A great source of CDK documentation or introductory reading is the CDK News, the quarterly newsletter of the CDK team.
Once you have managed to download the CDK source code, you can refer to the test classes in src/test/org/openscience/cdk/. They are sorted by topic (packages) and contain small codes snippets that show nicely how to use each aspect of CDK. Of course, the user list is the place to ask questions. Feel free to contribute to the Frequently Asked Questions.
- Groovy Cheminformatics with the Chemistry Development Kit, Egon Willighagen
Documentation of the Java API
The JavaDoc for the CDK library is available from the Nightly pages for the two releases (stable and unstable) and various patches at SuperNightly. The below links may be outdated, but you can always find to most up to date JavaDoc via SuperNightly.
Request for Comments (RFC)
Request for Comments are a formal means of the CDK developers to discuss core API designs. While recently no longer used a lot, as the API has been stabilizing, they were actively used in the past. More information can be found at Request for Comments.
- The Graph Representation
- C.Hoppe, Atom types in the Chemistry Development Kit, CDK News, 2005, 2(3):60-61. PDF
- S.Kuhn, Stereochemistry detection in the CDK, CDK News, 2005, 2(3):64-66. PDF
- ChemFormats and ChemObjectReaders
- E.L.Willighagen, Customizing file IO, CDK News, 2004, 1(2):2-4. PDF
- Descriptor Calculation
- R.Guha, Using the CDK as a backend to R, CDK News, 2005, 2(1):2-6. PDF
- R.Guha, Using R to provide statistical functionality for QSAR modeling in CDK, CDK News, 2005, 2(1):7-13. PDF
Integration with R
Installation Help - Tips and Tricks
- You can find help for the installation on different systems and with different methods under Installation. Moreover you can find there Tips and Tricks for the usage of the CDK.