I've fixed this. It's a minor change so you could apply it locally if
you want. I just moved the call to DeleteHydrogens past the stereo
section when reading the InChI:
https://github.com/baoilleach/openbabel/commit/428ac8790d3b5307305912b892e9953c793b80dc
- Noel
On 26 June 2013 14:42, Jon Fuller <jonathan.ful...@gmail.com> wrote:
> Dear Chris and Fredrik,
>
> Thanks for the information regarding this problem. The solution that I've
> been using is to use an older version 2.3.0 to run my script.
>
> Additional thanks for the information about the differences between obabel
> and babel.
>
> Best,
>
> Jon
>
>
> On 26 June 2013 15:01, Chris Morley <c.mor...@gaseq.co.uk> wrote:
>>
>> I think this is due to a bug in the stereo perception code which
>> appeared in v2.3.2 . It has been mentioned before on this and the
>> development list but a fix is not yet committed to the development code.
>> Version 2.3.1 works ok for me.
>>
>> Incidentally, prefer obabel to the older babel. obabel is safer with
>> incorrect input and can handle commandline options with parameters much
>> better than babel.
>>
>> Chris
>>
>> On 26/06/2013 11:57, Fredrik Wallner wrote:
>> > Hi,
>> >
>> > No, I never found a solution to this. I managed a workaround for the
>> > specific problem (although I cannot remember for sure I believe I
>> > accepted some help from ChemDraw…) so my needs fainted…
>> >
>> > Kind regards,
>> > Fredrik
>> >
>> > 25 jun 2013 kl. 14:33 skrev Jon Fuller <jonathan.ful...@gmail.com
>> > <mailto:jonathan.ful...@gmail.com>>:
>> >
>> >> Hi Fredrik,
>> >>
>> >> Did you find a solution to this problem? I found a similar example:
>> >> I pasted example code for pybel, but running the command below with
>> >> both inchis in the file inchi.txt:
>> >> babel -iinchi inchi.txt -osdf inchi.sdf
>> >> Will result in "Segmentation fault: 11"
>> >> Remove the second inchi and the command works.
>> >>
>> >> mol1 = pybel.readstring("inchi",
>> >>
>> >> "InChI=1S/C19H22N2O/c1-4-15-7-6-8-16(5-2)18(15)10-9-14-11-17(13-21-12-14)19(22)20-3/h6-13H,4-5H2,1-3H3,(H,20,22)/b10-9+")
>> >>
>> >> print"molecule one works"
>> >>
>> >>
>> >> mol2smiles = pybel.readstring("smiles",
>> >>
>> >> "O=C(OC[C@H](\C3=C2/[C@@H](O[C@H]1O[C@@H]([C@@H](O)[C@H](OC(=O)C)[C@H]1O)COC(\C=C)(C)C)[C@H](O)[C@H](C)[C@H]4C(=C/[C@@]2(C)[C@@H](O)C3)\[C@@H](COC)CC4)C)C")
>> >>
>> >> print"smiles works for molecule two!"
>> >>
>> >> print mol2smiles
>> >>
>> >>
>> >> mol2inchichemspider = pybel.readstring("inchi",
>> >>
>> >> "InChI=1S/C36H56O12/c1-10-35(6,7)45-17-26-30(41)33(46-21(5)38)31(42)34(47-26)48-32-28-24(18(2)15-44-20(4)37)13-27(39)36(28,8)14-25-22(16-43-9)11-12-23(25)19(3)29(32)40/h10,14,18-19,22-23,26-27,29-34,39-42H,1,11-13,15-17H2,2-9H3/b25-14-/t18-,19-,22-,23+,26-,27+,29-,30-,31-,32-,33+,34-,36+/m1/s1")
>> >>
>> >> print"inchi does not work for molecule two"
>> >>
>> >> print mol2inchichemspider
>> >>
>> >>
>> >> Best,
>> >>
>> >> Jon
>> >>
>> >>
>> >>
>> >> On 11 April 2013 16:21, Fredrik Wallner <fred...@wallner.nu
>> >> <mailto:fred...@wallner.nu>> wrote:
>> >>
>> >> Hi again,
>> >>
>> >> Some more information…
>> >> The InChI
>> >> "InChI=1S/C8H12/c1-2-4-6-8-7-5-3-1/h1-2,7-8H,3-6H2/b2-1-,8-7-"
>> >> gives the same problem.
>> >> I have now updated the ubuntu box to also run ob 2.3.2 and it
>> >> segfaults now as well, so it seems it has something to do with
>> >> differences between 2.3.1 and 2.3.2.
>> >>
>> >> Kind regards,
>> >> Fredrik
>> >>
>> >> 11 apr 2013 kl. 14:45 skrev Fredrik Wallner <fred...@wallner.nu
>> >> <mailto:fred...@wallner.nu>>:
>> >>
>> >> > Hi,
>> >> >
>> >> > I get a segmentation fault when running the following command:
>> >> > obabel -iinchi
>> >>
>> >> -:"InChI=1S/2C8H12.Ni/c2*1-2-4-6-8-7-5-3-1;/h2*1-2,7-8H,3-6H2;/b2*2-1-,8-7-;"
>> >> -osmi
>> >> >
>> >> > I'm running Open Babel 2.3.2 on a MacBook Pro, OSX 10.8.3
>> >> (installed via homerbrew).
>> >> > I have also tried it on an Ubuntu box (10.04.4) running ob 2.3.1
>> >> and here it's working without problem. Is there anyone else having
>> >> problems with this, or is it just me?
>> >> >
>> >> > Kind regards,
>> >> > Fredrik
>> >> >
>> >>
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