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 >> > >> >> ------------------------------------------------------------------------------ >> > Precog is a next-generation analytics platform capable of advanced >> > analytics on semi-structured data. The platform includes APIs >> for building >> > apps and a phenomenal toolset for data science. Developers can use >> > our toolset for easy data analysis & visualization. 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