Fixed in r4321. There were two issues with atom typing (of As and Sb), and one with perception of cis/trans stereo centers (C=RuR3 is not a stereo center). A reduced set of non-redundant test cases (38) are included in the test suite.
If you're interested in further testing, that'd be great. If you find any more segfaults converting between the common cheminformatics formats, just send them to the list and we'll try to sort them out. - Noel On 24 November 2010 06:56, Steffen Neumann <sneum...@ipb-halle.de> wrote: > 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 3D Game App & Earn a Chance To Win $500! > Tap into the largest installed PC base & get more eyes on your game by > optimizing for Intel(R) Graphics Technology. Get started today with the > Intel(R) Software Partner Program. Five $500 cash prizes are up for grabs. > http://p.sf.net/sfu/intelisp-dev2dev > _______________________________________________ > OpenBabel-Devel mailing list > OpenBabel-Devel@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-devel > ------------------------------------------------------------------------------ Increase Visibility of Your 3D Game App & Earn a Chance To Win $500! Tap into the largest installed PC base & get more eyes on your game by optimizing for Intel(R) Graphics Technology. Get started today with the Intel(R) Software Partner Program. Five $500 cash prizes are up for grabs. http://p.sf.net/sfu/intelisp-dev2dev _______________________________________________ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
