`openff.toolkit.utils.exceptions`

Exceptions

`AmbiguousAtomChemicalAssignment`(res_name, ...)	Exception raised when substructure does not contain enough information
`AmbiguousBondChemicalAssignment`(res_name, ...)	Exception raised when substructure does not contain enough information
`AntechamberNotFoundError`(msg)	The antechamber executable was not found
`AtomMappingWarning`	A warning when dealing with atom maping or indices.
`AtomNotInTopologyError`(msg)	An atom was not found in a topology.
`BondExistsError`(msg)	The program attempted to add a bond that already exists
`BondNotInTopologyError`(msg)	An bond was not found in a topology.
`CallbackRegistrationError`(msg)	Error raised when callback registration fails.
`ChargeCalculationError`(msg)	An unhandled error occurred in an external toolkit during charge calculation
`ChargeMethodUnavailableError`(msg)	A toolkit does not support the requested partial_charge_method combination
`ChemicalEnvironmentParsingError`(msg)	Exception for when SMARTS/SMIRKS are not parseable by a wrapped toolkit
`ConformerGenerationError`(msg)	Conformer generation via a wrapped toolkit failed.
`ConstraintExsistsError`(msg)	Attempting to override a constraint that already exists with a specified distance.
`DuplicateParameterError`(msg)	Exception raised when trying to add a ParameterType that already exists
`DuplicateUniqueMoleculeError`(msg)	Exception for when the user provides indistinguishable unique molecules when trying to identify atoms from a PDB
`DuplicateVirtualSiteTypeException`(msg)	Exception raised when trying to register two different virtual site classes with the same 'type'
`FractionalBondOrderInterpolationMethodUnsupportedError`(msg)	Exception for when an unsupported fractional bond order interpolation assignment method is called.
`GAFFAtomTypeWarning`	A warning raised if a loaded mol2 file possibly uses GAFF atom types.
`HierarchyIteratorNameConflictError`(msg)	Exception raised when trying to access a hierarchy scheme with a name that already exists as a Topology or Molecule attribute.
`HierarchySchemeNotFoundException`(msg)	Exception raised when trying to access a HierarchyScheme from a molecule that doesn't have one with the given iterator name
`HierarchySchemeWithIteratorNameAlreadyRegisteredException`(msg)	Exception raised when trying to add a HierarchyScheme to a molecule that already has one with the same iterator name
`InChIParseError`(msg)	The InChI record could not be parsed.
`IncompatibleParameterError`(msg)	Exception for when a set of parameters is scientifically/technically incompatible with another
`IncompatibleShapeError`(msg)	Exception for when a value is in the wrong shape
`IncompatibleTypeError`(msg)	Exception for when a value is in an incompatible type
`IncompatibleUnitError`(msg)	Exception for when a parameter is in the wrong units for a ParameterHandler's unit system
`InconsistentStereochemistryError`(msg)	Error raised when stereochemistry is inconsistent before and after conversions between molecule representations.
`IncorrectNumConformersError`(msg)	The requested partial_charge_method expects a different number of conformers than was provided
`IncorrectNumConformersWarning`	The requested partial_charge_method expects a different number of conformers than was provided
`InvalidAromaticityModelError`(msg)	General exception for errors while setting the aromaticity model of a Topology.
`InvalidAtomMetadataError`(msg)	The program attempted to set atom metadata to an invalid type
`InvalidBondOrderError`(msg)	Exception for passing a non-int to Molecule.bond_order
`InvalidBoxVectorsError`(msg)	Exception for setting invalid box vectors
`InvalidConformerError`(msg)	This error is raised when the conformer added to the molecule has a different connectivity to that already defined.
`InvalidIUPACNameError`(msg)	Failed to parse IUPAC name
`InvalidPeriodicityError`(msg)	Exception for setting invalid periodicity
`InvalidQCInputError`(msg)	This error is raised when an input to Molecule.from_qcschema is invalid.
`InvalidToolkitError`(msg)	A non-toolkit object was received when a toolkit object was expected
`InvalidToolkitRegistryError`(msg)	An object other than a ToolkitRegistry or toolkit wrapper was received
`LicenseError`(msg)	This function requires a license that cannot be found.
`MissingCMILESError`(msg)	Error raised when attempting to convert an QC input to an OFF Molecule, but the CMILES can't be found or isn't present.
`MissingConformersError`(msg)	Error raised when a molecule is missing conformer(s) in a context in which it is expected to have them.
`MissingIndexedAttributeError`(msg)	Error raised when an indexed attribute does not exist
`MissingPackageError`(msg)	This function requires a package that is not installed.
`MissingPartialChargesError`(msg)	Error raised when a molecule is missing partial charges in a context in which it is expected to have them.
`MissingUniqueMoleculesError`(msg)	Exception for when unique_molecules is required but not found
`MoleculeNotInTopologyError`(msg)	A molecule was not found in a topology.
`MoleculeParseError`(msg)	The molecule could not be created from the given format
`MultipleMoleculesInPDBError`(msg)	Error raised when a multiple molecules are found when one was expected
`NonUniqueSubstructureName`(duplicate_keys)	Exception raised when nonunique names are given
`NotAttachedToMoleculeError`(msg)	Exception for when a component does not belong to a Molecule object, but is queried
`NotBondedError`(msg)	Exception for when a function requires a bond between two atoms, but none is present
`NotEnoughPointsForInterpolationError`(msg)	Exception for when less than two points are provided for interpolation
`NotInTopologyError`(msg)	An object was not found in a topology.
`OpenEyeError`(msg)	Error raised when an OpenEye Toolkits operation fails.
`OpenEyeImportError`(msg)	Error raised when importing an OpenEye module fails.
`OpenFFToolkitException`(msg)	Base exception for custom exceptions raised by the OpenFF Toolkit
`ParameterHandlerRegistrationError`(msg)	Exception for errors in ParameterHandler registration
`ParameterLookupError`(msg)	Exception raised when something goes wrong in a parameter lookup in ParameterHandler.__getitem__
`PartialChargeVirtualSitesError`(msg)	Exception thrown when partial charges cannot be computed for a Molecule because the ForceField applies virtual sites.
`RadicalsNotSupportedError`(msg)	The OpenFF Toolkit does not currently support parsing molecules with radicals.
`RemapIndexError`(msg)	An error with indices used to remap a molecule
`SMILESParseError`(msg)	The record could not be parsed into the given format
`SMIRKSMismatchError`(msg)	Exception for cases where smirks are inappropriate for the environment type they are being parsed into
`SMIRKSParsingError`(msg)	Exception for when SMIRKS are not parseable for any environment
`SMIRNOFFAromaticityError`(msg)	Exception thrown when an incompatible SMIRNOFF aromaticity model is checked for compatibility.
`SMIRNOFFParseError`(msg)	Error for when a SMIRNOFF data structure is not parseable by a ForceField
`SMIRNOFFSpecError`(msg)	Exception for when data is noncompliant with the SMIRNOFF data specification.
`SMIRNOFFSpecUnimplementedError`(msg)	Exception for when a portion of the SMIRNOFF specification is not yet implemented.
`SMIRNOFFVersionError`(msg)	Exception thrown when an incompatible SMIRNOFF version data structure is attempted to be read.
`SmilesParsingError`(msg)	This error is raised when parsing a SMILES string results in an error.
`SubstructureAtomSmartsInvalid`(name, ...)	Exception raised when atom or bond smarts are found to be improperly formatted
`SubstructureBondSmartsInvalid`(name, bond, ...)
`SubstructureImproperlySpecified`(name, reason)	Exception raised when substructure does not contain enough information
`ToolkitUnavailableException`(msg)	The requested toolkit is unavailable.
`UnassignedAngleParameterException`(msg)	Exception raised when there are angle terms for which a ParameterHandler can't find parameters.
`UnassignedBondParameterException`(msg)	Exception raised when there are bond terms for which a ParameterHandler can't find parameters.
`UnassignedChemistryInPDBError`([msg, ...])	Error raised when a bond or atom in a polymer could not be assigned chemical information.
`UnassignedMoleculeChargeException`(msg)	Exception raised when no charge method is able to assign charges to a molecule.
`UnassignedProperTorsionParameterException`(msg)	Exception raised when there are proper torsion terms for which a ParameterHandler can't find parameters.
`UnassignedValenceParameterException`(msg)	Exception raised when there are valence terms for which a ParameterHandler can't find parameters.
`UndefinedStereochemistryError`(msg)	A molecule was attempted to be loaded with undefined stereochemistry
`UnsupportedFileTypeError`(msg)	Error raised when attempting to parse an unsupported file type.
`UnsupportedMoleculeConversionError`(msg)	Error raised when attempting to instantiate a Molecule with insufficient inputs.
`VirtualSitesUnsupportedError`(msg)	Exception raised when trying to store virtual sites in a Molecule or Topology object.
`WrongShapeError`(msg)	Error raised when an array of the wrong shape is found

exception openff.toolkit.utils.exceptions.OpenFFToolkitException(msg: str)[source]

Base exception for custom exceptions raised by the OpenFF Toolkit

with_traceback(): Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

exception openff.toolkit.utils.exceptions.IncompatibleUnitError(msg: str)[source]

Exception for when a parameter is in the wrong units for a ParameterHandler’s unit system

with_traceback(): Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

exception openff.toolkit.utils.exceptions.IncompatibleShapeError(msg: str)[source]

Exception for when a value is in the wrong shape

with_traceback(): Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

exception openff.toolkit.utils.exceptions.IncompatibleTypeError(msg: str)[source]

Exception for when a value is in an incompatible type

with_traceback(): Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

exception openff.toolkit.utils.exceptions.MissingPackageError(msg: str)[source]

This function requires a package that is not installed.

with_traceback(): Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

exception openff.toolkit.utils.exceptions.ToolkitUnavailableException(msg: str)[source]

The requested toolkit is unavailable.

with_traceback(): Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

exception openff.toolkit.utils.exceptions.LicenseError(msg: str)[source]

This function requires a license that cannot be found.

with_traceback(): Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

exception openff.toolkit.utils.exceptions.InvalidToolkitError(msg: str)[source]

A non-toolkit object was received when a toolkit object was expected

with_traceback(): Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

exception openff.toolkit.utils.exceptions.InvalidToolkitRegistryError(msg: str)[source]

An object other than a ToolkitRegistry or toolkit wrapper was received

with_traceback(): Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

exception openff.toolkit.utils.exceptions.UndefinedStereochemistryError(msg: str)[source]

A molecule was attempted to be loaded with undefined stereochemistry

with_traceback(): Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

exception openff.toolkit.utils.exceptions.GAFFAtomTypeWarning[source]

A warning raised if a loaded mol2 file possibly uses GAFF atom types.

with_traceback(): Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

exception openff.toolkit.utils.exceptions.ChargeMethodUnavailableError(msg: str)[source]

A toolkit does not support the requested partial_charge_method combination

with_traceback(): Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

exception openff.toolkit.utils.exceptions.IncorrectNumConformersError(msg: str)[source]

The requested partial_charge_method expects a different number of conformers than was provided

with_traceback(): Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

exception openff.toolkit.utils.exceptions.IncorrectNumConformersWarning[source]

The requested partial_charge_method expects a different number of conformers than was provided

with_traceback(): Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

exception openff.toolkit.utils.exceptions.ChargeCalculationError(msg: str)[source]

An unhandled error occurred in an external toolkit during charge calculation

with_traceback(): Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

exception openff.toolkit.utils.exceptions.ConformerGenerationError(msg: str)[source]

Conformer generation via a wrapped toolkit failed.

with_traceback(): Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

exception openff.toolkit.utils.exceptions.InvalidIUPACNameError(msg: str)[source]

Failed to parse IUPAC name

with_traceback(): Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

exception openff.toolkit.utils.exceptions.AntechamberNotFoundError(msg: str)[source]

The antechamber executable was not found

with_traceback(): Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

exception openff.toolkit.utils.exceptions.MoleculeParseError(msg: str)[source]

The molecule could not be created from the given format

with_traceback(): Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

exception openff.toolkit.utils.exceptions.SMILESParseError(msg: str)[source]

The record could not be parsed into the given format

with_traceback(): Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

exception openff.toolkit.utils.exceptions.AtomMappingWarning[source]

A warning when dealing with atom maping or indices.

with_traceback(): Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

exception openff.toolkit.utils.exceptions.InChIParseError(msg: str)[source]

The InChI record could not be parsed.

with_traceback(): Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

exception openff.toolkit.utils.exceptions.RadicalsNotSupportedError(msg: str)[source]

The OpenFF Toolkit does not currently support parsing molecules with radicals.

with_traceback(): Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

exception openff.toolkit.utils.exceptions.InvalidConformerError(msg: str)[source]

This error is raised when the conformer added to the molecule has a different connectivity to that already defined. or any other conformer related issues.

with_traceback(): Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

exception openff.toolkit.utils.exceptions.InvalidQCInputError(msg: str)[source]

This error is raised when an input to Molecule.from_qcschema is invalid.

with_traceback(): Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

exception openff.toolkit.utils.exceptions.SmilesParsingError(msg: str)[source]

This error is raised when parsing a SMILES string results in an error.

with_traceback(): Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

exception openff.toolkit.utils.exceptions.NotAttachedToMoleculeError(msg: str)[source]

Exception for when a component does not belong to a Molecule object, but is queried

with_traceback(): Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

exception openff.toolkit.utils.exceptions.NotInTopologyError(msg: str)[source]

An object was not found in a topology.

with_traceback(): Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

exception openff.toolkit.utils.exceptions.RemapIndexError(msg: str)[source]

An error with indices used to remap a molecule

with_traceback(): Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

exception openff.toolkit.utils.exceptions.AtomNotInTopologyError(msg: str)[source]

An atom was not found in a topology.

with_traceback(): Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

exception openff.toolkit.utils.exceptions.BondNotInTopologyError(msg: str)[source]

An bond was not found in a topology.

with_traceback(): Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

exception openff.toolkit.utils.exceptions.MoleculeNotInTopologyError(msg: str)[source]

A molecule was not found in a topology.

with_traceback(): Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

exception openff.toolkit.utils.exceptions.InvalidAtomMetadataError(msg: str)[source]

The program attempted to set atom metadata to an invalid type

with_traceback(): Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

exception openff.toolkit.utils.exceptions.BondExistsError(msg: str)[source]

The program attempted to add a bond that already exists

with_traceback(): Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

exception openff.toolkit.utils.exceptions.ConstraintExsistsError(msg: str)[source]

Attempting to override a constraint that already exists with a specified distance.

with_traceback(): Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

exception openff.toolkit.utils.exceptions.DuplicateUniqueMoleculeError(msg: str)[source]

Exception for when the user provides indistinguishable unique molecules when trying to identify atoms from a PDB

with_traceback(): Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

exception openff.toolkit.utils.exceptions.NotBondedError(msg: str)[source]

Exception for when a function requires a bond between two atoms, but none is present

with_traceback(): Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

exception openff.toolkit.utils.exceptions.InvalidBondOrderError(msg: str)[source]

Exception for passing a non-int to Molecule.bond_order

with_traceback(): Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

exception openff.toolkit.utils.exceptions.InvalidBoxVectorsError(msg: str)[source]

Exception for setting invalid box vectors

with_traceback(): Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

exception openff.toolkit.utils.exceptions.InvalidPeriodicityError(msg: str)[source]

Exception for setting invalid periodicity

with_traceback(): Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

exception openff.toolkit.utils.exceptions.MissingUniqueMoleculesError(msg: str)[source]

Exception for when unique_molecules is required but not found

with_traceback(): Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

exception openff.toolkit.utils.exceptions.SMIRKSMismatchError(msg: str)[source]

Exception for cases where smirks are inappropriate for the environment type they are being parsed into

with_traceback(): Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

exception openff.toolkit.utils.exceptions.SMIRKSParsingError(msg: str)[source]

Exception for when SMIRKS are not parseable for any environment

with_traceback(): Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

exception openff.toolkit.utils.exceptions.ChemicalEnvironmentParsingError(msg: str)[source]

Exception for when SMARTS/SMIRKS are not parseable by a wrapped toolkit

with_traceback(): Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

exception openff.toolkit.utils.exceptions.ParameterHandlerRegistrationError(msg: str)[source]

Exception for errors in ParameterHandler registration

with_traceback(): Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

exception openff.toolkit.utils.exceptions.SMIRNOFFVersionError(msg: str)[source]

Exception thrown when an incompatible SMIRNOFF version data structure is attempted to be read.

with_traceback(): Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

exception openff.toolkit.utils.exceptions.SMIRNOFFAromaticityError(msg: str)[source]

Exception thrown when an incompatible SMIRNOFF aromaticity model is checked for compatibility.

with_traceback(): Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

exception openff.toolkit.utils.exceptions.InvalidAromaticityModelError(msg: str)[source]

General exception for errors while setting the aromaticity model of a Topology.

with_traceback(): Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

exception openff.toolkit.utils.exceptions.SMIRNOFFParseError(msg: str)[source]

Error for when a SMIRNOFF data structure is not parseable by a ForceField

with_traceback(): Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

exception openff.toolkit.utils.exceptions.PartialChargeVirtualSitesError(msg: str)[source]

Exception thrown when partial charges cannot be computed for a Molecule because the ForceField applies virtual sites.

with_traceback(): Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

exception openff.toolkit.utils.exceptions.SMIRNOFFSpecError(msg: str)[source]

Exception for when data is noncompliant with the SMIRNOFF data specification.

with_traceback(): Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

exception openff.toolkit.utils.exceptions.SMIRNOFFSpecUnimplementedError(msg: str)[source]

Exception for when a portion of the SMIRNOFF specification is not yet implemented.

with_traceback(): Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

exception openff.toolkit.utils.exceptions.FractionalBondOrderInterpolationMethodUnsupportedError(msg: str)[source]

Exception for when an unsupported fractional bond order interpolation assignment method is called.

with_traceback(): Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

exception openff.toolkit.utils.exceptions.NotEnoughPointsForInterpolationError(msg: str)[source]

Exception for when less than two points are provided for interpolation

with_traceback(): Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

exception openff.toolkit.utils.exceptions.IncompatibleParameterError(msg: str)[source]

Exception for when a set of parameters is scientifically/technically incompatible with another

with_traceback(): Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

exception openff.toolkit.utils.exceptions.UnassignedValenceParameterException(msg: str)[source]

Exception raised when there are valence terms for which a ParameterHandler can’t find parameters.

with_traceback(): Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

exception openff.toolkit.utils.exceptions.UnassignedBondParameterException(msg: str)[source]

Exception raised when there are bond terms for which a ParameterHandler can’t find parameters.

with_traceback(): Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

exception openff.toolkit.utils.exceptions.UnassignedAngleParameterException(msg: str)[source]

Exception raised when there are angle terms for which a ParameterHandler can’t find parameters.

with_traceback(): Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

exception openff.toolkit.utils.exceptions.UnassignedProperTorsionParameterException(msg: str)[source]

Exception raised when there are proper torsion terms for which a ParameterHandler can’t find parameters.

with_traceback(): Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

exception openff.toolkit.utils.exceptions.UnassignedMoleculeChargeException(msg: str)[source]

Exception raised when no charge method is able to assign charges to a molecule.

with_traceback(): Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

exception openff.toolkit.utils.exceptions.DuplicateParameterError(msg: str)[source]

Exception raised when trying to add a ParameterType that already exists

with_traceback(): Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

exception openff.toolkit.utils.exceptions.ParameterLookupError(msg: str)[source]

Exception raised when something goes wrong in a parameter lookup in ParameterHandler.__getitem__

with_traceback(): Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

exception openff.toolkit.utils.exceptions.DuplicateVirtualSiteTypeException(msg: str)[source]

Exception raised when trying to register two different virtual site classes with the same ‘type’

with_traceback(): Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

exception openff.toolkit.utils.exceptions.CallbackRegistrationError(msg: str)[source]

Error raised when callback registration fails.

with_traceback(): Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

exception openff.toolkit.utils.exceptions.HierarchySchemeWithIteratorNameAlreadyRegisteredException(msg: str)[source]

Exception raised when trying to add a HierarchyScheme to a molecule that already has one with the same iterator name

with_traceback(): Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

exception openff.toolkit.utils.exceptions.HierarchySchemeNotFoundException(msg: str)[source]

Exception raised when trying to access a HierarchyScheme from a molecule that doesn’t have one with the given iterator name

with_traceback(): Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

exception openff.toolkit.utils.exceptions.HierarchyIteratorNameConflictError(msg: str)[source]

Exception raised when trying to access a hierarchy scheme with a name that already exists as a Topology or Molecule attribute.

with_traceback(): Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

exception openff.toolkit.utils.exceptions.VirtualSitesUnsupportedError(msg: str)[source]

Exception raised when trying to store virtual sites in a Molecule or Topology object.

with_traceback(): Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

exception openff.toolkit.utils.exceptions.MissingIndexedAttributeError(msg: str)[source]

Error raised when an indexed attribute does not exist

with_traceback(): Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

exception openff.toolkit.utils.exceptions.MissingPartialChargesError(msg: str)[source]

Error raised when a molecule is missing partial charges in a context in which it is expected to have them.

with_traceback(): Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

exception openff.toolkit.utils.exceptions.MissingConformersError(msg: str)[source]

Error raised when a molecule is missing conformer(s) in a context in which it is expected to have them.

with_traceback(): Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

exception openff.toolkit.utils.exceptions.MissingCMILESError(msg: str)[source]

Error raised when attempting to convert an QC input to an OFF Molecule, but the CMILES can’t be found or isn’t present.

with_traceback(): Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

exception openff.toolkit.utils.exceptions.UnsupportedMoleculeConversionError(msg: str)[source]

Error raised when attempting to instantiate a Molecule with insufficient inputs.

with_traceback(): Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

exception openff.toolkit.utils.exceptions.InconsistentStereochemistryError(msg: str)[source]

Error raised when stereochemistry is inconsistent before and after conversions between molecule representations.

with_traceback(): Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

exception openff.toolkit.utils.exceptions.UnsupportedFileTypeError(msg: str)[source]

Error raised when attempting to parse an unsupported file type.

with_traceback(): Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

exception openff.toolkit.utils.exceptions.OpenEyeError(msg: str)[source]

Error raised when an OpenEye Toolkits operation fails.

with_traceback(): Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

exception openff.toolkit.utils.exceptions.OpenEyeImportError(msg: str)[source]

Error raised when importing an OpenEye module fails.

with_traceback(): Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

exception openff.toolkit.utils.exceptions.MultipleMoleculesInPDBError(msg: str)[source]

Error raised when a multiple molecules are found when one was expected

with_traceback(): Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

exception openff.toolkit.utils.exceptions.WrongShapeError(msg: str)[source]

Error raised when an array of the wrong shape is found

with_traceback(): Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

exception openff.toolkit.utils.exceptions.UnassignedChemistryInPDBError(msg: str | None = None, substructure_library: dict[str, list[tuple]] | None = None, omm_top: OpenMMTopology | None = None, unassigned_bonds: list[tuple[int, int]] | None = None, unassigned_atoms: list[int] | None = None, matches: DefaultDict[int, list[str]] | None = None)[source]

Error raised when a bond or atom in a polymer could not be assigned chemical information.

with_traceback(): Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

exception openff.toolkit.utils.exceptions.NonUniqueSubstructureName(duplicate_keys)[source]

Exception raised when nonunique names are given

with_traceback(): Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

exception openff.toolkit.utils.exceptions.SubstructureAtomSmartsInvalid(name, atom_smarts, smarts, reason)[source]

Exception raised when atom or bond smarts are found to be improperly formatted

with_traceback(): Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

exception openff.toolkit.utils.exceptions.SubstructureBondSmartsInvalid(name, bond, valid_bond_types)[source]

with_traceback(): Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

exception openff.toolkit.utils.exceptions.SubstructureImproperlySpecified(name, reason)[source]

Exception raised when substructure does not contain enough information

with_traceback(): Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

exception openff.toolkit.utils.exceptions.AmbiguousAtomChemicalAssignment(res_name, mol_atom, query_atom, reason)[source]

Exception raised when substructure does not contain enough information

with_traceback(): Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

exception openff.toolkit.utils.exceptions.AmbiguousBondChemicalAssignment(res_name, mol_bond, query_bond, reason)[source]

Exception raised when substructure does not contain enough information

with_traceback(): Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.