chemdraw-mcp 0.2.0__tar.gz

chemdraw_mcp-0.2.0/.github/workflows/ci.yml

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+name: CI
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v6
+
+      # setup-uv publishes no floating major tag for v8+ — pin the exact version
+      - uses: astral-sh/setup-uv@v8.2.0
+        with:
+          enable-cache: true
+
+      - uses: actions/setup-node@v6
+        with:
+          node-version: 22
+
+      - name: Install backend dependencies
+        run: uv sync
+
+      - name: Install frontend dependencies
+        run: npm --prefix chemdraw_tool/ui install
+
+      - name: Install Playwright Chromium
+        working-directory: chemdraw_tool/ui
+        run: npx playwright install --with-deps chromium
+
+      # The pixel snapshot is platform-specific (see svgToPng.e2e.mjs). On the
+      # very first CI run the linux golden file doesn't exist yet — generate it
+      # so ./test.sh below can run, and publish it as an artifact. Download that
+      # artifact and commit it as
+      #   chemdraw_tool/ui/src/utils/__fixtures__/aspirin.expected.linux.png
+      # — from then on this step is a no-op and the comparison is a real
+      # regression check. Never regenerate it just to make a diff disappear.
+      - name: Bootstrap linux snapshot (first run only)
+        run: |
+          if [ ! -f chemdraw_tool/ui/src/utils/__fixtures__/aspirin.expected.linux.png ]; then
+            echo "::warning::linux golden file missing — bootstrapping (commit the artifact!)"
+            UPDATE_SNAPSHOTS=1 npm --prefix chemdraw_tool/ui run test:e2e
+          fi
+
+      - name: Run the gate (backend + frontend)
+        run: ./test.sh
+
+      - name: Upload fixtures (for snapshot bootstrap)
+        uses: actions/upload-artifact@v7
+        if: always()
+        with:
+          name: ui-fixtures
+          path: chemdraw_tool/ui/src/utils/__fixtures__/

chemdraw_mcp-0.2.0/.github/workflows/publish.yml

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+name: Publish to PyPI
+
+# Trusted Publishing (OIDC) — no API token stored anywhere.
+# One-time setup on pypi.org: Account → Publishing → Add pending publisher
+#   PyPI project name: chemdraw-mcp
+#   Owner: jurimaxam-dotcom   Repository: chemdraw-mcp
+#   Workflow name: publish.yml   Environment: (leave empty)
+on:
+  release:
+    types: [published]
+  workflow_dispatch:
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v6
+      - uses: astral-sh/setup-uv@v8.2.0
+      - run: uv build
+      - uses: actions/upload-artifact@v7
+        with:
+          name: dist
+          path: dist/
+
+  publish:
+    needs: build
+    runs-on: ubuntu-latest
+    permissions:
+      id-token: write
+    steps:
+      - uses: actions/download-artifact@v8
+        with:
+          name: dist
+          path: dist/
+      - uses: pypa/gh-action-pypi-publish@release/v1

chemdraw_mcp-0.2.0/.gitignore

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+# Python
+.venv/
+__pycache__/
+*.pyc
+
+# Node
+node_modules/
+package-lock.json
+
+# OS / IDE / local agent config
+.DS_Store
+.idea/
+.ai/
+.claude/settings.local.json
+CLAUDE.local.md

chemdraw_mcp-0.2.0/CLAUDE.md

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+# chemdraw-mcp
+
+MCP server for Claude Desktop that turns molecule names or SMILES into
+publication-style 2D structure drawings. PNG/SVG are the primary outputs
+(rendered offline via RDKit) — ChemDraw CDXML is an optional extra format,
+never a runtime requirement.
+
+## Build / Run
+
+```bash
+./install.sh                 # one-command setup: uv + deps + Claude Desktop config
+uv sync                      # deps only
+uv run chemdraw-tool-server  # run the MCP server (stdio) manually
+```
+
+`install.sh` registers the server in Claude Desktop via
+`scripts/install_claude_config.py` (idempotent merge, writes a `.bak` backup,
+never touches other configured MCP servers).
+
+**After changing server code or dependencies, restart Claude Desktop** —
+it keeps the server process alive, and a stale process mixes old in-memory
+modules with new files (manifests as confusing RDKit/Boost signature errors).
+
+## Auto-Gate (the project's green/red)
+
+```bash
+./test.sh                                     # full pipeline: backend + frontend
+npm --prefix chemdraw_tool/ui run test:watch  # JS unit tests in watch mode
+```
+
+One-time frontend setup: `cd chemdraw_tool/ui && npm install && npx playwright install chromium`
+
+The e2e test rasters a real RDKit SVG in headless Chromium and compares an
+exact pixel snapshot. The snapshot is machine-specific: regenerate once per
+machine with `npm --prefix chemdraw_tool/ui run test:e2e:update` — never
+regenerate it just to make a diff disappear.
+
+## Architecture
+
+```
+chemdraw_tool/
+├── resolver.py            — SMILES detection + name→SMILES cascade:
+│                            OPSIN (offline, needs Java; degrades gracefully)
+│                            → PubChem → NCI
+├── generator.py           — RDKit 2D coordinates
+├── image_export.py        — PNG/SVG file rendering (primary output path)
+├── svg_renderer.py        — SVG for the embedded UI preview (shared BOND_LINE_WIDTH)
+├── spectrum.py            — schematic spectra from peak lists (matplotlib → PNG/SVG)
+├── cdxml_writer.py        — RDKit mol → ChemDraw CDXML (optional format)
+├── layout.py              — reaction scheme layout (arrows, +, conditions)
+├── mechanism*.py           — reaction mechanism definitions/coords/rendering
+├── databases.py           — PubChem / ChEBI / KEGG / UniProt lookups
+├── validator.py           — input validation + CDXML round-trip validation
+├── calculator/            — Ph.Eur. content-determination math (pure functions)
+├── payloads.py            — Pydantic models for MCP structured output
+├── chemdraw.py            — optional macOS AppleScript bridge to ChemDraw
+├── server.py              — FastMCP server (stdio) + tool definitions
+└── ui/                    — embedded MCP App UI (React/Vite, served as resource)
+```
+
+Pipeline: input (name/SMILES) → resolver → RDKit 2D → image_export (PNG/SVG)
+[→ cdxml_writer if requested] → `~/ChemDraw-Output/`
+
+Output formats: `generate_*` tools accept `formats=["png","svg","cdxml"]`,
+default `["png","svg"]`. CDXML only on explicit request.
+
+## Conventions
+
+- Python 3.11+, package manager: `uv`
+- Tests: pytest, TDD (red first — no production code without a failing test)
+- UI preview and exported files must stay visually consistent
+  (shared constants like `BOND_LINE_WIDTH`; parity is test-enforced)
+- Dependencies: rdkit, lxml, requests, mcp, Pillow, matplotlib, py2opsin
+  (OPSIN needs a JRE at runtime; without one the resolver degrades to
+  PubChem/NCI — never make Java a hard requirement)

chemdraw_mcp-0.2.0/LICENSE

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chemdraw_mcp-0.2.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: chemdraw-mcp
+Version: 0.2.0
+Summary: MCP server that turns molecule names or SMILES into publication-style 2D structure drawings (PNG/SVG via RDKit) — reaction schemes, mechanisms, spectra. Unofficial, not affiliated with Revvity.
+Project-URL: Repository, https://github.com/jurimaxam-dotcom/chemdraw-mcp
+Project-URL: Issues, https://github.com/jurimaxam-dotcom/chemdraw-mcp/issues
+Author: jurimaxam-dotcom
+License-Expression: Apache-2.0
+License-File: LICENSE
+Keywords: chemistry,claude,mcp,rdkit,smiles,structure-drawing
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Science/Research
+Classifier: Programming Language :: Python :: 3
+Classifier: Topic :: Scientific/Engineering :: Chemistry
+Requires-Python: >=3.11
+Requires-Dist: genanki>=0.13.1
+Requires-Dist: lxml
+Requires-Dist: matplotlib>=3.10.9
+Requires-Dist: mcp
+Requires-Dist: pillow
+Requires-Dist: py2opsin>=1.2.0
+Requires-Dist: rdkit
+Requires-Dist: requests
+Description-Content-Type: text/markdown
+
+# chemdraw-mcp
+
+<!-- mcp-name: io.github.jurimaxam-dotcom/chemdraw-mcp -->
+
+[![CI](https://github.com/jurimaxam-dotcom/chemdraw-mcp/actions/workflows/ci.yml/badge.svg)](https://github.com/jurimaxam-dotcom/chemdraw-mcp/actions/workflows/ci.yml)
+[![Release](https://img.shields.io/github/v/release/jurimaxam-dotcom/chemdraw-mcp)](https://github.com/jurimaxam-dotcom/chemdraw-mcp/releases)
+[![License: Apache-2.0](https://img.shields.io/badge/license-Apache--2.0-blue)](LICENSE)
+
+**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.
+
+<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>
+
+*"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>
+
+*"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` / `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:
+
+<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
+
+- **`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
+
+```bash
+git clone https://github.com/jurimaxam-dotcom/chemdraw-mcp.git
+cd chemdraw-mcp && ./install.sh
+```
+
+The installer sets up everything: installs [uv](https://docs.astral.sh/uv/)
+if missing, resolves Python + RDKit, and registers the server in Claude
+Desktop's config (idempotent, with backup — existing MCP servers are left
+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](https://github.com/dan2097/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
+
+```bash
+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](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.