Source code for MDAnalysis.selections.charmm
# -*- 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
#
"""
CHARMM selections
=================
Write :class:`MDAnalysis.core.AtomGroup.AtomGroup` selection to a `str` file
that defines a `CHARMM selection`_. To be used in CHARMM_ like this::
stream macro.str
The selection is named *mdanalysis001*.
.. autoclass:: SelectionWriter
:inherited-members:
.. _CHARMM: http://www.charmm.org
.. _CHARMM selection: http://www.charmm.org/documentation/c34b1/select.html
"""
import base
[docs]class SelectionWriter(base.SelectionWriter):
format = "CHARMM"
ext = "str"
continuation = '-'
commentfmt = "! %s"
default_numterms = 4 # be conservative because CHARMM only reads 72 columns
def _translate(self, atoms, **kwargs):
# CHARMM index is 1-based
def _index(atom):
return "BYNUM %d" % (atom.number + 1)
return base.join(atoms, ' .or.', _index)
def _write_head(self, out, **kwargs):
out.write(self.comment("MDAnalysis CHARMM selection"))
out.write("DEFINE %(name)s SELECT " % kwargs + self.continuation + '\n')
def _write_tail(self, out, **kwargs):
out.write("END")