The Chemistry Development Kit (CDK) is a library of Java classes for chemo-, bioinformatics, computational chemistry, and chemometrics. It provides important algorithms like substructure search, SMILES, Gasteiger charges, QSAR descriptor calculation, 3D structure generation, 2D layout and rendering, many IO formats, atom typing, and more.
QuartzCrystal is an application for rendering Quartz compositions to QuickTime movies and image sequences. It supports third party plugins (using both the official and unofficial API), as well as unsafe patches. It also supports spatial supersampling (antialiasing) and temporal supersampling (motion blur).