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I tried doing this a little while ago, but couldn't get OpenGL to render properly to an image, so I put it on hold. I'll take another look it it.
In the meantime, you can do a crude version of this by holding the suspend and home buttons on the iPad at the same time, which takes a snapshot of the screen. You could then crop the molecule portion of the screen and use Instant Alpha in Keynote to remove the black background.