Hi Steffen, This is really useful. I've been looking at your bug reports, and will try and sort out these out today.
- 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
