@cavall/heimdall-mcp-server

The prebuilt stdio MCP server that backs the Heimdall skills. Heimdall turns an image or PDF of drawn chemical structures into SMILES with Ketcher as the source of truth — the model transcribes the visible marks, a backend interprets them into a chemical graph, and Ketcher exports the SMILES. No SMILES is ever free-styled by the LLM.

This package ships the server, a headless Ketcher UI bundle, and a small Indigo shim. It is normally installed for you by the Heimdall plugin; install it directly only if you are wiring the MCP server into a client by hand.

Run

npx -y @cavall/heimdall-mcp-server

Register it as an MCP server (key heimdall) in your client. For example, in .mcp.json:

{
  "mcpServers": {
    "heimdall": {
      "command": "npx",
      "args": ["-y", "@cavall/heimdall-mcp-server"]
    }
  }
}

Tools are then addressed as mcp__heimdall__<tool>.

Tools

The server exposes 16 tools (ingest, build-from-graph, validate, crop, render, export, refuse) — no editing or chemistry-derivation surface. See docs/tool-reference.md in the main repo for the full list and arguments.

Configuration

• HEIMDALL_PYTHON — Python interpreter used to probe/run Indigo (default python3). Indigo is optional: it enables canonical SMILES and improved stereo perception. Without it the server still runs; exports carry a "degraded" advisory.
• HEIMDALL_SKIP_BROWSER — set to skip the Chromium download in the postinstall step (the headless Ketcher canvas needs Chromium at runtime, so only skip this if Chromium is already provisioned by other means).

Links

• Main repository: https://github.com/CAVALL-ORG/Heimdall
• Tool reference: https://github.com/CAVALL-ORG/Heimdall/blob/main/docs/tool-reference.md
• Architecture: https://github.com/CAVALL-ORG/Heimdall/blob/main/docs/architecture.md

Cavall Labs · [email protected]