Importing PDB files via web crashes

[cryos]

http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=570230

Greetings,

Avogadro crashes when importing (File->Import->Fetch from PDB) with
PDB code 3B75 (Crystal Structure of Glycated Human Haemoglobin
DOI:10.2210/pdb3b75/pdb).

The console only shows this:

QStackedLayout::setCurrentWidget: Widget 0x9e23de8 not contained in stack
libpng warning: Ignoring attempt to set cHRM RGB triangle with zero area
Segmentation fault (core dumped)

In fact, other PDB codes seem to crash as well, I tried with 1QNF, 1DNP and 1IQR, and all of them crashed. So far, I could not find a PDB code which loaded fine. Downloading and converting the .pdbs with OpenBabel works fine.

Reported by: @mbanck

[cryos]

Hrm, no idea why SF now sets the priority to 1 by default - I don't believe I changed then when entering the bug.

Original comment by: @mbanck

[cryos]

Reproducible.
Backtrace:

Program received signal SIGSEGV, Segmentation fault.
[Switching to Thread 0xf581c6e0 (LWP 30650)]
OpenBabel::OBMol::expand_kekulize (this=0x8f19ac8, bond_idx=4324,
atomState=@0xffd47438, bondState=@0xffd47420)
at /mnt/storage/openbabel/trunk/include/openbabel/atom.h:223
223 unsigned int GetIdx() const { return((int)_idx); }
(gdb)
(gdb) bt
#0 OpenBabel::OBMol::expand_kekulize (this=0x8f19ac8, bond_idx=4324,
atomState=@0xffd47438, bondState=@0xffd47420)
at /mnt/storage/openbabel/trunk/include/openbabel/atom.h:223
#1 0xf7b1e11b in OpenBabel::OBMol::expand_kekulize (this=0x8f19ac8,
bond_idx=4323, atomState=@0xffd47438, bondState=@0xffd47420)
at /mnt/storage/openbabel/trunk/src/kekulize.cpp:438
#2 0xf7b1e11b in OpenBabel::OBMol::expand_kekulize (this=0x8f19ac8,
bond_idx=4322, atomState=@0xffd47438, bondState=@0xffd47420)
at /mnt/storage/openbabel/trunk/src/kekulize.cpp:438
#3 0xf7b1e11b in OpenBabel::OBMol::expand_kekulize (this=0x8f19ac8,
bond_idx=4321, atomState=@0xffd47438, bondState=@0xffd47420)
at /mnt/storage/openbabel/trunk/src/kekulize.cpp:438
#4 0xf7b1e11b in OpenBabel::OBMol::expand_kekulize (this=0x8f19ac8,
bond_idx=4320, atomState=@0xffd47438, bondState=@0xffd47420)
at /mnt/storage/openbabel/trunk/src/kekulize.cpp:438
#5 0xf7b1e11b in OpenBabel::OBMol::expand_kekulize (this=0x8f19ac8,
bond_idx=4319, atomState=@0xffd47438, bondState=@0xffd47420)
at /mnt/storage/openbabel/trunk/src/kekulize.cpp:438
#6 0xf7b1e11b in OpenBabel::OBMol::expand_kekulize (this=0x8f19ac8,
bond_idx=4318, atomState=@0xffd47438, bondState=@0xffd47420)
at /mnt/storage/openbabel/trunk/src/kekulize.cpp:438
#7 0xf7b1e11b in OpenBabel::OBMol::expand_kekulize (this=0x8f19ac8,
bond_idx=4317, atomState=@0xffd47438, bondState=@0xffd47420)

Original comment by: @annulen

[cryos]

From the backtrace, this appears to be #2841031 in openbabel.

The question is why avogadro runs expand_kekulize() for PDB files loaded via the web, and not for those opened via File or the command-line.

Original comment by: @mbanck

[cryos]

This bug has been fixed in OB trunk.

Original comment by: @timvdm

[cryos]

I also can't reproduce this with Open Babel, but did crash the Mac 1.0 release of Avogadro. I'm building a full debug build to try to find the crash. I can attest that OB 2.2.3 seems immune, so I'm confused.

Original comment by: @ghutchis

[cryos]

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).

Original comment by: sf-robot