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 awardshttp://p.sf.net/sfu/Bonitasoft
>
>
>
> _______________________________________________
> OpenBabel-discuss mailing
> listOpenBabel-discuss@lists.sourceforge.nethttps://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
