The Chemistry Development Kit (CDK)is a JAVA based open source project aimed at cheminformatics. Several core people around the Steinbeck group developed the code. According to Ohloh the development took 84 Person Years and translated into several million dollars in development cost. One personal criticism (I support and advertise the CDK but I am not a developer) is that there are too few useful examples which can be used by non-programming people. This includes tools with GUIs and command line tools. Such issues were better solved in related projects like JChemPaint or JMOL or BioClipse or OpenBabel.

CDK examples can be found in the java test package and CDK code snippets and on Rajarshi Guha site.