5 ms·

The caffeine example is laughable. https://penrose.cs.cmu.edu/try/?examples=structural-formula/molecules/caffeine https://penrose.cs.cmu.edu/try/?examples=struc

• xigoi 3y ago
  What is laughable about it?
  • jugoetz 3y ago
    It's completely, utterly wrong. To point out just one problem, the two central rings should be planar. Good thing they picked this one to show in the landing page carousel. That example was enough for me to close the page again.
  • shrx 3y ago
    The displayed structure has nothing to do with how it really looks like [0]. It seems they just used a naive algorithm for automatic atom placement with a goal to minimize overlaps between the atoms. [0] https://en.wikipedia.org/wiki/Caffeine https://en.wikipedia.org/wiki/Caffeine
    • bmitc 3y ago
      That naive algorithm isn't even good since it can clearly be laid out without any edge crossings.
  • sestep 3y ago
    By the way, just for clarity, note that the comments in this subthread were written before we updated the random seed for that example to result in a much better diagram: https://github.com/penrose/penrose/commit/134533830dab25642a153b60112f6f310622a247 https://github.com/penrose/penrose/commit/134533830dab25642a...
• sestep 3y ago
  Yeah :( To be honest, I think we got a bit overeager about this one, since none of us on the project are chemistry experts. At least for the front page, we should probably replace that with a different diagram from our registry. I think this is actually a fairly deep issue with our approach where we try to express everything in terms of numerical optimization, pairwise energies on shapes, etc. Especially since Style is not a Turing-complete programming language and also doesn't support calling out to existing libraries written in, e.g., JavaScript, there isn't a way to do actually-correct layout of the caffeine molecule, so instead we do the "lazy" thing and just try to make the atoms not overlap. To anyone who actually knows what a caffeine molecule looks like, obviously this looks ridiculous. In the same vein as the other HN comment about separation of substance and style, I think we could do a much better job on chemistry diagrams by actually placing the atoms where they should be in 3D space, then projecting onto a 2D SVG diagram. To illustrate what I mean, consider this other diagram in our registry, showing a methane combustion reaction: https://penrose.cs.cmu.edu/try/?examples=structural-formula/reactions/methane-combustion https://penrose.cs.cmu.edu/try/?examples=structural-formula/... As you can see on that example, the methane molecule looks weird because all the bonds are drawn "below" the carbon atom, and the carbon dioxide molecule is all bent out of shape. In contrast, by just writing a bit of Python code, you can make the diagram both easier to specify https://github.com/samestep/diagrams/blob/3d7fe855b3a9634d17b2ddb54819c192f8f23454/combustion.py#L382-L387 https://github.com/samestep/diagrams/blob/3d7fe855b3a9634d17... (compared to the 70-line Penrose Substance file) and also more correct: https://raw.githubusercontent.com/samestep/diagrams/2c8fb3345cf34331abe87b8010b04352c0bdf7d9/combustion.svg https://raw.githubusercontent.com/samestep/diagrams/2c8fb334... I think that a general-purpose text-based diagramming tool needs to support a variety of different layout engines.
  • shrx 3y ago
    The combustion diagram does look nicer, since it doesn't contain complex overlaps of bonds. However, it's still physically inaccurate. The carbon dioxide molecule should be linear, for example. Molecules have atoms arranged following very specific rules arising from quantum mechanics and the theory of molecular orbitals, you can't solve this with a graph optimization algorithm.