6.5. Base classes for the selection writers
Specialized SelectionWriters are derived from
SelectionWriter. Override the _write_head(),
_translate(), and _write_tail()
methods.
-
class MDAnalysis.selections.base.SelectionWriter(filename, mode='wa', numterms=None, preamble=None, **kwargs)
Export a selection in MDAnalysis to a format usable in an external package.
The SelectionWriter writes a selection string to a file
that can be used in another package such as VMD, PyMOL,
Gromacs or CHARMM. In this way, analysis and visualization
can be done with the best or most convenient tools at hand.
SelectionWriter is a base class and child classes are
derived with the appropriate customizations for the package file
format.
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()
|
-
__init__(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()
|
-
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]
|
-
_translate(atoms, **kwargs)
Translate atoms into a list of native selection terms.
build list of ALL selection terms as if this was a single line, e.g.
['index 12 |', 'index 22 |', 'index 33']
only one term per atom!!
terms must be strings
- something like::
” ”.join(terms)
must work
-
_write_head(out, **kwargs)
Initial output to open file object out.
-
_write_tail(out, **kwargs)
Last output to open file object out.
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.
-
MDAnalysis.selections.base.join(seq, string='', func=None)
Create a list from sequence.
string is appended to each element but the last.
func is applied to every element before appending string.
-
MDAnalysis.selections.base.get_writer(filename, defaultformat)
Return a SelectionWriter for filename or a defaultformat.