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#1076 Chi descriptors hang on covalent bonded metals

cdk-1.4.x
open
Rajarshi Guha
cdk-qsar module (68)
9
2012-11-03
2010-06-30
Peter Maas
No

Any of the Kier & Hall Chi Descriptors will hang on structures contain covalent drawn metals. Examples are taken from the EBI's CHEMBL database.
Idnumbers: 285037, 111737, 426537. This only has been tested using Guha's CDKDescGui. I did try to add hydrogens externally or not add hydrogrens at all. In all cases the application hangs.

Discussion

  • Peter Maas

    Peter Maas - 2010-06-30

    3 entries from chembl containing Zn, Sn and Pt

     
    TestCovalentMetals.sdf

  • Rajarshi Guha

    Rajarshi Guha - 2010-06-30

    I have added test cases to all the Chi descriptors in the CDK code and they do not hang the code. But note that they may throw an NPE as some metals do not have a valency entry in the valency table. (what the valency should be is something I'm not sure about).

    But at least, within the CDK the first two examples do not cause a hang. I will look at the GUI a little later.

    Note that I checked on master, which is what the GUI is using. Is there a reason you set this for 1.2.x?

     

  • Peter Maas

    Peter Maas - 2010-06-30

    No I do not have a reason to set it to 1.2.x other then it seemed like the most appropriete. I used CDKDescUI 1.0.1 and retested it using 1.0.5. I just noticed it does complain about the valance. The exact message:
    Exception in thread "Thread-4" java.lang.NullPointerException
    at org.openscience.cdk.qsar.AtomValenceTool.getValence(AtomValenceTool.java:88)
    at org.openscience.cdk.qsar.descriptors.molecular.ChiIndexUtils.getValenceElectronCount(ChiIndexUtils.java:179)
    at org.openscience.cdk.qsar.descriptors.molecular.ChiIndexUtils.evalValenceIndex(ChiIndexUtils.java:166)
    at org.openscience.cdk.qsar.descriptors.molecular.ChiChainDescriptor.calculate(ChiChainDescriptor.java:197)
    at net.guha.apps.cdkdesc.workers.DescriptorSwingWorker$ActualTask.evalToTextFile(DescriptorSwingWorker.java:224)
    at net.guha.apps.cdkdesc.workers.DescriptorSwingWorker$ActualTask.<init>(DescriptorSwingWorker.java:365)
    at net.guha.apps.cdkdesc.workers.DescriptorSwingWorker$1.construct(DescriptorSwingWorker.java:101)
    at net.guha.apps.cdkdesc.SwingWorker$2.run(SwingWorker.java:121)
    at java.lang.Thread.run(Unknown Source)

     

  • Rajarshi Guha

    Rajarshi Guha - 2010-06-30

    OK, switched the report to master.

    So the valence error is expected - is it crashing the UI, or does it catch it and carry on?

    In general, the Chi desc's were not designed for metal containing compounds (what would be the valence e count for Pt or Zr?)

    Doe the UI still hang?