Rdkit

Rdkit: Open-source cheminformatics. A collection of cheminformatics and machine-learning software written in C++ and Python. NOTE: the RDKit source code and downloads are now in github: https://github.com/rdkit/rdkit. The core algorithms and data structures are written in C++. Wrappers are provided to use the toolkit from either Python or Java. Additionally, the RDKit distribution includes a PostgreSQL-based cartridge that allows molecules to be stored in relational database and retrieved via substructure and similarity searches.