Source code for MDAnalysis.selections.pymol

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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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"""
PyMOL selections
=================

Write :class:`MDAnalysis.core.groups.AtomGroup` selection to a
script `pml`_ file that defines PyMOL_ atomselect macros. To be used
in PyMOL like this::

  @macros.pml

The selections should appear in the user interface.

.. _PyMOL: http://www.pymol.org
.. _pml: http://pymol.sourceforge.net/newman/user/S0210start_cmds.html#6_5_1

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

from . import base

class SelectionWriter(base.SelectionWriterBase):
    format = ["PyMol", "pml"]
    ext = "pml"
    continuation = '\\'  # quoted backslash!
    commentfmt = "# %s"
    default_numterms = 6

    def _translate(self, atoms, **kwargs):
        # PyMol index is 1-based
        def _index(atom):
            return "index {0:d}".format((atom.index + 1))

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

    def _write_head(self, out, **kwargs):
        out.write(self.comment("MDAnalysis PyMol selection"))
        out.write("select {name!s}, ".format(**kwargs) + self.continuation + '\n')