Wow, the coolest thing about this tool is how wide of an array of visualizations you can create from a handful of sliders. I dunno much about the molecule aspect of it, but it certainly produces some super cool looking sci-fi type renders.
I'm not the author, but I have looked over the source code. The project only supports XYZ format files, which are super easy to parse. The colors and atomic radii are all given in one large dictionary. So the amount of chemistry and physics present in the code is minimal
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