Source code for MDAnalysis.selections.pymol
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
#
# MDAnalysis --- http://mdanalysis.googlecode.com
# Copyright (c) 2006-2011 Naveen Michaud-Agrawal,
# Elizabeth J. Denning, Oliver Beckstein,
# and contributors (see website for details)
# 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')