Mark is working in my group on a CDK-based plugin for Oracle to enable chemistry searching: Similarity and Substructure. In his talk at the CDK workshop, he points out in the beginning that this is not a cartridge as defined by Oracle. It is a set of java classes loaded by the Oracle Java virtual machine (called “Aurora”).
Mark points out a few performance issues (finding all rings in a Bucky Ball ).
He then goes into how (and why) to use a combination of the CDK fingerprinter and the CDK subgraph ismorphism to achieve a good performance in chemical database searching. Mark has put up an exercise on http://www.ebi.ac.uk/~markr.
Feel free to go ahead and fill the gaps.