Chemdraw MCP Server

live-chemdraw-mcp

MCP server that connects AI assistants to a live ChemDraw window on Windows via COM automation — draw, edit, and organize structures directly in the document you have open.

Capabilities:

• Insert & export — SMILES, name, molfile, InChI, CDXML; export as an image, structure text, or straight to the clipboard
• Substrate-scope tables — build a whole scope figure in one call, sized for journal columns, with labels/yields placed under each structure
• Shorthand groups — detect and contract functional groups inline (chemdraw_contract_group: Ph, TES, Boc, Ts... ~40 groups, SMARTS-matched via RDKit), or contract/expand a whole structure to a single label, including a one-call bulk expand across the whole document
• Figure layout — chemdraw_describe_canvas gives one semantic read of a whole page (structures, captions matched to their owners, panel boxes, overlap/overflow violations); chemdraw_arrange_in_region fits structures into a panel box in one call, captions riding along, nothing ever rescaled; chemdraw_get_layout/chemdraw_move_objects for raw-geometry plans with automatic collateral-movement detection
• Chemistry QC — read/set stereochemistry (wedge/hash, "and1"/"or1" enhanced-stereo grouping), duplicate detection, valence warnings, IUPAC naming, HRMS text generation
• Publication tools — journal style presets, reaction schemes, and derivative-library enumeration with RDKit-computed properties
• Annotations — mechanism/reaction arrows (chemdraw_make_arrow: solid/ hollow/angle heads, single-barb "fishhook" electron-pushing arrows, crossed-out "no-go" pathway markers, dipole markers) and symbols (chemdraw_make_symbol: racemic/absolute/relative stereo-descriptor labels; lone pairs/radicals/daggers also place but currently render at a tiny, apparently unscalable default size — see the tool's own docstring). Isotope labeling (chemdraw_edit_atom(..., isotope=13, ...)) survives export as real isotope notation, not just a ChemDraw-display label. Limitation: arrows/symbols are free-floating — moving a nearby structure with chemdraw_move_objects/chemdraw_transform will NOT carry them along, the same class of gap already documented for captions below. Curved/arc arrows and true double-object ⇌ equilibrium-arrow pairs aren't supported yet — both were probed live and need more COM investigation before a design commitment (see docs/com_typelib/)
• Polymer repeat-unit brackets (chemdraw_make_bracket: square/curly/ round glyph, SRU/monomer/copolymer/crosslink/... usage with ChemDraw's own auto-generated abbreviation label — "n"/"mon"/"xl"/etc.) wraps a structure (or an explicit rectangle) with an opening + closing bracket pair. Limitations, confirmed live, not solved: RepeatCount/SRULabel/ ComponentOrder cannot be set via COM at all (both get and put reliably raise); the pair's mirrored orientation ("[...]" vs two identically- oriented marks) is unreliable once a second bracket exists in one automation session — always check the exported image; brackets are purely decorative (not bound to real atom/bond membership despite ChemDraw exposing InsideAtoms/ContainedAtoms/CrossingBonds properties — confirmed these don't reflect true geometry) and share the same free-floating/doesn't-move-with-the-structure limitation as arrows/ symbols above
• TLC plates (chemdraw_make_tlc_plate: rectangular plate outline with labeled Rf-spot lanes for reaction-monitoring figures) — a spot's vertical position is driven entirely by its rf (0-1) property, which ChemDraw itself interpolates between the plate's origin/solvent-front lines (confirmed live via measured screenshot pixel positions, within ~1% of the expected fraction) — no manual position math needed. Supports show_rf (auto "Rf = 0.NN" label), filled/bold/dashed (a hollow dashed-outline circle is visually confirmed distinct from a solid dot), and an experimental tail (comet-tail smear) whose visual effect could not be confirmed at available screenshot resolution. Hard limit, confirmed live and enforced by the tool (raises before any COM call): a single lane can hold at most 2 spots — ChemDraw's own AddSpot is a silent no-op past that, with no error at all. Same free-floating/ doesn't-move-with-the-structure limitation as arrows/symbols/brackets above.

This README covers setup and usage — not a per-tool reference (each tool's exact parameters, return shape, and usage notes live in its own docstring, visible to any MCP client via its tool listing) and not internal architecture or ChemDraw-COM implementation notes (see AGENTS.md for those — useful reading whenever you're looking at the source, whether you're debugging something, curious how it works, or extending it, not only for the last one).

Built and validated against ChemDraw 26 (Revvity) on Windows 11 / Python 3.14.

This is an independent, unofficial project. It is not affiliated with, endorsed by, or supported by Revvity or PerkinElmer. "ChemDraw" is a trademark of its respective owner; it's referenced here only to describe compatibility. You'll need your own licensed copy of ChemDraw to use this.

Setup

cd live-chemdraw-mcp
python -m venv .venv
.venv\Scripts\python -m pip install pywin32 rdkit "mcp[cli]" pytest

Register in %APPDATA%\Claude\claude_desktop_config.json (replace C:\\path\\to\\live-chemdraw-mcp with wherever you cloned it):

"mcpServers": {
  "chemdraw": {
    "command": "C:\\path\\to\\live-chemdraw-mcp\\.venv\\Scripts\\python.exe",
    "args": ["C:\\path\\to\\live-chemdraw-mcp\\server.py"]
  }
}

Restart the Claude desktop app. No ChemDraw-side installation is needed — the server attaches to a running ChemDraw (or launches one) over COM.

Testing

• .venv\Scripts\python -m pytest — unit tests for the pure logic, all running against fakes/fixtures with no live ChemDraw required: layout math, style presets, HRMS text, dedup, numbering, diff, RDKit enumeration, CDXML parsing/graph-building, substructure/SMARTS matching, canvas/caption classification, reagent-text subscript formatting, and bond-splitting, plus connector-internals coverage for the COM worker's timeout/nudge state machine and targets.py's target-resolution and stale-cache-retry logic.
• .venv\Scripts\python test_smoke_visual.py — live smoke test; drives a visible ChemDraw window end to end. Watch it run.

Development

Package layout, and the ChemDraw COM quirks this connector was built around (COM crash traps, silent no-ops, timing/caching gotchas) — see AGENTS.md whenever you're looking at the source, not only if you're extending it. None of it matters if you're just talking to the server through Claude (that's what the rest of this README covers), but it's the fastest way to understand why the code is shaped the way it is if you're reading it for any reason.

Troubleshooting

• In-progress canvas text edit / text tool left active — puts ChemDraw's UI thread in a modal loop that blocks COM. The connector auto-recovers: on a timeout it posts an Escape to ChemDraw's focused control via Win32 (com/nudge.py, a channel separate from the blocked COM one) and retries, so a stray edit no longer wedges the session. Only if that fails do you see the "not responding" error below.
• "ChemDraw is not responding to automation" — a modal dialog is open (or an edit the auto-nudge couldn't clear); dismiss the dialog or press Escape / click empty canvas, then retry.
• "ChemDraw stopped responding during this operation" — ChemDraw crashed and was relaunched; recover unsaved work from the automatic backups at %LOCALAPPDATA%\chemdraw-mcp\backups.
• Tools report structure ids like claude-a1b2c3d4; if one "no longer exists," the structure was deleted/rebuilt — ask Claude to call chemdraw_get_document_state to re-inventory the page.

License

MIT