Source code for MDAnalysis.selections.jmol

# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
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# Please cite your use of MDAnalysis in published work:
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# 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
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# MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations.
# J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787
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"""
Jmol selections
=================

Write :class:`MDAnalysis.core.groups.AtomGroup` selection to a `str` file
that defines a `Jmol selection`_. To be used in Jmol_ like this::

  script macro.spt
  select ~selection

The selection is named *mdanalysis001*.TODO

.. autoclass:: SelectionWriter
   :inherited-members:

.. _Jmol: http://wiki.jmol.org/index.php/Main_Page
.. _Jmol selection: http://chemapps.stolaf.edu/jmol/docs/#define
"""
from . import base


class SelectionWriter(base.SelectionWriterBase):
    format = ["Jmol", "spt"]
    ext = "spt"
    default_numterms = None
    commentfmt = '#'

    def _translate(self, atoms, **kwargs):
        # Jmol indexing is 0 based when using atom bitsets
        def _index(atom):
            return str(atom.index)

        return base.join(atoms, ' ', _index)

    def _write_head(self, out, **kwargs):
        out.write("@~{name!s} ({{".format(**kwargs))

    def _write_tail(self, out, **kwargs):
        out.write("});")