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