openff-interchange documentation

Index

_

__init__() (openff.interchange.interop.external.InteroperabilityWrapper method) (openff.interchange.interop.external.ParmEdWrapper method) (openff.interchange.types.ArrayQuantity method) (openff.interchange.types.FloatQuantity method) (openff.interchange.types.QuantityEncoder method)

A

add_handler() (openff.interchange.components.interchange.Interchange method) allowed_parameter_handlers() (openff.interchange.components.smirnoff.SMIRNOFFAngleHandler class method) (openff.interchange.components.smirnoff.SMIRNOFFBondHandler class method) (openff.interchange.components.smirnoff.SMIRNOFFConstraintHandler class method) (openff.interchange.components.smirnoff.SMIRNOFFElectrostaticsHandler class method) (openff.interchange.components.smirnoff.SMIRNOFFImproperTorsionHandler class method) (openff.interchange.components.smirnoff.SMIRNOFFPotentialHandler class method) (openff.interchange.components.smirnoff.SMIRNOFFProperTorsionHandler class method) (openff.interchange.components.smirnoff.SMIRNOFFvdWHandler class method) (openff.interchange.components.smirnoff.SMIRNOFFVirtualSiteHandler class method)

AmberError AmberExecutableNotFoundError ArrayQuantity (class in openff.interchange.types) as_integer_ratio() (openff.interchange.types.ArrayQuantity method) (openff.interchange.types.FloatQuantity method) associated_handler (openff.interchange.models.PotentialKey attribute) atom_indices (openff.interchange.models.TopologyKey attribute) (openff.interchange.models.VirtualSiteKey attribute)

B

bond_order (openff.interchange.models.PotentialKey attribute) (openff.interchange.models.TopologyKey attribute)

box (openff.interchange.components.interchange.Interchange property)

C

charges (openff.interchange.components.base.BaseElectrostaticsHandler property) (openff.interchange.components.foyer.FoyerElectrostaticsHandler attribute) (openff.interchange.components.smirnoff.SMIRNOFFElectrostaticsHandler property) charges_with_virtual_sites (openff.interchange.components.foyer.FoyerElectrostaticsHandler property) (openff.interchange.components.smirnoff.SMIRNOFFElectrostaticsHandler property) check_supported_parameters() (openff.interchange.components.smirnoff.SMIRNOFFPotentialHandler class method) compare() (openff.interchange.drivers.report.EnergyReport method) compare_forcefields() (in module openff.interchange.utils) conjugate() (openff.interchange.types.ArrayQuantity method) (openff.interchange.types.FloatQuantity 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.smirnoff.SMIRNOFFConstraintHandler attribute) ConversionError custom_quantity_encoder() (in module openff.interchange.types) cutoff (openff.interchange.components.foyer.FoyerElectrostaticsHandler attribute) (openff.interchange.components.foyer.FoyerVDWHandler attribute) (openff.interchange.components.nonbonded.BuckinghamvdWHandler attribute)

D

data (openff.interchange.components.potentials.WrappedPotential.InnerData attribute)

default() (openff.interchange.types.QuantityEncoder method)

E

encode() (openff.interchange.types.QuantityEncoder method) energies (openff.interchange.drivers.report.EnergyReport attribute) EnergyError exclusion_policy (openff.interchange.components.smirnoff.SMIRNOFFVirtualSiteHandler attribute) 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.BuckinghamvdWHandler attribute) (openff.interchange.components.potentials.PotentialHandler attribute) (openff.interchange.components.smirnoff.SMIRNOFFAngleHandler attribute) (openff.interchange.components.smirnoff.SMIRNOFFBondHandler attribute) (openff.interchange.components.smirnoff.SMIRNOFFConstraintHandler attribute) (openff.interchange.components.smirnoff.SMIRNOFFElectrostaticsHandler attribute) (openff.interchange.components.smirnoff.SMIRNOFFImproperTorsionHandler attribute) (openff.interchange.components.smirnoff.SMIRNOFFPotentialHandler attribute) (openff.interchange.components.smirnoff.SMIRNOFFProperTorsionHandler attribute) (openff.interchange.components.smirnoff.SMIRNOFFvdWHandler attribute) (openff.interchange.components.smirnoff.SMIRNOFFVirtualSiteHandler attribute)

F

f_from_toolkit() (openff.interchange.components.smirnoff.SMIRNOFFAngleHandler class method) FloatQuantity (class in openff.interchange.types) fractional_bond_order_interpolation (openff.interchange.components.smirnoff.SMIRNOFFBondHandler attribute) (openff.interchange.components.smirnoff.SMIRNOFFProperTorsionHandler attribute) fractional_bond_order_method (openff.interchange.components.smirnoff.SMIRNOFFBondHandler attribute) (openff.interchange.components.smirnoff.SMIRNOFFProperTorsionHandler attribute)

from_foyer() (openff.interchange.components.interchange.Interchange class method) from_gromacs() (openff.interchange.components.interchange.Interchange 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) fromhex() (openff.interchange.types.ArrayQuantity method) (openff.interchange.types.FloatQuantity method)

G

get_all_energies() (in module openff.interchange.drivers.all) get_amber_energies() (in module openff.interchange.drivers.amber) get_charges() (openff.interchange.components.smirnoff.SMIRNOFFElectrostaticsHandler method) get_force_field_parameters() (openff.interchange.components.potentials.PotentialHandler method) get_gromacs_energies() (in module openff.interchange.drivers.gromacs) get_handlers_callable() (in module openff.interchange.components.foyer) get_lammps_energies() (in module openff.interchange.drivers.lammps) get_mapping() (openff.interchange.components.potentials.PotentialHandler method) get_nonbonded_force_from_openmm_system() (in module openff.interchange.utils) get_openmm_energies() (in module openff.interchange.drivers.openmm) get_param_matrix() (openff.interchange.components.potentials.PotentialHandler 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_partial_charges_from_openmm_system() (in module openff.interchange.utils) get_summary_data() (in module openff.interchange.drivers.all) get_system_parameters() (openff.interchange.components.potentials.PotentialHandler method) get_test_file_path() (in module openff.interchange.utils) get_test_files_dir_path() (in module openff.interchange.utils) GMXGromppError GMXMdrunError GMXRunError

H

handlers (openff.interchange.components.interchange.Interchange property) HAS_GROMACS (in module openff.interchange.testing.utils)

HAS_LAMMPS (in module openff.interchange.testing.utils) hex() (openff.interchange.types.ArrayQuantity method) (openff.interchange.types.FloatQuantity method)

I

id (openff.interchange.models.PotentialKey attribute) imag (openff.interchange.types.ArrayQuantity attribute) (openff.interchange.types.FloatQuantity attribute) independent_variables (openff.interchange.components.potentials.PotentialHandler property) InternalInconsistencyError InteroperabilityWrapper (class in openff.interchange.interop.external) InvalidBoxError

InvalidExpressionError InvalidParameterHandlerError InvalidTopologyError is_integer() (openff.interchange.types.ArrayQuantity method) (openff.interchange.types.FloatQuantity method) item_separator (openff.interchange.types.QuantityEncoder attribute) iterencode() (openff.interchange.types.QuantityEncoder method)

J

json_loader() (in module openff.interchange.types)

K

key_separator (openff.interchange.types.QuantityEncoder attribute)

L

LAMMPSRunError

library_charge_from_molecule() (in module openff.interchange.components.smirnoff)

M

map_key (openff.interchange.components.potentials.Potential attribute) match (openff.interchange.models.VirtualSiteKey attribute) MDP_HEADER (in module openff.interchange.drivers.gromacs) method (openff.interchange.components.base.BaseElectrostaticsHandler attribute) (openff.interchange.components.base.BasevdWHandler attribute) (openff.interchange.components.foyer.FoyerElectrostaticsHandler attribute) (openff.interchange.components.foyer.FoyerVDWHandler attribute) (openff.interchange.components.nonbonded.BuckinghamvdWHandler attribute) (openff.interchange.components.smirnoff.SMIRNOFFElectrostaticsHandler attribute) (openff.interchange.components.smirnoff.SMIRNOFFvdWHandler attribute) MissingBondOrdersError MissingBoxError MissingEnergyError MissingNonbondedCompatibilityError MissingParameterHandlerError MissingParametersError MissingPositionsError MissingUnitError mixing_rule (openff.interchange.components.base.BasevdWHandler attribute) (openff.interchange.components.foyer.FoyerVDWHandler attribute) (openff.interchange.components.nonbonded.BuckinghamvdWHandler attribute) (openff.interchange.components.smirnoff.SMIRNOFFvdWHandler attribute) 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.mdtraj openff.interchange.components.nonbonded openff.interchange.components.potentials openff.interchange.components.smirnoff 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.drivers.utils openff.interchange.exceptions openff.interchange.interop openff.interchange.interop.external openff.interchange.interop.intermol openff.interchange.interop.openmm openff.interchange.interop.parmed openff.interchange.models openff.interchange.testing openff.interchange.testing.utils openff.interchange.types openff.interchange.utils

mult (openff.interchange.models.PotentialKey attribute) (openff.interchange.models.TopologyKey attribute)

N

NonbondedCompatibilityError

NonbondedEnergyError

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.mdtraj module openff.interchange.components.nonbonded module openff.interchange.components.potentials module openff.interchange.components.smirnoff 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.drivers.utils module openff.interchange.exceptions module openff.interchange.interop module openff.interchange.interop.external module openff.interchange.interop.intermol module openff.interchange.interop.openmm module openff.interchange.interop.parmed module openff.interchange.models module openff.interchange.testing module openff.interchange.testing.utils module openff.interchange.types module openff.interchange.utils module

P

parameter_handler_precedence() (openff.interchange.components.smirnoff.SMIRNOFFElectrostaticsHandler class method) (openff.interchange.components.smirnoff.SMIRNOFFvdWHandler class method) parameters (openff.interchange.components.potentials.Potential attribute) (openff.interchange.components.potentials.WrappedPotential property) parametrize() (openff.interchange.components.potentials.PotentialHandler method) parametrize_partial() (openff.interchange.components.potentials.PotentialHandler method)

ParmEdWrapper (class in openff.interchange.interop.external) pint_to_openmm() (in module openff.interchange.utils) positions (openff.interchange.components.interchange.Interchange property) POTENTIAL_KEY_SEPARATOR (in module openff.interchange.components.foyer) potentials (openff.interchange.components.potentials.PotentialHandler attribute) (openff.interchange.components.smirnoff.SMIRNOFFPotentialHandler attribute)

Q

QuantityEncoder (class in openff.interchange.types)

R

raise_on_missing_params (openff.interchange.components.foyer.FoyerPeriodicProperHandler attribute) (openff.interchange.components.foyer.FoyerRBProperHandler attribute)

real (openff.interchange.types.ArrayQuantity attribute) (openff.interchange.types.FloatQuantity attribute) remove_handler() (openff.interchange.components.interchange.Interchange method)

S

SanderError scale_13 (openff.interchange.components.foyer.FoyerElectrostaticsHandler attribute) (openff.interchange.components.foyer.FoyerVDWHandler attribute) (openff.interchange.components.nonbonded.BuckinghamvdWHandler attribute) scale_14 (openff.interchange.components.foyer.FoyerElectrostaticsHandler attribute) (openff.interchange.components.foyer.FoyerVDWHandler attribute) (openff.interchange.components.nonbonded.BuckinghamvdWHandler attribute) scale_15 (openff.interchange.components.foyer.FoyerElectrostaticsHandler attribute) (openff.interchange.components.foyer.FoyerVDWHandler attribute) (openff.interchange.components.nonbonded.BuckinghamvdWHandler attribute) set_force_field_parameters() (openff.interchange.components.potentials.PotentialHandler method) slot_map (openff.interchange.components.potentials.PotentialHandler attribute) (openff.interchange.components.smirnoff.SMIRNOFFPotentialHandler attribute) SMIRNOFF_POTENTIAL_HANDLERS (in module openff.interchange.components.interchange) (in module openff.interchange.components.smirnoff) SMIRNOFFHandlersNotImplementedError SMIRNOFFParameterAttributeNotImplementedError store_charges() (openff.interchange.components.foyer.FoyerElectrostaticsHandler method) store_constraints() (openff.interchange.components.smirnoff.SMIRNOFFConstraintHandler method) store_matches() (openff.interchange.components.foyer.FoyerConnectedAtomsHandler method) (openff.interchange.components.foyer.FoyerVDWHandler method) (openff.interchange.components.potentials.PotentialHandler method) (openff.interchange.components.smirnoff.SMIRNOFFBondHandler method) (openff.interchange.components.smirnoff.SMIRNOFFElectrostaticsHandler method) (openff.interchange.components.smirnoff.SMIRNOFFImproperTorsionHandler method) (openff.interchange.components.smirnoff.SMIRNOFFPotentialHandler method) (openff.interchange.components.smirnoff.SMIRNOFFProperTorsionHandler method) (openff.interchange.components.smirnoff.SMIRNOFFVirtualSiteHandler method)

store_potentials() (openff.interchange.components.foyer.FoyerConnectedAtomsHandler method) (openff.interchange.components.foyer.FoyerVDWHandler method) (openff.interchange.components.potentials.PotentialHandler method) (openff.interchange.components.smirnoff.SMIRNOFFAngleHandler method) (openff.interchange.components.smirnoff.SMIRNOFFBondHandler method) (openff.interchange.components.smirnoff.SMIRNOFFElectrostaticsHandler method) (openff.interchange.components.smirnoff.SMIRNOFFImproperTorsionHandler method) (openff.interchange.components.smirnoff.SMIRNOFFProperTorsionHandler method) (openff.interchange.components.smirnoff.SMIRNOFFvdWHandler method) (openff.interchange.components.smirnoff.SMIRNOFFVirtualSiteHandler method) supported_parameters() (openff.interchange.components.smirnoff.SMIRNOFFAngleHandler class method) (openff.interchange.components.smirnoff.SMIRNOFFBondHandler class method) (openff.interchange.components.smirnoff.SMIRNOFFConstraintHandler class method) (openff.interchange.components.smirnoff.SMIRNOFFElectrostaticsHandler class method) (openff.interchange.components.smirnoff.SMIRNOFFImproperTorsionHandler class method) (openff.interchange.components.smirnoff.SMIRNOFFPotentialHandler class method) (openff.interchange.components.smirnoff.SMIRNOFFProperTorsionHandler class method) (openff.interchange.components.smirnoff.SMIRNOFFvdWHandler class method) (openff.interchange.components.smirnoff.SMIRNOFFVirtualSiteHandler class method) switch_width (openff.interchange.components.smirnoff.SMIRNOFFvdWHandler attribute)

T

T (in module openff.interchange.components.smirnoff) to_crd() (openff.interchange.components.interchange.Interchange method) to_file() (openff.interchange.interop.external.ParmEdWrapper method) to_gro() (openff.interchange.components.interchange.Interchange method) to_inpcrd() (openff.interchange.components.interchange.Interchange method) to_lammps() (openff.interchange.components.interchange.Interchange method) to_openmm() (in module openff.interchange.interop.openmm) (openff.interchange.components.interchange.Interchange method) to_prmtop() (openff.interchange.components.interchange.Interchange method) to_psf() (openff.interchange.components.interchange.Interchange method) to_top() (openff.interchange.components.interchange.Interchange method) ToolkitTopologyConformersNotFoundError topology (openff.interchange.components.interchange.Interchange property) TP (in module openff.interchange.components.smirnoff) 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.BuckinghamvdWHandler attribute) (openff.interchange.components.potentials.PotentialHandler attribute) (openff.interchange.components.smirnoff.SMIRNOFFAngleHandler attribute) (openff.interchange.components.smirnoff.SMIRNOFFBondHandler attribute) (openff.interchange.components.smirnoff.SMIRNOFFConstraintHandler attribute) (openff.interchange.components.smirnoff.SMIRNOFFElectrostaticsHandler attribute) (openff.interchange.components.smirnoff.SMIRNOFFImproperTorsionHandler attribute) (openff.interchange.components.smirnoff.SMIRNOFFPotentialHandler attribute) (openff.interchange.components.smirnoff.SMIRNOFFProperTorsionHandler attribute) (openff.interchange.components.smirnoff.SMIRNOFFvdWHandler attribute) (openff.interchange.components.smirnoff.SMIRNOFFVirtualSiteHandler attribute) (openff.interchange.models.VirtualSiteKey attribute)

TYPE_CHECKING (in module openff.interchange.components.foyer) (in module openff.interchange.components.interchange) (in module openff.interchange.components.mbuild) (in module openff.interchange.components.potentials) (in module openff.interchange.components.smirnoff) (in module openff.interchange.drivers.all) (in module openff.interchange.drivers.amber) (in module openff.interchange.drivers.gromacs) (in module openff.interchange.drivers.utils) (in module openff.interchange.interop.openmm) (in module openff.interchange.interop.parmed) (in module openff.interchange.types)

U

UnimplementedCutoffMethodError UnitValidationError UnsupportedBoxError

UnsupportedCutoffMethodError UnsupportedExportError UnsupportedParameterError update_energies() (openff.interchange.drivers.report.EnergyReport method)

V

valence_terms() (openff.interchange.components.smirnoff.SMIRNOFFAngleHandler class method) (openff.interchange.components.smirnoff.SMIRNOFFBondHandler class method) validate_energies() (openff.interchange.drivers.report.EnergyReport class method)

validate_parameters() (openff.interchange.components.potentials.Potential class method) validate_type() (openff.interchange.types.ArrayQuantity class method) (openff.interchange.types.FloatQuantity class method) virtual_site_key_topology_index_map (openff.interchange.components.smirnoff.SMIRNOFFVirtualSiteHandler attribute)

W

write_formats (openff.interchange.interop.external.InteroperabilityWrapper property) (openff.interchange.interop.external.ParmEdWrapper property)