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Friday, June 22, 2012

CDK 1.4.11: the changes, the authors, and the reviewers

The CDK 1.4 series is really getting into slower waters. With only one new feature anticipated, we still see bug fixes though, and I'm sure there are a few left to review.

For me, the most important patch is that of Kevin for finding the position of double bond positions, important when taking SMILES input (see SMILES, Bioclipse, double bonds and Finding where to put double bonds...). The other two changes are files for developing CDK with NetBeans and for roundtripping 2D-based stereoinformation for bonds in CML.

The changes

  • CML Bond Conversion Test [patch:3530233] 63f0aeb
  • Improved conversion of AtomContainer to CMLMolecule b4e480c
  • Provide the necessary project files for netBeans 8caf84c
  • Changes to avoid inadvertent alteration of passed IMolecule and to deal with molecules lacking implicit hydrogen atom information 710af3e
  • Added the tool to the smiles module, and the tests to the module's test suite 575dd2c
  • Class to fix bond orders for aromatic rings 7867bd6
The authors
2  Kevin Lawson
2  John May
2  Egon Willighagen
1  Jonty Lawson

The reviewers
2  Egon Willighagen 
2  Nina Jeliazkova