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Monday, August 22, 2011

CDK 1.4.2: the changes, the authors, and the reviewers

Not so long since the CDK 1.4.1 blog post, but about a month after the actual release, there was already more than enough content for the next minor release. The 1.4.2 release adds another batch of atom type by Asad, Nimish, and Gilleain, which constitutes the majority of the patches. There is also some fixing of the creation of JavaDoc, and it seems that the link to the Git repository got broken somewhere. It turns out that the Tag.position()-returned SourcePosition class no longer returns the full file name path, but only the ClassName.java in some intermediate folder, causing all package information to be lost. And, more apparently got lost, because we no longer seem to have module pages. Clearly, some help with project maintenance is appreciated!

Other cool changes include a patch by Thorsten to speed up Morgan number calculation, a reference to the paper by Miguel on metabolite identification (DOI:10.1093/bioinformatics/btr409) for which he wrote a lot of code for the CDK, a bug fix, code clean up patches by Dmitry allowing this branch to be compiled with Java5 again, and the first patches by my son :)

The Changes
  • Apparently something changed in the JavaDoc API, and I only get the file name now, so added this work around to be at least somewhat useful 819f2fc
  • Module pages are lost, remove the link for now f1ffaca
  • cleaner patch for Fe atomtype test cases added ed3a554
  • cleaner patch for Fe atomtype data added b92b8b1
  • cleaner patch for Fe atomtype added da8d3d0
  • Hg Atom type owl added 66d6321
  • Hg Atom type added d9fc795
  • Hg Test cases added 0e3d587
  • Added Nimish who did a lot of the hard work from the atom type patches from Asad's lab, which are going in under Gillieain's name 888ab40
  • Added new contributor's name to the copyright/license header f006ffb
  • made the creation of morgan numbers N times faster, where N is the number of atoms in the AtomContainer 1c5ba83
  • Added the new CDK contributor of the previous two patches 5d268f5
  • changed assertEquals(true to assertTrue( and the same for false 2 cd467ca
  • changed assertEquals(true to assertTrue( and the same for False d3e08a2
  • Fixed charge in unit test: +4 not 0 c8bf1f1
  • Te final 17d6044
  • Rb final af5f764
  • Ra final 5ebe425
  • Made the code Java 5 compilable. 7406c2b
  • Removed usefull JavaDoc f6076d5
  • closed @cdk.bug 3273205 and created a test. Control that IsotopeContainer doesn't get null. 9733d0e
  • MolecularFormulaManipulatorTest: Cleaned up javadoc - removed all empty/meaningless javadoc - wrote short oneliner javadoc for the more complicated methods 681cef8
  • MolecularFormulaManipulatorTest: Updated testGenerateOrderEle to match updated method 9028b3c
  • Cr final fce1c7a
  • Be final ac15cb5
  • Ba final d9632c1
  • Au final 936d2d3
  • Ag final 75036b8
  • Cl final 5920102
  • In final 78b3d27
  • Hooked in Cd atom type perception bd3ca4d
  • Cd final 4d68c27
  • Pu final 0eebd74
  • Th final c684298
  • Include CDK deps in the classpath, to not get false positive warnings about missing CDK classes 2701ea6
  • Added citation:RojasCherto2011 which uses some CDK classes to generate elemental formulas. 99ac224
The Authors

13 Gilleain Torrance
11 Egon Willighagen
 6  Syed Asad Rahman
 2  Jules Kerssemakers
 2  Lars Willighagen
 2  Miguel Rojas Cherto
 1  Thorsten Fl├╝gel
 1  Dmitry Katsubo

These are patches from four countries and six independent groups. I am still hoping to find some time (or someone else) to make a Google Map that plots the commits in time on a world map :)

The Reviewers

25  Egon Willighagen 
  2  Syed Asad Rahman 

Yeah, we're still short on people interested in doing review work for the CDK. Feel free to put that up on your CV, along side reviewing work for journals!