chemdraw-mcp

# chemdraw-mcp

<!-- mcp-name: io.github.jurimaxam-dotcom/chemdraw-mcp -->

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**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: **structures, reaction schemes, curved-arrow mechanisms and
substrate-scope figures** — the drawing a report or a slide actually asks for.

For the same lab report, also:

| | |
|---|---|
| **Lab graphics** | TLC plates, titration curves, schematic spectra, calibration lines |
| **Look up** | PubChem/GHS data sheets, expected IR bands |
| **Bench maths** | weighing and dilutions, Ph.Eur. content determination, pH and buffers |
| **Exam prep** | Anki decks with the structures rendered in |

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](https://docs.astral.sh/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.

<p align="center"><img src="https://raw.githubusercontent.com/jurimaxam-dotcom/chemdraw-mcp/main/assets/demo.gif" alt="Live demo: 'Draw Caffein' renders an interactive structure panel in Claude Desktop" width="560"></p>

## Example output

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

<p align="center"><img src="https://raw.githubusercontent.com/jurimaxam-dotcom/chemdraw-mcp/main/assets/caffeine.png" alt="Caffeine structure, rendered by generate_molecule" width="420"></p>

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

<p align="center"><img src="https://raw.githubusercontent.com/jurimaxam-dotcom/chemdraw-mcp/main/assets/reaction-demo.gif" alt="Reaction scheme with conditions appearing live in the chat panel" width="640"></p>

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

<p align="center"><img src="https://raw.githubusercontent.com/jurimaxam-dotcom/chemdraw-mcp/main/assets/mechanism-demo.gif" alt="Step-by-step Fischer esterification mechanism with curved arrows in the chat panel" width="560"></p>

*"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:

<p align="center"><img src="https://raw.githubusercontent.com/jurimaxam-dotcom/chemdraw-mcp/main/assets/scope-suzuki.png" alt="Substrate scope figure: Suzuki coupling equation with conditions on top, below it four biphenyl products labeled 3a to 3d with yields and ee/dr notes" width="760"></p>

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

<p align="center"><img src="https://raw.githubusercontent.com/jurimaxam-dotcom/chemdraw-mcp/main/assets/ethyl-acetate-ir.png" alt="Schematic IR spectrum of ethyl acetate with labeled bands" width="560"></p>

*"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:

<p align="center"><img src="https://raw.githubusercontent.com/jurimaxam-dotcom/chemdraw-mcp/main/assets/tlc-esterification.png" alt="TLC plate sketch with four lanes: educt at Rf 0.30, reaction lane with a faint educt spot and the ester at 0.65, co-spot lane with both, reference lane at 0.65" width="520"></p>

*"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:

<p align="center"><img src="https://raw.githubusercontent.com/jurimaxam-dotcom/chemdraw-mcp/main/assets/3d-demo.gif" alt="Rotating 3D ball-and-stick caffeine model inside the concave viewer" width="560"></p>

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

<p align="center"><img src="https://raw.githubusercontent.com/jurimaxam-dotcom/chemdraw-mcp/main/assets/compare-profens.png" alt="Ibuprofen, naproxen and ketoprofen side by side with differences highlighted" width="680"></p>

*"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:

<p align="center">
  <img src="https://raw.githubusercontent.com/jurimaxam-dotcom/chemdraw-mcp/main/assets/titration-phosphoric.png" alt="Titration curve of phosphoric acid with three equivalence points and phenolphthalein band" width="420">
  <img src="https://raw.githubusercontent.com/jurimaxam-dotcom/chemdraw-mcp/main/assets/species-phosphoric.png" alt="Species distribution of phosphoric acid over pH with pKa crossovers" width="420">
</p>

*"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:

<p align="center"><img src="https://raw.githubusercontent.com/jurimaxam-dotcom/chemdraw-mcp/main/assets/anki-demo.gif" alt="Split screen: asking Claude for an Anki deck, cards appear in Anki via AnkiConnect" width="760"></p>

## 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 `method`s
- **`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 assu