Hi, I imported ~28 million compounds from PubChem into the postgres pgchem database, and found (only) 58 failures (SEGV).
They can be reproduced using openbabel command line tools, where the conversion from the PubChem provided canonical smiles to InChI fails with a SEGV in ob-2.3.TRUNK. In addition to the tracker items #3107834 and #3116415 I now have a full list of smiles which brake openbabel when called as in: echo "C1=CC=C(C=C1)C(=O)SC2=C(SC(=P(C3=CC=CC=C3)(C4=CC=CC=C4)C5=CC=CC=C5)S2)SC(=O)C6=CC=CC=C6" | babel -i smi - -o inchi - The first bugreport mentioned above also has a gdb stack trace. All of the smiles below convert fine in openbabel-2.2.3 Anything where I can help debugging this ? Maybe the list (or a part of it) could be added to the test/files directory, but i am unsure which test program would use them best. Yours, Steffen C1=CC=C(C=C1)[AsH](C2=CC=CC=C2)(C3=CC=CC=C3)C4=CC=CC=C4 C1=CC=C(C=C1)C(=O)SC2=C(SC(=P(C3=CC=CC=C3)(C4=CC=CC=C4)C5=CC=CC=C5)S2)SC(=O)C6=CC=CC=C6 CC1(C[N+](=P(C2=CC=CC=C2)(C3=CC=CC=C3)C4=CC=CC=C4)C1)COS(=O)(=O)C.CS(=O)(=O)[O-] COC(=O)C1=C([Se]C(=P(C2=CC=CC=C2)(C3=CC=CC=C3)C4=CC=CC=C4)[Se]1)C(=O)OC C[C]1[C]([C]([C]([C]1C)C)C)C.C1CCC(CC1)N2C=CN(C2=[Ru](=CC3=CC=CC=C3)(Cl)Cl)C4CCCCC4.Cl[Rh+]Cl CC1=CC=C(C=C1)C(=P(C2=CC=CC=C2)(C3=CC=CC=C3)C4=CC=CC=C4)C5=CC=C(C=C5)C CC1=CC=C(C=C1)C(C)C.C1CCC(CC1)N2C=CN(C2=[Ru](=CC3=CC=CC=C3)(Cl)Cl)C4CCCCC4.Cl[Ru]Cl CC1=CC(=C(C(=C1)C)N2C3CCCCC3N(C2=[Ru](=CC4=CC=CC=C4)(Cl)Cl)C5=C(C=C(C=C5C)C)C)C.C1CCC(CC1)P(C2CCCCC2)C3CCCCC3 CC1=CC(=C(C(=C1)C)N2CCN(C2=[Ru](=CC3=CC=CC=C3)(Cl)Cl)C4=C(C=C(C=C4C)C)C)C.C1CCC(CC1)P(C2CCCCC2)C3CCCCC3 CC1=CC(=C(C(=C1)C)N2CCN(C2=[Ru](=CC3=C(C(=CC=C3)OC)OC(C)C)(Cl)Cl)C4=C(C=C(C=C4C)C)C)C CC1=CC(=C(C(=C1)C)N2CCN(C2=[Ru](=C=CC(C)(C)C)(Cl)Cl)C3=C(C=C(C=C3C)C)C)C.C1CCC(CC1)P(C2CCCCC2)C3CCCCC3 CC1=CC(=C(C(=C1)C)N2CCN(C2=[Ru](=CC3=C(C=CC(=C3)[N+](=O)[O-])OC(C)C)(Cl)Cl)C4=C(C=C(C=C4C)C)C)C CC1=CC(=C(C(=C1)C)N2CCN(C2=[Ru](=CC3=CC(=C(C=C3OC)OC)OC)(Cl)Cl)C4=C(C=C(C=C4C)C)C)C CC(C)C1=CC=CC=C1N2C(C(N(C2=[Ru](=CC3=CC=CC=C3)(Cl)Cl)C4=CC=CC=C4C(C)C)C5=CC=CC=C5)C6=CC=CC=C6.C1CCC(CC1)P(C2CCCCC2)C3CCCCC3 CC1=CC(=C(C(=C1)C)N2CC(CN(C2=[Ru](=CC3=CC=CC=C3)(Cl)Cl)C4=C(C=C(C=C4C)C)C)(C)C)C.C1CCC(CC1)P(C2CCCCC2)C3CCCCC3 CC1=CC(=C(C(=C1)C)N2CCN(C2=[Ru](=CC3=CC=CC(=C3OC(C)C)C4=CC=CC=C4)(Cl)Cl)C5=C(C=C(C=C5C)C)C)C CC1=CC(=C(C(=C1)C)N2CCN(C2=[Ru](=CC3=C(C=C(C=C3)OC(C)C)OC(C)C)(Cl)Cl)C4=C(C=C(C=C4C)C)C)C CC1=CC(=C(C(=C1)C)N2CCN(C2=[Ru](=CC3=C(C=CC(=C3)CCCN4C=C[N+](=C4)C)OC(C)C)(Cl)Cl)C5=C(C=C(C=C5C)C)C)C.F[P-](F)(F)(F)(F)F CC1=CC(=C(C(=C1)C)N2CCN(C2=[Ru](=CC3=CC4=CC=CC=C4C(=C3OC(C)C)C5=C(C=CC6=CC=CC=C65)OC(C)C)(Cl)Cl)C7=C(C=C(C=C7C)C)C)C CC1=CC(=C(C(=C1)C)N2CCN(C2=[Ru](=CC3=CC=CC=C3C(=O)OC)(Cl)Cl)C4=C(C=C(C=C4C)C)C)C CC1=CC(=C(C(=C1)C)N2C=CN(C2=[Ru](=CC=C(C)C)(Cl)Cl)C3=C(C=C(C=C3C)C)C)C.C1CCC(CC1)P(C2CCCCC2)C3CCCCC3 CC1=CC(=C(C(=C1)C)N2CCN(C2=[Ru](=CC3=C(C=C(C=C3)[N+](=O)[O-])OC(C)C)(Cl)Cl)C4=C(C=C(C=C4C)C)C)C CC1=CC(=C(C(=C1)C)N2CCN(C2=[Ru](=CC3=CC=CC=C3)(Cl)Cl)C4=C(C=C(C=C4C)C)C)C.C1=CC=C(C=C1)P(C2=CC=CC=C2)C3=CC=CC=C3 CC1=CC(=C(C(=C1)C)N2CCN(C2=[Ru](=CC3=CC=CC=C3OC(C)C)(Cl)Cl)C4=C(C=C(C=C4C)C)C)C C1=CC=C(C=C1)N2C(=O)C(=P(C3=CC=CC=C3)(C4=CC=CC=C4)C5=CC=CC=C5)C(=O)N(C2=O)C6=CC=CC=C6 C1=CC=C(C=C1)P(C2=CC=CC=C2)C(=P(C3=CC=CC=C3)(C4=CC=CC=C4)C5=CC=CC=C5)P(C6=CC=CC=C6)C7=CC=CC=C7 C1=CC=C(C=C1)N2C(=NN=N2)C(=P(C3=CC=CC=C3)(C4=CC=CC=C4)C5=CC=CC=C5)C6=NN=NN6C7=CC=CC=C7 C1=CC=C(C=C1)C(=O)C(=O)C(=P(C2=CC=CC=C2)(C3=CC=CC=C3)C4=CC=CC=C4)C(=O)C(=O)C5=CC=CC=C5 C1CCC(CC1)N2C=CN(C2=[Ru](=CC3=CC=CC=C3)(Cl)Cl)C4CCCCC4.C1CCC(CC1)P(C2CCCCC2)C3CCCCC3 CC1=CC(=C(C(=C1)C)N2CCN(C2=[Ru](=CC3=CC=CC=C3)(Cl)Cl)C4=C(C=C(C=C4C)C)C)C.C1CCC(CC1)[PH+](C2CCCCC2)C3CCCCC3 CC1=CC(=C(C(=C1)C)N2CCN(C2=[Ru](=CC3=C(C=CC(=C3)CCC(=O)OCCC[Si](C)(C)CCC[Si](CCC[Si](C)(C)CCCOC(=O)CCC4=CC(=C(C=C4)OC(C)C)C=[Ru](=C5N(CCN5C6=C(C=C(C=C6C)C)C)C7=C(C=C(C=C7C)C)C)(Cl)Cl)(CCC[Si](C)(C)CCCOC(=O)CCC8=CC(=C(C=C8)OC(C)C)C=[Ru](=C9N(CCN9C1=C(C=C(C=C1C)C)C)C1=C(C=C(C=C1C)C)C)(Cl)Cl)CCC[Si](C)(C)CCCOC(=O)CCC1=CC(=C(C=C1)OC(C)C)C=[Ru](=C1N(CCN1C1=C(C=C(C=C1C)C)C)C1=C(C=C(C=C1C)C)C)(Cl)Cl)OC(C)C)(Cl)Cl)C1=C(C=C(C=C1C)C)C)C C1(C(C2C(=O)O[SbH]3(O2)OC(C(C(C4C(=O)O[SbH]5(O4)OC1C(=O)O5)O)O)C(=O)O3)O)O CC(C1=CC=CC2=CC=CC=C21)N3C=CN(C3=[Ru](=CC4=CC=CC=C4)(Cl)Cl)C(C)C5=CC=CC6=CC=CC=C65.C1CCC(CC1)P(C2CCCCC2)C3CCCCC3 C1=CC=C(C=C1)C2=C3C4=CC=CC5=C4C(=CC=C5)C3=C(C2=P(C6=CC=CC=C6)(C7=CC=CC=C7)C8=CC=CC=C8)C9=CC=CC=C9 CC(C1=CC=CC2=CC=CC=C21)N3C=CN(C3=[Ru](=CC4=CC=CC=C4)(Cl)Cl)C(C)C5=CC=CC6=CC=CC=C65.C1CCC(CC1)P(C2CCCCC2)C3CCCCC3 CC(C)(C1C=CC(=P(C2=CC=CC=C2)(C3=CC=CC=C3)C4=CC=CC=C4)C=C1)C(=O)OC C1CN2CCN(CCN1CC[N+](=P(CO)(O)O)CC2)P(=O)(CO)O CC1=CC(=C(C(=C1)C)N2CCN(C2=[Ru](=C=CC3=CC=CC=C3)(Cl)Cl)C4=C(C=C(C=C4C)C)C)C.C1CCC(CC1)P(C2CCCCC2)C3CCCCC3 CC1(C(=O)C(=P(C2=CC=CC=C2)(C3=CC=CC=C3)C4=CC=CC=C4)C1=O)[P+](C5=CC=CC=C5)(C6=CC=CC=C6)C7=CC=CC=C7 CC1C([N+]1=P(C2=CC=CC=C2)(C3=CC=CC=C3)C4=CC=CC=C4)C.[I-] [C-]#[N+][O-].[C-]#[N+][O-].[C-]#[N+][O-].[C-]#[N+][O-].C1=CC=C(C=C1)[AsH](C2=CC=CC=C2)(C3=CC=CC=C3)C4=CC=CC=C4.[Cd+2] C1=CC(=S(=O)([NH3+])[O-])C=CC1=NNC2=C(N=NC2=O)N C1=CC=C(C=C1)C(=O)C(=[As](C2=CC=CC=C2)(C3=CC=CC=C3)C4=CC=CC=C4)C(=O)C5=CC=CC=C5 CC1C([N+]1=P(C2=CC=CC=C2)(C3=CC=CC=C3)C4=CC=CC=C4)C C1=CC=C(C=C1)[AsH2](CC[AsH2](C2=CC=CC=C2)C3=CC=CC=C3)C4=CC=CC=C4 C1=CC=C(C=C1)N=NC(=P(C2=CC=CC=C2)(C3=CC=CC=C3)C4=CC=CC=C4)N=NC5=CC=CC=C5 COC1=CC=C(C=C1)S(=O)(=O)C(=P(C2=CC=CC=C2)(C3=CC=CC=C3)O)S(=O)(=O)C4=CC=C(C=C4)OC C[SbH]1(CC2CCCC(C2)C[SbH](CC3CCCC(C3)C1)(C)C)C CC[AsH](C1=CC=CC=C1)(C2=CC=CC=C2)C3=CC=CC=C3 COC(=O)C[AsH](C1=CC=CC=C1)(C2=CC=CC=C2)C3=CC=CC=C3 C1=CC=C(C=C1)C2=CC=C(C=C2)[AsH](C3=CC=C(C=C3)C4=CC=CC=C4)(C5=CC=C(C=C5)C6=CC=CC=C6)C7=CC=C(C=C7)C8=CC=CC=C8 C1=CC=C(C=C1)C(=P(C2=CC=CC=C2)(C3=CC=CC=C3)C4=CC=CC=C4)C5=CC=CC=C5 CC1=CC(=C(C(=C1)C)N2CCN(C2=[Ru](=CC3=CC=CC=C3)(Cl)Cl)C4=C(C=C(C=C4C)C)C)C C[Si](C)(C)C1(C2C=CC=CN2[SbH]1(C(C3=CC=CC=N3)([Si](C)(C)C)[Si](C)(C)C)Cl)[Si](C)(C)C COC1=CC=C(C=C1)C(=P(C2=CC=CC=C2)(C3=CC=CC=C3)C4=CC=CC=C4)C5=CC=C(C=C5)OC C1=CC=C(C=C1)[AsH2](CC[AsH2](C2=CC=CC=C2)C3=CC=CC=C3)C4=CC=CC=C4.Cl[Pt]Cl C1=CC=C(C=C1)P(=C2C(=O)C(=P(C3=CC=CC=C3)(C4=CC=CC=C4)C5=CC=CC=C5)C2=O)(C6=CC=CC=C6)C7=CC=CC=C7 CC1=CC2=C(C=C1)C3=C(C2=P(C4=CC=CC=C4)(C5=CC=CC=C5)C6=CC=CC=C6)C=C(C=C3)C -- IPB Halle AG Massenspektrometrie & Bioinformatik Dr. Steffen Neumann http://www.IPB-Halle.DE Weinberg 3 http://msbi.bic-gh.de 06120 Halle Tel. +49 (0) 345 5582 - 1470 +49 (0) 345 5582 - 0 sneumann(at)IPB-Halle.DE Fax. +49 (0) 345 5582 - 1409 ------------------------------------------------------------------------------ Increase Visibility of Your 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