Source code for MDAnalysis.selections.gromacs
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# MDAnalysis --- http://mdanalysis.googlecode.com
# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver Beckstein
# and contributors (see AUTHORS for the full list)
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# Released under the GNU Public Licence, v2 or any higher version
#
# Please cite your use of MDAnalysis in published work:
#
# 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
#
"""
Gromacs selections
==================
Write :class:`MDAnalysis.core.AtomGroup.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:
"""
import base
[docs]class SelectionWriter(base.SelectionWriter):
format = "Gromacs"
ext = "ndx"
default_numterms = 12
def _translate(self, atoms, **kwargs):
# Gromacs index is 1-based; MDAnalysis is 0-based
return [str(atom.number + 1) for atom in atoms]
def _write_head(self, out, **kwargs):
out.write("[ %(name)s ]\n" % kwargs)