Live 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:

image, structure text, or straight to the clipboard

• Insert & export — SMILES, name, molfile, InChI, CDXML; export as an

for journal columns, with labels/yields placed under each structure

• Substrate-scope tables — build a whole scope figure in one call, sized

(chemdrawcontractgroup: 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

• Shorthand groups — detect and contract functional groups inline

whole page (structures, captions matched to their owners, panel boxes, overlap/overflow violations); chemdrawarrangeinregion fits structures into a panel box in one call, captions riding along, nothing ever rescaled; chemdrawgetlayout/chemdrawmove_objects for raw-geometry plans with automatic collateral-movement detection

• Figure layout — chemdrawdescribecanvas gives one semantic read of a

enhanced-stereo grouping), duplicate detection, valence warnings, IUPAC naming, HRMS text generation

• Chemistry QC — read/set stereochemistry (wedge/hash, "and1"/"or1"

derivative-library enumeration with RDKit-computed properties

• Publication tools — journal style presets, reaction schemes, and

hollow/angle heads, single-barb "fishhook" electron-pushing arrows, crossed-out "no-go" pathway markers, dipole markers) and symbols (chemdrawmakesymbol: 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 (chemdraweditatom(..., 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 chemdrawmoveobjects/chemdrawtransform 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/comtypelib/)

• Annotations — mechanism/reaction arrows (chemdrawmakearrow: solid/

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

• Polymer repeat-unit brackets (chemdrawmakebracket: square/curly/

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

• TLC plates (chemdrawmaketlc_plate: rectangular plate outline with

Shortened. The full README is on GitHub.