cheminformatics-rdkit

Cheminformatics (RDKit MCP)

Overview

The rdkit MCP server (tandemai-inc/rdkit-mcp-server, MIT) exposes 74 cheminformatics tools - a license-free, standalone alternative to the bundled-RDKit path inside the schrodinger server. Use it for molecular descriptors, fingerprints, similarity, substructure/scaffold work on SMILES or structures.

• Local checkout: C:\Users\agentuser\source\repos\rdkit-mcp-server
• Capability categories (call the server's tool list at runtime for exact names): molecular descriptors / physchem properties, fingerprints, similarity scoring, substructure search, and scaffold analysis.

Registration (verified, stdio)

• command: C:\Users\agentuser\source\repos\rdkit-mcp-server\.venv\Scripts\python.exe
• args: C:\Users\agentuser\source\repos\rdkit-mcp-server\run_server.py --transport stdio
• env: none.
• Cross-platform: on POSIX, point command at rdkit-mcp-server/.venv/bin/python and keep run_server.py --transport stdio.

Two Install Gotchas (load-bearing)

1. Dead RDKit pin: upstream pins rdkit==2025.3.1, which is unavailable. Install a working RDKit (here rdkit 2026.3.3) and then install the package WITHOUT re-resolving the dead pin: pip install --no-deps . inside the venv. Skipping --no-deps re-pulls the broken pin and the install fails.
2. Transport default: the server defaults to SSE on port 8000. You MUST pass --transport stdio in the args (as registered above) or the MCP client cannot connect over stdio.

Quick Workflow

When to Use vs the Schrodinger Server

Common Mistakes

Related Skills