Dear Pascal,
thank you for reporting this - apologies for missing your previous
message. It was a while ago, but I remember that I was attempting to
infer the correct formal charges in the absence of explicit information
in the MOL2 format. It may well be that I inadvertently messed up
something. I'll have a look and see what's going wrong, then I'll get
back to the list.
Sorry for the inconvenience, cheers
p.
On 04/07/14 09:32, Pascal Muller wrote:
---------- Forwarded message ----------
From: *Pascal Muller* <pascal.jm.mul...@gmail.com
<mailto:pascal.jm.mul...@gmail.com>>
Date: 2014-05-09 10:51 GMT+02:00
Subject: Re: [Open Babel] C++ / segfault / "open file" change?
To: babel <openbabel-discuss@lists.sourceforge.net
<mailto:openbabel-discuss@lists.sourceforge.net>>
Hi,
Well, I got a little further.
Now, it's working with version 2.3.1, but not 2.3.2 and 2.3.90.
It seems somehow related to a "patch by Paolo Tosco 2012-06-07" in
mol2format.cpp (not yet present in 2.3.1).
What I have with 2.3.2, when going line after line in mol2format.cpp:
370 FOR_BONDS_OF_ATOM(bond3, partner) {
(gdb)
372 n_h_bonded++;
(gdb)
Program received signal SIGSEGV, Segmentation fault.
0x02207c48 in OpenBabel::MOL2Format::ReadMolecule (this=0x220a488,
pOb=0xbfffed50, pConv=0xbfffebd4)
at /opt/OPENBABEL/openbabel-2.3.2/src/src/formats/mol2format.cpp:372
372 n_h_bonded++;
And with 2.3.90, which has some additionnal conditions:
384 FOR_BONDS_OF_MOL(bond, mol)
(gdb)
386 if (bv[bond->GetIdx()] || (bond->GetBO() != 5))
(gdb)
391 if ( (bond->FindSmallestRing())->Size() != 6 )
(gdb)
Program received signal SIGSEGV, Segmentation fault.
OpenBabel::MOL2Format::ReadMolecule (this=0x22cc5d0, pOb=0xbfffed50,
pConv=0xbfffebd4)
at /opt/OPENBABEL/openbabel-2.3.90/src/src/formats/mol2format.cpp:391
391 if ( (bond->FindSmallestRing())->Size() != 6 )
My program read two mol2 files: a protein site and a ligand. With
obabel, I can convert the ligand, but conversion of the protein site
is raising a segfault with 2.3.2 and 2.3.90, too.
The conversion of the protein site with 2.3.1 is OK.
According to gdb, the segfault with obabel is happening on the same
line of mol2format.cpp.
obabel 3ku0_site27res.mol2 -O 3ku0_site27res_bab.mol2
I attach the site mol2 file to see if somebody else has the same problem.
Regards,
Pascal
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Turn processes into business applications with Bonita BPM Community Edition
Quickly connect people, data, and systems into organized workflows
Winner of BOSSIE, CODIE, OW2 and Gartner awards
http://p.sf.net/sfu/Bonitasoft
_______________________________________________
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