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6. Selection exporters

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6.2. PyMOL selections

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6.1. VMD selections

Write MDAnalysis.core.AtomGroup.AtomGroup selection to a VMD tcl file that defines atomselect macros. To be used in VMD like this:

source macros.vmd
set sel [atomselect top mdanalysis001]  # use macro 001
class MDAnalysis.selections.vmd.SelectionWriter(filename, mode='wa', numterms=None, preamble=None, **kwargs)

Set up for writing to filename.

Arguments :
filename

output file

mode

overwrite (“w”) for every write, append (“a”) to existing file, or overwrite an existing file and then append (“wa”) [“wa”]

numterms

number of individual index numbers per line for output formats that write multiple entries in one line. If set to 0 or False then no special formatting is done [8]

preamble

string that is written as a comment at the top of the file []

kwargs

use as defaults for write()

comment(s)

Return string s interpolated into the comment format string.

If no SelectionWriter.commentfmt is 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.

write(selection, number=None, name=None, frame=None, mode=None)

Write selection to the output file.

Arguments :
selection

a MDAnalysis.core.AtomGroup.AtomGroup

number

selection will be named “mdanalysis<number>” (None auto increments between writes; useful when appending) [None]

name

selection will be named name (instead of numbered) [None]

frame

write selection of this frame (or the current one if None [None]

write_preamble()

Write a header, depending on the file format.