Athanor MCP server
The Athanor MCP server lets any AI assistant that supports MCP convert, name, draw, check and screen structures, look compounds up, and build and edit a whole Athanor document, with Athanor's own engine. It is free and needs no account.
The Athanor MCP server lets an AI assistant use Athanor's own chemistry engine: it can convert a structure, name it, work out its properties, draw it in a journal style, check it for drawing mistakes, run the safety screen, look a compound up in Athanor's library, and turn a structure in perspective. It can also build a whole Athanor document call by call and hand it back as a file. It speaks the Model Context Protocol, so any assistant that supports MCP can use it.
Free for everyone, with no account. The server is at:
https://mcp-athanor.arbastro.com/mcpConnect your assistant takes a minute. The tools lists each one with a real example. To run it offline on your own computer, see the local MCP server.
What it can do
| Tool | What it does |
|---|---|
convert |
A structure to canonical SMILES, MOL V3000, MOL V2000, or XYZ with 3D coordinates |
name |
The systematic IUPAC name from Athanor's own rules, and the common name when the library knows it |
properties |
Formula, charge, exact and average mass, and descriptors |
depict |
An SVG drawing in a journal style (ACS Document 1996 by default) |
check |
Everything Athanor's editor would flag: valence, charge, stereo, each with a fix |
screen |
The safety screen as a synthesis target (controlled substances, CWC, Australia Group) |
library_search |
A compound by name, synonym or CAS number, from Athanor's library |
perspective_rotate |
The drawing turned in 3D and projected back, every R and S kept |
Every tool above takes a structure as SMILES, a molfile, an InChI or a common name.
Build a document
Twelve document_ tools work on an Athanor document, the same document the app edits. document_create starts one, empty or from a structure or an .athanor file, and returns a handle the other tools take. The assistant can then add structures, arrows and text, change atoms (element, charge, isotope) and bonds (order, wedge or hash), flip, rotate or turn in perspective, clean up, list problems, draw the page as SVG, and export it as .athanor, CDXML, MOL, SMILES or SVG. Open the .athanor file in Athanor to keep working on it.
Security and privacy
- The structure tools only read what you give them and return a result. They keep nothing.
- A document made with
document_createis a working copy held in the server's memory, not storage. It is deleted two hours after its last use, holds up to 2 MB, and is reached only by its handle. Export it to keep it. - Nothing is tied to an account, and nothing reaches your arbastro account or library.
- It needs no sign-in, so it never sees your arbastro account.
- Limits: 60 calls a minute per address, and structures up to 20,000 characters.
Coming next
Signing in with your arbastro account will add the tools that run on your plan: product prediction, retrosynthesis, Build mechanism and NMR prediction.
Troubleshooting
See MCP troubleshooting.
Is this helpful?
Last updated Nov 12, 2026
- Still stuck? Read the FAQ or contact support.
- Something wrong on this page? Tell us.
- For AI tools: llms.txt