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> 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>:
>
> > 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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