7. 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 MDAnalysis.core.groups.AtomGroup. Such cross-package interoperability allows a user to combine their favourite tools with MDAnalysis for further visualization or simulation.

Table of supported exporters and recognized file name extensions.
Name extension IO remarks
vmd tcl w VMD macros, available in Representations; module MDAnalysis.selections.vmd
pymol pml w simple PyMOL selection string; module MDAnalysis.selections.pymol
gromacs ndx w Gromacs index file; module MDAnalysis.selections.gromacs
charmm str w CHARMM selection of individual atoms; module MDAnalysis.selections.charmm
jmol spt w Jmol selection commands; module MDAnalysis.selections.jmol

7.1. How to write selections

7.1.1. Single AtomGroup

The typical situation is that one has an 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 AtomGroup (named g in the example below) and then use its write method with the appropriate file extension (see Table of supported exporters and recognized file name extensions. 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

source selection.vmd
set sel [atomselect top mda_mdanalysis]

and in the GUI the macro appears in the Graphics ‣ Representations window in the list Selections: Singlewords as “mda_protein”.

7.1.2. Multiple selections

The 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 SelectionWriter itself as a context manager and write each 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 SelectionWriter for each format, as described next.

7.2. Selection writers

There exist different SelectionWriterBase classes for different packages. The get_writer() function can automatically pick the appropriate one, based on the file name extension in the Table of supported exporters and recognized file name extensions..

MDAnalysis.selections.get_writer(filename, defaultformat)[source]

Return a SelectionWriter for filename or a defaultformat.

Parameters:
  • filename (str) – name of the output file; the extension is used to guess the file format
  • defaultformat (str) – if filename does not have an extension, use defaultformat instead
Returns:

SelectionWriter – the writer class for the detected format

Return type:

type

Raises:

NotImplementedError – for any format that is not defined

Formats

Each module implements a SelectionWriter for a specific format.