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#127 OBConversion segfaults using Python

2.0.x
closed
Geoff Hutchison
File Translation (240)
8
2012-10-23
2006-02-21
Noel O'Boyle
No

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

Discussion

  • Geoff Hutchison

    Geoff Hutchison - 2006-02-23

    Logged In: YES
    user_id=21420

    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

    SourceForge Robot - 2006-03-10

    Logged In: YES
    user_id=1312539

    This Tracker item was closed automatically by the system. It was
    previously set to a Pending status, and the original submitter
    did not respond within 14 days (the time period specified by
    the administrator of this Tracker).