Interesting! You'd think this is something that would have been worked out -- or is this not an intended use of RDKit? Either way, you'd also think that if OpenAI meant for this to be useful, they would have ironed out that kink when they integrated it into ChatGPT - ThreadSky

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brittanytrang.com • 11 days ago

Interesting! You'd think this is something that would have been worked out -- or is this not an intended use of RDKit?

Either way, you'd also think that if OpenAI meant for this to be useful, they would have ironed out that kink when they integrated it into ChatGPT

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drchrispook.bsky.social•11 days ago

Oh, it's absolutely what rdkit is meant to do. But it's a massive package and written for free by a condition of mostly end users. And, as with any Python library, there's several different ways to do everything and each has it's own bugs and glitches.

drchrispook.bsky.social•11 days ago

Consortium not condition

supersciencegrl.co.uk•10 days ago

It's an issue I've run into at work recently. The fact is, it's very hard to come up with a good algorithm for making any structure look pretty in 2D. Whatever the proprietary algorithm in ChemDraw is, it does it excellently (inb4 people cherry-picking things that even that can't do well)

supersciencegrl.co.uk•10 days ago

Also tbf, I would say that as "things that rdkit is meant to do" go, prettiness is a thing but not super high on the list. Most of the time, people tolerate lack of structure prettiness in software (such as med chem tools and inventories) without even thinking about it, as do chemoinformaticians

supersciencegrl.co.uk•10 days ago

Sorry, that wasn't meant to be so authoritative; I did not design rdkit 😂😂

drchrispook.bsky.social•10 days ago

Very much agree. Pretty it is not. Functional, it is (with a bit of work). If I want pretty molecules I export them to SVG. I tried to work out how to do that directly from rdkit. It's one of the buggy things I ran into.

drchrispook.bsky.social•10 days ago

One of the coolest things it does is align molecules on a common substructure. It's so useful if you want to visualise differences.
https://www.rdkit.org/docs/GettingStartedInPython.html#working-with-2d-molecules-generating-depictions

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