> 1) automatic conversion 2D to 3D
> 2) minimal molecular mechanics support

That's courageous, Bob!
That feature would be a dream for me. For that, I am using 
ChemSketch, which is a Windows-only program. I don't think you can 
get any code out of it, as it is a commercial venture (but they offer 
the freeware version which I use).


> d) What people know about code that is already out there in any language 
> that we could adopt.

Avogadro includes a molecule builder and "cheap" 3D optimization 
(which can run on-the-fly as you draw the model by dragging new 
atoms):
http://avogadro.openmolecules.net/wiki/Main_Page
Donald and Marcus, two of the main developers, were present at the 
Runcorn meeting last week.
That could be a good source of code.


> e) Who wants to help.

Sorry, I can't do any Java coding. But do count on me for testing



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