Source code for MDAnalysis.coordinates.XTC

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"""
Gromacs XTC file IO --- :mod:`MDAnalysis.coordinates.XTC`
=========================================================

The Gromacs `XTC trajectory format`_ is a format with lossy
compression. Coordinates are only stored with a fixed precision (by
default, 1/1000 of a nm). The XTC format can only store
*coordinates*. Its main advantage is that it requires less disk space
than e.g. TRR or DCD trajectories and the loss of precision is usually
not a problem.

If one wants to store Gromacs trajectories without loss of precision
or with velocities and/or forces then one should use the TRR format
(see module :mod:`~MDAnalysis.coordinates.TRR`).

The XTC I/O interface uses
:mod:`~MDAnalysis.coordinates.xdrfile.libxdrfile2` to implement random
access to frames. This works by initially building an internal index
of all frames and then using this index for direct seeks. Building the
index is triggered by
:func:`~MDAnalysis.coordinates.xdrfile.libxdrfile2.read_xtc_numframes`,
which typically happens when one accesses the
:attr:`XTCReader.numframes` attribute for the first time. Building the
index may take many minutes for large trajectories but afterwards
access is faster than with native Gromacs tools.

.. _XTC trajectory format:
   http://www.gromacs.org/Documentation/File_Formats/.xtc_File

.. versionchanged:: 0.8.0
   The XTC I/O interface now uses
   :mod:`~MDAnalysis.coordinates.xdrfile.libxdrfile2`, which has
   seeking and indexing capabilities. Note that unlike
   :mod:`~MDAnalysis.coordinates.xdrfile.libxdrfile` before it,
   :mod:`~MDAnalysis.coordinates.xdrfile.libxdrfile2` is distributed
   under the GNU GENERAL PUBLIC LICENSE, version 2 (or higher).
   :class:`~MDAnalysis.coordinates.XTC.Timestep` now correctly
   deals with presence/absence of coordinate/velocity/force
   information on a per-frame basis.

Module reference
----------------

.. autoclass:: Timestep
   :members:
   :inherited-members:

.. autoclass:: XTCReader
   :members:
   :inherited-members:

.. autoclass:: XTCWriter
   :members:
   :inherited-members:

"""

from .xdrfile.XTC import XTCReader, XTCWriter, Timestep