Source code for MDAnalysis.coordinates.core

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Common functions for coordinate reading --- :mod:`MDAnalysis.coordinates.core`

Important base classes are collected in :mod:`MDAnalysis.coordinates.base`.

.. autofunction:: reader
.. autofunction:: writer

Helper functions:

.. autofunction:: get_reader_for
.. autofunction:: get_writer_for

from __future__ import absolute_import

import six

from ..lib import util
from ..lib.mdamath import triclinic_box, triclinic_vectors, box_volume
from ..core._get_readers import get_reader_for, get_writer_for

[docs]def reader(filename, format=None, **kwargs): """Provide a trajectory reader instance for *filename*. This function guesses the file format from the extension of *filename* and it will throw a :exc:`TypeError` if the extension is not recognized. In most cases, no special keyword arguments are necessary. All other keywords are passed on to the underlying Reader classes; see their documentation for details. Parameters ---------- filename : str or tuple filename (or tuple of filenames) of the input coordinate file kwargs Keyword arguments for the selected Reader class. Returns ------- :class:`~base.Reader` A trajectory Reader instance See Also -------- :ref:`Supported coordinate formats` """ if isinstance(filename, tuple): Reader = get_reader_for(filename[0], format=filename[1]) filename = filename[0] else: Reader = get_reader_for(filename, format=format) try: return Reader(filename, **kwargs) except ValueError: six.raise_from( TypeError( 'Unable to read {fn} with {r}.'.format( fn=filename, r=Reader ) ), None)
[docs]def writer(filename, n_atoms=None, **kwargs): """Initialize a trajectory writer instance for *filename*. Parameters ---------- filename : str Output filename of the trajectory; the extension determines the format. n_atoms : int (optional) The number of atoms in the output trajectory; can be ommitted for single-frame writers. multiframe : bool (optional) ``True``: write a trajectory with multiple frames; ``False`` only write a single frame snapshot; ``None`` first try to get a multiframe writer and then fall back to single frame [``None``] kwargs : optional Keyword arguments for the writer; all trajectory Writers accept ``start``: starting time [0], ``step``: step size in frames [1], ``dt``: length of time between two frames, in ps [1.0] Some readers accept additional arguments, which need to be looked up in the documentation of the reader. Returns ------- :class:`~base.Writer` A trajectory Writer instance See Also -------- :ref:`Supported coordinate formats` .. versionchanged:: 0.7.6 Added `multiframe` keyword. See also :func:`get_writer_for`. """ Writer = get_writer_for(filename, format=kwargs.pop('format', None), multiframe=kwargs.pop('multiframe', None)) return Writer(filename, n_atoms=n_atoms, **kwargs)