Chemdraw MCP Server

chemdraw-mcp

Chat → chemical structure. An MCP server for Claude Desktop: you describe a molecule, a reaction or a lab result in plain words, and it draws the figure — a print-ready PNG/SVG rendered locally with RDKit, plus an interactive preview inside the chat. "Draw aspirin" is already a complete command.

Built for pharmacy and chemistry students who spend too much time clicking hexagons. 20 tools cover what a report or a slide actually needs: structures, reaction schemes, step-by-step mechanisms, substrate-scope figures, TLC plates, titration curves, schematic spectra, substance data sheets, Ph.Eur. assay calculations and Anki decks.

What it costs you: one install command. Apache-2.0, no API key, no sign-up for the server, no ChemDraw licence — you need Claude Desktop and uv, everything else is fetched once. Rendering runs entirely on your machine; only name resolution and the database lookups reach the internet. ChemDraw CDXML is an optional extra format for people who want to keep editing there, never a requirement.

Example output

"Draw caffeine" — print-ready PNG, generated by generate_molecule:

"Show the Fischer esterification of ethanol with acetic acid" — generate_reaction renders the scheme with conditions above the arrow, live in the chat panel:

"Show the Fischer esterification mechanism step by step" — generate_mechanism renders curved electron-flow arrows in the interactive panel:

"Make a scope figure of my Suzuki couplings: 3a 92%, 3b 88% after 12 h, 3c 64% with ee 94% and dr 10:1, 3d 71%" — generate_scope_table sets the general equation with its conditions on top and the products below it, on a shared bond length and a shared caption baseline:

"Sketch the IR spectrum of ethyl acetate" — generate_spectrum (draws the peaks it is given, with per-type axis conventions):

"TLC of my esterification: educt at 0.30, product at 0.65, the co-spot shows both, some educt left" — generate_tlc draws the plate the lab report asks for, with mobile phase and detection as its caption:

"Show caffeine in 3D" — generate_3d embeds the molecule (ETKDG + force field) and opens a drag-to-rotate ball-and-stick viewer in the chat panel:

"What distinguishes ibuprofen from naproxen and ketoprofen?" — compare_molecules keeps the shared scaffold (MCS) neutral and highlights everything that differs:

"Titration curve of phosphoric acid with NaOH, phenolphthalein as indicator" — generate_titration_curve computes pH from the exact charge balance, with equivalence points, buffer points (pH = pKa) and the indicator band; its sibling generate_species_distribution shows which protonation species dominates at every pH:

"Create an Anki deck with important molecules and open it in Anki" — export_anki_deck builds a ready-to-import .apkg with rendered structures embedded; with the optional AnkiConnect add-on the cards land straight in the running Anki, no clicks:

Features

All 20 tools the server exposes. Files are written to ~/ChemDraw-Output/; every drawing tool also returns a live preview for the in-chat panel.

Structures and schemes

• generate_molecule — name/SMILES → 2D structure as PNG + SVG (optionally CDXML), with properties, functional-group detection and a Lipinski rule-of-five check
• batch_generate — a whole list of structures in one call
• generate_reaction — educts + products + conditions → reaction scheme with the conditions set above the arrow
• generate_mechanism — curved-arrow mechanisms (SN1, SN2, Fischer esterification) step by step
• generate_scope_table — the substrate-scope figure of the methodology literature: the general equation with its conditions on top, below it a grid of products, each with identifier ("1a") and yield ("78%") plus optional ee/dr/time. All structures share one bond length, all captions one baseline; an entry that cannot be resolved is reported, not fatal
• compare_molecules — 2–4 structures side by side, differences highlighted, shared scaffold (MCS) neutral
• generate_3d — rotatable 3D ball-and-stick conformer in the chat panel (ETKDGv3 + force field) plus SDF export

Lab results and analysis

• generate_spectrum — schematic spectra from peak lists (IR, NIR, Raman, UV/Vis, fluorescence, ORD, CD, ¹H/¹³C NMR, MS) with per-type axis conventions — draws given peaks, does not predict spectra
• generate_tlc — TLC plate sketch from Rf values: start line at the bottom, solvent front at the top, one captioned lane per application point (educt / reaction / co-spot), Rf annotated at every spot, mobile phase and detection printed as a caption — the sketch a lab report asks for
• generate_titration_curve — pH vs. titrant volume from the exact charge balance, with equivalence points, buffer points (pH = pKa) and indicator transition band
• generate_species_distribution — protonation species fractions over pH (Henderson–Hasselbalch) with pKa crossovers marked
• generate_calibration_curve — least-squares line through your standards, and the unknowns read back off it the way you would with a ruler. A sample outside the calibrated range is labelled as extrapolated rather than quietly reported; limits of detection and quantitation (DIN 32645) come along for the validation question

Bench maths (the number and the working — a lab report asks for both)

• calculate_solution — what to weigh (m = c · V · M), what you actually got, dilutions (C₁V₁ = C₂V₂ with the solvent volume spelled out), the mixing cross, and molar masses including hydrates like CuSO₄·5H₂O. Warns when the calculated portion falls below what an analytical balance resolves — then diluting a larger portion is the right move
• calculate_content — a content determination the way the protocol wants it: one content per measurement → Grubbs outlier test → mean, s, RSD → t-test against the declared content. Titration (with titer determination from reference titrations) and photometry, plus the fat characteristics (acid, saponification, ester and iodine value) and Karl Fischer water content as further methods
• calculate_ph — weak and strong acids and bases, buffers, and buffer recipes down to weighable masses. Solved through the exact charge balance with the textbook approximation printed beside it: where the two disagree, the approximation has lost its assumptions and says so. 10⁻⁸ M HCl comes out at pH 6.98, not 8

Substance data (online lookups)

• lookup — the facts as text, one topic per question: properties (formula, mass, CAS, InChIKey — the default), safety (GHS hazard statements, pictograms, signal word), physical (melting/boiling point, solubility, density), biochem (ChEBI classification plus related UniProt entries), pathway (metabolic pathways from KEGG)
• lookup_molecule_data — PubChem + GHS combined into one data sheet for the in-chat panel, structure included
• predict_spectrum — which IR bands a structure should show (with intensity and band shape), what a measured wavenumber could belong to, and how many ¹H signals to expect with their integral ratio. Deterministic, so it says what it cannot do: no chemical shifts in ppm, and diastereotopic protons are counted as one signal

Exam prep

• export_anki_deck — flashcards as a ready-to-import Anki .apkg: structure↔name drills (optionally reversed: one note, both directions), cloze/fill-in-the-blank cards, identity/detection reactions, spectrum band assignment — with rendered images embedded, per-card tags, Parent::Child subdecks; re-exporting a deck updates cards instead of duplicating them. Optional delivery straight into the running Anki via the AnkiConnect add-on. Pass curated_deck_id instead of your own cards for a small, formula-verified starter deck (classic analgesics, Ph.Eur. identity reactions)

Every tool belongs to one of five areas — draw, lab graphics, look up, calculate, Anki — and each says what it is not for, in both directions, so "draw aspirin" cannot end up in a substrate-scope grid and "what pH is my buffer?" cannot end up in a plotting tool. One tool sits outside them: save_png is the server half of the panel's export button, called when you click it, never on its own.

Two optional vault tools (search_vault, read_vault_entry) appear only when CHEMDRAW_VAULT_PATH is set; without it the server exposes exactly the 20 tools above.

Options on the drawing tools

• formats — ["png","svg"] by default; "cdxml" on top of that for generate_molecule, generate_reaction and batch_generate. The figure tools (generate_scope_table, generate_tlc, generate_spectrum) reject CDXML with a clear error instead of writing something meaningless.
• abbreviate_groups=True — draws common substituents as the labels chemists actually write: Ph, Bn, OMe, OAc, tBu, CO₂H, Boc, Ts, TBS. Worth it whenever cells get small — a scope figure stays readable because only what differs between the substrates remains spelled out. Available on generate_molecule, generate_reaction, generate_scope_table, batch_generate.
• render_style — a named look instead of a pile of render parameters, on the same four tools. "compact" (thin bonds, capped label size, tight margins) for a small figure in a two-column layout, "presentation" (double bond width, minimum font size, more padding) for a lecture slide, "grayscale" for black-and-white printing, where red and blue would otherwise become two indistinguishable greys. Empty means the default look, untouched.
• annotate_stereo=True — prints CIP descriptors (R/S, E/Z) on the 2D drawing (generate_molecule, batch_generate).

Installation

Three ways in; pick one. Options 1 and 2 merge into the config idempotently, back it up first and leave every other MCP server you have configured untouched. Afterwards restart Claude Desktop and ask: "draw caffeine".

Option 1 — clone the repo (recommended if you want to read or change the code; installs uv if missing, syncs dependencies, registers the server):

git clone https://github.com/jurimaxam-dotcom/chemdraw-mcp.git
cd chemdraw-mcp && ./install.sh

Option 2 — from PyPI, no clone (needs uv):

uv tool install chemdraw-mcp
chemdraw-install

chemdraw-install writes the Claude Desktop entry for you, using the absolute path of the installed launcher, and prints the start command it registered.

Option 3 — edit the config by hand. Add this to claude_desktop_config.json under mcpServers (macOS: ~/Library/Application Support/Claude/claude_desktop_config.json):

"chemdraw-tool": {
  "command": "/opt/homebrew/bin/uvx",
  "args": ["chemdraw-mcp"]
}

The one pitfall that breaks every manual install: Claude Desktop does not start MCP servers from a login shell — it uses the minimal GUI PATH. A bare "uvx" or "uv" cannot be resolved there, and the server fails to start without saying so. Always put the absolute path that which uvx prints on your machine into command. Options 1 and 2 do this for you.

Optional extras

• A Java runtime (e.g. brew install openjdk) lets OPSIN parse systematic IUPAC names offline — including ones no database indexes. Without Java the resolver simply continues with the PubChem/NCI online lookup.
• The AnkiConnect add-on lets export_anki_deck push cards straight into a running Anki. Without it you get the .apkg file and import it yourself.
• ChemDraw (macOS) is never required: request formats=["cdxml"] and open the file yourself if you want to keep editing there.

Something not working? Run the doctor

chemdraw-doctor                            # after "uv tool install chemdraw-mcp"
uv run chemdraw-doctor                     # in the cloned repo
uvx --from chemdraw-mcp chemdraw-doctor    # without installing anything

This is the first thing to try — it turns "the server does nothing" into a named cause. It checks the six things that make the server look dead in the chat (RDKit rendering, the Java/OPSIN runtime, the uv path, the Claude Desktop entry, the name databases, the output directory) and prints, for every problem, the exact command that fixes it. Three levels are distinguished: [OK], [LIMITED] (works, but restricted) and [FAIL] (broken); [NOTE] marks checks that simply do not apply, such as not having Claude Desktop installed. The exit code stays 0 as long as the server is usable, so it can run in scripts. (From a PyPI install the uv and Claude Desktop checks report [NOTE] — they relate to the repo installer.)

Limitations

Stated up front, so nothing surprises you in a report:

• Java is optional, and that has a price. Without a JRE, OPSIN is skipped and names are resolved online via PubChem/NCI — so name lookups need an internet connection and only work for names those databases index. SMILES input never touches the network.
• Spectra are schematic. generate_spectrum draws the peaks it is handed, with the right axis conventions for the spectrum type. It measures nothing and predicts nothing — if the peak values came from the chat rather than from your instrument, verify them before they go into a report.
• TLC intensity is a drawing hint. The optional intensity (0…1) makes a spot fainter on the sketch. It is not densitometry and carries no quantitative meaning.
• CDXML is a side path. It is written from the RDKit molecule and round-trip validated, but PNG/SVG are the primary outputs and the ones the pixel tests cover. CDXML is off by default and limited to structures and reaction schemes — TLC plates, scope figures and spectra reject it.
• 3D is one conformer. generate_3d embeds with ETKDGv3 and optimizes with MMFF (UFF as fallback). That is a plausible geometry for looking at, not a conformational search and not an energy statement.
• The ChemDraw bridge is macOS-only and needs a locally installed ChemDraw. Everything else works without it.

How it works

name / SMILES
   │
   ▼
resolver ──► OPSIN (systematic IUPAC names, offline) ──► PubChem / NCI (names)  ·  direct parse (SMILES)
   │
   ▼
RDKit 2D coordinates ──► validation (sanity, round-trip)
   │
   ├──► image_export   → PNG + SVG files          (primary, offline)
   ├──► svg_renderer   → interactive chat preview (MCP App resource)
   └──► cdxml_writer   → ChemDraw CDXML           (optional, on request)

Development

Python 3.11+, package manager uv.

uv sync                      # backend deps
cd chemdraw_tool/ui && npm install && npx playwright install chromium  # frontend, once
./test.sh                    # the gate: pytest + JS unit + headless-Chromium e2e

600+ tests, written test-first. The e2e test rasters a real RDKit SVG in headless Chromium and compares it against an exact pixel snapshot — the export path and the in-chat preview are held to the same drawing constants.

License

Apache-2.0 — see LICENSE. Copyright 2026 jurimaxam-dotcom.

Disclaimer: This is an unofficial, independent project, not affiliated with or endorsed by Revvity. ChemDraw is a trademark of Revvity Signals Software, Inc. This tool does not include or require ChemDraw; it can optionally export files in the open CDXML format.