YAJOGLB (Yet Another Java OpenGL Binding) allows Java programmers to access their native OpenGL library. The library is implemented using Java's JAWT to access the native windowing system, along with JNI calls to OpenGL. Programs using the binding must use the shared library provided, since this is not a pure Java library.
The Deimos Project is a 3D space combat simulator and modular game library collection. It includes a 3D modeler designed with a programmer's needs in mind. It allows you to construct 3D models by writing Java source code. All you need to design a model is a computer, some graph paper, and a pencil. The modeler's internals function as a simple OpenGL scene graph API, without preventing the use of low-level OpenGL commands. For storing settings and other hierarchically-representable data, the project provides a Hierarchy library that stores data atomically using XML. It also features a timing library, a game object container system, and many other features.
BRL-CAD is a powerful constructive solid geometry solid modeling system that includes an interactive geometry editor, ray-tracing support for rendering and geometric analysis, path-tracing for realistic image synthesis, network distributed framebuffer support, and image and signal-processing tools.
Equalizer is middleware for creating and deploying parallel OpenGL-based applications. It enables applications to benefit from multiple graphics cards, processors, and computers to scale rendering performance, visual quality, and display size. An Equalizer-based application runs unmodified on any visualization system, from a simple workstation to large scale graphics clusters, multi-GPU workstations, and Virtual Reality installations.
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.
Jmol is a Free, Open Source molecule viewer and editor. It is a collaboratively developed visualization and measurement tool for chemical scientists. Jmol is an active project, and there are new features being added to it on a daily basis. Users are encouraged to modify it to fit their needs and to contribute their changes to the project.