How to run Athanor's MCP server on your own computer

The hosted server at mcp-athanor.arbastro.com needs a connection. athanor mcp is the offline version: the same engine, running on your computer, talking to your AI client over standard input and output. Nothing leaves your machine.

Steps

1. Install the athanor command line, for example as C:\Tools\athanor.exe.
2. Add it to your MCP client as a local (stdio) server, with the command set to the binary and one argument, mcp. In clients configured with JSON, such as Claude Desktop or Cursor:

{
  "mcpServers": {
    "athanor": {
      "command": "C:\\Tools\\athanor.exe",
      "args": ["mcp"]
    }
  }
}

In Claude Code:

claude mcp add athanor -- C:\Tools\athanor.exe mcp

3. Restart the client. It should list Athanor's tools.

The tools

A structure is passed as text: SMILES, a molfile, CDXML, MRV, CML or XYZ. Its format is read from the text when not given.

The local server has these five. Drawing (depict), the library lookup, perspective and the document tools are on the hosted server.

Check it by hand

The server reads one JSON-RPC message per line. This asks for ethanol's name:

printf '%s\n' '{"jsonrpc":"2.0","id":1,"method":"initialize","params":{"protocolVersion":"2025-06-18","capabilities":{},"clientInfo":{"name":"test","version":"1"}}}' '{"jsonrpc":"2.0","id":2,"method":"tools/call","params":{"name":"name","arguments":{"structure":"CCO"}}}' | athanor mcp

The last line of the reply carries "text":"ethanol".