CS-Miner stands for Chemical Space Miner and is a software tool for navigating in chemical space of compound databases. It helps for deriving appropriate classification models and performing virtual screening.
Download it via:
http://csminer.com/csm/?p=7
A quick tutorial is available through:
http://csminer.com/csm/?p=8
JOELib/JOELib2 is a cheminformatics library which supports SMARTS substructure search, descriptor calculation, processing/filtering pipes, conversion of file formats, 100% pure Java, and interfaces to external programs (e.g. Ghemical) are available.