Saturday, December 31, 2011

CDK 1.4.6: the changes, the authors, and the reviewers

OK, I forgot to write those up again :(

Release 1.4.6 of about a month ago, fixes a few bugs, including broken JavaDoc, atom type perception when SMILES are parsed while keeping the lower case formalism as aromaticity indicators (I will not discuss the pros and cons of that here), and the Chi index descriptors for sulphurs. This release also introduces a new fingerprint, based on an extensive list of biologically-relevant substructures identified by Klekota and Roth in 2008 (doi:10.1093/bioinformatics/btn479). This functionality was backported by Jonathan from the PaDeL software by Yap Chun Wei. The rest is a bunch of small code and dependency clean ups as well as new unit tests.

The changes
  • Added missing unit tests 9119aa2
  • Added get-methods for information needed for extensions 4525cbe
  • A few missing unit tests in the 'qsar' module 2356a10
  • Added further methods needed for CDK-JChemPaint 804a6f5
  • Added missing JavaDoc. e316210
  • No longer complain about missing testing for abstract classes 284ff84
  • Typo: there → their 640b6e6
  • Added unit testing 05216f0
  • Throw a descriptive exception when 2D coordinates are missing (fixes #3355921) cdc4cbd
  • Fixed the cheminf.bibx well-formedness (fixes #3435367) 7bc0772
  • Added missing @cdk.githash. fdd3d22
  • Updaetd chi index util to correctly evaluate deltav for sulphurs. Fixes bug 3434741. Added unit test 8225175
  • Use interfaces instead of implementations 434c9b1
  • Use interfaces instead of implementations 76dcdf7
  • Use interfaces instead of implementations 5bef796
  • Use interfaces instead of implementations b6ed6a7
  • Moved the pi-contact descriptor (atom-pair) to qsarmolecular, removing the depedency of qsar on reaction d902312
  • Added a missing dependency; it now finds PDBPolymer f03eb3c
  • Fixed test method names f6562cb
  • Added a missing test a853c91
  • Fixed TestClass annotation d37961d
  • Added tests for the isomorphism module to the proper suite 657c3a7
  • fixed dependency for fingerprint tests 135edeb
  • added test for getSubstructure d1eb951
  • lookup SMARTS at index in Substructurefingerprint 65602db
  • Wrote test for KlekotaRothFingerprinter 2b1288b
  • adapted to CDK 84aefixesd70
  • Import from the source code of PaDEL-descriptor (doi:10.1002/jcc.21707) 291def4
  • Fix to use interfaces as argument instead of classes 5e828f5
  • Perceive atom types also when aromaticity from the SMILES is kept 2e76ff6
  • Added unit test to make sure atom types are also perceived when aromaticity from SMILES is kept b315ee6
The authors

25  Egon Willighagen
  5  Jonathan Alvarsson
  2  Rajarshi Guha
  1  Nina Jeliazkova
  1  Yap Chun Wei

The reviewers

13  Rajarshi  Guha 
  8  Egon Willighagen 
  1  Nina Jeliazkova 

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