Source code for MDAnalysis.selections.charmm

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"""
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 __future__ import absolute_import

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")