#380 Ensure proper Burden matrix diagnonal values

Needs_Revision
closed
cdk-1.4.x (181)
master
5
2013-10-07
2011-07-01
No

Correctly sets the diagonal of the Burden matrix with charge values. Fixes bug 3347528

Discussion

  • Egon Willighagen

    Looks good to me. Funny bug!

    I'll apply it later.

     
  • Egon Willighagen

    Rajarshi, one unit test value changes:

    Testcase: testAromaticity(org.openscience.cdk.qsar.descriptors.molecular.BCUTDescriptorTest): FAILED
    element 2 does not match expected:<-0.18066486607184457> but was:<-0.21175815206924314>
    junit.framework.AssertionFailedError: element 2 does not match expected:<-0.18066486607184457> but was:<-0.21175815206924314>
    at org.openscience.cdk.qsar.descriptors.molecular.BCUTDescriptorTest.testAromaticity(BCUTDescriptorTest.java:148)

    If that is OK, please provide a patch.

    The current patch is applied and pushed.

     
  • Rajarshi Guha

    Rajarshi Guha - 2011-07-17

    The problem is not in the BCUT descriptor - instead, the partial charges calculted for the two forms of the molecule (kekule and aromatic) differ - hence the difference. If the charges are meant to differ, then I can update the new BCUT descriptor values to go away.

    But I think partial charges should not be representation dependent

     
  • John May

    John May - 2013-10-06

    This can be closed (I think it's already applied) - the failing test went away with the new SMILES code giving a kekule structure. It will come back again though with the new patches to keep the aromatic specification from SMILES. As Rajarshi says it's the charges which correctly give different values.

     
  • Egon Willighagen

    • status: open --> closed
    • Branch: --> master
     

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