16. Custom exceptions and warnings — MDAnalysis.exceptions

exception MDAnalysis.exceptions.ApplicationError[source]

Raised when an external application failed.

The error code is specific for the application.

New in version 0.7.7.

exception MDAnalysis.exceptions.ConversionWarning[source]

Warning indicating a problem with converting between units.

exception MDAnalysis.exceptions.DuplicateWarning[source]

Warning indicating possible problems arising from an AtomGroup / ResidueGroup / SegmentGroup containing duplicate Atoms / Residues / Segments.

New in version 0.19.0.

exception MDAnalysis.exceptions.FileFormatWarning[source]

Warning indicating possible problems with a file format.

exception MDAnalysis.exceptions.MissingDataWarning[source]

Warning indicating is that required data are missing.

exception MDAnalysis.exceptions.NoDataError[source]

Raised when empty input is not allowed or required data are missing.

This exception is raised in the following scenarios:

  • Raised when a TopologyAttr (e.g., bonds, charges) is not present in the data.

  • Raised when data is missing in an analysis class because the run() method has not been called, e.g. PersistenceLength.

  • Raised when timestep data is missing, such as positions, velocities, or forces.

  • Raised in the nojump transformation if there is no box information in the universe.

This exception should not be raised in cases where arrays have zero width, or AtomGroups are empty.

Changed in version 1.0.0: Now a subclass of AttributeError as well as ValueError

exception MDAnalysis.exceptions.SelectionError[source]

Raised when a atom selection failed.

exception MDAnalysis.exceptions.SelectionWarning[source]

Warning indicating a possible problem with a selection.

exception MDAnalysis.exceptions.StreamWarning[source]

Warning indicating a possible problem with a stream.

StreamWarning is used when streams are substituted for simple access by filename (see in particular NamedStream). This does not work everywhere in MDAnalysis (yet).