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.
aiSee reads a textual, easy-to-read, and easy-to-learn graph specification and automatically calculates a customizable graph layout. This layout is then displayed, and can be printed or interactively explored. aiSee features 15 basic graph layout algorithms (including force-directed layout), recursive subgraph nesting, fish-eye views, and an animation interface. It has been optimized to handle huge graphs automatically generated by applications (e.g. compilers).
Mage is a 3D vector display program that shows "kinemage" graphics used in both teaching and research, in applications ranging from estuary ecology to X-ray crystallography model quality assessments. It displays the 3D relationships between data in an interactive environment, which facilitates both open-ended exploration and structured presentation. It includes many tools for on-screen measurement, construction, and editing of the display objects, and can write either kinemage output or various types of 2D images.