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.
KOJAC is a set of Java classes implementing optical elements and optics laws in order to build and simulate optical systems. It is also aimed at being a demonstrator of optics for educational purposes. Optical systems are composed of objects with defined properties that may be modified by the user through the applet's buttons and scrollbars. Such basic devices are lenses, apertures, interfaces, and may be themselves composite sets of other elements. KOJAC is able to do exact raytracing in 3 dimensions, taking into account the wavelength of the rays, and simulating real materials.
JOELib/JOELib2 is a cheminformatics library which supports SMARTS substructure search, descriptor calculation, processing/filtering pipes, and conversion of different chemical file formats. It is written in 100% pure Java, and interfaces to external programs (e.g. Ghemical) are available.
Koalog Constraint Solver is a powerful constraint solver written in Java. It provides cutting-edge technology for solving satisfaction and optimization problems, including scheduling, time-tabling, resource-allocation, puzzles (sudoku.koalog.com is powered by Koalog Constraint Solver), and configuration (Koalog Configurator is powered by Koalog Constraint Solver).
Ptplot is a set of Java classes that can be used as an applet or an application for graphing datasets. It reads PlotML, binary, or ASCII data, is autoranging, and automatically or manually labels axes and tick marks. It can plot live, animated plots and provides zooming. It also includes Bourne shell scripts and DOS .bat files that can be used as a replacement for xgraph, the X11 graphing tool.