schrodinger.application.jaguar.autots_exceptions module

Custom AutoTS exceptions

exception schrodinger.application.jaguar.autots_exceptions.TemplateGuessFailure

Bases: schrodinger.application.jaguar.exceptions.JaguarUserFacingException

Templating failed to generate a TS guess.

exception schrodinger.application.jaguar.autots_exceptions.TemplateAtomMapFailure

Bases: schrodinger.application.jaguar.exceptions.JaguarUserFacingException

unable to generate atom mapping for input->template

exception schrodinger.application.jaguar.autots_exceptions.CategoryOrderError

Bases: schrodinger.application.jaguar.exceptions.JaguarUserFacingException

reaction category order is out of acceptable range

exception schrodinger.application.jaguar.autots_exceptions.UnknownChiralityError

Bases: schrodinger.application.jaguar.exceptions.JaguarUserFacingException

Unable to determine chirality of a chiral center.

exception schrodinger.application.jaguar.autots_exceptions.ActiveBondSearchFailure

Bases: schrodinger.application.jaguar.exceptions.JaguarUserFacingException

Failure to locate active bonds by simple search.

exception schrodinger.application.jaguar.autots_exceptions.GhostAtomIndexError

Bases: schrodinger.application.jaguar.exceptions.JaguarUserFacingException

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

exception schrodinger.application.jaguar.autots_exceptions.UFFFailure

Bases: schrodinger.application.jaguar.exceptions.JaguarUserFacingException

Failed to optimize with UFF

exception schrodinger.application.jaguar.autots_exceptions.MCSFailure

Bases: schrodinger.application.jaguar.exceptions.JaguarUserFacingException

canvas mcs failed

exception schrodinger.application.jaguar.autots_exceptions.MappingError

Bases: schrodinger.application.jaguar.exceptions.JaguarUserFacingException

indicates a mapping between incorrect atom types

exception schrodinger.application.jaguar.autots_exceptions.Sn2Failure

Bases: schrodinger.application.jaguar.exceptions.JaguarUserFacingException

failed to do sn2 renumbering

exception schrodinger.application.jaguar.autots_exceptions.IsomerError

Bases: schrodinger.application.jaguar.exceptions.JaguarUserFacingException

two structures are not isomers and are being compared

exception schrodinger.application.jaguar.autots_exceptions.UndefinedBondOperation

Bases: schrodinger.application.jaguar.exceptions.JaguarUserFacingException

the bond operation is undefined

exception schrodinger.application.jaguar.autots_exceptions.UnsupportedReaction

Bases: schrodinger.application.jaguar.exceptions.JaguarUserFacingException

Reaction type is unsupported for complex formation

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

Bases: schrodinger.application.jaguar.exceptions.JaguarUserFacingException

Failure to correctly type the FF

__init__(msg, st=None)

exception schrodinger.application.jaguar.autots_exceptions.InsertionError

Bases: schrodinger.application.jaguar.exceptions.JaguarUserFacingException

failed to insert into min_list

exception schrodinger.application.jaguar.autots_exceptions.ConnectionError

Bases: schrodinger.application.jaguar.exceptions.JaguarUserFacingException

tried to connect same two structures twice

exception schrodinger.application.jaguar.autots_exceptions.IRCFailure

Bases: schrodinger.application.jaguar.exceptions.JaguarUserFacingException

exception schrodinger.application.jaguar.autots_exceptions.IRCVettingFailure

Bases: ValueError

TS failed IRC vetting

exception schrodinger.application.jaguar.autots_exceptions.ChiralityMismatchError

Bases: schrodinger.application.jaguar.exceptions.JaguarUserFacingException

exception schrodinger.application.jaguar.autots_exceptions.TransformError

Bases: schrodinger.application.jaguar.exceptions.JaguarUserFacingException

exception schrodinger.application.jaguar.autots_exceptions.TSFailure

Bases: schrodinger.application.jaguar.exceptions.JaguarUserFacingException

exception schrodinger.application.jaguar.autots_exceptions.FinalTSFailure

Bases: schrodinger.application.jaguar.exceptions.JaguarUserFacingException

exception schrodinger.application.jaguar.autots_exceptions.TSEnergyError

Bases: schrodinger.application.jaguar.exceptions.JaguarUserFacingException

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

Bases: schrodinger.application.jaguar.exceptions.JaguarUserFacingException

transition state has wrong number of imaginary frequencies

__init__(msg, n_neg_freqs)

exception schrodinger.application.jaguar.autots_exceptions.TSDisplacementError

Bases: schrodinger.application.jaguar.exceptions.JaguarUserFacingException

TS has wrong number of modes but displacement criteria were neglected

exception schrodinger.application.jaguar.autots_exceptions.BondError

Bases: schrodinger.application.jaguar.exceptions.JaguarUserFacingException

no bonds are broken/formed in relax_ts

exception schrodinger.application.jaguar.autots_exceptions.JobFailure

Bases: schrodinger.application.jaguar.exceptions.JaguarUserFacingException

a jaguar job failed

exception schrodinger.application.jaguar.autots_exceptions.OptimizationFailure

Bases: schrodinger.application.jaguar.exceptions.JaguarUserFacingException

a jaguar optimization ran out of cycles

exception schrodinger.application.jaguar.autots_exceptions.IRCEndpointError

Bases: schrodinger.application.jaguar.exceptions.JaguarUserFacingException

the irc endpoints are the same geometry

exception schrodinger.application.jaguar.autots_exceptions.CriticalPointsFailure

Bases: schrodinger.application.jaguar.exceptions.JaguarUserFacingException

generic error in critical_points.py, output summary was printed

exception schrodinger.application.jaguar.autots_exceptions.PathFailure

Bases: schrodinger.application.jaguar.exceptions.JaguarUserFacingException

failure in fitting the path

exception schrodinger.application.jaguar.autots_exceptions.SpectatorMoleculeError

Bases: schrodinger.application.jaguar.exceptions.JaguarUserFacingException

Spectator molecules are unsupported