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.. Contains the formatted docstrings for the core modules located in 'mdanalysis/MDAnalysis/core'
.. _`Selection exporters`:
*******************
Selection exporters
*******************
The classes in this module allow writing a selection to a file that can be read by
*another program* to select the atoms in a MDAnalysis
:class:`MDAnalysis.core.groups.AtomGroup`. Such cross-package interoperability
allows a user to combine their favourite tools with MDAnalysis for further
visualization or simulation.
.. _Supported selection exporters:
.. table:: Table of supported exporters and recognized file name extensions.
+---------------+-----------+-------+--------------------------------------------+
|Name | extension | IO | remarks |
+===============+===========+=======+============================================+
| vmd | tcl | w | VMD_ macros, available in Representations; |
| | | | module :mod:`MDAnalysis.selections.vmd` |
+---------------+-----------+-------+--------------------------------------------+
| pymol | pml | w | simple PyMOL_ selection string; |
| | | | module :mod:`MDAnalysis.selections.pymol` |
+---------------+-----------+-------+--------------------------------------------+
| gromacs | ndx | w | Gromacs_ index file; |
| | | | module :mod:`MDAnalysis.selections.gromacs`|
+---------------+-----------+-------+--------------------------------------------+
| charmm | str | w | CHARMM_ selection of individual atoms; |
| | | | module :mod:`MDAnalysis.selections.charmm` |
+---------------+-----------+-------+--------------------------------------------+
| jmol | spt | w | Jmol_ selection commands; |
| | | | module :mod:`MDAnalysis.selections.jmol` |
+---------------+-----------+-------+--------------------------------------------+
How to write selections
=======================
Single AtomGroup
----------------
The typical situation is that one has an
:class:`~MDAnalysis.core.groups.AtomGroup` and wants to work with the
same selection of atoms in a different package, for example, to
visualize the atoms in VMD_. First create an :class:`AtomGroup` (named
``g`` in the example below) and then use its
:class:`~MDAnalysis.core.groups.AtomGroup.write` method with the
appropriate *file extension* (see :ref:`Supported selection
exporters` for the recognized *extension*)::
g = u.select_atoms('protein")
g.write("selections.vmd", name="mda_protein")
In VMD_, sourcing the file ``selections.vmd`` (written in Tcl) defines
the "macro" ``mda_protein`` that contains the atom indices to select
.. code-block:: tcl
source selection.vmd
set sel [atomselect top mda_mdanalysis]
and in the GUI the macro appears in the :menuselection:`Graphics -->
Representations` window in the list :guilabel:`Selections: Singlewords` as
"mda_protein".
Multiple selections
-------------------
The :class:`~MDAnalysis.core.groups.AtomGroup.write` method can take
additional keyword arguments, including ``mode``. The default is
``mode="w"``, which will overwrite the provided file. If ``mode="a"``
then the selection is *appended* to the file.
Alternatively, one may use the
:class:`~MDAnalysis.selections.base.SelectionWriter` itself as a
context manager and write each :class:`AtomGroup` inside the
context. For example, to write multiple groups that were selected to
mark different parts of a lipid bilayer to Gromacs_ index file named
"leaflets.ndx"::
with mda.selections.gromacs.SelectionWriter('leaflets.ndx', mode='w') as ndx:
ndx.write(upper_saturated, name='upper_sat')
ndx.write(lower_saturated, name='lower_sat')
ndx.write(upper_unsaturated, name='upper_unsat')
ndx.write(lower_unsaturated, name='lower_unsat')
There is a separate :class:`SelectionWriter` for each format, as
described next.
Selection writers
=================
There exist different :class:`~MDAnalysis.selections.base.SelectionWriterBase`
classes for different packages. The
:func:`~MDAnalysis.selections.get_writer` function can automatically pick
the appropriate one, based on the file name extension in the :ref:`Supported
selection exporters`.
.. autofunction:: MDAnalysis.selections.get_writer
.. rubric:: Formats
Each module implements a :class:`SelectionWriter` for a specific format.
.. toctree::
:maxdepth: 1
selections/vmd
selections/pymol
selections/gromacs
selections/charmm
selections/jmol
selections/base
.. _CHARMM: http://www.charmm.org
.. _Gromacs: http://www.gromacs.org
.. _VMD: http://www.ks.uiuc.edu/Research/vmd/
.. _PyMOL: http://www.pymol.org
.. _Jmol: https://jmol.sourceforge.net/
|
