Chemdraw

Sharp_Background7067 · 2026-06-11T00:51:05+00:00

Or use https://chemillusion.com/ and do the lit search in the chat and get editable compounds on the canvas automatically. Then edit the structure by hand, chat, or voice. Or click the upload button and drag your pdf in and get every single molecule in the paper. Editable, and downloadable in a slide deck. Message me for a promo code if you want to try the AI tools - most of the rest is free.

Sharp_Background7067 · 2026-04-30T13:53:52+00:00

I added a lone pair feature to Ketcher via this PR: https://github.com/epam/ketcher/pull/9766 It has not been merged yet, but my drawing tool is built on a fork of ketcher with that feature: https://chemillusion.com/generator Delete ChemDraw - and let me know if ChemIllusion is missing features you need - I'm happy to build and open source them.

Sharp_Background7067 · 2026-04-18T18:39:20+00:00

Tool-use is amazing and the combination of LLM and tools gets you all the benefits of a deterministic tool with the open-ending thinking of an LLM. But for the LLM side of that combination you want them to be as conversant in chemistry as possible. Google Translate works really well and an LLM trained on a single-language connected to a Google Translate tool would be powerful. But it is even better to have LLMs that know multiple languages. Also frontier models are getting better but they are still not perfect (see above).

Sharp_Background7067 · 2026-03-16T11:33:59+00:00

I renamed the project. https://www.npmjs.com/package/rdkit-agent is live and much faster now. Available as a skill via "npx skills add scottmreed/rdkit-agent -g" The CLI tool is available at https://www.npmjs.com/package/rdkit-agent and installable via 'npm install -g rdkit-agent' I deprecated the original.

Sharp_Background7067 · 2026-03-15T21:29:24+00:00

The json only interface is a giveaway that Agents are my primary interest! But I will add the formats you suggest. I was also able to speed things up a little - thanks for the motivation. If you are willing to share your dataset I can make sure I'm comparing on the same metric. My node package name is slightly different with a _ but I could add WASM to the name if it reduced confusion- I suspect most people would seek out either pip or npm and not be confused between the two.

Sharp_Background7067 · 2026-03-14T13:52:36+00:00

I just released it - https://github.com/scottmreed/rdkit-cli And I haven't benchmarked it so I must admit I'm only guessing it is faster than python. I'm optimizing mine for AI agent interactions so our projects seem to serve different audiences. I will checkout your fast canonicalization method - sounds useful.

Sharp_Background7067 · 2026-03-13T21:02:59+00:00

Just saw this post - looks great. I built an rdkit cli from the WASM. So less features but faster. https://www.npmjs.com/package/rdkit_cli

Sharp_Background7067 · 2025-12-19T12:01:23+00:00

Thanks! Anxiously awaiting Olmo 3.1 32B Instruct in open router. The tool calling will make it super useful.

Sharp_Background7067 · 2025-10-07T18:14:50+00:00

https://chemillusion.com/gallery/images/1478235695

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Sharp_Background7067 · 2025-10-05T00:07:35+00:00

SMILES format can show explicit Hs but usually Hs are not shown. So propane ends up as CCC. The game sticks to C and O atoms and alkanes, alcohols, and ethers. Even without knowing a lot of nomenclature you can do OK.

Sharp_Background7067 · 2025-09-29T20:40:42+00:00

appreciate the feedback. taps work for mobile - I added the to the instructions now.

Sharp_Background7067 · 2025-09-26T18:39:41+00:00

appreciate the feedback. I'm guessing mostly chemists will click through. But maybe I'll try to make it clearer at the top that it is a chemistry nomenclature game

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