RE: [PyMOL] pymol sys.argv, winnt, barks

[DeLano, W. <wa...@su...>]

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 =3D copy.deepcopy(argv)

Directly under "def parse_args(argv):" (line 79) in
PyMOL/modules/pymol/invocation.py. =20

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: =20

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?=20

- Warren


--
mailto:wa...@su...
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=20
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> Andrey,
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> I deduce you're referring to windows?  I think this is what=20
> you get when python gets installed in C:\Program Files\python=20
> or some other location that is not on the (hardcoded?) search=20
> path of pymol, which means it can't find the tcltk libraries.=20
>  The solution is to install python on C:\python, and=20
> everything is hunky-dory -- I think you don't even have to=20
> reinstall pymol, but you can check that, it doesn't take long.=20
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> Good luck
> phx.
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> From:	Andrey Khavryuchenko
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> Hi!
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> Is it only me who gets the following:
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> for i in argv:
>     print i
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> [...]
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> $ pymol -c mov.py
> [...]
>  Hit ESC anytime to toggle between text and graphics.
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>  Command mode. No graphics front end.
> Traceback (most recent call last):
>   File "C:\Program Files\DeLano=20
> 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.
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> Linux version and plain python under winnt are ok.  It's only=20
> pymol that
> gives that strange behaviour.
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> --=20
> Andrey V Khavryuchenko          http://www.kds.com.ua/
> Offshore Software Development
>=20
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