One such open-source Java library is the Chemistry Development Kit (CDK), which is useful for chemo- and bioinformatics

Abstract

If you're interested in structural chemistry or bioinformatics, you may get your hands on the open-source Chemistry Development Kit (CDK) collection of Java programs. Its design, features, and development as an open-source project by a group of worldwide academic and business partners are detailed. Molecular informatics procedures, structures, 2D and 3D chemical structure rendering, input/output routines, SMILES creation and parsing, ring searches, isomorphism verification, structure diagram production, etc. are all provided by the CDK. Interested users and potential contributors are provided with access information and application possibilities..