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

.. _CHARMM selection:
from __future__ import absolute_import

from . import base

[docs]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")