Source code for MDAnalysis.exceptions

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# MDAnalysis --- https://www.mdanalysis.org
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# Please cite your use of MDAnalysis in published work:
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# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler,
# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein.
# MDAnalysis: A Python package for the rapid analysis of molecular dynamics
# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th
# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy.
# doi: 10.25080/majora-629e541a-00e
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# N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein.
# MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations.
# J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787
#

"""
Custom exceptions and warnings --- :mod:`MDAnalysis.exceptions`
===============================================================

"""


[docs] class SelectionError(Exception): """Raised when a atom selection failed."""
[docs] class NoDataError(ValueError, AttributeError): """Raised when empty input is not allowed or required data are missing. This exception is raised in the following scenarios: * Raised when a :class:`~MDAnalysis.core.topologyattrs.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. :class:`~MDAnalysis.analysis.polymer.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. .. versionchanged:: 1.0.0 Now a subclass of AttributeError as well as ValueError """
[docs] class ApplicationError(OSError): """Raised when an external application failed. The error code is specific for the application. .. versionadded:: 0.7.7 """
[docs] class SelectionWarning(Warning): """Warning indicating a possible problem with a selection."""
[docs] class MissingDataWarning(Warning): """Warning indicating is that required data are missing."""
[docs] class ConversionWarning(Warning): """Warning indicating a problem with converting between units."""
[docs] class FileFormatWarning(Warning): """Warning indicating possible problems with a file format."""
[docs] class StreamWarning(Warning): """Warning indicating a possible problem with a stream. :exc:`StreamWarning` is used when streams are substituted for simple access by filename (see in particular :class:`~MDAnalysis.lib.util.NamedStream`). This does not work everywhere in MDAnalysis (yet). """
[docs] class DuplicateWarning(UserWarning): """Warning indicating possible problems arising from an :class:`~MDAnalysis.core.groups.AtomGroup` / :class:`~MDAnalysis.core.groups.ResidueGroup` / :class:`~MDAnalysis.core.groups.SegmentGroup` containing duplicate :class:`Atoms<MDAnalysis.core.groups.Atom>` / :class:`Residues<MDAnalysis.core.groups.Residue>` / :class:`Segments<MDAnalysis.core.groups.Segment>`. .. versionadded:: 0.19.0 """