Source code for MDAnalysis.selections.pymol

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PyMOL selections

Write :class:`MDAnalysis.core.groups.AtomGroup` selection to a
script `pml`_ file that defines PyMOL_ atomselect macros. To be used
in PyMOL like this::


The selections should appear in the user interface.

.. _PyMOL:
.. _pml:

.. autoclass:: SelectionWriter
from . import base

[docs]class SelectionWriter(base.SelectionWriterBase): format = ["PyMol", "pml"] ext = "pml" continuation = '\\' # quoted backslash! commentfmt = "# %s" default_numterms = 6 def _translate(self, atoms, **kwargs): # PyMol index is 1-based def _index(atom): return "index {0:d}".format((atom.index + 1)) return base.join(atoms, ' |', _index) def _write_head(self, out, **kwargs): out.write(self.comment("MDAnalysis PyMol selection")) out.write("select {name!s}, ".format(**kwargs) + self.continuation + '\n')