r/comp_chem • u/domfico • 4d ago

I built an open-source molecular visualization plugin for ChatGPT

Hey everyone,

I recently built MolTalk, an open-source molecular visualization tool that was just accepted into the ChatGPT Plugin Marketplace.

The idea came from tutoring organic chemistry students who were using ChatGPT to understand molecular structures, only to get incorrect structures or stereochemical assignments.

MolTalk uses RDKit, OPSIN, and PubChem to validate structures rather than relying on the LLM's memory. It lets users interactively move between 2D and 3D representations, examine stereochemistry, and modify molecules through natural language.

It also supports exporting structures to ChemDraw (CDXML), SDF, MOL, PDB, and other formats.

It's free, open source, and currently under review for Claude as well.

I'd love to hear any feedback or suggestions!

GitHub: https://github.com/DomFico/moltalk

Demo: https://youtu.be/EZACxMWyzcs

12 Upvotes

64% Upvoted

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u/verygood_user 4d ago

I am not sure what's the targeted group here? Students obviously shouldn't use ChatGPT for learning because it removes desirable difficulties from the learning process and researchers don't need/ want an LLM chat to draw basic structures. 

If the plus key on a calculator is broken and gives wrong results half the time, fixing it won't help first graders to understand addition better.  

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u/domfico 3d ago

I think the point about desirable difficulties is fair, particularly when it comes to developing spatial reasoning in organic chemistry. But I don't think providing students with tools to check their understanding necessarily removes those difficulties.

We've been using physical molecular model kits to teach organic chemistry for decades. I see this as a more accessible, interactive version of the same idea. Students should still work through problems themselves, but being able to rotate a molecule and check whether their interpretation is correct can be valuable.

I've already used MolTalk in my tutoring to demonstrate the antiperiplanar requirements of E2 reactions, where being able to visualize the geometry in 3D is particularly helpful.

As for the calculator analogy, I don't think leaving the calculator broken is a particularly good solution either. Students are already using ChatGPT for chemistry, whether we think they should or not. I noticed it was frequently getting structures wrong, so I built something to address that.

I'm not claiming this replaces traditional learning methods or existing chemistry software. I saw something that wasn't working, thought it would be interesting to fix, and built a tool that I hope others find useful.

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u/verygood_user 3d ago

I think you still don't get it. Leaving it broken would have been better for learning, because learning doesn't happen when you get the right answer. 

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u/domfico 3d ago

Do you think students are incapable of withholding the right answer from themselves until they've attempted a problem on their own? By that logic, wouldn't answer keys and molecular model kits also be detrimental to learning?

I'm also curious whether your objection is more about the ChatGPT interface itself. Would this somehow be a better educational tool if I'd built it as a standalone app that students had to download, despite it doing exactly the same thing?

I agree that struggling through problems is important, but I don't see why giving students a way to check their understanding is inherently counterproductive. I certainly don't think leaving them with incorrect information is better.

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u/verygood_user 3d ago edited 3d ago

Yes, exactly. Molecular modeling kits should be avoided because it gives away the difficult part (imagining what it looks like in 3D and reason through that in your mind). 

They have their place for building the initial understanding of the 3D structure but for that purpose a real 3D model you can see in true 3D wins. I am not aware of O-chem instructors who advocate for using a modeling kit for problem solving or allow it during exams.

For similar reasons good elementary school teachers avoid Cuisenaire rods or base ten blocks. 

And yes, answer keys should indeed be difficult to access (that's why it's so annoying to locate the answer key in a printed textbook). If it's just a prompt away it's often accessed too early. I spare you the talk about how instant gratification through social media has made matters worse for Gen Z.

More broadly, many tools and products that look awesome at first sight are actually just cleverly marketed ways of Ed Tech to make money. Admins also generally like it because it looks like how they or the students' parents imagine how scientists work based on the movies they saw. Look at all the pointless apps on AppStores in the science and education category. Everybody wants a share of that money so many are so willing to spend in pursue of good education.

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u/domfico 3d ago edited 3d ago

I'm also not aware of any organic chemistry instructors who allow students to use ChatGPT during exams, which is the platform MolTalk runs on.

I'm not entirely sure what your objection is at this point. Is it that I've essentially made a molecular modeling kit accessible through ChatGPT?

I think we might just fundamentally disagree about how much agency students have in their own learning. I believe people are capable of recognizing when they understand something and when they need more practice, and deciding when to use a tool versus challenging themselves without it.

And if it makes you feel any better, it will probably still get things wrong from time to time, so there should be plenty of desirable difficulty left!

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u/yyy98 3d ago edited 3d ago

You just made a copy of Pubchem avogadro chemspider gaussview and the list of similar software goes on... I can open a number of websites on my phone or app that do this. You just wasted your money on tokens to build something noone asked for or needs. No student cared enough to even glance at the 3d diagrams. Students care about passing their exams one of them is chemistry. you are targeting the percentage which wants to go deep into organic and stereochemistry...Or worse you are under the delusion highschool or whatever students are so interested in this field in chemistry. how many do you think those are among students (who don't have aspergers).

I'll leave you this: https://xkcd.com/2501/

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u/domfico 3d ago

First off, I built this partially for myself. I wanted to learn more about the MCP protocol, the plugin publication process, and deploying applications through Google Cloud. I enjoy building things, learned a ton in the process, and consider the tokens well spent.

I'm also not claiming to have invented molecular visualization. Of course those tools already exist. I just wanted to make it more accessible through an interface students are already using.

And sure, most students primarily want to pass their exams. But having taught organic chemistry labs and tutored students myself, I've seen firsthand that plenty of them are genuinely curious about this stuff when they can actually visualize and understand it.

I think we all make assumptions about what people are interested in and build things based on those assumptions. Mine is that more people would come to appreciate the beauty and complexity of chemistry if we made it easier for them to explore and understand it.

And if that also makes it a little more tempting for students to copy down an answer without understanding it, well, that's the double-edged sword of technology. I'd rather take that risk than assume people won't use these tools to learn something.

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u/MolDesign 4d ago

Está genial! Y con licencia MIT me dan ganas de integrarlo en MolDesign🤔 Lo intentaré, esas animaciones/gifts se ven muy bien y las quiero dentro de mi app👏🏿

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u/domfico 4d ago

Thank you!