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
>>>
>>>
>>>
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Turn processes into business applications with Bonita BPM Community Edition
Quickly connect people, data, and systems into organized workflows
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http://p.sf.net/sfu/Bonitasoft
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