Source code for MDAnalysis.exceptions

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# MDAnalysis --- https://www.mdanalysis.org
# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#
# Released under the GNU Public Licence, v2 or any higher version
#
# Please cite your use of MDAnalysis in published work:
#
# 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
#
# 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`
===============================================================

"""




class SelectionError(Exception):
    """Raised when a atom selection failed."""





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
    """





class ApplicationError(OSError):
    """Raised when an external application failed.

    The error code is specific for the application.

    .. versionadded:: 0.7.7
    """





class SelectionWarning(Warning):
    """Warning indicating a possible problem with a selection."""





class MissingDataWarning(Warning):
    """Warning indicating is that required data are missing."""





class ConversionWarning(Warning):
    """Warning indicating a problem with converting between units."""





class FileFormatWarning(Warning):
    """Warning indicating possible problems with a file format."""





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).
    """





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
    """