The massXpert software package is a mass spectrometry environment for linear (bio-)polymers. It inherits all the innovations of GNU polyxmass. It allows the detailed definition of new polymer chemistries in the XpertDef module. These chemistry definitions are then used in the desktop calculator-like mass calculator (XpertCalc) and in the sophisticated polymer sequence editor and (bio-)chemical/mass spectrometric simulations module (XpertEdit). Available simulations include polymer and monomer chemical modifications, polymer sequence cleavage, gas-phase fragmentation, m/z ratio calculations, and more.
license (follow up)
And now I stumble on this:
The component classes are released in Java byte-code form for personal use, and NOT for commercial use. If you need the source code for personal use, you MUST sign a non-disclosure agreement and send it via fax at +39(0)11 3473522. If you want to use my program for making money, it will cost you 200 US$; in this case, or if you need a modified version, you should contact me.
(from one of the examples mentioned by the author of parent article: http://www.ilpiola.it/roberto/jchart/index_e.html).
How about Free Software?
It should not take more than one minute to find the licensing of a piece of software from that software's web page.
I could not find the license of the stuff on http://jdrawing.sourceforge.net ---even if it is said in the article that the material is in the public domain.
See http://www.polyxmass.org/ for an example :-)