#76 Problems with different aromaticity concepts

closed
5
2012-10-08
2003-07-15
Stefan Kuhn
No

I have got two MDLs, both containing 2-Chlor-Naphtalin.
The difference is one has got the aromaticity as
double-single-bonds, the other as an aromatic circle
(hope that's the term). If I read them and run the
AromaticityDetector on them and then produces the
fingerprint, the fingerprints are different.

Discussion

  • Kai Hartmann

    Kai Hartmann - 2003-07-15

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    I think this may be due to the aromaticity flag of the ring
    not being set in the HueckelAromaticityDetector. See my
    comment on bug item #716259. My plan was to implement this
    when the aromaticity detection works fine.

     
  • Egon Willighagen

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    Stefan, could you please upload those two MDL files
    (commited, or attached to this report), so that I can make a
    JUnit for it to confirm the bug?

     
  • Stefan Kuhn

    Stefan Kuhn - 2003-07-22
     
  • Christoph Steinbeck

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    This could also be due to the Chlorine atom which causes
    problems due to the string inversion in the FingerPrinter.
    See newly filed bug

    799672 "Wrong handling of multi-letter atom symbols". We'll

    see....

     
  • Christoph Steinbeck

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    user_id=54358

    Seems like Kai was right. The recent CVS version of CDK
    produce identical strings for this molecule.

     

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