visualize¶
Interfaces for molecular viewers¶
The viewers defined here are meant to be used for quick interactive structure
and trajectory display. All viewer functions are actually callable instances of
ViewFactory
, and thus have the same call signature:
- ViewFactory.__call__(obj, logfile=None, structfile=None, disp=False, keepfiles=False, tmpdir='/tmp', wait=True, bg=False, options='')[source]¶
Call viewer.
The executed shell command is:
<cmd> <options> <structfile> > <logfile>
- Parameters:
obj (Structure or Trajectory)
logfile (str, optional) – Filename of a logfile for the viewer’s text output.
structfile (str, optional) – Filename of a file to write the structure to.
disp (bool) – Display text output (i.e. logfile’s content).
keepfiles (bool) – Keep structfile and logfile on disk.
tmpdir (str, optional) – Directory where temp files are written to.
wait (bool, optional) – wait passed to common.system(), wait (or not) for command to exit
bg (bool) – Background mode. If True then this is an alias for wait=False + keepfiles=True. The latter is needed b/c with just wait=False, temp files will be deleted right after the shell call and the viewer program may complain.
VMD¶
Use view_vmd_xyz()
or view_vmd_axsf()
. To execute a tcl script
after the struct has loaded (in the shell: vmd -e script.tcl foo.xyz
), use:
>>> tr = crys.Trajectory(...)
>>> view_vmd_axsf(tr, options='-e script.tcl')
Note that the viewer (in this case VMD) is simply called like vmd
structfile
, which can take very long for big MD data b/c the VMD default
is to use smth like mol new ... waitfor 1
, which is slow. In that case you
want to call VMD directly:
$ vmd
vmd > mol new /tmp/foo.axsf type xsf waitfor all
vmd > set molid 0
vmd > source ~/work/vmd/ca_salt.tcl
The trick here is ... waitfor all
. See the VMD manual for the mol
command. Or you place these lines in a script and use:
$ vmd script_to_execute.tcl
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Factory for creating interface functions to external molecular viewers. |
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str(object='') -> str str(bytes_or_buffer[, encoding[, errors]]) -> str |
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Factory for creating interface functions to external molecular viewers. |
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Factory for creating interface functions to external molecular viewers. |
|
Factory for creating interface functions to external molecular viewers. |
|
Factory for creating interface functions to external molecular viewers. |
|
Factory for creating interface functions to external molecular viewers. |