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# -*- 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 Lesser GNU Public Licence, v2.1 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 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 ..lib import util
from ..lib.mdamath import triclinic_box, triclinic_vectors, box_volume
from ..core._get_readers import get_reader_for, get_writer_for
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:
errmsg = f"Unable to read {filename} with {Reader}."
raise TypeError(errmsg) from None
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)
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