculeConversionError method) (openff.toolkit.utils.exceptions.VirtualSitesUnsupportedError method) (openff.toolkit.utils.exceptions.WrongShapeError method) WrongShapeError X XMLParameterIOHandler (class in openff.toolkit.typing.engines.smirnoff.io)