RMG Exceptions (rmgpy.exceptions)

This module contains classes which extend Exception for usage in the RMG module

exception rmgpy.exceptions.ActionError

An exception class for errors that occur while applying reaction recipe actions. Pass a string describing the circumstances that caused the exceptional behavior.

with_traceback()

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

exception rmgpy.exceptions.AtomTypeError

An exception to be raised when an error occurs while working with atom types. Pass a string describing the circumstances that caused the exceptional behavior.

with_traceback()

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

exception rmgpy.exceptions.ChemicallySignificantEigenvaluesError

An exception raised when the chemically significant eigenvalue method is unsuccessful for any reason. Pass a string describing the cause of the exceptional behavior.

with_traceback()

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

exception rmgpy.exceptions.ChemkinError

An exception class for exceptional behavior involving Chemkin files. Pass a string describing the circumstances that caused the exceptional behavior.

with_traceback()

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

exception rmgpy.exceptions.CollisionError

An exception class for when RMG is unable to calculate collision efficiencies for the single exponential down pressure dependent solver. Pass a string describing the circumstances that caused the exceptional behavior.

with_traceback()

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

exception rmgpy.exceptions.CoreError

An exception raised if there is a problem within the model core

with_traceback()

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

exception rmgpy.exceptions.DatabaseError

A exception that occurs when working with an RMG database. Pass a string giving specifics about the exceptional behavior.

with_traceback()

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

exception rmgpy.exceptions.DependencyError

An exception that occurs when an error is encountered with a dependency. Pass a string describing the circumstances that caused the exception.

with_traceback()

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

exception rmgpy.exceptions.ElementError

An exception class for errors that occur while working with elements. Pass a string describing the circumstances that caused the exceptional behavior.

with_traceback()

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

exception rmgpy.exceptions.ForbiddenStructureException

An exception passed when RMG encounters a forbidden structure. These are usually caught and the reaction that created it is ignored.

with_traceback()

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

exception rmgpy.exceptions.ImplicitBenzeneError

An exception class when encountering a group with too many implicit benzene atoms. These groups are hard to create sample molecules and hard for users to interpret. Pass a string describing the limitation.

with_traceback()

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

exception rmgpy.exceptions.InchiException

An exception used when encountering a non-valid Inchi expression are encountered. Pass a string describing the error.

with_traceback()

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

exception rmgpy.exceptions.InputError

An exception raised when parsing an input file for any module in RMG: mechanism generation, Arkane, conformer creation, etc. Pass a string describing the error.

with_traceback()

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

exception rmgpy.exceptions.InvalidActionError

An exception to be raised when an invalid action is encountered in a reaction recipe.

with_traceback()

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

exception rmgpy.exceptions.InvalidAdjacencyListError

An exception used to indicate that an RMG-style adjacency list is invalid. Pass a string describing the reason the adjacency list is invalid

with_traceback()

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

exception rmgpy.exceptions.InvalidMicrocanonicalRateError(message, k_ratio=1.0, Keq_ratio=1.0)

Used in pressure dependence when the k(E) calculation does not give the correct kf(T) or Kc(T)

badness()

How bad is the error?

Returns the max of the absolute logarithmic errors of kf and Kc

with_traceback()

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

exception rmgpy.exceptions.KekulizationError

An exception to be raised when encountering an error while kekulizing an aromatic molecule. Can pass a string to indicate the reason for failure.

with_traceback()

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

exception rmgpy.exceptions.KineticsError

An exception class for problems with kinetics. This can be used when finding degeneracy in reaction generation, modifying KineticsData objects, or finding the kinetics of reactions. Unable Pass a string describing the problem.

with_traceback()

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

exception rmgpy.exceptions.ModifiedStrongCollisionError

An exception raised when the modified strong collision method is unsuccessful for any reason. Pass a string describing the cause of the exceptional behavior.

with_traceback()

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

exception rmgpy.exceptions.NegativeBarrierException

This Exception occurs when the energy barrier for a hindered Rotor is negative. This can occur if the scan or fourier fit is poor.

with_traceback()

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

exception rmgpy.exceptions.NetworkError

Raised when an error occurs while working with a pressure-dependent reaction network

with_traceback()

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

exception rmgpy.exceptions.OutputError

This exception is raised whenever an error occurs while saving output information. Pass a string describing the circumstances of the exceptional behavior.

with_traceback()

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

exception rmgpy.exceptions.PressureDependenceError

An exception class to use when an error involving pressure dependence is encountered. Pass a string describing the circumstances of the exceptional behavior.

with_traceback()

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

exception rmgpy.exceptions.QuantityError

An exception to be raised when an error occurs while working with physical quantities in RMG. Pass a string describing the circumstances of the exceptional behavior.

with_traceback()

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

exception rmgpy.exceptions.ReactionError

An exception class for exceptional behavior involving Reaction objects. Pass a string describing the circumstances that caused the exceptional behavior.

with_traceback()

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

exception rmgpy.exceptions.ReactionPairsError

An exception to be raised when an error occurs while working with reaction pairs.

with_traceback()

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

exception rmgpy.exceptions.ReservoirStateError

An exception raised when the reservoir state method is unsuccessful for any reason. Pass a string describing the cause of the exceptional behavior.

with_traceback()

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

exception rmgpy.exceptions.ResonanceError

An exception class for when RMG is unable to generate resonance structures.

with_traceback()

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

exception rmgpy.exceptions.SettingsError

An exception raised when dealing with settings.

with_traceback()

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

exception rmgpy.exceptions.SpeciesError

An exception class for exceptional behavior that occurs while working with chemical species. Pass a string describing the circumstances that caused the exceptional behavior.

with_traceback()

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

exception rmgpy.exceptions.StatmechError

An exception used when an error occurs in estimating Statmech.

with_traceback()

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

exception rmgpy.exceptions.StatmechFitError

An exception used when attempting to fit molecular degrees of freedom to heat capacity data. Pass a string describing the circumstances of the exceptional behavior.

with_traceback()

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

exception rmgpy.exceptions.UndeterminableKineticsError(reaction, message='')

An exception raised when attempts to estimate appropriate kinetic parameters for a chemical reaction are unsuccessful.

with_traceback()

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

exception rmgpy.exceptions.UnexpectedChargeError(graph)

An exception class when encountering a group/molecule with unexpected charge Curently in RMG, we never expect to see -2/+2 or greater magnitude charge, we only except +1/-1 charges on nitrogen, oxygen, sulfur or specifically carbon monoxide/monosulfide.

Attributes: graph is the molecule or group object with the unexpected charge

with_traceback()

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

exception rmgpy.exceptions.VF2Error

An exception raised if an error occurs within the VF2 graph isomorphism algorithm. Pass a string describing the error.

with_traceback()

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