Source code for MDAnalysis.selections.vmd

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# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler,
# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein.
# MDAnalysis: A Python package for the rapid analysis of molecular dynamics
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# MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations.
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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: http://www.ks.uiuc.edu/Research/vmd/
.. _atomselect macros: http://www.ks.uiuc.edu/Research/vmd/current/ug/node120.html

.. autoclass:: SelectionWriter
   :inherited-members:

"""
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("}")