Index _ | A | B | C | D | E | F | G | I | K | L | M | N | O | P | R | S | T | U | V | W _ __init__() (openff.interchange.components.interchange.TopologyEncoder method) (openff.interchange.interop.external.InteroperabilityWrapper method) (openff.interchange.interop.external.ParmEdWrapper method) A allowed_parameter_handlers() (openff.interchange.plugins.SMIRNOFFCollection class method) AMBER_COULOMBS_CONSTANT (in module openff.interchange.constants) (in module openff.interchange.interop.internal.amber) AmberError AmberExecutableNotFoundError associated_handler (openff.interchange.models.PotentialKey attribute) atom_indices (openff.interchange.models.AngleKey attribute) (openff.interchange.models.BondKey attribute) (openff.interchange.models.ChargeIncrementTopologyKey property) (openff.interchange.models.ChargeModelTopologyKey property) (openff.interchange.models.LibraryChargeTopologyKey property) (openff.interchange.models.ProperTorsionKey attribute) (openff.interchange.models.TopologyKey attribute) (openff.interchange.models.VirtualSiteKey attribute) B bond_order (openff.interchange.models.BondKey attribute) (openff.interchange.models.PotentialKey attribute) (openff.interchange.models.ProperTorsionKey attribute) box (openff.interchange.components.interchange.Interchange attribute) (openff.interchange.Interchange attribute) C CannotInferEnergyError CannotInferNonbondedEnergyError CannotSetSwitchingFunctionError charges (openff.interchange.components.base.BaseElectrostaticsHandler property) (openff.interchange.components.foyer.FoyerElectrostaticsHandler attribute) charges_with_virtual_sites (openff.interchange.components.foyer.FoyerElectrostaticsHandler property) check_openmm_requirements() (openff.interchange.plugins.SMIRNOFFCollection class method) check_supported_parameters() (openff.interchange.plugins.SMIRNOFFCollection class method) collections (openff.interchange.components.interchange.Interchange attribute) (openff.interchange.Interchange attribute) compare() (openff.interchange.drivers.report.EnergyReport method) connection_attribute (openff.interchange.components.foyer.FoyerConnectedAtomsHandler attribute) (openff.interchange.components.foyer.FoyerHarmonicAngleHandler attribute) (openff.interchange.components.foyer.FoyerPeriodicImproperHandler attribute) (openff.interchange.components.foyer.FoyerPeriodicProperHandler attribute) (openff.interchange.components.foyer.FoyerRBImproperHandler attribute) (openff.interchange.components.foyer.FoyerRBProperHandler attribute) constraints (openff.interchange.components.mdconfig.MDConfig attribute) ConversionError coul_cutoff (openff.interchange.components.mdconfig.MDConfig attribute) coul_method (openff.interchange.components.mdconfig.MDConfig attribute) create() (openff.interchange.plugins.SMIRNOFFCollection class method) cutoff (openff.interchange.components.foyer.FoyerElectrostaticsHandler attribute) (openff.interchange.components.foyer.FoyerVDWHandler attribute) (openff.interchange.components.nonbonded.BuckinghamvdWCollection attribute) D data (openff.interchange.components.potentials.WrappedPotential.InnerData attribute) default() (openff.interchange.components.interchange.TopologyEncoder method) diff() (openff.interchange.drivers.report.EnergyReport method) DuplicateMoleculeError E encode() (openff.interchange.components.interchange.TopologyEncoder method) energies (openff.interchange.drivers.report.EnergyReport attribute) EnergyError expression (openff.interchange.components.base.BaseAngleHandler attribute) (openff.interchange.components.base.BaseBondHandler attribute) (openff.interchange.components.base.BaseElectrostaticsHandler attribute) (openff.interchange.components.base.BaseImproperTorsionHandler attribute) (openff.interchange.components.base.BaseProperTorsionHandler attribute) (openff.interchange.components.base.BasevdWHandler attribute) (openff.interchange.components.foyer.FoyerElectrostaticsHandler attribute) (openff.interchange.components.foyer.FoyerHarmonicAngleHandler attribute) (openff.interchange.components.foyer.FoyerHarmonicBondHandler attribute) (openff.interchange.components.foyer.FoyerPeriodicProperHandler attribute) (openff.interchange.components.foyer.FoyerRBProperHandler attribute) (openff.interchange.components.foyer.FoyerVDWHandler attribute) (openff.interchange.components.nonbonded.BuckinghamvdWCollection attribute) (openff.interchange.components.potentials.Collection attribute) F from_foyer() (openff.interchange.components.interchange.Interchange class method) (openff.interchange.Interchange class method) from_gro() (in module openff.interchange.interop.internal.gromacs) from_gromacs() (openff.interchange.components.interchange.Interchange class method) (openff.interchange.Interchange class method) from_interchange() (openff.interchange.components.mdconfig.MDConfig class method) from_intermol_system() (in module openff.interchange.interop.intermol) from_openmm() (in module openff.interchange.interop.openmm) from_smirnoff() (openff.interchange.components.interchange.Interchange class method) (openff.interchange.Interchange class method) from_top() (in module openff.interchange.interop.internal.gromacs) G get_all_energies() (in module openff.interchange.drivers) (in module openff.interchange.drivers.all) get_amber_energies() (in module openff.interchange.drivers) (in module openff.interchange.drivers.amber) get_central_atom_index() (openff.interchange.models.ImproperTorsionKey method) get_force_field_parameters() (openff.interchange.components.potentials.Collection method) get_gromacs_energies() (in module openff.interchange.drivers) (in module openff.interchange.drivers.gromacs) get_handlers_callable() (in module openff.interchange.components.foyer) get_lammps_energies() (in module openff.interchange.drivers) (in module openff.interchange.drivers.lammps) get_mapping() (openff.interchange.components.potentials.Collection method) get_openmm_energies() (in module openff.interchange.drivers) (in module openff.interchange.drivers.openmm) get_param_matrix() (openff.interchange.components.potentials.Collection method) get_params_with_units() (openff.interchange.components.foyer.FoyerConnectedAtomsHandler method) (openff.interchange.components.foyer.FoyerHarmonicAngleHandler method) (openff.interchange.components.foyer.FoyerHarmonicBondHandler method) (openff.interchange.components.foyer.FoyerPeriodicProperHandler method) (openff.interchange.components.foyer.FoyerRBProperHandler method) get_summary_data() (in module openff.interchange.drivers) (in module openff.interchange.drivers.all) get_system_parameters() (openff.interchange.components.potentials.Collection method) GMXGromppError GMXMdrunError GMXRunError I id (openff.interchange.models.PotentialKey attribute) IncompatibleTolerancesError independent_variables (openff.interchange.components.potentials.Collection property) interchange_dumps() (in module openff.interchange.components.interchange) interchange_loader() (in module openff.interchange.components.interchange) InterchangeDeprecationWarning InternalInconsistencyError InteroperabilityWrapper (class in openff.interchange.interop.external) InvalidBoxError InvalidEnergyError InvalidExpressionError InvalidParameterHandlerError InvalidTopologyError InvalidWriterError is_plugin (openff.interchange.components.potentials.Collection attribute) (openff.interchange.plugins.SMIRNOFFCollection attribute) iterencode() (openff.interchange.components.interchange.TopologyEncoder method) K key_map (openff.interchange.components.potentials.Collection attribute) L LAMMPSRunError M map_key (openff.interchange.components.potentials.Potential attribute) match (openff.interchange.models.VirtualSiteKey attribute) mdconfig (openff.interchange.components.interchange.Interchange attribute) (openff.interchange.Interchange attribute) MDP_HEADER (in module openff.interchange.components.mdconfig) method (openff.interchange.components.base.BaseElectrostaticsHandler attribute) (openff.interchange.components.base.BasevdWHandler attribute) (openff.interchange.components.foyer.FoyerVDWHandler attribute) (openff.interchange.components.nonbonded.BuckinghamvdWCollection attribute) MissingBondOrdersError MissingBoxError MissingNonbondedCompatibilityError MissingParameterHandlerError MissingParametersError MissingPartialChargesError MissingPositionsError MissingUnitError mixing_rule (openff.interchange.components.base.BasevdWHandler attribute) (openff.interchange.components.foyer.FoyerVDWHandler attribute) (openff.interchange.components.mdconfig.MDConfig attribute) (openff.interchange.components.nonbonded.BuckinghamvdWCollection attribute) modify_openmm_forces() (openff.interchange.plugins.SMIRNOFFCollection method) module openff.interchange openff.interchange.components openff.interchange.components.base openff.interchange.components.foyer openff.interchange.components.interchange openff.interchange.components.mbuild openff.interchange.components.mdconfig openff.interchange.components.nonbonded openff.interchange.components.potentials openff.interchange.components.toolkit openff.interchange.constants openff.interchange.drivers openff.interchange.drivers.all openff.interchange.drivers.amber openff.interchange.drivers.gromacs openff.interchange.drivers.lammps openff.interchange.drivers.openmm openff.interchange.drivers.report openff.interchange.exceptions openff.interchange.interop openff.interchange.interop.external openff.interchange.interop.intermol openff.interchange.interop.internal openff.interchange.interop.internal.amber openff.interchange.interop.internal.gromacs openff.interchange.interop.internal.lammps openff.interchange.interop.openmm openff.interchange.interop.parmed openff.interchange.models openff.interchange.plugins openff.interchange.smirnoff openff.interchange.warnings mult (openff.interchange.models.PotentialKey attribute) (openff.interchange.models.ProperTorsionKey attribute) N name (openff.interchange.models.VirtualSiteKey attribute) NonbondedCompatibilityError NonbondedEnergyError NonIntegralMoleculeChargeError O offmol_to_compound() (in module openff.interchange.components.mbuild) offtop_to_compound() (in module openff.interchange.components.mbuild) openff.interchange module openff.interchange.components module openff.interchange.components.base module openff.interchange.components.foyer module openff.interchange.components.interchange module openff.interchange.components.mbuild module openff.interchange.components.mdconfig module openff.interchange.components.nonbonded module openff.interchange.components.potentials module openff.interchange.components.toolkit module openff.interchange.constants module openff.interchange.drivers module openff.interchange.drivers.all module openff.interchange.drivers.amber module openff.interchange.drivers.gromacs module openff.interchange.drivers.lammps module openff.interchange.drivers.openmm module openff.interchange.drivers.report module openff.interchange.exceptions module openff.interchange.interop module openff.interchange.interop.external module openff.interchange.interop.intermol module openff.interchange.interop.internal module openff.interchange.interop.internal.amber module openff.interchange.interop.internal.gromacs module openff.interchange.interop.internal.lammps module openff.interchange.interop.openmm module openff.interchange.interop.parmed module openff.interchange.models module openff.interchange.plugins module openff.interchange.smirnoff module openff.interchange.warnings module orientation_atom_indices (openff.interchange.models.VirtualSiteKey attribute) other_atom_indices (openff.interchange.models.ChargeIncrementTopologyKey attribute) P parameters (openff.interchange.components.potentials.Potential attribute) (openff.interchange.components.potentials.WrappedPotential property) parametrize() (openff.interchange.components.potentials.Collection method) parametrize_partial() (openff.interchange.components.potentials.Collection method) ParmEdWrapper (class in openff.interchange.interop.external) partial_charge_method (openff.interchange.models.ChargeModelTopologyKey attribute) periodic (openff.interchange.components.mdconfig.MDConfig attribute) periodic_potential (openff.interchange.components.foyer.FoyerElectrostaticsHandler attribute) phase (openff.interchange.models.ProperTorsionKey attribute) PluginCompatibilityError positions (openff.interchange.components.interchange.Interchange attribute) (openff.interchange.Interchange attribute) POTENTIAL_KEY_SEPARATOR (in module openff.interchange.components.foyer) potential_parameters() (openff.interchange.plugins.SMIRNOFFCollection class method) potentials (openff.interchange.components.potentials.Collection attribute) R raise_on_missing_params (openff.interchange.components.foyer.FoyerPeriodicProperHandler attribute) (openff.interchange.components.foyer.FoyerRBProperHandler attribute) S SanderError scale_13 (openff.interchange.components.foyer.FoyerElectrostaticsHandler attribute) (openff.interchange.components.foyer.FoyerVDWHandler attribute) (openff.interchange.components.nonbonded.BuckinghamvdWCollection attribute) scale_14 (openff.interchange.components.foyer.FoyerElectrostaticsHandler attribute) (openff.interchange.components.foyer.FoyerVDWHandler attribute) (openff.interchange.components.nonbonded.BuckinghamvdWCollection attribute) scale_15 (openff.interchange.components.foyer.FoyerElectrostaticsHandler attribute) (openff.interchange.components.foyer.FoyerVDWHandler attribute) (openff.interchange.components.nonbonded.BuckinghamvdWCollection attribute) set_force_field_parameters() (openff.interchange.components.potentials.Collection method) SMIRNOFFHandlersNotImplementedError SMIRNOFFParameterAttributeNotImplementedError SMIRNOFFVersionNotSupportedError store_charges() (openff.interchange.components.foyer.FoyerElectrostaticsHandler method) store_matches() (openff.interchange.components.foyer.FoyerConnectedAtomsHandler method) (openff.interchange.components.foyer.FoyerHarmonicAngleHandler method) (openff.interchange.components.foyer.FoyerHarmonicBondHandler method) (openff.interchange.components.foyer.FoyerRBProperHandler method) (openff.interchange.components.foyer.FoyerVDWHandler method) (openff.interchange.components.potentials.Collection method) (openff.interchange.plugins.SMIRNOFFCollection method) store_potentials() (openff.interchange.components.foyer.FoyerConnectedAtomsHandler method) (openff.interchange.components.foyer.FoyerVDWHandler method) (openff.interchange.components.potentials.Collection method) supported_parameters() (openff.interchange.plugins.SMIRNOFFCollection class method) switch_width (openff.interchange.components.foyer.FoyerVDWHandler attribute) switching_distance (openff.interchange.components.mdconfig.MDConfig attribute) switching_function (openff.interchange.components.mdconfig.MDConfig attribute) T this_atom_index (openff.interchange.models.ChargeIncrementTopologyKey attribute) (openff.interchange.models.ChargeModelTopologyKey attribute) (openff.interchange.models.LibraryChargeTopologyKey attribute) to_crd() (openff.interchange.components.interchange.Interchange method) (openff.interchange.Interchange method) to_file() (openff.interchange.interop.external.ParmEdWrapper method) to_gro() (in module openff.interchange.interop.internal.gromacs) (openff.interchange.components.interchange.Interchange method) (openff.interchange.Interchange method) to_inpcrd() (in module openff.interchange.interop.internal.amber) (openff.interchange.components.interchange.Interchange method) (openff.interchange.Interchange method) to_lammps() (in module openff.interchange.interop.internal.lammps) (openff.interchange.components.interchange.Interchange method) (openff.interchange.Interchange method) to_openmm() (in module openff.interchange.interop.openmm) (openff.interchange.components.interchange.Interchange method) (openff.interchange.Interchange method) to_openmm_positions() (in module openff.interchange.interop.openmm) to_openmm_topology() (in module openff.interchange.interop.openmm) (openff.interchange.components.interchange.Interchange method) (openff.interchange.Interchange method) to_pdb() (openff.interchange.components.interchange.Interchange method) (openff.interchange.Interchange method) to_prmtop() (in module openff.interchange.interop.internal.amber) (openff.interchange.components.interchange.Interchange method) (openff.interchange.Interchange method) to_psf() (openff.interchange.components.interchange.Interchange method) (openff.interchange.Interchange method) to_top() (in module openff.interchange.interop.internal.gromacs) (openff.interchange.components.interchange.Interchange method) (openff.interchange.Interchange method) topology (openff.interchange.components.interchange.Interchange attribute) (openff.interchange.Interchange attribute) TopologyEncoder (class in openff.interchange.components.interchange) total_energy (openff.interchange.drivers.report.EnergyReport property) type (openff.interchange.components.base.BaseAngleHandler attribute) (openff.interchange.components.base.BaseBondHandler attribute) (openff.interchange.components.base.BaseElectrostaticsHandler attribute) (openff.interchange.components.base.BaseImproperTorsionHandler attribute) (openff.interchange.components.base.BaseProperTorsionHandler attribute) (openff.interchange.components.base.BasevdWHandler attribute) (openff.interchange.components.foyer.FoyerElectrostaticsHandler attribute) (openff.interchange.components.foyer.FoyerHarmonicAngleHandler attribute) (openff.interchange.components.foyer.FoyerHarmonicBondHandler attribute) (openff.interchange.components.foyer.FoyerPeriodicImproperHandler attribute) (openff.interchange.components.foyer.FoyerPeriodicProperHandler attribute) (openff.interchange.components.foyer.FoyerRBImproperHandler attribute) (openff.interchange.components.foyer.FoyerRBProperHandler attribute) (openff.interchange.components.foyer.FoyerVDWHandler attribute) (openff.interchange.components.nonbonded.BuckinghamvdWCollection attribute) (openff.interchange.components.potentials.Collection attribute) (openff.interchange.models.VirtualSiteKey attribute) U UnassignedAngleError UnassignedBondError UnassignedTorsionError UnassignedValenceError UnimplementedCutoffMethodError UnitValidationError UnsupportedBoxError UnsupportedCombinationError UnsupportedCutoffMethodError UnsupportedExportError UnsupportedImportError UnsupportedMixingRuleError UnsupportedParameterError update() (openff.interchange.drivers.report.EnergyReport method) V validate_box() (openff.interchange.components.interchange.Interchange class method) (openff.interchange.Interchange class method) validate_energies() (openff.interchange.drivers.report.EnergyReport class method) validate_parameters() (openff.interchange.components.potentials.Potential class method) validate_topology() (openff.interchange.components.interchange.Interchange class method) (openff.interchange.Interchange class method) vdw_cutoff (openff.interchange.components.mdconfig.MDConfig attribute) vdw_method (openff.interchange.components.mdconfig.MDConfig attribute) velocities (openff.interchange.components.interchange.Interchange attribute) (openff.interchange.Interchange attribute) VirtualSiteTypeNotImplementedError visualize() (openff.interchange.components.interchange.Interchange method) (openff.interchange.Interchange method) W write_lammps_input() (openff.interchange.components.mdconfig.MDConfig method) write_mdp_file() (openff.interchange.components.mdconfig.MDConfig method) write_sander_input_file() (openff.interchange.components.mdconfig.MDConfig method)