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Solid little puzzle game, easy to learn with great presentation. A very difficult genre to pull off in such restrictive circumstances.
I'd love to see the addition of chirality or something that takes into account the rotation/pairing of the structures. I started ignoring the pretty animations pretty soon after I noticed the letters were the only thing I needed to look at.

You're right. The animation are here for the "style", but you can't play using it. That's why I added the letters.