Source code for MDAnalysis.selections.jmol

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Jmol selections

Write :class:`MDAnalysis.core.groups.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

.. _Jmol:
.. _Jmol selection:
from . import base

[docs]class SelectionWriter(base.SelectionWriterBase): format = ["Jmol", "spt"] 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("});")