Source code for MDAnalysis.selections.vmd

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VMD selections

Write :class:`MDAnalysis.core.groups.AtomGroup` selection to a VMD_ `tcl` file
(for example, "macros.vmd") that defines `atomselect macros`_. To be used in
VMD like this (assuming the default macro name "mdanalysis001"):

.. code-block:: tcl

   source macros.vmd
   set sel [atomselect top mdanalysis001]

In the VMD_ GUI the macro "mdanalysis001" appears in the
:menuselection:`Graphics --> Representations` window under
:guilabel:`Selections: Singlewords`.

.. _VMD:
.. _atomselect macros:

.. autoclass:: SelectionWriter

from __future__ import absolute_import

from . import base

[docs]class SelectionWriter(base.SelectionWriterBase): format = "VMD" ext = "vmd" continuation = '\\' commentfmt = "# %s" def _write_head(self, out, **kwargs): out.write(self.comment("MDAnalysis VMD selection")) out.write("atomselect macro {name!s} {{index ".format(**kwargs)) def _translate(self, atoms, **kwargs): # VMD index is 0-based (as is MDAnalysis) return [str(atom.index) for atom in atoms] def _write_tail(self, out, **kwargs): out.write("}")