Source code for MDAnalysis.auxiliary.core

# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
#
# 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
#

"""
Common functions for auxiliary reading --- :mod:`MDAnalysis.auxiliary.core`
===========================================================================

.. autofunction:: get_auxreader_for
.. autofunction:: auxreader
"""
from . import _AUXREADERS
from ..lib import util


[docs] def get_auxreader_for(auxdata=None, format=None): """Return the appropriate auxiliary reader class for *auxdata*/*format*. If *format* is provided, will attempt to find an AuxReader corresponding to that format. If *auxdata* is provided, the format will first be guessed. Parameters ---------- auxdata (Optional) The auxiliary data (e.g. filename of file containing auxiliary data). format (Optional). Known format of *auxdata*. Returns ------- :class:`~MDAnalysis.auxiliary.base.AuxReader` AuxReader class corresponding to the supplied/guessed format. Raises ------ ValueError If an AuxReader for the format (provided or guessed from *auxdata*) cannot be found. """ if not auxdata and not format: raise ValueError('Must provide either auxdata or format') if format is None: if isinstance(auxdata, str): ## assume it's a filename? format = util.guess_format(auxdata) else: ## TBA if add non-file-format readers pass format = format.upper() try: return _AUXREADERS[format] except KeyError: errmsg = f"Unknown auxiliary data format for auxdata: {auxdata}" raise ValueError(errmsg) from None else: try: return _AUXREADERS[format] except KeyError: errmsg = f"Unknown auxiliary data format {format}" raise ValueError(errmsg) from None
[docs] def auxreader(auxdata, format=None, **kwargs): """ Return an auxiliary reader instance for *auxdata*. An appropriate reader class is first obtained using :func:`get_auxreader_for`, and an auxiliary reader instance for *auxdata* then created and returned. Parameters ---------- auxdata Auxiliary data (e.g. filename of file containing auxiliary data). format (Optional). The format of *auxdata*, if known. **kwargs Additional AuxReader options. Returns ------- :class:`~MDAnalysis.auxiliary.base.AuxReader` instance Appropriate auxiliary reader instance for *auxdata*. """ reader = get_auxreader_for(auxdata, format=format) return reader(auxdata, **kwargs)