parmed.tools.exceptions module¶

Exceptions used in parmed script

exception parmed.tools.exceptions.AddPDBError(msg='parmed error')[source]¶: Bases: parmed.tools.exceptions.ParmError

exception parmed.tools.exceptions.AddPDBWarning(msg='parmed warning')[source]¶: Bases: parmed.tools.exceptions.ParmWarning

exception parmed.tools.exceptions.AmberIncompatibleWarning(msg='parmed warning')[source]¶: Bases: parmed.tools.exceptions.ParmWarning

exception parmed.tools.exceptions.AmbiguousParmError(msg='parmed error')[source]¶: Bases: parmed.tools.exceptions.ParmError

exception parmed.tools.exceptions.ArgumentError(msg='parmed error')[source]¶: Bases: parmed.tools.exceptions.ParmError

exception parmed.tools.exceptions.BadParmWarning(msg='parmed warning')[source]¶: Bases: parmed.tools.exceptions.ParmWarning

exception parmed.tools.exceptions.ChamberError(msg='parmed error')[source]¶: Bases: parmed.tools.exceptions.ParmError

exception parmed.tools.exceptions.ChangeLJPairError(msg='parmed error')[source]¶: Bases: parmed.tools.exceptions.ParmError

exception parmed.tools.exceptions.ChangeRadiiError(msg='parmed error')[source]¶: Bases: parmed.tools.exceptions.ParmError

exception parmed.tools.exceptions.ChangeStateError(msg='parmed error')[source]¶: Bases: parmed.tools.exceptions.ParmError

exception parmed.tools.exceptions.CoarseGrainError(msg='parmed error')[source]¶: Bases: parmed.tools.exceptions.ParmError

exception parmed.tools.exceptions.DeleteDihedralError(msg='parmed error')[source]¶: Bases: parmed.tools.exceptions.ParmError

exception parmed.tools.exceptions.DuplicateParamWarning(msg='parmed warning')[source]¶: Bases: parmed.tools.exceptions.SeriousParmWarning

exception parmed.tools.exceptions.DuplicateParm(msg='parmed error')[source]¶: Bases: parmed.tools.exceptions.ParmError

exception parmed.tools.exceptions.FileDoesNotExist(msg='parmed error')[source]¶: Bases: parmed.tools.exceptions.ParmError, OSError

exception parmed.tools.exceptions.FileExists(msg='parmed error')[source]¶: Bases: parmed.tools.exceptions.ParmError

exception parmed.tools.exceptions.FixableParmWarning(msg='parmed warning')[source]¶: Bases: parmed.tools.exceptions.ParmWarning

exception parmed.tools.exceptions.HMassRepartitionError(msg='parmed error')[source]¶: Bases: parmed.tools.exceptions.ParmError

exception parmed.tools.exceptions.IncompatibleParmsError(msg='parmed error')[source]¶: Bases: parmed.tools.exceptions.ParmError

exception parmed.tools.exceptions.InputError[source]¶

Bases: parmed.exceptions.ParmedError

When there is an error with input

exception parmed.tools.exceptions.InterpreterError(msg='parmed error')[source]¶: Bases: parmed.tools.exceptions.ParmError

exception parmed.tools.exceptions.LJ12_6_4Error(msg='parmed error')[source]¶: Bases: parmed.tools.exceptions.ParmError

exception parmed.tools.exceptions.LJ_TypeError(msg='parmed error')[source]¶: Bases: parmed.tools.exceptions.ParmError

exception parmed.tools.exceptions.LongBondWarning(msg='parmed warning')[source]¶: Bases: parmed.tools.exceptions.ParmWarning

exception parmed.tools.exceptions.MissingDisulfide(msg='parmed warning')[source]¶: Bases: parmed.tools.exceptions.ParmWarning

exception parmed.tools.exceptions.NoArgument(msg='parmed error')[source]¶: Bases: parmed.tools.exceptions.ParmError

exception parmed.tools.exceptions.NonUniversalWarning(msg='parmed warning')[source]¶: Bases: parmed.tools.exceptions.ParmWarning

exception parmed.tools.exceptions.NonexistentParm(msg='parmed error')[source]¶: Bases: parmed.tools.exceptions.ParmError

exception parmed.tools.exceptions.NonfatalWarning(msg='parmed warning')[source]¶: Bases: parmed.tools.exceptions.ParmWarning

exception parmed.tools.exceptions.ParmError(msg='parmed error')[source]¶

Bases: parmed.exceptions.ParmedError

Base parmed error

exception parmed.tools.exceptions.ParmFileNotFound(msg='parmed error')[source]¶: Bases: parmed.tools.exceptions.ParmError, FileNotFoundError

exception parmed.tools.exceptions.ParmIndexError(msg='parmed error')[source]¶: Bases: parmed.tools.exceptions.ParmError, IndexError

exception parmed.tools.exceptions.ParmWarning(msg='parmed warning')[source]¶

Bases: parmed.exceptions.ParmedWarning

Base parmed warning

exception parmed.tools.exceptions.ParmedAddLJTypeError(msg='parmed error')[source]¶: Bases: parmed.tools.exceptions.ParmError

exception parmed.tools.exceptions.ParmedChangeError(msg='parmed error')[source]¶: Bases: parmed.tools.exceptions.ParmError

exception parmed.tools.exceptions.ParmedError[source]¶

Bases: Exception

Base class for all non-trivial exceptions raised by ParmEd

exception parmed.tools.exceptions.ParmedMoleculeError(msg='parmed error')[source]¶: Bases: parmed.tools.exceptions.ParmError

exception parmed.tools.exceptions.ParmedUtilsError(msg='parmed error')[source]¶: Bases: parmed.tools.exceptions.ParmError

exception parmed.tools.exceptions.ParmedWarning[source]¶

Bases: Warning

Base class for all warnings raised by ParmEd

exception parmed.tools.exceptions.SeriousParmWarning(msg='parmed warning')[source]¶

Bases: parmed.tools.exceptions.ParmWarning

These warnings are more serious, and are fatal in strict operation

exception parmed.tools.exceptions.SimulationError(msg='parmed error')[source]¶: Bases: parmed.tools.exceptions.ParmError

exception parmed.tools.exceptions.SimulationWarning(msg='parmed warning')[source]¶: Bases: parmed.tools.exceptions.ParmWarning

exception parmed.tools.exceptions.TiMergeError(msg='parmed error')[source]¶: Bases: parmed.tools.exceptions.ParmError

exception parmed.tools.exceptions.UnhandledArgumentWarning(msg='parmed warning')[source]¶: Bases: parmed.tools.exceptions.SeriousParmWarning

class parmed.tools.exceptions.WarningList(empty_msg='No warnings found')[source]¶

Bases: list

List of warnings

Methods

`append`(*args)	Append object to the end of the list.
`clear`(/)	Remove all items from list.
`copy`(/)	Return a shallow copy of the list.
`count`(value, /)	Return number of occurrences of value.
`dump`([dest, ncols])	Dump a list of all warnings to the destination
`extend`(*args)	Append object to the end of the list.
`index`(value[, start, stop])	Return first index of value.
`insert`(index, object, /)	Insert object before index.
`pop`([index])	Remove and return item at index (default last).
`remove`(value, /)	Remove first occurrence of value.
`reverse`(/)	Reverse IN PLACE.
`sort`(*[, key, reverse])	Stable sort IN PLACE.
`warn`(msg[, exc_type])	Adds a warning to the list

append(*args)[source]¶: Append object to the end of the list.

dump(dest=<_io.TextIOWrapper name='<stderr>' mode='w' encoding='UTF-8'>, ncols=80)[source]¶: Dump a list of all warnings to the destination

extend(*args)¶: Append object to the end of the list.

warn(msg, exc_type=<class 'parmed.tools.exceptions.ParmWarning'>)[source]¶: Adds a warning to the list

exception parmed.tools.exceptions.WriteOFFError(msg='parmed error')[source]¶: Bases: parmed.tools.exceptions.ParmError