Source code for MDAnalysis.selections.gromacs

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# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler,
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"""
Gromacs selections
==================

Write :class:`MDAnalysis.core.groups.AtomGroup` selection to a `ndx`_ file
that defines a Gromacs_ index group. To be used in Gromacs like this::

  <GROMACS_COMMAND> -n macro.ndx

The index groups are named *mdanalysis001*, *mdanalysis002*, etc.

.. _Gromacs: http://www.gromacs.org
.. _ndx: http://www.gromacs.org/Documentation/File_Formats/Index_File

.. autoclass:: SelectionWriter
   :inherited-members:
"""
from __future__ import absolute_import

from . import base

class SelectionWriter(base.SelectionWriterBase):
    format = ["Gromacs", "ndx"]
    ext = "ndx"
    default_numterms = 12

    def _translate(self, atoms, **kwargs):
        # Gromacs index is 1-based; MDAnalysis is 0-based
        return [str(atom.index + 1) for atom in atoms]

    def _write_head(self, out, **kwargs):
        out.write("[ {name!s} ]\n".format(**kwargs))