[OpenBabel-scripting] Trying to get access to a gzipped SDF file in Python

[Andreas K. <ka...@in...>]

Hi all,

I hope I don't have to send this to the developer list...

I have installed the latest version of openbabel (2.1.0b3) including =20
the python bindings... (openbabel and pybel), Linux Suse 9.2
I wanted to parse a gzipped SDF file (zipped file size 14 M) to =20
extract specific molecules (by name), for this I first tried to do =20
the normal routine, i.e.:

sdfFileName =3D <someGzippedSDFFile>
obconversion =3D OBConversion()
obconversion.SetInFormat("sdf")
obconversion.SetOutFormat("smi")
obmol =3D OBMol()

notatend =3D obconversion.ReadFile(obmol,sdfFileName)
export =3D obconversion.WriteFile(obmol,'myTest.smi')
while notatend:
     obconversion.Write(obmol)
     obmol =3D OBMol()
     notatend =3D obconversion.Read(obmol)

On a normal (i.e. unzipped) SDF File it works fine. But not on a =20
gzipped one -> Segmentation Fault. It can only get access the first  =20
single molecule

The same is true when using the new pybel lib. -> Segmentation Fault!

I assume that OpenBabel keeps a pointer to the last read molecule in =20
the SDF file, which would not work when accessing the zipped one...

I don't want to unpack the file, as I have a few hundred of those.. =20
(disk space!)

Did anyone have the same problem and knows an elegant workaround?
I guess the problem should occur for other scripting languages as =20
well...

Regards,

A. Karwath
-----------------
Dr. Andreas Karwath
Machine Learning Lab
Institute for Computer Science
Albert-Ludwigs-Universit=E4t Freiburg
Georges-K=F6hler-Allee 079
D-79110 Freiburg
Germany