Hi all, I must be missing something obvious:
pybel.readfile( "sdf", sdf, opt = { "canonical" : None } ).next()
File "/opt/lib/pybel.py", line 145, in filereader
notatend = obconversion.ReadFile(obmol,filename)
TypeError: in method 'OBConversion_ReadFile', argument 3 of type
'std::string'
This is from the 'if' fork of
if infile == None :
sdfs = glob.glob( "%s/*.sdf" % (self._workdir) )
if len( sdfs ) < 1 : return False
filename = os.path.split( sdfs[0] )[1]
else :
filename = os.path.split( infile )[1]
sdf = "%s/%s" % (self._workdir, filename)
print >> sys.stderr, sdf
self._obmol = pybel.readfile( "sdf", sdf, opt={"canonical":None}).next()
The 'else' fork works. In both cases the filename is logged as (e.g.)
/var/tmp/bm30/92802.sdf and it is the same file.
Can anyone spot the problem?
Thanks,
--
Dimitri Maziuk
Programmer/sysadmin
BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu
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