ChemDraft MCP
A chemical structure editor with MCP, CLI and a skill: an agent draws molecules, computes properties and exports CDXML and SVG.
- 68 ★ on the repository
- Last commit
- Apache-2.0
Minimal access
Why this level
- The tools create files in an output folder and run local app programs.
Install
- Works in
Manual install
Download the ChemDraft release from GitHub Releases or chemdraft.ai, clone the repository and link `skills/chemdraft` into the agent skills directory. Register the `chemdraft-mcp` server and run `chemdraft --help`: all ten subcommands must appear.
Access and checks
How we reviewMinimal accessThe tool runs nothing and makes no network calls.
- The tools create files in an output folder and run local app programs.
This is third-party code. Review the repository files before installing.
What it does
ChemDraft is a free open-source chemical structure editor for macOS and Windows. Agents get three entry points: the `chemdraft` MCP server, a command line and the `skills/chemdraft` skill. MCP tools are `render_structure`, `render_grid`, `render_reaction`, `analyze_structure`, `name_to_structure`, `check_stereo`, `predict_nmr`, `export_structure`, `build_document` and `render_document`. The agent draws molecules and reaction schemes, builds structure grids for exams, converts names to structures through OPSIN, assigns R/S and E/Z, computes formula, masses, m/z, logP, TPSA and pKa, predicts NMR shifts and exports CDXML, SDF, MOL, PDF and SMILES. The skill demands that numbers and structures come from ChemDraft and not from model memory. Output goes to a separate folder and the user's open canvas is untouched.
Who it is for. Chemists, teachers and handout authors who need an agent to draw structures and compute properties without invented figures.
Good fit when
- An exam needs a grid of structures with answer options.
- A compound name has to become a structure with its formula checked.
- A reaction scheme is prepared for an article at one scale.
- Stereocentres and R and S configurations must be determined.
Not a fit when
- An edit of the user's open canvas is required: the tools run headless.
- The name is trivial and OPSIN cannot parse it.
- A structure is wanted from model memory without computation.
Example request
Draw the aspirin structure in document style, compute formula and exact mass and save SVG and CDXML.MCP
- Transport
- stdio
- Authentication
- not required
Limitations
macOS and Windows are targeted; Spin 3D in version 1.1.0 may not start on macOS 15 or earlier, with a fix promised in 1.1.1. PDF output currently misplaces atom labels and text, so every PDF should be viewed and SVG or PNG preferred for documents. The CLI needs Node.js, pnpm and a repository checkout, and MCP use requires registering the server on the machine that runs ChemDraft. OPSIN parses systematic names, not every trivial one.
How to disable. Remove the `chemdraft` server from the client MCP config and the link to `skills/chemdraft` from the agent skills directory. The app is removed like any macOS or Windows program.
FAQ
Which tools does the MCP server have?
`render_structure`, `render_grid`, `render_reaction`, `analyze_structure`, `name_to_structure`, `check_stereo`, `predict_nmr`, `export_structure`, `build_document` and `render_document`.
What if MCP is unavailable?
The skill falls back to the CLI through `pnpm chemdraft`, and if that is missing too it stops and points to the setup guide without substituting a guessed structure.
How should figures go into a document?
Use the `document` style and SVG: bond 14.4 pt, Arial 10 pt labels. Insert figures at natural size with no scaling.
Does the agent change my open drawing?
No. The tools create output in a separate folder and the app canvas stays as it was.
Is NMR prediction available?
Yes, `predict_nmr` returns predicted ¹H and ¹³C shifts and spectra; the app also has an optional official NMR plugin.
Discussion
No questions or reviews yet.
Related
MCP serversAn MCP server that links an agent to an open PyMOL: load structures, align, measure distances and render PNGs.
Plugin with 130-plus skills for atomistic materials research: relaxation, dynamics, DFT and structure databases through MCP.
A Claude Code agent for protein design: target research, antibody and nanobody generation, screening and candidate ranking.
Skills for computational chemistry: ASE, DFT codes, LAMMPS, DeePMD, RDKit, Open Babel and more, built for OpenClaw
MCP server for the ERD Editor: an agent adds tables, relations and indexes and the edits show up live on the canvas in VS Code, Obsidian and JetBrains
MCP server and CLI that turns paper text or data into academic figures, diagrams and plots
README in short
ChemDraft is described as a drawing application, yet it ships a CLI, an MCP server and a skill. The skill sets an order, MCP first and then the CLI, and two bans: no hand-drawn molecules and no numbers from memory.