Fungimol is a extensible system for designing atomic-scale objects.
This is release 0.1.1 of Fungimol. The low release number means that is has obvious known bugs, the API for plugins is likely to change, and even the URL for this document is likely to change. However, when it is used it seems fairly stable; I don't know any way to crash it right now, and there were no crashes in the recent past that were not firmly connected in my mind to subsequent bug fixes.