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DECIMER MCP Server

docminus/decimermcpserver

Connects Claude to DECIMER's chemical structure recognition engine via a FastAPI backend. Exposes two tools: server_health to ping the API and analyze_chemical_image to send a base64-encoded image and get back SMILES notation plus classifier confidence scores. You run the DECIMER API separately (Docker image or source available), then point this MCP adapter at it. Useful when you're working with chemical diagrams in papers or lab notebooks and need programmatic access to structure data. Returns structured JSON with the SMILES string, classifier decision, and fallback reasons when the image isn't recognized as a chemical structure. The server is a thin transport layer, not a standalone model runtime.

tools
2
transport
STDIO
last updated
Apr 13, 2026
View on GitHub

Tools

2 tools

Public tool metadata for what this MCP can expose to an agent.

server_healthChecks whether the DECIMER FastAPI server is reachable.

Checks whether the DECIMER FastAPI server is reachable.

No parameter schema in public metadata yet.

analyze_chemical_imageSends a base64-encoded image to `/image2smiles/` and returns structured output.

Sends a base64-encoded image to `/image2smiles/` and returns structured output.

No parameter schema in public metadata yet.

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Readme

DecimerMCPServer

mcp-name: io.github.DocMinus/decimer-mcp-server

MCP server that exposes DECIMER image-to-SMILES functionality as tool calls.

This project is a thin adapter over the existing FastAPI service in DecimerServerAPI. It does not run DECIMER models directly. The adapter sends JSON requests by default, with automatic fallback to form payloads for compatibility.

Tools

  • server_health: Checks whether the DECIMER FastAPI server is reachable.
  • analyze_chemical_image: Sends a base64-encoded image to /image2smiles/ and returns structured output.

Requirements

  • Python 3.10+
  • Running DECIMER API server (default: http://localhost:8099)

find it at either of these two versions:

Install

cd /Users/a/dev/DecimerMCPServer
uv venv
uv sync

Configuration

Copy .env.example values into your environment:

  • DECIMER_API_BASE_URL (default http://localhost:8099)
  • DECIMER_API_TIMEOUT_SECONDS (default 60)
  • DECIMER_MAX_IMAGE_BYTES (default 10000000)
  • DECIMER_MCP_LOG_LEVEL (default INFO)

Run (stdio transport)

View the full README on GitHub

Details

Repository
github.com/docminus/decimermcpserver
Package
decimer-mcp-server
Transport
STDIO
Registry
MCP registry, active