Source code for MDAnalysis.selections.jmol
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
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# MDAnalysis --- http://www.MDAnalysis.org
# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver Beckstein
# and contributors (see AUTHORS for the full list)
#
# 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
#
"""
Jmol selections
=================
Write :class:`MDAnalysis.core.AtomGroup.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 __future__ import absolute_import
from . import base
[docs]class SelectionWriter(base.SelectionWriter):
format = "Jmol"
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("});")