Saturday, June 11, 2011

CDK 1.3.10: the changes, the authors, and the reviewers

Release 1.3.10 is not much different from 1.3.9, as we are seriously converging towards CDK 1.4.0 now, with only the big CDK-JChemPaint renderbasic patch waiting. I'm hoping to merge that in this weekend, and to release the first Release Candidate then. The 2nd edition of the Groovy Cheminformatics book, in fact, is already based on 1.3.10, which I released a few days ago. This release has the following changes, mostly contained bug fixes in the 1.2 series:

  • Fixed dependency on specific molecule impl, so now we use IAtomContainer rather than Molecule fbdb989
  • Added a convenience test to see if a parameter has been registered to the model ad04b69
  • Updated JavaDoc checking to OpenJavaDocCheck 0.8 7bfb28b
  • Copy data files into the right folder of the puredist ae69740
  • Added a test to demonstrate the ClassPathException in bug #3305581 d8c4ca6
  • Test if the descriptor results are the same for two implementations (unfortunately, the nonotify IMolecule extends the data IMolecule, so it does not catch bug #3305581) 0f3f147
  • Factored out a method to test whether to descriptor calculations give the same results 861c304
  • Parameterized method to create water to allow alternative implementations 4d7c6b5
  • Updated code to avoid dependency on specific implementation of molecule object. Now use IAtomContainer 7cc943a
  • Added detection of a Te atom type, found in ChEMBL d114114
  • Added unit tests^Cor Te.3 atom type detection aa79a3f
  • Added note about required atom type perception 54d5ff9
  • Added unit tests to calculate tautomers from a handcrafted IAtomContainer 310cd0c
  • Fixed OJDCheck validation 67d76d0

The Authors
13  Egon Willighagen
 2  Rajarshi Guha
 1  Onkar Shinde
The Reviewers
 5  Rajarshi Guha 
 2  Jonathan Alvarsson
 2  Mark Rynbeek
 2  Egon Willighagen 

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