RDKit MCP Server (TandemAI)

MCP server that exposes the full RDKit 2025.3.1 surface as discrete tool calls — useful when local Python execution is disabled or undesirable.


Type	MCP server
Supplier	TandemAI Inc.
Availability	GA — targets RDKit 2025.3.1, actively developed
Pricing	Free / OSS (MIT)
Capabilities	Read/Write

Clone, install dependencies, and verify the server starts:

git clone https://github.com/tandemai-inc/rdkit-mcp-server
cd rdkit-mcp-server
pip install -r requirements.txt
python run_server.py --settings settings.yaml   # Ctrl-C once you confirm it boots

Then register with Claude Code (replace /path/to/rdkit-mcp-server with the absolute path — e.g., $(pwd) if still in that directory):

claude mcp add --transport stdio rdkit -- python /path/to/rdkit-mcp-server/run_server.py --settings /path/to/rdkit-mcp-server/settings.yaml

Or for Claude Desktop, add to claude_desktop_config.json:

{
  "mcpServers": {
    "rdkit": {
      "command": "python",
      "args": ["/path/to/rdkit-mcp-server/run_server.py", "--settings", "/path/to/rdkit-mcp-server/settings.yaml"]
    }
  }
}

Enumerate the available tools with python list_tools.py from inside the clone.

What it does

Auto-generated MCP wrappers around RDKit modules — descriptors, fingerprints, reactions, substructure matching, conformer generation, and more. settings.yaml controls which RDKit surface is exposed.

Primary use cases: Agent-driven cheminformatics where Claude calls RDKit as tools (not code execution), molecule manipulation pipelines, retrosynthesis support.

Notes

stdio transport. Differs from the K-Dense RDKit Skill: this exposes RDKit as discrete MCP tools (model calls them like any other function), while the skill instructs Claude to write and run Python locally. Pick the server if your environment forbids Bash/Python execution; pick the skill if it allows them and you want maximum flexibility.

Sources

tandemai-inc/rdkit-mcp-server

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