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\paragraph{Toolkits} (Table~\ref {})  The Biochemical Algorithms Library (BALL) \cite{Hildebrandt_2010} provides an object-oriented C++ library for structural bioinformatics, and its capabilities include molecular mechanics, support for reading and writing a variety of file formats, protein-ligand scoring, docking, and QSAR modeling.  The Chemistry Development Kit (CDK) \cite{Steinbeck_2006} is a cheminformatics toolkit written in Java. Its capabilities include support for reading and writing a variety of chemical formats, descriptor and fingerprint calculation, force field calculations, substructure search, and structure generation.