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rdkit-tools-mcp

rdkit-tools-mcp

by mtx-auto
OverviewSchemaSourceRelated ServersDiscussionsAdmin
Python
Remote

RDKit Tools MCP Server

A Model Context Protocol (MCP) server exposing core RDKit cheminformatics operations as tools, for use by AI agents (e.g. DIAL toolsets).

Complements other chemistry MCPs (SMILES visualization, ChEMBL database access) by covering the in-process cheminformatics operations they don't: descriptor/fingerprint calculation, similarity and substructure search, reaction enumeration, standardization, and 3D conformer generation.

Tools

Tool

Description

canonicalize_smiles

Parse a SMILES string, return its canonical form and basic identity info

standardize_molecule

Clean up a molecule: strip salts/solvents, keep the largest fragment, neutralize charges

calculate_descriptors

Compute descriptors (MolWt, LogP, TPSA, HBD/HBA, ring counts, QED, ...) for one SMILES

batch_calculate_descriptors

Same, for a batch of SMILES

calculate_fingerprint

Compute a fingerprint (morgan, rdkit, or maccs) and return its on-bit indices

tanimoto_similarity

Tanimoto similarity between two molecules

similarity_search

Rank candidate SMILES by similarity to a query molecule

substructure_search

Check which candidates match a SMARTS substructure pattern

enumerate_reaction

Apply a reaction SMARTS/SMIRKS template to reactants, return distinct products

generate_3d_conformer

Generate (optionally force-field optimized) 3D conformers as MOL blocks

Related MCP server: cmxflow

Running locally

pip install -r requirements.txt
python server.py --host 127.0.0.1 --port 8080

Docker

docker build -t rdkit-tools-mcp .
docker run -p 8080:8080 rdkit-tools-mcp

The server speaks MCP over HTTP Streamable transport at /mcp.

Tool Schema Changelog

Recent tool additions, removals, and schema changes observed during successful MCP inspections.

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