Re: [PyMOL] Command-line arguments when using PyMOL to launch ascript

[DeLano S. <de...@de...>]

In the current open-source and beta builds (1.1),

pymol -c script.py -- arg1 arg2

should give a sys.argv of

['script.py', 'arg1', 'arg2']

paralleling the behavior of Python, given similar inputs:

python script.py arg1 arg2

Cheers,
Warren

PS.  the "3D" after the equals sign is annoying mailing list / MIME
artifact.

--
DeLano Scientific LLC
Subscriber Support Services
mailto:de...@de...
 

> -----Original Message-----
> From: pym...@li... 
> [mailto:pym...@li...] On Behalf 
> Of Michael Lerner
> Sent: Friday, February 15, 2008 8:22 AM
> To: Josep Maria Campanera Alsina
> Cc: pym...@li...
> Subject: Re: [PyMOL] Command-line arguments when using PyMOL 
> to launch ascript
> 
> Hi,
> 
> First, the initial error you were seeing was a syntax error:
> 
> > from sys import argv
> > my_argv =3D argv[argv.index("--"):]
> > print my_argv[1], my_argv[2]
> 
> is failing because of the word "3D"
> 
> Second, that used to fail on Linux systems anyway (it worked 
> on some other systems). I tend to use optparse, which often 
> requires things to live in sys.argv. Here's my current workaround:
> 
>     #argv = sys.argv[sys.argv.index('--') + 1:]
>     try:
>         argv = sys.argv
>     except AttributeError:
>         argv = pymol_argv
>         sys.argv = pymol_argv # this is necessary for 
> optparse to handle the --help option.
>     try:
>         argv = argv[argv.index('--') + 1:]
>     except IndexError:
>         argv = []
> 
>     options,args = parser.parse_args(args=argv)
> 
> I haven't re-tested Linux recently, though. It might be that 
> the pymol_argv workaround is not necessary anymore.
> 
> -michael
> 
> --
> IRTA Postdoctoral Fellow
> Laboratory of Computational Biology NIH/NHLBI
> 5635 Fishers Lane, Room T909
> http://www.umich.edu/~mlerner
> 
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