My apologies if this has been corrected in the meantime, but at least part of the problem with that commit would be that in the first occurence of boundToNitrogen->IsHydrogen() (line 367 in that github commit), boundToNitrogen is a wild pointer - leading to the crash in Pascal Muller's case (apparently only on 32bit x86 - and even there doing a debug build is sufficient to mask the problem due to padding, but probably returning a completely spurious result. The initializsation of boundToNitrogen happens only in the second - suspiciously similar FOR_BONDS_OF_ATOM loop (around line 383 in the commited code segment.
Regards Martin > Dear David, > > thanks for the great pointer, that's very helpful. I am working on it, I hope > I'll manage to get it done during the weekend. > > Cheers, > p. > > > On 04 Jul 2014, at 10:59, David Hall <li...@cowsandmilk.net> wrote: > > > > Hi Paolo, > > > > Can you possibly look into what I describe in my message at > > > > http://sourceforge.net/p/openbabel/mailman/message/31507998/ > > > > Testing today, 20,081 out of 24,867 molecules from VEHICLe cannot be > > roundtripped through the mol2 format in openbabel and be preserved. > > > > removing the lines of code added to mol2format.cpp in this commit: > > > > https://github.com/openbabel/openbabel/commit/097636fd7cdba1c842d27a80ccab809c558d0b98#diff-d6e9941b72192e2ba1a2d244948450ae > > > > improves this to only 3,866 molecules not being successfully roundtripped. > > Unfortunately, deleting that code also means the pyridinium cation no > > longer works, which has made me not want to remove it, but instead try to > > find a fix that solves both this and the bug the code meant to fix. > > > > -David > > > > > > > > > >> On Fri, Jul 4, 2014 at 5:44 AM, Paolo Tosco <paolo.to...@unito.it> wrote: > >> 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> > >>> 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> > >>> > >>> > >>> 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 > >>> > >>> > >>> > >>> ------------------------------------------------------------------------------ > >>> Open source business process management suite built on Java and Eclipse > >>> 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 > >>> > >>> > >>> _______________________________________________ > >>> OpenBabel-discuss mailing list > >>> OpenBabel-discuss@lists.sourceforge.net > >>> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > >> > >> > >> ------------------------------------------------------------------------------ > >> Open source business process management suite built on Java and Eclipse > >> 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 > >> _______________________________________________ > >> OpenBabel-discuss mailing list > >> OpenBabel-discuss@lists.sourceforge.net > >> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > > > ------------------------------------------------------------------------------ > Open source business process management suite built on Java and Eclipse > 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> > _______________________________________________ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss -- Dr. Martin Kroeker mar...@ruby.chemie.uni-freiburg.de c/o Prof.Dr. Caroline Roehr Institut fuer Anorganische und Analytische Chemie der Universitaet Freiburg ------------------------------------------------------------------------------ Want fast and easy access to all the code in your enterprise? 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