> But in the meantime, as a workaround, fall back on __main__.pymol_argv if
> sys.argv is not defined.
Thanks! For what it's worth, I ended up with something like
try:
args = sys.argv
except AttributeError:
sys.argv = pymol_argv
args = sys.argv
because I'm using optparse to handle command line options. When
optparse generates its automatic help messages, it calls through to
sys.argv no matter what you tell it to do.
Here's a related question: when I call sys.exit from my script (or,
actually, when optparse calls it), it ends up causing a traceback. Is
there any way to turn that behavior off? At the moment, I'm using this
as a workaround:
from pymol import cmd
import sys
def exit(*args,**kwargs):
cmd.quit()
sys.exit = exit
but I thought that I remembered hearing about a better way once.
Thanks,
-michael
>
> Cheers,
> Warren
>
>
>
> --
> DeLano Scientific LLC
> Subscriber Support Services
> mailto:del...@delsci.info
>
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>
>
> > -----Original Message-----
> > From: pymol-users-boun...@lists.sourceforge.net
> > [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf
> > Of Michael Lerner
> > Sent: Tuesday, August 14, 2007 2:35 PM
> > To: pymol-users@lists.sourceforge.net
> > Subject: [PyMOL] Why can't I get to sys.argv on Linux?
> >
> > Hi,
> >
> > I'm using PyMOL as a front end to a few scripts. So, I need
> > to get my hands on sys.argv to process the command-line
> > arguments. On OS X, everything works just like I'd expect.
> > However, on Linux, I can't get sys.argv. Here's a very simple
> > Python script:
> >
> > #!/usr/bin/env python
> > import sys
> > print dir(sys)
> > print sys.argv
> >
> > When I run pymol -cr ./my_script.py on Linux, I get this:
> >
> > PyMOL>run ./x.py,main
> > ['__displayhook__', '__doc__', '__excepthook__', '__name__',
> > '__stderr__', '__stdin__', '__stdout__', '_getframe',
> > 'api_version', 'builtin_module_names', 'byteorder',
> > 'call_tracing', 'callstats', 'copyright', 'displayhook',
> > 'exc_clear', 'exc_info', 'exc_type', 'excepthook',
> > 'exec_prefix', 'executable', 'exit', 'exitfunc',
> > 'getcheckinterval', 'getdefaultencoding', 'getdlopenflags',
> > 'getfilesystemencoding', 'getrecursionlimit', 'getrefcount',
> > 'hexversion', 'maxint', 'maxunicode', 'meta_path', 'modules',
> > 'path', 'path_hooks', 'path_importer_cache', 'platform',
> > 'prefix', 'setcheckinterval', 'setdlopenflags', 'setprofile',
> > 'setrecursionlimit', 'settrace', 'stderr', 'stdin', 'stdout',
> > 'version', 'version_info', 'warnoptions'] Traceback (most
> > recent call last):
> > File "/users/mlerner/src/pymol/modules/pymol/parser.py",
> > line 287, in parse
> >
> > parsing.run_file(exp_path(args[nest][0]),__main__.__dict__,__m
> > ain__.__dict__)
> > File "/users/mlerner/src/pymol/modules/pymol/parsing.py",
> > line 407, in run_file
> > execfile(file,global_ns,local_ns)
> > File "./x.py", line 4, in ?
> > print sys.argv
> > AttributeError: 'module' object has no attribute 'argv'
> > PyMOL: normal program termination.
> >
> > While pawing around in the PyMOL sources, I found that
> > pymol_argv shows up. It seems to be what I want, but I don't
> > know how stable it is. Am I supposed to use it instead of sys.argv?
> >
> > Thanks,
> >
> > -michael
> >
> > --
> > Biophysics Graduate Student
> > Carlson Lab, University of Michigan
> > http://www.umich.edu/~mlerner
> >
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>
>
