6.3. Gromacs selections
Write MDAnalysis.core.AtomGroup.AtomGroup selection to a ndx file
that defines a Gromacs index group. To be used in Gromacs like this:
<GROMACS_COMMAND> -n macro.ndx
The index groups are named mdanalysis001, mdanalysis002, etc.
-
class MDAnalysis.selections.gromacs.SelectionWriter(filename, mode='wa', numterms=None, preamble=None, **kwargs)[source]
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()
|
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.