Friday, April 06, 2012

CDK 1.4.9: the changes, the authors, and the reviewers

This quick release does not indicate emergency fixes for CDK 1.4.8, but results more from a timing issue. It addresses some practical problems in our development flow. The earliest (bottom most) three patches have to do with the submission of the renderextra patch, while several others result from development work around the DeduceBondSystemTool. The third part is a fix for when the PubchemFingerprinter is used in a threaded environment. Additionally, there is a small fix in the build system to ensure that the dist-test-large includes all data files and core test classes.

The changes
  • Fixed bond order assignment when using the SilentCOB 1e936d0
  • Double bond orders are not properly assigned when using the SilentCOB fb37eab
  • Added testing of the number of double bonds found (fixes #3514176) a6597e3
  • But the test data should be added too 059da00
  • Added the missing cdk-test.jar (patch by Jonty Lawson) df12e2e
  • Updated PubchemFingerprinter to not use static variables. Allows it to be used in multithreaded scenarios 9bd6b45
  • Removed to unused imports, one of which causes trouble with free Java systems 7c5d18b
  • Added a unit test to check for multithreaded usage in PubchemFingerprint. Tests for bug 3510588 57a9c3f
  • Ensure that the totalBounds object returned is non-null c23740b
  • (renderbasic). Made AverageBondLengthCalculator public 1702f3e
  • (renderbasic). Pass the RendererModel to contained renderers. c59f344
The authors

7  Egon Willighagen
2  Arvid Berg
2  Rajarshi Guha

The reviewers

4  Egon Willighagen 
3  Nina Jeliazkova 
1  Arvid Berg 


  1. Ever since this release (1.4.9) I get an error when using the deducebondsystem tool

    DeduceBondSystemTool dbst = new DeduceBondSystemTool();
    iAtomContainer = dbst.fixAromaticBondOrders((IMolecule) iAtomContainer);

    results in:
    Exception in thread "main" java.lang.NullPointerException
    at org.openscience.cdk.smiles.DeduceBondSystemTool.removeExtraRings(
    at org.openscience.cdk.smiles.DeduceBondSystemTool.combineRetMols(
    at org.openscience.cdk.smiles.DeduceBondSystemTool.fixAromaticBondOrders(

    1. So, a regression? I noted that exception too, but was not sure if that was new... if so, can you file a bug report please? E.g. just copy/pasting the above?