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\Prekzursil\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\Prekzursil\source\repos\rdkit-mcp-server\.venv\Scripts\python.exe
• args: C:\Users\Prekzursil\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

1. Confirm the rdkit MCP server is connected (claude mcp get rdkit).
2. List the server's tools to get exact names/signatures - do not assume tool names from the 74-tool set.
3. Run the chemistry operation (descriptors / fingerprint / similarity / substructure / scaffold) on your SMILES or structure input.

When to Use vs the Schrodinger Server

• Use cheminformatics-rdkit for license-free RDKit cheminformatics (descriptors, fingerprints, similarity, scaffolds) - no Schrodinger token consumed.
• Use schrodinger-maestro-driver when you need suite-specific computation: LigPrep, Glide docking, QikProp ADMET, or .mae interchange. Note its molecule_properties and smiles_to_3d also use a bundled RDKit, so for pure descriptors either server works - prefer this one to avoid touching the licensed suite.

Common Mistakes

• Forgetting --transport stdio and getting an SSE:8000 server the client cannot reach.
• Running a plain pip install . and failing on the dead rdkit==2025.3.1 pin (use --no-deps with a separately installed working RDKit).
• Inventing tool names instead of listing the server's 74 tools at runtime.

Related Skills

• schrodinger-maestro-driver - licensed suite tools (LigPrep/Glide/QikProp) and its own bundled-RDKit descriptor panel.
• ddi-admet-research - ToolUniverse biomedical knowledge front-end.