pymol-users

[PyMOL] Command-line arguments when using PyMOL to launch a script

[Michael L. <mgl...@gm...>]

Hi,

I have a script that uses PyMOL to aid with a lot of calculations. So,
I run the script like this:

pymol -c script.py

The script has grown so that it has a lot of options. Right now, I
edit the script every time I want to change them. If it were a normal
Python script, I'd run it like

script.py --do=something --when=now

Is there a standard way to do this via PyMOL? Ideally, I'd like to say

pymol -qcr script.py --do=something --when=now
and have script.py think that sys.argv == ['script.py',
'--do=something', '--when=now'].

I pawed through pymol.invocation.py, and it looks like PyMOL respects
the convention where it won't parse arguments after a '--', so my
current workaround is to launch things like

pymol -qcr script.py -- -do=something --when=now

and then this in my script:

argv = sys.argv[sys.argv.index('--') + 1:]
...
# parse with optparse
options,args = parser.parse_args(args=argv)

So, is there a more standard way of doing this? If not, hopefully
google will find this for me the next time I have this question :).

Thanks,

-Michael
-- 
Biophysics Graduate Student
Carlson Lab, University of Michigan
http://www.umich.edu/~mlerner

[PyMOL] Command-line arguments when using PyMOL to launch a script

[Josep M. C. A. <cam...@ub...>]

Hi all,
I'd like to execute pymol like: pymol -c script.py arg1 arg2 arg3 arg4.

(1) Reading into PyMolWiki
http://www.pymolwiki.org/index.php/Scripting, I've learned that I have
to type:

pymol -c script.py -- arg1 arg2 arg3 arg4

and then add to my script:

from sys import argv
my_argv =3D argv[argv.index("--"):]
print my_argv[1], my_argv[2]

But it doesn work!

"Traceback (most recent call last):
File "/home/campa/SOFTWARE/pymol/modules/pymol/parser.py", line 285, in parse
    parsing.run_file(exp_path(args[nest][0]),pymol_names,pymol_names)
File "/home/campa/SOFTWARE/pymol/modules/pymol/parsing.py", line 407,
in run_file
    execfile(file,global_ns,local_ns)
File "rotamermod3.py", line 45
     my_argv =3D argv[argv.index("--"):]
               ^
 SyntaxError: invalid syntax"

(2) Then I found an alternatively procedure
http://sourceforge.net/mailarchive/message.php?msg_id=e4c539ed0708011206nf6dc1a1r257f7311f42aa59e%40mail.gmail.com

Identical command: pymol -c script.py -- arg1 arg2 arg3 arg4

But I have to add into my script.py the following:

argv = sys.argv[sys.argv.index('--') + 1:]
options,args = parser.parse_args(args=argv)

But it doesn't work neither:
AttributeError: 'module' object has no attribute 'argv'

Can someone give a light in how to call arguments in pymol -c script.py?

Thanks a lot,

Josep Maria Campanera,

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

[Michael L. <mgl...@gm...>]

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

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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