Hacker News Reader

Comment by shrx | Hacker News Reader

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

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/...

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/3d7fe855b3a9634d17... (compared to the 70-line Penrose Substance file) and also more correct: 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.

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.

Could you clarify what you mean when you say "it's still physically inaccurate" and "The carbon dioxide molecule should be linear"? In my post I was specifically contrasting the diagram in the Penrose registry (in which the carbon dioxide molecule is incorrect as you point out) with another version of that diagram which I generated using Python (in which the carbon dioxide molecule is correct). Did you only look at the one and not the other, perhaps?

What is laughable about it?

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.

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

That naive algorithm isn't even good since it can clearly be laid out without any edge crossings.

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/134533830dab25642a...

Reply on news.ycombinator.com