schrodinger.application.jaguar.autots_exceptions module

Custom AutoTS exceptions

exception schrodinger.application.jaguar.autots_exceptions.TemplateGuessFailure[source]

Bases: schrodinger.application.jaguar.exceptions.JaguarUserFacingException

Templating failed to generate a TS guess.

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

args
with_traceback()

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

exception schrodinger.application.jaguar.autots_exceptions.TemplateAtomMapFailure[source]

Bases: schrodinger.application.jaguar.exceptions.JaguarUserFacingException

unable to generate atom mapping for input->template

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

args
with_traceback()

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

exception schrodinger.application.jaguar.autots_exceptions.CategoryOrderError[source]

Bases: schrodinger.application.jaguar.exceptions.JaguarUserFacingException

reaction category order is out of acceptable range

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

args
with_traceback()

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

exception schrodinger.application.jaguar.autots_exceptions.UnknownChiralityError[source]

Bases: schrodinger.application.jaguar.exceptions.JaguarUserFacingException

Unable to determine chirality of a chiral center.

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

args
with_traceback()

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

exception schrodinger.application.jaguar.autots_exceptions.ActiveBondSearchFailure[source]

Bases: schrodinger.application.jaguar.exceptions.JaguarUserFacingException

Failure to locate active bonds by simple search.

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

args
with_traceback()

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

exception schrodinger.application.jaguar.autots_exceptions.GhostAtomIndexError[source]

Bases: schrodinger.application.jaguar.exceptions.JaguarUserFacingException

Ghost/dummy atoms are not at the end of the atom list.

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

args
with_traceback()

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

exception schrodinger.application.jaguar.autots_exceptions.UFFFailure[source]

Bases: schrodinger.application.jaguar.exceptions.JaguarUserFacingException

Failed to optimize with UFF

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

args
with_traceback()

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

exception schrodinger.application.jaguar.autots_exceptions.MCSFailure[source]

Bases: schrodinger.application.jaguar.exceptions.JaguarUserFacingException

canvas mcs failed

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

args
with_traceback()

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

exception schrodinger.application.jaguar.autots_exceptions.MappingError[source]

Bases: schrodinger.application.jaguar.exceptions.JaguarUserFacingException

indicates a mapping between incorrect atom types

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

args
with_traceback()

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

exception schrodinger.application.jaguar.autots_exceptions.Sn2Failure[source]

Bases: schrodinger.application.jaguar.exceptions.JaguarUserFacingException

failed to do sn2 renumbering

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

args
with_traceback()

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

exception schrodinger.application.jaguar.autots_exceptions.IsomerError[source]

Bases: schrodinger.application.jaguar.exceptions.JaguarUserFacingException

two structures are not isomers and are being compared

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

args
with_traceback()

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

exception schrodinger.application.jaguar.autots_exceptions.UndefinedBondOperation[source]

Bases: schrodinger.application.jaguar.exceptions.JaguarUserFacingException

the bond operation is undefined

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

args
with_traceback()

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

exception schrodinger.application.jaguar.autots_exceptions.UnsupportedReaction[source]

Bases: schrodinger.application.jaguar.exceptions.JaguarUserFacingException

Reaction type is unsupported for complex formation

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

args
with_traceback()

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

exception schrodinger.application.jaguar.autots_exceptions.MMTypingFailure(msg, st=None)[source]

Bases: schrodinger.application.jaguar.exceptions.JaguarUserFacingException

Failure to correctly type the FF

__init__(msg, st=None)[source]

Initialize self. See help(type(self)) for accurate signature.

args
with_traceback()

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

exception schrodinger.application.jaguar.autots_exceptions.InsertionError[source]

Bases: schrodinger.application.jaguar.exceptions.JaguarUserFacingException

failed to insert into min_list

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

args
with_traceback()

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

exception schrodinger.application.jaguar.autots_exceptions.ConnectionError[source]

Bases: schrodinger.application.jaguar.exceptions.JaguarUserFacingException

tried to connect same two structures twice

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

args
with_traceback()

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

exception schrodinger.application.jaguar.autots_exceptions.IRCFailure[source]

Bases: schrodinger.application.jaguar.exceptions.JaguarUserFacingException

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

args
with_traceback()

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

exception schrodinger.application.jaguar.autots_exceptions.IRCVettingFailure[source]

Bases: ValueError

TS failed IRC vetting

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

args
with_traceback()

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

exception schrodinger.application.jaguar.autots_exceptions.ChiralityMismatchError[source]

Bases: schrodinger.application.jaguar.exceptions.JaguarUserFacingException

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

args
with_traceback()

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

exception schrodinger.application.jaguar.autots_exceptions.TransformError[source]

Bases: schrodinger.application.jaguar.exceptions.JaguarUserFacingException

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

args
with_traceback()

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

exception schrodinger.application.jaguar.autots_exceptions.TSFailure[source]

Bases: schrodinger.application.jaguar.exceptions.JaguarUserFacingException

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

args
with_traceback()

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

exception schrodinger.application.jaguar.autots_exceptions.FinalTSFailure[source]

Bases: schrodinger.application.jaguar.exceptions.JaguarUserFacingException

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

args
with_traceback()

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

exception schrodinger.application.jaguar.autots_exceptions.TSEnergyError[source]

Bases: schrodinger.application.jaguar.exceptions.JaguarUserFacingException

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

args
with_traceback()

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

exception schrodinger.application.jaguar.autots_exceptions.TSFrequencyError(msg, n_neg_freqs)[source]

Bases: schrodinger.application.jaguar.exceptions.JaguarUserFacingException

transition state has wrong number of imaginary frequencies

__init__(msg, n_neg_freqs)[source]

Initialize self. See help(type(self)) for accurate signature.

args
with_traceback()

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

exception schrodinger.application.jaguar.autots_exceptions.TSDisplacementError[source]

Bases: schrodinger.application.jaguar.exceptions.JaguarUserFacingException

TS has wrong number of modes but displacement criteria were neglected

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

args
with_traceback()

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

exception schrodinger.application.jaguar.autots_exceptions.BondError[source]

Bases: schrodinger.application.jaguar.exceptions.JaguarUserFacingException

no bonds are broken/formed in relax_ts

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

args
with_traceback()

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

exception schrodinger.application.jaguar.autots_exceptions.JobFailure[source]

Bases: schrodinger.application.jaguar.exceptions.JaguarUserFacingException

a jaguar job failed

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

args
with_traceback()

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

exception schrodinger.application.jaguar.autots_exceptions.OptimizationFailure[source]

Bases: schrodinger.application.jaguar.exceptions.JaguarUserFacingException

a jaguar optimization ran out of cycles

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

args
with_traceback()

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

exception schrodinger.application.jaguar.autots_exceptions.IRCEndpointError[source]

Bases: schrodinger.application.jaguar.exceptions.JaguarUserFacingException

the irc endpoints are the same geometry

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

args
with_traceback()

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

exception schrodinger.application.jaguar.autots_exceptions.CriticalPointsFailure[source]

Bases: schrodinger.application.jaguar.exceptions.JaguarUserFacingException

generic error in critical_points.py, output summary was printed

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

args
with_traceback()

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

exception schrodinger.application.jaguar.autots_exceptions.PathFailure[source]

Bases: schrodinger.application.jaguar.exceptions.JaguarUserFacingException

failure in fitting the path

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

args
with_traceback()

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

exception schrodinger.application.jaguar.autots_exceptions.SpectatorMoleculeError[source]

Bases: schrodinger.application.jaguar.exceptions.JaguarUserFacingException

Spectator molecules are unsupported

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

args
with_traceback()

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