It looks like Andrey wants his script to be able to interpret command
line arguments. Unfortunately, PyMOL doesn't enable this in a
consistent way, since Launching under Windows (embedded Python) is quite
different than unix (non-embedded Python).
With embedded Python, arguments aren't making it to sys.argv. Instead,
they are being passed straight from C into PyMOL's invocation routine.
I will fix this in the next version by reassigning them to sys.argv, but
you can do this immediate by inserting
import sys
sys.argv = copy.deepcopy(argv)
Directly under "def parse_args(argv):" (line 79) in
PyMOL/modules/pymol/invocation.py.
I'd also like to provide a means by which certain can be ignored by
PyMOL and be available directly to Python scripts in PyMOL.
Here is my proposal:
Ignore any arguments after a double-hyphen ("--") sentinel. For
example:
pymol -c myscript.py -- -pymol -will -ignore -these -arguments
pymol -c myscript.py -- -your -script -interpret -them -instead
Any objections?
- Warren
--
mailto:[email protected]
Warren L. DeLano, Ph.D.
Informatics Scientist
Sunesis Pharmaceuticals, Inc.
341 Oyster Point Blvd.
S. San Francisco, CA 94080
(650)-266-3606 fax: (650)-266-3501
> From: Frank Vondelft
>
> Andrey,
>
> I deduce you're referring to windows? I think this is what
> you get when python gets installed in C:\Program Files\python
> or some other location that is not on the (hardcoded?) search
> path of pymol, which means it can't find the tcltk libraries.
> The solution is to install python on C:\python, and
> everything is hunky-dory -- I think you don't even have to
> reinstall pymol, but you can check that, it doesn't take long.
>
> Good luck
> phx.
>
> From: Andrey Khavryuchenko
>
> Hi!
>
> Is it only me who gets the following:
>
> for i in argv:
> print i
>
> [...]
>
> $ pymol -c mov.py
> [...]
> Hit ESC anytime to toggle between text and graphics.
>
> Command mode. No graphics front end.
> Traceback (most recent call last):
> File "C:\Program Files\DeLano
> Scientific\PyMOL/modules\pymol\parser.py", lin
> e 174, in parse
> execfile(args[nest][0],pymol_names,pymol_names)
> File "mov.py", line 90, in ?
> for i in sys.argv:
> AttributeError: 'sys' module has no attribute 'argv'
> Memory: 0 blocks expected, 0 found, 42 maximum allocated.
>
> Linux version and plain python under winnt are ok. It's only
> pymol that
> gives that strange behaviour.
>
> --
> Andrey V Khavryuchenko http://www.kds.com.ua/
> Offshore Software Development
>
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>
>
