Index _ | A | B | C | D | E | F | G | H | I | K | L | M | N | O | P | R | S | T | U | V | 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.chemistry.ChemicalEnvironment method) (openff.toolkit.typing.engines.smirnoff.AngleType method) (openff.toolkit.typing.engines.smirnoff.BondType method) (openff.toolkit.typing.engines.smirnoff.ChargeIncrementType method) (openff.toolkit.typing.engines.smirnoff.ConstraintType method) (openff.toolkit.typing.engines.smirnoff.ForceField method) (openff.toolkit.typing.engines.smirnoff.GBSAType method) (openff.toolkit.typing.engines.smirnoff.ImproperTorsionType method) (openff.toolkit.typing.engines.smirnoff.io.ParameterIOHandler method) (openff.toolkit.typing.engines.smirnoff.io.XMLParameterIOHandler method) (openff.toolkit.typing.engines.smirnoff.LibraryChargeType method) (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.IndexedMappedParameterAttribute method) (openff.toolkit.typing.engines.smirnoff.parameters.IndexedParameterAttribute method) (openff.toolkit.typing.engines.smirnoff.parameters.LibraryChargeHandler 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.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) (openff.toolkit.typing.engines.smirnoff.ParameterType method) (openff.toolkit.typing.engines.smirnoff.ProperTorsionType method) (openff.toolkit.typing.engines.smirnoff.vdWType method) (openff.toolkit.typing.engines.smirnoff.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.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.AngleType method) (openff.toolkit.typing.engines.smirnoff.BondType method) (openff.toolkit.typing.engines.smirnoff.ChargeIncrementType method) (openff.toolkit.typing.engines.smirnoff.ConstraintType method) (openff.toolkit.typing.engines.smirnoff.GBSAType method) (openff.toolkit.typing.engines.smirnoff.ImproperTorsionType method) (openff.toolkit.typing.engines.smirnoff.LibraryChargeType method) (openff.toolkit.typing.engines.smirnoff.parameters.AngleHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.AngleHandler.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.ChargeIncrementModelHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.ChargeIncrementModelHandler.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.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.ImproperTorsionHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.ImproperTorsionHandler.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.ParameterHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.ProperTorsionHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.ProperTorsionHandler.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.VirtualSiteHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.VirtualSiteHandler.VirtualSiteType method) (openff.toolkit.typing.engines.smirnoff.ParameterType method) (openff.toolkit.typing.engines.smirnoff.ProperTorsionType method) (openff.toolkit.typing.engines.smirnoff.vdWType method) (openff.toolkit.typing.engines.smirnoff.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_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) 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) 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.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) atoms (openff.toolkit.topology.FrozenMolecule property) (openff.toolkit.topology.Molecule property) (openff.toolkit.topology.Topology property) attribute_is_cosmetic() (openff.toolkit.typing.engines.smirnoff.AngleType method) (openff.toolkit.typing.engines.smirnoff.BondType method) (openff.toolkit.typing.engines.smirnoff.ChargeIncrementType method) (openff.toolkit.typing.engines.smirnoff.ConstraintType method) (openff.toolkit.typing.engines.smirnoff.GBSAType method) (openff.toolkit.typing.engines.smirnoff.ImproperTorsionType method) (openff.toolkit.typing.engines.smirnoff.LibraryChargeType method) (openff.toolkit.typing.engines.smirnoff.parameters.AngleHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.AngleHandler.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.ChargeIncrementModelHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.ChargeIncrementModelHandler.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.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.ImproperTorsionHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.ImproperTorsionHandler.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.ParameterHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.ProperTorsionHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.ProperTorsionHandler.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.VirtualSiteHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.VirtualSiteHandler.VirtualSiteType method) (openff.toolkit.typing.engines.smirnoff.ParameterType method) (openff.toolkit.typing.engines.smirnoff.ProperTorsionType method) (openff.toolkit.typing.engines.smirnoff.vdWType method) (openff.toolkit.typing.engines.smirnoff.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) BondHandler (class in openff.toolkit.typing.engines.smirnoff.parameters) BondHandler.BondType (class in openff.toolkit.typing.engines.smirnoff.parameters) 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) box_vectors (openff.toolkit.topology.Topology property) BuiltInToolkitWrapper (class in openff.toolkit.utils.toolkits) C call() (openff.toolkit.utils.toolkits.ToolkitRegistry method) 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) 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) 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) ChemicalEnvironment (class in openff.toolkit.typing.chemistry) 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) compute_partial_charges_am1bcc() (openff.toolkit.topology.FrozenMolecule method) (openff.toolkit.topology.Molecule method) (openff.toolkit.utils.toolkits.AmberToolsToolkitWrapper method) (openff.toolkit.utils.toolkits.OpenEyeToolkitWrapper method) conformers (openff.toolkit.topology.FrozenMolecule property) (openff.toolkit.topology.Molecule property) constrained_atom_pairs (openff.toolkit.topology.Topology property) 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) 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_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.AngleType method) (openff.toolkit.typing.engines.smirnoff.BondType method) (openff.toolkit.typing.engines.smirnoff.ChargeIncrementType method) (openff.toolkit.typing.engines.smirnoff.ConstraintType method) (openff.toolkit.typing.engines.smirnoff.GBSAType method) (openff.toolkit.typing.engines.smirnoff.ImproperTorsionType method) (openff.toolkit.typing.engines.smirnoff.LibraryChargeType method) (openff.toolkit.typing.engines.smirnoff.parameters.AngleHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.AngleHandler.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.ChargeIncrementModelHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.ChargeIncrementModelHandler.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.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.ImproperTorsionHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.ImproperTorsionHandler.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.ParameterHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.ProperTorsionHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.ProperTorsionHandler.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.VirtualSiteHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.VirtualSiteHandler.VirtualSiteType method) (openff.toolkit.typing.engines.smirnoff.ParameterType method) (openff.toolkit.typing.engines.smirnoff.ProperTorsionType method) (openff.toolkit.typing.engines.smirnoff.vdWType method) (openff.toolkit.typing.engines.smirnoff.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) 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) 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.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.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.LibraryChargeType class method) (openff.toolkit.typing.engines.smirnoff.parameters.LibraryChargeHandler.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.FrozenMolecule class method) (openff.toolkit.topology.Molecule 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 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) 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.Molecule method) get() (openff.toolkit.topology.ImproperDict method) (openff.toolkit.topology.ValenceDict method) (openff.toolkit.utils.collections.ValidatedDict 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_tagged_smarts_connectivity() (openff.toolkit.utils.toolkits.OpenEyeToolkitWrapper method) (openff.toolkit.utils.toolkits.RDKitToolkitWrapper method) get_type() (openff.toolkit.typing.chemistry.ChemicalEnvironment method) H has_unique_atom_names (openff.toolkit.topology.FrozenMolecule 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) HierarchyScheme (class in openff.toolkit.topology) 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) index() (openff.toolkit.typing.engines.smirnoff.parameters.ParameterList method) (openff.toolkit.utils.collections.ValidatedList method) index_of() (openff.toolkit.topology.ImproperDict static method) (openff.toolkit.topology.ValenceDict static method) IndexedMappedParameterAttribute (class in openff.toolkit.typing.engines.smirnoff.parameters) IndexedMappedParameterAttribute.UNDEFINED (class in openff.toolkit.typing.engines.smirnoff.parameters) IndexedParameterAttribute (class in openff.toolkit.typing.engines.smirnoff.parameters) IndexedParameterAttribute.UNDEFINED (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) 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.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) M MappedParameterAttribute (class in openff.toolkit.typing.engines.smirnoff.parameters) MappedParameterAttribute.UNDEFINED (class in openff.toolkit.typing.engines.smirnoff.parameters) mass (openff.toolkit.topology.Atom property) metadata (openff.toolkit.topology.Atom property) 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) molecules (openff.toolkit.topology.Topology property) 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.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_particles (openff.toolkit.topology.FrozenMolecule property) (openff.toolkit.topology.Molecule property) (openff.toolkit.topology.Topology property) n_propers (openff.toolkit.topology.FrozenMolecule property) (openff.toolkit.topology.Molecule property) (openff.toolkit.topology.Topology property) n_reference_molecules (openff.toolkit.topology.Topology property) n_topology_atoms (openff.toolkit.topology.Topology property) n_topology_bonds (openff.toolkit.topology.Topology property) n_topology_molecules (openff.toolkit.topology.Topology property) n_topology_particles (openff.toolkit.topology.Topology property) name (openff.toolkit.topology.Atom property) (openff.toolkit.topology.FrozenMolecule property) (openff.toolkit.topology.Molecule property) (openff.toolkit.topology.Particle property) nth_degree_neighbors() (openff.toolkit.topology.FrozenMolecule method) (openff.toolkit.topology.Molecule method) (openff.toolkit.topology.Topology method) O OpenEyeToolkitWrapper (class in openff.toolkit.utils.toolkits) ordered_connection_table_hash() (openff.toolkit.topology.FrozenMolecule method) (openff.toolkit.topology.Molecule method) P ParameterAttribute (class in openff.toolkit.typing.engines.smirnoff.parameters) ParameterAttribute.UNDEFINED (class in openff.toolkit.typing.engines.smirnoff.parameters) ParameterHandler (class in openff.toolkit.typing.engines.smirnoff.parameters) ParameterIOHandler (class in openff.toolkit.typing.engines.smirnoff.io) ParameterList (class in openff.toolkit.typing.engines.smirnoff.parameters) 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) parent_index (openff.toolkit.typing.engines.smirnoff.parameters.VirtualSiteHandler.VirtualSiteType property) (openff.toolkit.typing.engines.smirnoff.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) Particle (class in openff.toolkit.topology) particle() (openff.toolkit.topology.FrozenMolecule method) (openff.toolkit.topology.Molecule method) particle_index() (openff.toolkit.topology.FrozenMolecule method) (openff.toolkit.topology.Molecule method) (openff.toolkit.topology.Topology method) particles (openff.toolkit.topology.FrozenMolecule property) (openff.toolkit.topology.Molecule property) (openff.toolkit.topology.Topology property) 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) R RDKitToolkitWrapper (class in openff.toolkit.utils.toolkits) reference_molecules (openff.toolkit.topology.Topology property) 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) 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) setdefault() (openff.toolkit.topology.ImproperDict method) (openff.toolkit.topology.ValenceDict method) (openff.toolkit.utils.collections.ValidatedDict method) smirnoff_impropers (openff.toolkit.topology.FrozenMolecule property) (openff.toolkit.topology.Molecule property) (openff.toolkit.topology.Topology property) 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) 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.AngleType method) (openff.toolkit.typing.engines.smirnoff.BondType method) (openff.toolkit.typing.engines.smirnoff.ChargeIncrementType method) (openff.toolkit.typing.engines.smirnoff.ConstraintType method) (openff.toolkit.typing.engines.smirnoff.GBSAType method) (openff.toolkit.typing.engines.smirnoff.ImproperTorsionType method) (openff.toolkit.typing.engines.smirnoff.LibraryChargeType method) (openff.toolkit.typing.engines.smirnoff.parameters.AngleHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.AngleHandler.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.ChargeIncrementModelHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.ChargeIncrementModelHandler.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.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.ImproperTorsionHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.ImproperTorsionHandler.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.ParameterHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.ProperTorsionHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.ProperTorsionHandler.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.VirtualSiteHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.VirtualSiteHandler.VirtualSiteType method) (openff.toolkit.typing.engines.smirnoff.ParameterType method) (openff.toolkit.typing.engines.smirnoff.ProperTorsionType method) (openff.toolkit.typing.engines.smirnoff.vdWType method) (openff.toolkit.typing.engines.smirnoff.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.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.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.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.OpenEyeToolkitWrapper property) (openff.toolkit.utils.toolkits.RDKitToolkitWrapper property) (openff.toolkit.utils.toolkits.ToolkitWrapper property) toolkit_version (openff.toolkit.utils.toolkits.AmberToolsToolkitWrapper property) (openff.toolkit.utils.toolkits.BuiltInToolkitWrapper 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) ToolkitWrapper (class in openff.toolkit.utils.toolkits) Topology (class in openff.toolkit.topology) topology_atoms (openff.toolkit.topology.Topology property) topology_bonds (openff.toolkit.topology.Topology property) topology_molecules (openff.toolkit.topology.Topology property) topology_particles (openff.toolkit.topology.Topology property) 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.VirtualSiteType class method) U unit_to_string() (in module openff.toolkit.utils.utils) 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) validate() (openff.toolkit.typing.chemistry.ChemicalEnvironment method) validate_smirks() (openff.toolkit.typing.chemistry.ChemicalEnvironment class method) 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) VirtualSiteHandler (class in openff.toolkit.typing.engines.smirnoff.parameters) VirtualSiteHandler.VirtualSiteType (class in openff.toolkit.typing.engines.smirnoff.parameters) VirtualSiteType (class in openff.toolkit.typing.engines.smirnoff) visualize() (openff.toolkit.topology.Molecule method) X XMLParameterIOHandler (class in openff.toolkit.typing.engines.smirnoff.io)