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.BondChargeVirtualSite method) (openff.toolkit.topology.DivalentLonePairVirtualSite method) (openff.toolkit.topology.FrozenMolecule method) (openff.toolkit.topology.ImproperDict method) (openff.toolkit.topology.Molecule method) (openff.toolkit.topology.MonovalentLonePairVirtualSite method) (openff.toolkit.topology.Particle method) (openff.toolkit.topology.Topology method) (openff.toolkit.topology.TopologyAtom method) (openff.toolkit.topology.TopologyBond method) (openff.toolkit.topology.TopologyMolecule method) (openff.toolkit.topology.TopologyVirtualParticle method) (openff.toolkit.topology.TopologyVirtualSite method) (openff.toolkit.topology.TrivalentLonePairVirtualSite method) (openff.toolkit.topology.ValenceDict method) (openff.toolkit.topology.VirtualParticle method) (openff.toolkit.topology.VirtualSite method) (openff.toolkit.typing.chemistry.ChemicalEnvironment method) (openff.toolkit.typing.engines.smirnoff.forcefield.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.BondHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.ChargeIncrementModelHandler 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.ParameterType 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.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_bond_charge_virtual_site() (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.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.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.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.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) add_divalent_lone_pair_virtual_site() (openff.toolkit.topology.Molecule method) add_molecule() (openff.toolkit.topology.Topology method) add_monovalent_lone_pair_virtual_site() (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.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_particle() (openff.toolkit.topology.Topology method) add_toolkit() (openff.toolkit.utils.toolkits.ToolkitRegistry method) add_trivalent_lone_pair_virtual_site() (openff.toolkit.topology.Molecule method) add_virtual_site() (openff.toolkit.topology.Atom 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) (openff.toolkit.topology.TopologyMolecule 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) (openff.toolkit.topology.TopologyMolecule property) 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.ForceField property) assert_bonded() (openff.toolkit.topology.Topology method) assign_charge_from_molecules() (openff.toolkit.typing.engines.smirnoff.parameters.ElectrostaticsHandler 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_parameters() (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.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) 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.TopologyAtom property) atom() (openff.toolkit.topology.Topology method) (openff.toolkit.topology.TopologyMolecule method) (openff.toolkit.topology.TopologyVirtualParticle method) atom_is_in_ring() (openff.toolkit.utils.toolkits.OpenEyeToolkitWrapper method) (openff.toolkit.utils.toolkits.RDKitToolkitWrapper method) atom_start_topology_index (openff.toolkit.topology.TopologyMolecule property) atomic_number (openff.toolkit.topology.Atom property) (openff.toolkit.topology.TopologyAtom property) atoms (openff.toolkit.topology.BondChargeVirtualSite property) (openff.toolkit.topology.DivalentLonePairVirtualSite property) (openff.toolkit.topology.FrozenMolecule property) (openff.toolkit.topology.Molecule property) (openff.toolkit.topology.MonovalentLonePairVirtualSite property) (openff.toolkit.topology.TopologyBond property) (openff.toolkit.topology.TopologyMolecule property) (openff.toolkit.topology.TopologyVirtualParticle property) (openff.toolkit.topology.TrivalentLonePairVirtualSite property) (openff.toolkit.topology.VirtualParticle property) (openff.toolkit.topology.VirtualSite 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.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.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.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.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) author (openff.toolkit.typing.engines.smirnoff.forcefield.ForceField property) B Bond (class in openff.toolkit.topology) bond (openff.toolkit.topology.TopologyBond property) bond() (openff.toolkit.topology.Topology method) (openff.toolkit.topology.TopologyMolecule method) bond_is_in_ring() (openff.toolkit.utils.toolkits.OpenEyeToolkitWrapper method) (openff.toolkit.utils.toolkits.RDKitToolkitWrapper method) bond_order (openff.toolkit.topology.TopologyBond property) bond_start_topology_index (openff.toolkit.topology.TopologyMolecule property) BondChargeVirtualSite (class in openff.toolkit.topology) 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.TopologyMolecule property) 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) charge_model (openff.toolkit.topology.Topology property) ChargeIncrementModelHandler (class in openff.toolkit.typing.engines.smirnoff.parameters) ChargeIncrementModelHandler.ChargeIncrementType (class in openff.toolkit.typing.engines.smirnoff.parameters) check_charges_assigned() (openff.toolkit.typing.engines.smirnoff.parameters.ChargeIncrementModelHandler static method) (openff.toolkit.typing.engines.smirnoff.parameters.ElectrostaticsHandler static method) (openff.toolkit.typing.engines.smirnoff.parameters.LibraryChargeHandler static method) (openff.toolkit.typing.engines.smirnoff.parameters.ToolkitAM1BCCHandler static method) (openff.toolkit.typing.engines.smirnoff.parameters.vdWHandler static method) (openff.toolkit.typing.engines.smirnoff.parameters.VirtualSiteHandler static method) 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.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) compute_position_from_atom_positions() (openff.toolkit.topology.VirtualParticle method) compute_position_from_conformer() (openff.toolkit.topology.VirtualParticle method) compute_positions_from_atom_positions() (openff.toolkit.topology.BondChargeVirtualSite method) (openff.toolkit.topology.DivalentLonePairVirtualSite method) (openff.toolkit.topology.MonovalentLonePairVirtualSite method) (openff.toolkit.topology.TrivalentLonePairVirtualSite method) (openff.toolkit.topology.VirtualSite method) compute_positions_from_conformer() (openff.toolkit.topology.BondChargeVirtualSite method) (openff.toolkit.topology.DivalentLonePairVirtualSite method) (openff.toolkit.topology.MonovalentLonePairVirtualSite method) (openff.toolkit.topology.TrivalentLonePairVirtualSite method) (openff.toolkit.topology.VirtualSite method) compute_virtual_site_positions_from_atom_positions() (openff.toolkit.topology.FrozenMolecule method) (openff.toolkit.topology.Molecule method) compute_virtual_site_positions_from_conformer() (openff.toolkit.topology.FrozenMolecule method) (openff.toolkit.topology.Molecule method) conformers (openff.toolkit.topology.FrozenMolecule property) (openff.toolkit.topology.Molecule property) constrained_atom_pairs (openff.toolkit.topology.Topology property) 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_openff_virtual_sites() (openff.toolkit.typing.engines.smirnoff.parameters.VirtualSiteHandler method) create_openmm_system() (openff.toolkit.typing.engines.smirnoff.forcefield.ForceField method) D date (openff.toolkit.typing.engines.smirnoff.forcefield.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.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.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.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.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) deregister_parameter_handler() (openff.toolkit.typing.engines.smirnoff.forcefield.ForceField method) deregister_toolkit() (openff.toolkit.utils.toolkits.ToolkitRegistry method) distance (openff.toolkit.topology.BondChargeVirtualSite property) (openff.toolkit.topology.DivalentLonePairVirtualSite property) (openff.toolkit.topology.MonovalentLonePairVirtualSite property) (openff.toolkit.topology.TrivalentLonePairVirtualSite property) DivalentLonePairVirtualSite (class in openff.toolkit.topology) E ElectrostaticsHandler (class in openff.toolkit.typing.engines.smirnoff.parameters) element (openff.toolkit.topology.Atom property) (openff.toolkit.topology.TopologyAtom property) 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.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.forcefield) formal_charge (openff.toolkit.topology.Atom property) fractional_bond_order_model (openff.toolkit.topology.Topology property) from_bson() (openff.toolkit.topology.Atom class method) (openff.toolkit.topology.Bond class method) (openff.toolkit.topology.BondChargeVirtualSite class method) (openff.toolkit.topology.DivalentLonePairVirtualSite class method) (openff.toolkit.topology.FrozenMolecule class method) (openff.toolkit.topology.Molecule class method) (openff.toolkit.topology.MonovalentLonePairVirtualSite class method) (openff.toolkit.topology.Particle class method) (openff.toolkit.topology.Topology class method) (openff.toolkit.topology.TopologyAtom class method) (openff.toolkit.topology.TopologyBond class method) (openff.toolkit.topology.TopologyVirtualParticle class method) (openff.toolkit.topology.TopologyVirtualSite class method) (openff.toolkit.topology.TrivalentLonePairVirtualSite class method) (openff.toolkit.topology.VirtualParticle class method) (openff.toolkit.topology.VirtualSite 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.BondChargeVirtualSite class method) (openff.toolkit.topology.DivalentLonePairVirtualSite class method) (openff.toolkit.topology.FrozenMolecule class method) (openff.toolkit.topology.Molecule class method) (openff.toolkit.topology.MonovalentLonePairVirtualSite class method) (openff.toolkit.topology.Particle class method) (openff.toolkit.topology.Topology class method) (openff.toolkit.topology.TopologyAtom class method) (openff.toolkit.topology.TopologyBond class method) (openff.toolkit.topology.TopologyMolecule class method) (openff.toolkit.topology.TopologyVirtualParticle class method) (openff.toolkit.topology.TopologyVirtualSite class method) (openff.toolkit.topology.TrivalentLonePairVirtualSite class method) (openff.toolkit.topology.VirtualParticle class method) (openff.toolkit.topology.VirtualSite 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.BondChargeVirtualSite class method) (openff.toolkit.topology.DivalentLonePairVirtualSite class method) (openff.toolkit.topology.FrozenMolecule class method) (openff.toolkit.topology.Molecule class method) (openff.toolkit.topology.MonovalentLonePairVirtualSite class method) (openff.toolkit.topology.Particle class method) (openff.toolkit.topology.Topology class method) (openff.toolkit.topology.TopologyAtom class method) (openff.toolkit.topology.TopologyBond class method) (openff.toolkit.topology.TopologyVirtualParticle class method) (openff.toolkit.topology.TopologyVirtualSite class method) (openff.toolkit.topology.TrivalentLonePairVirtualSite class method) (openff.toolkit.topology.VirtualParticle class method) (openff.toolkit.topology.VirtualSite 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 static method) from_messagepack() (openff.toolkit.topology.Atom class method) (openff.toolkit.topology.Bond class method) (openff.toolkit.topology.BondChargeVirtualSite class method) (openff.toolkit.topology.DivalentLonePairVirtualSite class method) (openff.toolkit.topology.FrozenMolecule class method) (openff.toolkit.topology.Molecule class method) (openff.toolkit.topology.MonovalentLonePairVirtualSite class method) (openff.toolkit.topology.Particle class method) (openff.toolkit.topology.Topology class method) (openff.toolkit.topology.TopologyAtom class method) (openff.toolkit.topology.TopologyBond class method) (openff.toolkit.topology.TopologyVirtualParticle class method) (openff.toolkit.topology.TopologyVirtualSite class method) (openff.toolkit.topology.TrivalentLonePairVirtualSite class method) (openff.toolkit.topology.VirtualParticle class method) (openff.toolkit.topology.VirtualSite class method) (openff.toolkit.utils.serialization.Serializable class method) from_molecule() (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_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.BondChargeVirtualSite class method) (openff.toolkit.topology.DivalentLonePairVirtualSite class method) (openff.toolkit.topology.FrozenMolecule class method) (openff.toolkit.topology.Molecule class method) (openff.toolkit.topology.MonovalentLonePairVirtualSite class method) (openff.toolkit.topology.Particle class method) (openff.toolkit.topology.Topology class method) (openff.toolkit.topology.TopologyAtom class method) (openff.toolkit.topology.TopologyBond class method) (openff.toolkit.topology.TopologyVirtualParticle class method) (openff.toolkit.topology.TopologyVirtualSite class method) (openff.toolkit.topology.TrivalentLonePairVirtualSite class method) (openff.toolkit.topology.VirtualParticle class method) (openff.toolkit.topology.VirtualSite class method) (openff.toolkit.utils.serialization.Serializable 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.BondChargeVirtualSite class method) (openff.toolkit.topology.DivalentLonePairVirtualSite class method) (openff.toolkit.topology.FrozenMolecule class method) (openff.toolkit.topology.Molecule class method) (openff.toolkit.topology.MonovalentLonePairVirtualSite class method) (openff.toolkit.topology.Particle class method) (openff.toolkit.topology.Topology class method) (openff.toolkit.topology.TopologyAtom class method) (openff.toolkit.topology.TopologyBond class method) (openff.toolkit.topology.TopologyVirtualParticle class method) (openff.toolkit.topology.TopologyVirtualSite class method) (openff.toolkit.topology.TrivalentLonePairVirtualSite class method) (openff.toolkit.topology.VirtualParticle class method) (openff.toolkit.topology.VirtualSite 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.BondChargeVirtualSite class method) (openff.toolkit.topology.DivalentLonePairVirtualSite class method) (openff.toolkit.topology.FrozenMolecule class method) (openff.toolkit.topology.Molecule class method) (openff.toolkit.topology.MonovalentLonePairVirtualSite class method) (openff.toolkit.topology.Particle class method) (openff.toolkit.topology.Topology class method) (openff.toolkit.topology.TopologyAtom class method) (openff.toolkit.topology.TopologyBond class method) (openff.toolkit.topology.TopologyVirtualParticle class method) (openff.toolkit.topology.TopologyVirtualSite class method) (openff.toolkit.topology.TrivalentLonePairVirtualSite class method) (openff.toolkit.topology.VirtualParticle class method) (openff.toolkit.topology.VirtualSite 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.BondChargeVirtualSite class method) (openff.toolkit.topology.DivalentLonePairVirtualSite class method) (openff.toolkit.topology.FrozenMolecule class method) (openff.toolkit.topology.Molecule class method) (openff.toolkit.topology.MonovalentLonePairVirtualSite class method) (openff.toolkit.topology.Particle class method) (openff.toolkit.topology.Topology class method) (openff.toolkit.topology.TopologyAtom class method) (openff.toolkit.topology.TopologyBond class method) (openff.toolkit.topology.TopologyVirtualParticle class method) (openff.toolkit.topology.TopologyVirtualSite class method) (openff.toolkit.topology.TrivalentLonePairVirtualSite class method) (openff.toolkit.topology.VirtualParticle class method) (openff.toolkit.topology.VirtualSite 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) 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.forcefield) 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_openmm_virtual_site() (openff.toolkit.topology.BondChargeVirtualSite method) (openff.toolkit.topology.DivalentLonePairVirtualSite method) (openff.toolkit.topology.MonovalentLonePairVirtualSite method) (openff.toolkit.topology.TrivalentLonePairVirtualSite method) 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.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.ForceField method) get_parameter_io_handler() (openff.toolkit.typing.engines.smirnoff.forcefield.ForceField method) get_partial_charges() (openff.toolkit.typing.engines.smirnoff.forcefield.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) hill_formula (openff.toolkit.topology.FrozenMolecule property) (openff.toolkit.topology.Molecule property) I ImproperDict (class in openff.toolkit.topology) impropers (openff.toolkit.topology.FrozenMolecule property) (openff.toolkit.topology.Molecule property) (openff.toolkit.topology.Topology property) (openff.toolkit.topology.TopologyMolecule property) ImproperTorsionHandler (class in openff.toolkit.typing.engines.smirnoff.parameters) ImproperTorsionHandler.ImproperTorsionType (class in openff.toolkit.typing.engines.smirnoff.parameters) in_plane_angle (openff.toolkit.topology.MonovalentLonePairVirtualSite property) 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) index_of_orientation() (openff.toolkit.topology.BondChargeVirtualSite method) (openff.toolkit.topology.DivalentLonePairVirtualSite method) (openff.toolkit.topology.MonovalentLonePairVirtualSite method) (openff.toolkit.topology.TrivalentLonePairVirtualSite method) (openff.toolkit.topology.VirtualSite 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.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.ForceField method) LibraryChargeHandler (class in openff.toolkit.typing.engines.smirnoff.parameters) LibraryChargeHandler.LibraryChargeType (class in openff.toolkit.typing.engines.smirnoff.parameters) local_frame_position (openff.toolkit.topology.BondChargeVirtualSite property) (openff.toolkit.topology.DivalentLonePairVirtualSite property) (openff.toolkit.topology.MonovalentLonePairVirtualSite property) (openff.toolkit.topology.TrivalentLonePairVirtualSite property) (openff.toolkit.topology.VirtualSite property) local_frame_weights (openff.toolkit.topology.BondChargeVirtualSite property) (openff.toolkit.topology.DivalentLonePairVirtualSite property) (openff.toolkit.topology.MonovalentLonePairVirtualSite property) (openff.toolkit.topology.TrivalentLonePairVirtualSite property) (openff.toolkit.topology.VirtualSite property) M MappedParameterAttribute (class in openff.toolkit.typing.engines.smirnoff.parameters) MappedParameterAttribute.UNDEFINED (class in openff.toolkit.typing.engines.smirnoff.parameters) mark_charges_assigned() (openff.toolkit.typing.engines.smirnoff.parameters.ChargeIncrementModelHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.ElectrostaticsHandler method) (openff.toolkit.typing.engines.smirnoff.parameters.LibraryChargeHandler 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) mass (openff.toolkit.topology.Atom property) Molecule (class in openff.toolkit.topology) molecule (openff.toolkit.topology.Atom property) (openff.toolkit.topology.BondChargeVirtualSite property) (openff.toolkit.topology.DivalentLonePairVirtualSite property) (openff.toolkit.topology.MonovalentLonePairVirtualSite property) (openff.toolkit.topology.Particle property) (openff.toolkit.topology.TopologyAtom property) (openff.toolkit.topology.TopologyBond property) (openff.toolkit.topology.TopologyVirtualParticle property) (openff.toolkit.topology.TopologyVirtualSite property) (openff.toolkit.topology.TrivalentLonePairVirtualSite property) (openff.toolkit.topology.VirtualParticle property) (openff.toolkit.topology.VirtualSite property) molecule_atom_index (openff.toolkit.topology.Atom property) molecule_bond_index (openff.toolkit.topology.Bond property) molecule_particle_index (openff.toolkit.topology.Atom property) (openff.toolkit.topology.BondChargeVirtualSite property) (openff.toolkit.topology.DivalentLonePairVirtualSite property) (openff.toolkit.topology.MonovalentLonePairVirtualSite property) (openff.toolkit.topology.Particle property) (openff.toolkit.topology.TrivalentLonePairVirtualSite property) (openff.toolkit.topology.VirtualParticle property) (openff.toolkit.topology.VirtualSite property) molecule_virtual_site_index (openff.toolkit.topology.BondChargeVirtualSite property) (openff.toolkit.topology.DivalentLonePairVirtualSite property) (openff.toolkit.topology.MonovalentLonePairVirtualSite property) (openff.toolkit.topology.TrivalentLonePairVirtualSite property) (openff.toolkit.topology.VirtualSite property) MonovalentLonePairVirtualSite (class in openff.toolkit.topology) N n_angles (openff.toolkit.topology.FrozenMolecule property) (openff.toolkit.topology.Molecule property) (openff.toolkit.topology.Topology property) (openff.toolkit.topology.TopologyMolecule property) n_atoms (openff.toolkit.topology.FrozenMolecule property) (openff.toolkit.topology.Molecule property) (openff.toolkit.topology.TopologyMolecule property) n_bonds (openff.toolkit.topology.FrozenMolecule property) (openff.toolkit.topology.Molecule property) (openff.toolkit.topology.TopologyMolecule 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) (openff.toolkit.topology.TopologyMolecule property) n_particles (openff.toolkit.topology.BondChargeVirtualSite property) (openff.toolkit.topology.DivalentLonePairVirtualSite property) (openff.toolkit.topology.FrozenMolecule property) (openff.toolkit.topology.Molecule property) (openff.toolkit.topology.MonovalentLonePairVirtualSite property) (openff.toolkit.topology.TopologyMolecule property) (openff.toolkit.topology.TopologyVirtualSite property) (openff.toolkit.topology.TrivalentLonePairVirtualSite property) (openff.toolkit.topology.VirtualSite property) n_propers (openff.toolkit.topology.FrozenMolecule property) (openff.toolkit.topology.Molecule property) (openff.toolkit.topology.Topology property) (openff.toolkit.topology.TopologyMolecule 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) n_topology_virtual_sites (openff.toolkit.topology.Topology property) n_virtual_particles (openff.toolkit.topology.FrozenMolecule property) (openff.toolkit.topology.Molecule property) n_virtual_sites (openff.toolkit.topology.FrozenMolecule property) (openff.toolkit.topology.Molecule property) (openff.toolkit.topology.TopologyMolecule property) name (openff.toolkit.topology.Atom property) (openff.toolkit.topology.BondChargeVirtualSite property) (openff.toolkit.topology.DivalentLonePairVirtualSite property) (openff.toolkit.topology.FrozenMolecule property) (openff.toolkit.topology.Molecule property) (openff.toolkit.topology.MonovalentLonePairVirtualSite property) (openff.toolkit.topology.Particle property) (openff.toolkit.topology.TrivalentLonePairVirtualSite property) (openff.toolkit.topology.VirtualParticle property) (openff.toolkit.topology.VirtualSite property) nth_degree_neighbors() (openff.toolkit.topology.FrozenMolecule method) (openff.toolkit.topology.Molecule method) (openff.toolkit.topology.Topology method) (openff.toolkit.topology.TopologyMolecule method) O OpenEyeToolkitWrapper (class in openff.toolkit.utils.toolkits) orientations (openff.toolkit.topology.BondChargeVirtualSite property) (openff.toolkit.topology.DivalentLonePairVirtualSite property) (openff.toolkit.topology.MonovalentLonePairVirtualSite property) (openff.toolkit.topology.TrivalentLonePairVirtualSite property) (openff.toolkit.topology.VirtualSite property) out_of_plane_angle (openff.toolkit.topology.DivalentLonePairVirtualSite property) (openff.toolkit.topology.MonovalentLonePairVirtualSite property) 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.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_index (openff.toolkit.typing.engines.smirnoff.parameters.VirtualSiteHandler.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.ForceField method) parse_sources() (openff.toolkit.typing.engines.smirnoff.forcefield.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.TopologyMolecule method) particles (openff.toolkit.topology.BondChargeVirtualSite property) (openff.toolkit.topology.DivalentLonePairVirtualSite property) (openff.toolkit.topology.FrozenMolecule property) (openff.toolkit.topology.Molecule property) (openff.toolkit.topology.MonovalentLonePairVirtualSite property) (openff.toolkit.topology.TopologyMolecule property) (openff.toolkit.topology.TopologyVirtualSite property) (openff.toolkit.topology.TrivalentLonePairVirtualSite property) (openff.toolkit.topology.VirtualSite property) 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) postprocess_system() (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.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) propers (openff.toolkit.topology.FrozenMolecule property) (openff.toolkit.topology.Molecule property) (openff.toolkit.topology.Topology property) (openff.toolkit.topology.TopologyMolecule 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) R RDKitToolkitWrapper (class in openff.toolkit.utils.toolkits) reference_molecule (openff.toolkit.topology.TopologyMolecule property) reference_molecules (openff.toolkit.topology.Topology property) register_parameter_handler() (openff.toolkit.typing.engines.smirnoff.forcefield.ForceField method) register_parameter_io_handler() (openff.toolkit.typing.engines.smirnoff.forcefield.ForceField method) register_toolkit() (openff.toolkit.utils.toolkits.ToolkitRegistry method) registered_parameter_handlers (openff.toolkit.typing.engines.smirnoff.forcefield.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) (openff.toolkit.topology.TopologyMolecule property) sort() (openff.toolkit.typing.engines.smirnoff.parameters.ParameterList method) (openff.toolkit.utils.collections.ValidatedList method) stereochemistry (openff.toolkit.topology.Atom property) strip_atom_stereochemistry() (openff.toolkit.topology.FrozenMolecule method) (openff.toolkit.topology.Molecule method) 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.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.BondChargeVirtualSite method) (openff.toolkit.topology.DivalentLonePairVirtualSite method) (openff.toolkit.topology.FrozenMolecule method) (openff.toolkit.topology.Molecule method) (openff.toolkit.topology.MonovalentLonePairVirtualSite method) (openff.toolkit.topology.Particle method) (openff.toolkit.topology.Topology method) (openff.toolkit.topology.TopologyAtom method) (openff.toolkit.topology.TopologyBond method) (openff.toolkit.topology.TopologyVirtualParticle method) (openff.toolkit.topology.TopologyVirtualSite method) (openff.toolkit.topology.TrivalentLonePairVirtualSite method) (openff.toolkit.topology.VirtualParticle method) (openff.toolkit.topology.VirtualSite method) (openff.toolkit.utils.serialization.Serializable method) to_dict() (openff.toolkit.topology.Atom method) (openff.toolkit.topology.Bond method) (openff.toolkit.topology.BondChargeVirtualSite method) (openff.toolkit.topology.DivalentLonePairVirtualSite method) (openff.toolkit.topology.FrozenMolecule method) (openff.toolkit.topology.Molecule method) (openff.toolkit.topology.MonovalentLonePairVirtualSite method) (openff.toolkit.topology.Particle method) (openff.toolkit.topology.Topology method) (openff.toolkit.topology.TopologyAtom method) (openff.toolkit.topology.TopologyBond method) (openff.toolkit.topology.TopologyMolecule method) (openff.toolkit.topology.TopologyVirtualParticle method) (openff.toolkit.topology.TopologyVirtualSite method) (openff.toolkit.topology.TrivalentLonePairVirtualSite method) (openff.toolkit.topology.VirtualParticle method) (openff.toolkit.topology.VirtualSite 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.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.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.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) to_file() (openff.toolkit.topology.FrozenMolecule method) (openff.toolkit.topology.Molecule method) (openff.toolkit.topology.Topology method) (openff.toolkit.typing.engines.smirnoff.forcefield.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.BondChargeVirtualSite method) (openff.toolkit.topology.DivalentLonePairVirtualSite method) (openff.toolkit.topology.FrozenMolecule method) (openff.toolkit.topology.Molecule method) (openff.toolkit.topology.MonovalentLonePairVirtualSite method) (openff.toolkit.topology.Particle method) (openff.toolkit.topology.Topology method) (openff.toolkit.topology.TopologyAtom method) (openff.toolkit.topology.TopologyBond method) (openff.toolkit.topology.TopologyVirtualParticle method) (openff.toolkit.topology.TopologyVirtualSite method) (openff.toolkit.topology.TrivalentLonePairVirtualSite method) (openff.toolkit.topology.VirtualParticle method) (openff.toolkit.topology.VirtualSite 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.BondChargeVirtualSite method) (openff.toolkit.topology.DivalentLonePairVirtualSite method) (openff.toolkit.topology.FrozenMolecule method) (openff.toolkit.topology.Molecule method) (openff.toolkit.topology.MonovalentLonePairVirtualSite method) (openff.toolkit.topology.Particle method) (openff.toolkit.topology.Topology method) (openff.toolkit.topology.TopologyAtom method) (openff.toolkit.topology.TopologyBond method) (openff.toolkit.topology.TopologyVirtualParticle method) (openff.toolkit.topology.TopologyVirtualSite method) (openff.toolkit.topology.TrivalentLonePairVirtualSite method) (openff.toolkit.topology.VirtualParticle method) (openff.toolkit.topology.VirtualSite 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 static method) to_openmm() (openff.toolkit.topology.Topology method) to_pickle() (openff.toolkit.topology.Atom method) (openff.toolkit.topology.Bond method) (openff.toolkit.topology.BondChargeVirtualSite method) (openff.toolkit.topology.DivalentLonePairVirtualSite method) (openff.toolkit.topology.FrozenMolecule method) (openff.toolkit.topology.Molecule method) (openff.toolkit.topology.MonovalentLonePairVirtualSite method) (openff.toolkit.topology.Particle method) (openff.toolkit.topology.Topology method) (openff.toolkit.topology.TopologyAtom method) (openff.toolkit.topology.TopologyBond method) (openff.toolkit.topology.TopologyVirtualParticle method) (openff.toolkit.topology.TopologyVirtualSite method) (openff.toolkit.topology.TrivalentLonePairVirtualSite method) (openff.toolkit.topology.VirtualParticle method) (openff.toolkit.topology.VirtualSite 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 class 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.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.BondChargeVirtualSite method) (openff.toolkit.topology.DivalentLonePairVirtualSite method) (openff.toolkit.topology.FrozenMolecule method) (openff.toolkit.topology.Molecule method) (openff.toolkit.topology.MonovalentLonePairVirtualSite method) (openff.toolkit.topology.Particle method) (openff.toolkit.topology.Topology method) (openff.toolkit.topology.TopologyAtom method) (openff.toolkit.topology.TopologyBond method) (openff.toolkit.topology.TopologyVirtualParticle method) (openff.toolkit.topology.TopologyVirtualSite method) (openff.toolkit.topology.TrivalentLonePairVirtualSite method) (openff.toolkit.topology.VirtualParticle method) (openff.toolkit.topology.VirtualSite 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.BondChargeVirtualSite method) (openff.toolkit.topology.DivalentLonePairVirtualSite method) (openff.toolkit.topology.FrozenMolecule method) (openff.toolkit.topology.Molecule method) (openff.toolkit.topology.MonovalentLonePairVirtualSite method) (openff.toolkit.topology.Particle method) (openff.toolkit.topology.Topology method) (openff.toolkit.topology.TopologyAtom method) (openff.toolkit.topology.TopologyBond method) (openff.toolkit.topology.TopologyVirtualParticle method) (openff.toolkit.topology.TopologyVirtualSite method) (openff.toolkit.topology.TrivalentLonePairVirtualSite method) (openff.toolkit.topology.VirtualParticle method) (openff.toolkit.topology.VirtualSite method) (openff.toolkit.utils.serialization.Serializable method) to_yaml() (openff.toolkit.topology.Atom method) (openff.toolkit.topology.Bond method) (openff.toolkit.topology.BondChargeVirtualSite method) (openff.toolkit.topology.DivalentLonePairVirtualSite method) (openff.toolkit.topology.FrozenMolecule method) (openff.toolkit.topology.Molecule method) (openff.toolkit.topology.MonovalentLonePairVirtualSite method) (openff.toolkit.topology.Particle method) (openff.toolkit.topology.Topology method) (openff.toolkit.topology.TopologyAtom method) (openff.toolkit.topology.TopologyBond method) (openff.toolkit.topology.TopologyVirtualParticle method) (openff.toolkit.topology.TopologyVirtualSite method) (openff.toolkit.topology.TrivalentLonePairVirtualSite method) (openff.toolkit.topology.VirtualParticle method) (openff.toolkit.topology.VirtualSite 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 (openff.toolkit.topology.TopologyMolecule property) topology_atom_index (openff.toolkit.topology.TopologyAtom property) topology_atoms (openff.toolkit.topology.Topology property) topology_bond_index (openff.toolkit.topology.TopologyBond property) topology_bonds (openff.toolkit.topology.Topology property) (openff.toolkit.topology.TopologyAtom property) topology_molecule (openff.toolkit.topology.TopologyAtom property) (openff.toolkit.topology.TopologyBond property) (openff.toolkit.topology.TopologyVirtualParticle property) (openff.toolkit.topology.TopologyVirtualSite property) topology_molecules (openff.toolkit.topology.Topology property) topology_parent_atom_index (openff.toolkit.topology.TopologyVirtualParticle property) topology_particle_index (openff.toolkit.topology.TopologyAtom property) (openff.toolkit.topology.TopologyVirtualParticle property) topology_particles (openff.toolkit.topology.Topology property) topology_virtual_particle_start_index (openff.toolkit.topology.TopologyVirtualSite property) topology_virtual_site_index (openff.toolkit.topology.TopologyVirtualSite property) topology_virtual_sites (openff.toolkit.topology.Topology property) TopologyAtom (class in openff.toolkit.topology) TopologyBond (class in openff.toolkit.topology) TopologyMolecule (class in openff.toolkit.topology) TopologyVirtualParticle (class in openff.toolkit.topology) TopologyVirtualSite (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) TrivalentLonePairVirtualSite (class in openff.toolkit.topology) type (openff.toolkit.topology.BondChargeVirtualSite property) (openff.toolkit.topology.DivalentLonePairVirtualSite property) (openff.toolkit.topology.MonovalentLonePairVirtualSite property) (openff.toolkit.topology.TopologyVirtualParticle property) (openff.toolkit.topology.TopologyVirtualSite property) (openff.toolkit.topology.TrivalentLonePairVirtualSite property) (openff.toolkit.topology.VirtualSite property) type_to_parent_index() (openff.toolkit.typing.engines.smirnoff.parameters.VirtualSiteHandler.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) 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) virtual_particle (openff.toolkit.topology.TopologyVirtualParticle property) virtual_particle_start_topology_index (openff.toolkit.topology.TopologyMolecule property) virtual_site (openff.toolkit.topology.TopologyVirtualParticle property) (openff.toolkit.topology.TopologyVirtualSite property) virtual_site() (openff.toolkit.topology.Topology method) (openff.toolkit.topology.TopologyMolecule method) virtual_site_particle_index (openff.toolkit.topology.VirtualParticle property) virtual_site_start_topology_index (openff.toolkit.topology.TopologyMolecule property) virtual_sites (openff.toolkit.topology.Atom property) (openff.toolkit.topology.FrozenMolecule property) (openff.toolkit.topology.Molecule property) (openff.toolkit.topology.TopologyMolecule property) VirtualParticle (class in openff.toolkit.topology) VirtualSite (class in openff.toolkit.topology) VirtualSiteHandler (class in openff.toolkit.typing.engines.smirnoff.parameters) VirtualSiteHandler.VirtualSiteType (class in openff.toolkit.typing.engines.smirnoff.parameters) visualize() (openff.toolkit.topology.Molecule method) X XMLParameterIOHandler (class in openff.toolkit.typing.engines.smirnoff.io)