The Chemistry Development Kit (CDK) is a scientific, LGPL-ed library for bio- and cheminformatics and computational chemistry written in Java.
The main home page of the CDK is now at: http://cdk.github.io
Fast search using a standard SQL on Oracle or PostgreSQL database. The package includes the database creator, loader and web application. It supports SMILES and SMARTS substructure searches, similarity search, stereochemistry.