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.
JFreeChart is a chart library for the Java platform that supports a wide range of charts including pie charts (2D and 3D), bar charts (horizontal and vertical, regular or stacked, with optional 3D-effects), line charts, XY plots, scatter plots, time series charts, high/low/open/close charts, candlestick plots, Gantt charts, Pareto charts, combination charts, and more. It is suitable for use in applications, applets, servlets, and JSP.