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.
Parameters: - *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()
-
__delattr__
¶ x.__delattr__(‘name’) <==> del x.name
-
__format__
()¶ default object formatter
-
__getattribute__
¶ x.__getattribute__(‘name’) <==> x.name
-
__hash__
¶
-
__reduce__
()¶ helper for pickle
-
__reduce_ex__
()¶ helper for pickle
-
__repr__
¶
-
__setattr__
¶ x.__setattr__(‘name’, value) <==> x.name = value
-
__sizeof__
() → int¶ size of object in memory, in bytes
-
__str__
¶
-
comment
(s)[source]¶ 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)[source]¶ Write selection to the output file.
Parameters: - *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
]
- *selection* – a