#127 OBConversion segfaults using Python

[Noel O'Boyle]

I am trying to read a PDB file into an OBMol with
Python but without any luck.

It seems that ReadFile only segfaults if the output
format is unset. That is, in the example below, Choice
1 completes normally, but Choice 2 segfaults.

========================================
import openbabel

obConversion = openbabel.OBConversion()

Choice 1: no seg fault

obConversion.SetInAndOutFormats("sdf", "mol2")

Choice 2: seg faults when reading the file

obConversion.SetInFormat("sdf")

mol = openbabel.OBMol()
obConversion.ReadFile(mol, "3d.head.sdf")

print mol.NumAtoms()

Regards,
Noel

[Geoff Hutchison]

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Thanks for the bug report -- obviously if there's a crash, it's because the
underlying C++ code is dead, not just the scripting wrapper. :-)

This one didn't take long to debug after that report. OBConversion::ReadFile()
was checking pOutFormat (which was a NULL pointer) rather than pInFormat.

Fixed in the CVS version shortly. I can send you a snapshot of the 2.0.1 code
if you like.

Thanks!
-Geoff

[SourceForge Robot]

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