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Synthetica is a Java program that is used to synthesize, analyze and simulate spatial linkages. Its' open architecture allows advanced users to add Java code to the system. It runs on Win32, MacOSX, Linux, Solaris and uses JOGL (OpenGL) for 3d graphics.
ChemVisio is software which might be useful for educational purposes (non-organic chemistry, crystallography etc.). It might be a good visualization support for all people who need better illustrations than that you could see in books.
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The application included in this project provides some facilities in processing results of molecular dynamic modeling and close experiments.