Source code for MDAnalysis.selections.pymol

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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
#


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

Write :class:`MDAnalysis.core.AtomGroup.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:
"""

import base


[docs]class SelectionWriter(base.SelectionWriter): format = "PyMol" 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 %d" % (atom.number + 1) return base.join(atoms, ' |', _index) def _write_head(self, out, **kwargs): out.write(self.comment("MDAnalysis PyMol selection")) out.write("select %(name)s, " % kwargs + self.continuation + '\n')