Hi all,
I'm trying to pretty up the next version of the APBS plugin and I've
run into two issues that I'm hoping others have solved:
1. Does anyone have any experience with PMW's OptionMenu? I've been
trying something where I call an OptionMenu's setitem() and it keeps
failing no matter what I do. Perhaps someone can just point me at some
working sample code.
2. I'm having trouble launching command-line Python scripts from my
plugin on OS X. Scripts complain about things like "import time"
failing that work from the command line. I have a wrapper function
that works on Windows, OS X and Linux for normal binaries, and I've
included it below. It looks to me like programs launched via PyMOL
(either via os.system or via subprocess.call) just don't get a proper
environment set up, thus causing Python imports to fail, but I'm not
entirely sure.
I typically work around this in an ugly way: I mess around with
sys.path, import whatever.py and then call whatever.main() directly.
This is obviously quite fragile and depends on whatever.py to have a
nice whatever.main() defined. It gets substantially worse when
whatever.py wants lots of things in its own path.
Has anyone else experienced this? Do you know a nice workaround?
Thanks,
-Michael
def run(prog,args):
'''
wrapper to handle spaces on windows.
prog is the full path to the program.
args is a string that we will split up for you.
or a tuple. or a list. your call.
return value is (retval,prog_out)
e.g.
(retval,prog_out) = run("/bin/ls","-al /tmp/myusername")
'''
import subprocess,tempfile
if type(args) == type(''):
args = tuple(args.split())
elif type(args) in (type([]),type(())):
args = tuple(args)
args = (prog,) + args
try:
output_file = tempfile.TemporaryFile(mode="w+") # <--
shouldn't this point to the temp dir
except IOError:
print "Error opening output_file when trying to run the APBS command."
print "Running:\n\tprog=%s\n\targs=%s" % (prog,args)
retcode =
subprocess.call(args,stdout=output_file.fileno(),stderr=subprocess.STDOUT)
output_file.seek(0)
#prog_out = output_file.read()
prog_out = ''.join(output_file.readlines())
output_file.close() #windows doesn't do this automatically
if DEBUG:
print "Results were:"
print "Return value:",retcode
print "Output:"
print prog_out
return (retcode,prog_out)
--
Michael Lerner, Ph.D.
IRTA Postdoctoral Fellow
Laboratory of Computational Biology NIH/NHLBI
5635 Fishers Lane, Room T909, MSC 9314
Rockville, MD 20852 (UPS/FedEx/Reality)
Bethesda MD 20892-9314 (USPS)
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