Aha! Success, thanks to Rajarshi

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!


Christoph said…
shows that this has all been working once :-)