RDKit Agent

Agent-first cheminformatics toolkit powered by RDKit compiled to WebAssembly — validate, repair, convert, and analyze chemical notation with structured JSON output and no Python runtime.

   
Type MCP server (also ships as a CLI, Node library, and Claude Code skill/plugin)
Supplier scottmreed
Availability Alpha — npm rdkit-agent v0.1.1, published 2026-03-16
Pricing Free / OSS (MIT)
Capabilities Read/Write — read-only chemistry analysis; writes SVG/PNG images and edited structures
Verified works · 2026-07-20
Security caution · 2026-07-20 — npm rdkit-agent 0.1.1 MIT + GitHub resolve, no OSV advisories, Alpha single-maintainer (9 stars)

How to install

Prerequisite: Node.js ≥ 16. RDKit runs as WebAssembly, so there is no native build step or Python dependency.

  • Claude Code — MCP server (stdio). Install the CLI globally, then register it. Claude Code launches the process itself via stdio — you do not need to keep rdkit-agent mcp running in a separate terminal. 
    npm install -g rdkit-agent
claude mcp add --transport stdio rdkit-agent -- rdkit-agent mcp

    To verify the server boots before registering, run rdkit-agent mcp once and Ctrl-C after it starts.

  • Claude Desktop — MCP server (stdio). After npm install -g rdkit-agent, add to claude_desktop_config.json: 
    {
  "mcpServers": {
    "rdkit-agent": {
      "command": "rdkit-agent",
      "args": ["mcp"]
    }
  }
}
  • Claude Code — as a skill (auto-invoked for cheminformatics tasks): 
    npx skills add scottmreed/rdkit-agent -g

    The upstream README shows the skill shortcut as bare /rdkit-agent. When installed as a plugin, plugin skills resolve as /<plugin>:<skill> — invoke /rdkit-agent:rdkit-agent if the bare form does not resolve.

  • Claude Code — as a plugin: 
    claude plugin install scottmreed/rdkit-agent

What it does

Exposes 20+ cheminformatics subcommands as MCP tools:

  • check — validate SMILES / SMIRKS / reactions
  • repair-smiles — reconstruct malformed SMILES
  • convert — format conversion (SMILES ↔ InChI / InChIKey / MOL / SDF)
  • descriptors — molecular properties (MW, LogP, TPSA, HBD, HBA, …)
  • similarity — Tanimoto similarity
  • filter — descriptor-based filtering (e.g., Lipinski rules)
  • draw — SVG / PNG rendering with atom/bond highlighting
  • react — apply reaction SMIRKS to reactants
  • stereo — stereocenter analysis
  • atom-map — manage atom mapping
  • balance, fg, subsearch, fingerprint, scaffold, rings, stats, edit, schema, version

Primary use cases: SMILES validation and repair, notation interconversion, descriptor calculation, reaction manipulation and atom mapping — without executing Python locally.

Notes

stdio transport. RDKit runs as WebAssembly (@rdkit/rdkit ≥ 2022.03 for reaction support), so there is no Python runtime — the author reports ~1 ms warm-path latency. Distinct from the TandemAI RDKit MCP Server (Python-based, exposes RDKit modules) and the K-Dense RDKit Skill (writes and runs Python locally): this one is Node/WASM and adds SMILES repair, reaction balancing, and atom-mapping tools not present in those. Same author as ChemCP (interactive molecule rendering), but a separate package.

Early-stage (v0.1.x) → availability: Alpha. Community project, not vendor-affiliated.

Sources

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