Aha! Success, thanks to Rajarshi

So:
it sortof works...

The missing piece of the puzzle was this line:

GeometryTools.scaleMolecule(molecule, getPreferredSize(), 0.9);

where getPreferredSize() is just a container call, and the 0.9 is a scale factor. This is too magical for my tastes. You apparently don't have to scale benzene, but you do have to scale pyridine!

Comments

Christoph said…
http://progz-jchem.blogspot.com/2007/07/innerbonds-including-funky-colors.html
shows that this has all been working once :-)