Source code for MDAnalysis.auxiliary.core

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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)