Like all release in the 1.2 series after CDK 1.2.0, release 1.2.6 is a bug fix release. Anyone running a CDK 1.2 version is advised to upgrade. New in this release is the availability of a torrent for the cdk-1.2.6.jar (see BitTorrents for Science). Please find below the changes and the authors that contributed to this release.

The changes

  • Updated the DebugBond unit test too now: new DebugBond() has zero atoms 6ef1fb1b36
  • Backport patch, to make the patches compile with cdk-1.2.x ce9b1bd9b3
  • Additional patch to reduce atom count on setAtom(null, int) and unit tests for the setAtom(IAtom, int) behavior. 6cf95db428
  • Also fix the new NNBond() == 0 atoms for the nonotify module 23d96855fa
  • Fixed Bond() constructor to create a bond with zero atoms. Also fixed setAtom(IAtom, int) to increase the atom count if a null entry is filled with a non-null IAtom. 916ab96c4e
  • Updated test to assume new Bond() creates a bond with zero atoms 4ac711194a
  • Exceptions when clone atomless ISingleElectron and ILonePair too c5d4cd3b9e
  • Unit test for ArrayIndexOutOfBoundsException occuring when trying to clone an IAtomContainer with an IBond with no IAtoms d71c31caf8
  • Added unit tests for SMILES with failing atom typing, from email on the cdk-devel mailing list June 11 2010 890d0f573c
  • Added the N.oxide atom type, for structures like (CH3)N=O bb431e3768
  • Fixed reading of SD properties: keep the first line too 3133a18574
  • Added missing dependency 14003dce2f
  • Fixed unit test: surely there is no atom with symbol 0... how long has this been failing?? c888e4fd44
  • Added a test class to aromaticity of three compounds: the last incorrectly fails a454ab84a7
  • Also except N.amide as part of an aromatic ring 3357113d0a
  • Added a test class to repeat atom type perception and test consistency 0bd5b421d3
  • Unit test fix: the molecules *is* aromatic, as we should assume it is. Fixes a big goof up cd83236c3a
  • Replace special chars where spaces are supposed to occur, fixing the fail of the unit tests every now and then 483c856e3a
  • Improved javadoc generation using a link tag, so that references to java library classes are resolved properly 1f8bb2d7a1
  • Removed use of the proprietary DocCheck utility 1523f66152
  • Use the new tests in more situations e8b13b27e2
  • Introducing PMD test for CDK specific issues: 406930b292
  • Added copyright and license header d6b6c65f5a
  • Replaced outdated URL with entry in WikiPedia (fixes #3002741) ad2bd3ed63
  • Fixed a ClassCastException in a unit test; I messed up (mea culpa) b5fa3dca01
  • Fixed NullPointerExceptions for LonePair's and SingleElectron's constructed with the no-argument constructors 5f34897eb8
  • Added missing cloning of single electrons 2d4c1220c3
  • Do not try to clone the atom if it does not exist 9672df0df7
  • converted uses of indexOf to startsWith/contains 7b9d84e44a
  • Updated HIN reader to fix bug 2984581 f95c6324a8
  • Added unit test to see of arrays are properly cloned, and that array entries of the original are not overwritten 38d5f8d191
  • Unit test that the IAtom[] array is properly cloned, and overwriting entries in the clone does not overwrite entries on the original 3c1b07e26f
  • Removed duplication of cloning. 216c1600b9
  • Apparently the super.clone() does not clone the pointer to the IAtomContainer[], causing a clone() followed by changing containers in the clone to overwrite the original IAtomContainer[]. Fixed by creating a new array. 4e5d6a120f
  • Moved test from the specific class to the abstract tests, as the behavior should be the same for NNMoleculeSet and DebugMoleculeSet too 068fb3b9b2
  • Two more tests for the issue: atom typing works fine; aromaticity detection fails: one ring is detected as aromatic (that with two nitrogesn), so that it does not consider the double ring, marking the other ring as non-aromatic 3be2367b36
  • Fixed taking into account larger ring systems when one ring is in itself already aromatic (fixes #2976054) 891049f59a
  • Fixed cloning of properties with null values by always using HashMap (fixes #2975800) 2f722f09f8
  • Added four and six coordinate neutral platinum atom types. 407d79323e
  • Shortened the SMILES to only contain the aromatic atoms, allowing a foreach loop: replaced for-loop by a foreach-loop, solving also the not testing all atoms in the testAromaticty() test. 6fcc3d08a0
  • Added InChI, and link to existing pyrolle test, using a different SMILES f088cd6a39
  • Added tests for two cases of aromatic rings c26ae95649
  • Added @cdk.bug annotation, and restricted testing to the bug 3b08f1a5dc
  • Removed try/catch to retain the stacktrace of where the NPE occurs ce11b521e1
  • Test checking for NPE when cloning with property with null as value 0aa632a876
  • Improved JavaDoc: 19a976c3fa
  • Loosened the perception of N.planar3 atom types: the Hueckel system consist of more than one ring, so looking just at the ring to which the atom belongs does not make sense d651c2597a
  • Added unit tests for atom type perception of more N.planar3 atom types 83423a7a30
  • Removed unused import e1c03fbff0
  • Removed last bits of implementation details from the API: now uses List<> instead of ArrayList<> 7727b72d7f
  • Removed output to STDOUT 14e1d12d71
  • Fixed some spelling errors and added JavaDoc links 677b3f6336
  • Synchronized behavior with the MDLV2000Reader (addressing bug #2942196) 2ceef95e74
  • Ant has a release 1.8 that should be accepted in build.xml 4398cc45a4
  • The IMapping interface had a class comment which probably was a copy&paste artefact. Changed this. 05c857cc4e
  • Fixed license info .meta file for JavaCC d9e15bbca9
  • Bumped version to differ form the 1.2.5 release 17a6f08a07

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.

49  Egon Willighagen
 3  Rajarshi Guha
 2  Stefan Kuhn
 1  Arvid Berg
 1  Mark Rynbeek
 1  maclean

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.

41  Rajarshi Guha
 3  Egon Willighagen
cdk