Sunday, September 12, 2010

CDK 1.2.7: the changes, the authors, and the reviewers

CDK 1.2.7 is the latest of bug fix releases in the 1.2 series. It brings a number of JavaDoc fixes, but, importantly, also bug fixes in SMILES handling and atom type perception. I am really pleased to see the application domain of various algorithms in the CDK continously grow: SMILES parsing for some transition metals has been fixed, and the SMILES generation for some types of ring closures too. Additionally, an important bug was fixed in the atom type perception algorithm, which failed for custom atom types with formal charges. Everyone using the CDK 1.2 series is advised to upgrade to this version.

The changes
  • Compare values not objects (fixes #3061263) 324f7f5
  • Unit test to reproduce failing atom type perception with one of the options to create a -1 Integer object 9c1b95a
  • Removed output to STDOUT 223fc9a
  • Fix for branching bracket issue when generating SMILES for BrC1C(Br)C(Br)C(Br)C(Br)C1Br b9b2272
  • Unit test for bug #3040273. 6d9b3d2
  • Fixed hybridization information: these are sp3 hybridized systems a01de91
  • More missing elements for SMILES parsing problems reported in bug #3048501 31f7462
  • Unit tests for SMILES parsing bugs reported in #3048501 bf8defd
  • A few more missing elements in the SMILES two-character element symbol parsing 5cf9334
  • Added missing elements, fixing several problems reported in bug #3048501 6ab74bc
  • Upper case the first character to also properly recognize lower cased 'aromatic' two-character element symbols (fixes SMILES parsign of things like c1[se]ccccc1 3ec1480
  • JavaDoc fixes: correct @cdk.cite use, and small typo 394f9ed
  • Updated the JavaDoc for an API changed a while ago: the getInChIToStructure() method now takes an IChemObjectBuilder as second argument (fixes #3035890) be56aac
  • Updated the JavaDoc for the atoms() Iterable API change (fixes #3034824) 38873dc

The authors
The below numbers are based on the number of commits, but keep in mind that some developers, like myself, need more commits for the same number of changed lines.
13  Egon Willighagen
 2  Saravanaraj
The reviewers
The below list is based on who signed off the patches. Anyone who reviews patches in the patch tracker can basically do this. Ask on cdk-devel on how to do this.
 8  Rajarshi Guha 
 4  Gilleain Torrance
 2  Egon Willighagen