Source code for MDAnalysis.selections.gromacs

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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:
.. _ndx:

.. autoclass:: SelectionWriter
from __future__ import absolute_import

from . import base

[docs]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))