Tuesday, November 01, 2011

CDK 1.4.5: the changes, the authors, and the reviewers

CDK 1.4.5 just got uploaded to SourceForge, about a month after the 1.4.4, though mere minutes after the 1.4.4 release notes. CDK 1.4.5 is the fifth bug fix release of the 1.4 series and brings another few bug fixes.

The changes include fixes to the JavaDoc generation, now outputting proper citations of PhD thesis and books, a fix in the SDFWriter to inherit the IO options from the underlying (used) MDLV2000Writer, restored atom type perception in SMILES parsing if aromaticity is not actively perceived (in line with earlier 1.4.x behavior that unfortunately got broken due to another fix), a fix in the MDLV2000Reader to deal with pseudo atoms with numbers greater than 9 (thanx to John May!), a fix in the sorting of IAtomContainers, and a fix for the elusive bug in the AWTRenderer causing thin bonds (e.g. due to zooming) to become grey.

The changes
  • Use a minimal stroke width in the AWT output (fixes #3295256) 1387b7b
  • Changed how data files are copied: copy those specified in the src/META-INF/*.datafiles (fixes #3430342) 68536e1
  • Perceive atom types also when aromaticity from the SMILES is kept 2413197
  • Added unit test to make sure atom types are also perceived when aromaticity from SMILES is kept d6b8c8e
  • Removed broken link and fixed syntax of @cdk.cites. 22c59fc
  • The SDFWriter now accepts all MDLV2000Writer's IOSettings too (fixes #3392485) aa6ca5f
  • Unit test for bug #3392485: SDFWriter not accepting MDLV2000Writer IO settings ab54ed5
  • Fixed @TestClass annotation to point to the correct class a7cbe48
  • Updated unit test to be independent of atom index and just match the coordinates 8d3eed0
  • Fixed bugged when reading MDL V2000 files. If the atom number of a pseudo atom was greater then 9 it would not be read correctly fd90ed5
  • Depend on standard to, to have access to AtomContainerComparator 76db769
  • Create IMolecule's instead of IAtomContainer's because IMoleculeSet can only contain the former; fixed the exception currently thrown by e.g. MoleculeSetTest 1aae7fa
  • Fixed sorting with null IAtomContainers (based on a suggestion by Mark in the bug report #3093241) 1bf194b
  • Missing unit test for AtomContainerSet.sort(Comparator) 0585bcd
  • Added a unit test to check that molecular descriptors do not throw Exceptions when disconnected structures are passed 853ca50
  • Added support for book and phdthesis reference types 277dd03
The authors
17  Egon Willighagen
 1  John May
The reviewers
10  Rajarshi Guha