chemdraw-mcp

chemdraw-mcp

Chat → chemical structure. An MCP server for Claude Desktop that turns molecule names or SMILES into publication-style 2D structure drawings — "draw aspirin" produces a print-ready PNG/SVG, rendered fully offline with RDKit. No ChemDraw required; ChemDraw CDXML is available as an optional extra format for users who want to keep editing there.

Built for pharmacy/chemistry students who spend too much time clicking hexagons: structures, full reaction schemes, step-by-step mechanisms, substance data sheets and Ph.Eur. assay calculations — straight from the chat, with an interactive preview panel rendered inline.

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:

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

"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 / export_curated_deck build 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

• generate_molecule — name/SMILES → 2D structure as PNG + SVG (optionally CDXML), with properties, functional-group detection and a Lipinski rule-of-five check
• generate_reaction — educts + products + conditions → reaction scheme
• batch_generate — a whole list of structures in one call
• generate_mechanism — curved-arrow mechanisms (SN1, SN2, Fischer esterification) step by step
• 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
• export_anki_deck — exam-prep 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
• export_curated_deck — small, formula-verified starter decks (classic analgesics, Ph.Eur. identity reactions)
• 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
• 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 (ETKDG + force field) plus SDF export; stereo descriptors (R/S, E/Z) available on 2D drawings via annotate_stereo
• lookup_* — substance data from PubChem, ChEBI, KEGG and UniProt (properties, GHS safety, pathways)
• calculate_validation — Ph.Eur.-style content determination with full calculation steps, t-test/F-test statistics
• Interactive in-chat UI (MCP App): hover atoms, inspect functional groups, export PNG with one click
• macOS ChemDraw bridge (optional): open any generated structure directly in ChemDraw via open_chemdraw_file

Installation

Option 1 — straight from PyPI (needs uv): add this to your Claude Desktop config (claude_desktop_config.json → mcpServers):

"chemdraw": {
  "command": "uvx",
  "args": ["chemdraw-mcp"]
}

Option 2 — one-command installer (clones the repo and registers the server in Claude Desktop automatically):

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

Both are idempotent and leave existing MCP servers untouched. Restart Claude Desktop, then ask: "draw caffeine".

Optional: with a Java runtime installed (e.g. brew install openjdk), systematic IUPAC names — including ones no database indexes — are parsed offline via OPSIN. Without Java the server falls back to the PubChem/NCI online lookup.

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

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

~400 tests, written test-first. The e2e test rasters a real RDKit SVG in headless Chromium and compares it against an exact pixel snapshot.

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.