ChemCP MCP server

ChemCP - Molecule Viewer MCP App

An MCP App that renders interactive 2D molecular structure diagrams from SMILES notation using RDKit.js. Ask your AI assistant to show you any molecule, and ChemCP displays the structure with computed properties — right inside the chat.

What you get

• 2D structure diagrams rendered from any valid SMILES string
• Molecular properties — molecular weight, LogP, H-bond donors/acceptors, TPSA, rotatable bonds, rings, and more
• Interactive UI — type your own SMILES, click example molecules, all without leaving the conversation
• Powered by RDKit (the same cheminformatics toolkit used by pharma and biotech)

For more functionality try: ChemIllusion

Prerequisites

• Node.js 18+ — download here
• Claude Desktop (recommended) or Claude.ai paid plan (Pro/Max/Team) — the interactive molecule viewer requires a host that supports MCP Apps

Note: Claude Desktop has full MCP Apps support. Claude.ai custom connectors are experimental and may have CSP limitations that prevent RDKit.js from loading. If you see "RDKit.js failed to load" in Claude.ai, use Claude Desktop instead.

Setup: Claude Desktop

Claude Desktop supports local MCP servers out of the box. No tunnels or remote hosting needed.

Step 1: Install ChemCP

npm install -g chemcp

Verify it installed:

chemcp --help

(It will start the MCP server on stdio — you can Ctrl+C to stop it.)

Step 2: Configure Claude Desktop

Open your Claude Desktop config file:

Add ChemCP to the mcpServers section:

{
  "mcpServers": {
    "chemcp": {
      "command": "npx",
      "args": ["chemcp"]
    }
  }
}

Tip: If you already have other MCP servers configured, just add the "chemcp" entry alongside them inside the existing "mcpServers" object.

Step 3: Restart Claude Desktop

Quit and reopen Claude Desktop. You should see ChemCP listed in the MCP tools (click the hammer icon at the bottom of the chat input).

Step 4: Try it out

Type a message like:

• "Show me the molecule for aspirin"
• "Render the structure of caffeine"
• "Display SMILES: CC(=O)Oc1ccccc1C(=O)O"

Claude will call the render_molecule tool, and an interactive molecule viewer will appear in the conversation showing the 2D structure and molecular properties.

Setup: Claude.ai (Web) — Experimental

⚠️ Experimental: Claude.ai custom connectors have experimental MCP Apps support. CSP restrictions may prevent RDKit.js from loading. Use Claude Desktop for the best experience.

Claude.ai supports remote MCP servers via custom connectors. This requires a paid Claude plan (Pro, Max, or Team).

Step 1: Install and start the server

npm install -g chemcp

Start in HTTP mode:

chemcp --http

This starts the server on http://localhost:3001/mcp.

Step 2: Expose with a tunnel

In a separate terminal, create a public tunnel to your local server:

npx cloudflared tunnel --url http://localhost:3001

Copy the generated URL (e.g., https://random-name.trycloudflare.com).

Step 3: Add as a custom connector in Claude.ai

Shortened. The full README is on GitHub.