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#900 -p 7.0 crashes obabel

2.3.x
open
nobody
None
1
2013-10-25
2013-10-23
Björn Grüning
No

Hi,

the following command will crash obabel 2.3.2.
Please note if you omit the -p 7.0 option it works.

echo 'N=[N+]=NC1=C(C(=O)C)C(=O)c2c3c1cccc3ccc2' | obabel -i smi - -o smi -e -b -p 7.0

Thanks!
Bjoern

Discussion

  • Hi,

    turnes out PubChem has a few more compounds that are crashing obabel.

    echo 'N=[N+]=NC1=NC(=O)C2(NN1)c1ccccc1c1c2cccc1' | obabel -i smi - -o can -p 7.0
    echo 'N=[N+]=NC1=NN=NC2=NC=NC12' | obabel -i smi - -o can -p 7.0
    echo 'N=[N+]=NC1=NS(=O)(=O)c2c1cccc2' | obabel -i smi - -o can -p 7.0

    I think I can see a pattern :)

    Cheers,
    Bjoern

     
  • Processing the whole pubchem resulted in.

    Passed:
    N=[N+]=NC1=C(OC)C(=O)c2c(C1=O)nccc2 6332313
    N=[N+]=NC1=C(OC)C(=O)C(=C(C1=O)OC)N=[N+]=N 6332557
    N=[N+]=NC1=C(OC)C(=O)c2c(C1=O)cccc2 6333422
    N=[N+]=NC1=C(Cl)/C(=N\S(=O)(=O)c2ccccc2)/C(=C/C/1=N\S(=O)(=O)c1ccccc1)C(C)(C)C 9573588

    Chrashed:
    N=[N+]=NC1=C(C(=O)C)C(=O)c2c3c1cccc3ccc2 21858521
    N=[N+]=NC1=NC(=O)C2(NN1)c1ccccc1c1c2cccc1 53298809
    N=[N+]=NC1=NS(=O)(=O)c2c1cccc2 6332151
    N=[N+]=NC1=NCCN1 6332157
    N=[N+]=NC1=C(Cl)C(=O)C(=C(C1=O)Cl)Cl 6332168
    N=[N+]=NC1=C(Cl)C(=O)C(=C(C1=O)Cl)N=[N+]=N 6332169
    N=[N+]=NC1=C(N=[N+]=N)C(=O)c2c(C1=O)nccc2 6332312
    N=[N+]=NC1=C(Cl)C(=O)c2c(C1=O)cccn2 6332314
    N=[N+]=NC1=NN=NC2=NC=NC12 6332367
    N=[N+]=NC1=NC2=NC=NC2C(=N1)N=[N+]=N 6332433
    N=[N+]=NC1=NC2=NC=NC2C(=N1)N 6332434
    N=[N+]=NC1=NC(=NC2=NC=NC12)Cl 6332462
    N=[N+]=NC1=C(C)C(=O)C(=C(C1=O)C)N=[N+]=N 6332534
    N=[N+]=NC1=C(c2ccccc2)C(=O)C(=C(C1=O)c1ccccc1)N=[N+]=N 6332563
    N=[N+]=NC1=C(Br)C(=O)OC1COC(=O)c1ccccc1 6333049
    N=[N+]=NC1=C(/C=C/c2ccccc2)C(=O)c2c(C1=O)cccc2 6333408
    N=[N+]=NC1=C(C)C(=O)c2c(C1=O)cccc2 6333417
    N=[N+]=NC1=CC(=O)C(=CC1=O)c1ccccc1 6333418
    N=[N+]=NC1=C(Cl)C(=O)c2c(C1=O)cccc2 6333420
    N=[N+]=NC1=C(C(=O)C(=C(C1=O)C(C)(C)C)N=[N+]=N)C(C)(C)C 6333421
    N=[N+]=NC1=C(C(=O)C=C(C1=O)C(C)(C)C)C(C)(C)C 6333423
    N=[N+]=NC1=CC(=O)C(=CC1=O)C(C)(C)C 6333425
    N=[N+]=NC1=C(C(=O)C=C(C1=O)c1ccccc1)c1ccccc1 6333426
    N=[N+]=NC1=C(C(=O)C(=C(C1=O)C(CC)(C)C)N=[N+]=N)C(CC)(C)C 6333430
    N=[N+]=NC1=C(N=[N+]=N)C(=O)c2c(C1=O)cccc2 6333447
    N=[N+]=NC1=CC=NC2=NN=NC12 6333539
    N=[N+]=NC1=NCS(=O)(=O)c2c1cccc2 6334211
    N=[N+]=NC1=C2C=CC=CC2N+C=C1 6334285

    Interestingly obabel 2.3.1 has no problems with such molecules.

    Salve,
    Bjoern