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codex-chemdraw-skill

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SUMMARY

Windows-first ChemDraw Skill and MCP adapter for Codex

README.md

Codex ChemDraw Skill

简体中文

A Codex Skill and MCP server for ChemDraw and cdxml-toolkit workflows on Windows. It gives Codex task-level tools for drawing, cleaning, merging, rendering, recognizing, analyzing, and embedding chemical structures.

This is an independent community project. It is not affiliated with or endorsed by Revvity, Anthropic, OpenAI, or the DECIMER project.

Capabilities

  • Resolve names, SMILES, InChI, and common structure identifiers.
  • Compare single molecules or bounded batches with ChemScript identity and RDKit fingerprints.
  • Draw and edit structures and reaction schemes as CDXML.
  • Clean, merge, polish, segment, and render ChemDraw documents.
  • Convert images with local DECIMER models or an explicitly confirmed remote request.
  • Embed CDXML objects in PowerPoint and Word files on supported Windows systems.
  • Discover experiment files and process selected LCMS, RDF, and lab-book workflows.
  • Inspect and execute the installed public ChemScript SDK through a controlled, isolated program.
  • Optionally serve the same tools over authenticated Streamable HTTP with health and Prometheus endpoints.

Requirements

  • Windows 10 or later.
  • A licensed, activated ChemDraw installation for native rendering and automation.
  • Python 3.10 or later; Python 3.12 is the tested configuration.
  • cdxml-toolkit==0.5.17 for the tested configuration.
  • mcp==2.0.0 for the tested MCP runtime; SDK 1.x remains compatible.
  • Codex CLI or Codex desktop for Skill and MCP integration.

ChemDraw, Microsoft Office, and local DECIMER model weights are not bundled.

Quick Start

git clone https://github.com/ZiChenWang114514/codex-chemdraw-skill.git
Set-Location codex-chemdraw-skill

conda create -n cdxml python=3.12 -y
conda run -n cdxml python -m pip install "mcp==2.0.0" "cdxml-toolkit==0.5.17"
$python = (conda run -n cdxml python -c "import sys; print(sys.executable)" | Select-Object -Last 1)
Set-ExecutionPolicy -Scope Process Bypass
& .\scripts\install.ps1 -Python $python -Apply -ConfigureMcp

Restart Codex after installation, then verify the integration:

codex mcp get cdxml-toolkit --json
& "$HOME\.codex\skills\chemdraw\scripts\health_check.ps1" -Python $python

The installer is read-only unless -Apply is supplied. Existing Skill and MCP configuration files are backed up before replacement.

stdio remains the default. For a ChemDraw workstation shared through a private network, see the authenticated Streamable HTTP setup before exposing a listening port.

Documentation

  • Project guide: installation, runtime discovery, architecture, testing, safety, and third-party boundaries.
  • Contributing: development workflow and pull-request expectations.
  • Security: private vulnerability reporting and supported versions.

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

Safety

Remote image recognition is disabled unless the caller explicitly confirms upload. Modifying tools create a new output path by default and reject accidental overwrites. Chemical outputs must be checked against the source material before scientific use.

License

Repository-authored code and documentation are licensed under the MIT License. Third-party software keeps its own license: ChemDraw, cdxml-toolkit, and DECIMER.

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