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# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
#
# MDAnalysis --- https://www.mdanalysis.org
# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#
# Released under the Lesser GNU Public Licence, v2.1 or any higher version
#
# Please cite your use of MDAnalysis in published work:
#
# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler,
# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein.
# MDAnalysis: A Python package for the rapid analysis of molecular dynamics
# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th
# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy.
# doi: 10.25080/majora-629e541a-00e
#
# 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.groups.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
"""
from . import base
class SelectionWriter(base.SelectionWriterBase):
format = ["CHARMM", "str"]
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 {0:d}".format((atom.index + 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 ".format(**kwargs)
+ self.continuation
+ "\n"
)
def _write_tail(self, out, **kwargs):
out.write("END")
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