ChemDraw Skill

ChemDraw Skill: controlled CDXML workflows from a chemistry request to a checked native ChemDraw artifact

Turn chemistry requests into editable CDXML, native ChemDraw renders, molecule comparisons, recognition candidates, and Office-embedded structures through a client-independent Skill and MCP server.

Reproduce a paper figure

Start with the whole figure, then follow one route:

Inspect → crop structures → DECIMER → match orientation → inspect side-by-side → correct chemistry → assemble conditions and layout → native preview.

Use the ChemDraw Skill to reproduce this paper figure. Read the whole scheme,
crop each complete structure, and obtain DECIMER candidates. Match the original
orientation, inspect actual side-by-side previews, and correct only the affected
structures. Transcribe conditions visually, then deliver editable CDXML and a
native preview with unresolved chemistry or visual differences stated clearly.

The image below is a self-authored native depiction test, illustrating editable multi-reactant layout and stereo bonds; it is not a paper-replication accuracy claim.

Native ChemDraw reaction with multiple reactants and S stereochemistry

Editable reaction · Fast replication guide · Minimal task template · Replayable figure example

Need	Ready-to-use route
Crop and review an image	Existing crop/mask and comparison helpers; keep region-to-result mapping
Match a folded chain or bridged ring	Trace source coordinates, then check crossings and bond order
Correct stereochemistry	Inspect atom indices, apply an explicit edit, and read back final CDXML
Assemble the final scheme	Fixed-coordinate figures, rich conditions, arrows and native preview
Work beyond drawing	RDKit stereo/tautomer enumeration, MCS and R-group decomposition

Remote DECIMER calls require upload authorization. Visual review remains an agent task; pixel metrics do not certify chemistry or universal 1:1 fidelity.

What It Handles

Structures and reactions: resolve names and identifiers; draw, edit, clean, merge, polish, segment, convert, and render CDXML or CDX documents.
Molecule comparison: use ChemScript exact-identity checks together with RDKit fingerprint similarity for one molecule pair or a bounded batch.
Image recognition: extract candidate structures, confidence values, and bounding boxes with local DECIMER models or an explicitly confirmed remote request. Recognition candidates still require source review.
Office documents: embed editable ChemDraw objects in supported desktop versions of Word and PowerPoint.
Experimental records: discover files and process selected LCMS, SciFinder RDF, and lab-book workflows.
ChemScript SDK: inspect the installed public catalog and run supported declarative calls in a separate worker process. Process separation limits stalled calls; it is not an operating-system security sandbox.
Remote workstation access: keep stdio as the default or expose the Windows host through optional Streamable HTTP with health and Prometheus endpoints.

The project audits 594 public cdxml-toolkit-community symbols. That number describes the toolkit inventory, not the 38-tool full MCP profile. Full public ChemScript catalog coverage means the interface can be discovered and reported; successful execution still depends on the installed SDK, license, architecture, and individual member behavior.

Choose the Required Components

Goal	Add to the core setup
Create and edit CDXML	Any agent, 64-bit Python 3.10-3.13, MCP 1.x or 2.x, and `cdxml-toolkit-community` at the commit pinned in Quick Start; runs on Windows, macOS, and Linux
Native PNG, CDX, or ChemDraw cleanup	Licensed and activated Windows desktop ChemDraw with working COM automation
Molecule comparison or ChemScript SDK calls	Installed ChemScript DLLs compatible with the selected worker runtime
Editable Word or PowerPoint objects	Supported desktop Microsoft Word and/or PowerPoint
Local optical structure recognition	DECIMER model weights and their runtime dependencies
Remote access to a ChemDraw workstation	A Windows host plus authenticated HTTP configuration and an encrypted network path

ChemDraw, Microsoft Office, ChemScript, and DECIMER model weights are not bundled. For a first installation, use the step-by-step Chinese guide or the detailed English guide.

Quick Start: any agent

Load skill/chemdraw/SKILL.md in your agent, then connect MCP or use Python/CLI. Clients with Skill discovery can install the whole chemdraw folder in their own Skill directory. Otherwise, point the agent's project instructions to the file.

git clone https://github.com/ZiChenWang114514/chemdraw-skill.git
Set-Location .\chemdraw-skill
python -m pip install "cdxml-toolkit-community @ git+https://github.com/ZiChenWang114514/cdxml-toolkit-community.git@57db286ea4fa1c74a524e7a329dd5ba3f39dc21e"
python -m cdxml_toolkit.mcp_runtime

This starts a stdio server with the full 38-tool collection. Register the same absolute Python executable and arguments in your client's MCP settings. Image reconstruction needs vision or human visual review.

On Windows, preview scripts/install.ps1 -Destination <your-skill-directory>, then add -Apply. Its default storage path is $HOME/.agents/skills/chemdraw; individual clients may use different discovery paths. Client configuration is not changed by default. On macOS/Linux, copy the entire Skill folder directly.

Generic MCP, CLI and optional client adapters · Windows native setup · Chinese walkthrough

# Generic health check; no particular agent CLI or native application required
.\skill\chemdraw\scripts\health_check.ps1 -Python <absolute-python-path> -SkipNativeChemDraw

For native rendering, ChemScript or Office, add the corresponding dependencies and select the checks described in the setup guide.

Validation and Safety

GitHub Actions validates the portable runtime on Windows and Linux with Python 3.12, MCP 1.28.1 and 2.0.0, and cdxml-toolkit-community at the commit pinned in Quick Start. Python 3.10-3.13 is supported.
Native ChemDraw, ChemScript, and Office behavior must be checked on a licensed local Windows host because those applications are unavailable in hosted CI.
Structural changes can be checked with source identity, MCS-based diffs, chemistry metadata, and native rendering. Scientific acceptance remains the user's responsibility.
Standard modifying tools create a new output path and reject accidental replacement. ChemScript SDK file access and replacement are available only when their explicit permission and overwrite options are enabled.
Remote image recognition refuses upload unless the caller explicitly confirms it. The guided replication route requires explicit structure-role assignment and visual review; it is not an unattended reaction-image converter.
The built-in HTTP listener does not provide TLS. Non-loopback use requires bearer authentication and an allowed Host; place it behind an encrypted tunnel or HTTPS reverse proxy. /health exposes status only, while /metrics requires authentication.
Worker processes provide timeout and failure isolation, but they do not sandbox ChemDraw, Office, Python dependencies, or filesystem access. Review the security policy before enabling native file operations or remote access.

Documentation

The deployable Skill lives in skill/chemdraw. Repository-specific contributor instructions are in AGENTS.md.

License

Repository-authored code and documentation are licensed under the MIT License. ChemDraw, Microsoft Office, agent clients, cdxml-toolkit-community, the MCP Python SDK, RDKit, DECIMER, and their dependencies retain their respective licenses and usage terms.

This is an independent community project. It is not affiliated with or endorsed by Revvity, OpenAI, Microsoft, or the maintainers of the upstream cdxml-toolkit, the MCP Python SDK, RDKit, or DECIMER.