9.2.5. Jmol selections
MDAnalysis.core.groups.AtomGroup selection to a str file
that defines a Jmol selection. To be used in Jmol like this:
script macro.spt select ~selection
The selection is named mdanalysis001.TODO
- class MDAnalysis.selections.jmol.SelectionWriter(filename, mode='w', numterms=None, preamble=None, **kwargs)[source]
Set up for writing to filename.
filename – output file
mode – create a new file (“w”), or append (“a”) to existing file [“w”]
numterms – number of individual index numbers per line for output formats that write multiple entries in one line. If set to 0 or
Falsethen no special formatting is done 
preamble – string that is written as a comment at the top of the file 
kwargs – use as defaults for
Close the file
New in version 0.16.0.
Return string s interpolated into the comment format string.
SelectionWriterBase.commentfmtis defined (None) then the empty string is returned because presumably there is no way to enter comments into the file.
A newline is appended to non-empty strings.
- commentfmt = '#'
Comment format string; should contain ‘%s’ or
Nonefor no comments.
- continuation = ''
Special character to continue a line across a newline.
- default_numterms = None
- ext = 'spt'
Extension of output files.
- format = ['Jmol', 'spt']
Name of the format.
- write(selection, number=None, name=None, frame=None, mode=None)
Write selection to the output file.
selection – a
number – selection will be named “mdanalysis<number>” (
Noneauto increments between writes; useful when appending) [
name – selection will be named name (instead of numbered) [
frame – write selection of this frame (or the current one if
Write a header, depending on the file format.