MCP Servers

pubchem-mcp

Enables querying PubChem compound properties and structure images through MCP, providing formula, molecular weight, SMILES, IUPAC name, and image URLs.

README

PubChem MCP

中文说明

A small stdio MCP server for querying PubChem compound properties and structure images.

Tools

query_pubchem: returns formula, molecular weight, charge, SMILES, IUPAC name, atoms, bonds, and hydrogen-bond counts.
img: returns PubChem structure-image URLs and MCP image objects.

Setup

Requires Python 3.10+.

python -m venv .venv
# Windows PowerShell
.\.venv\Scripts\Activate.ps1
# macOS/Linux
source .venv/bin/activate

pip install -r requirements.txt

Add the server to an MCP client (replace both paths with absolute paths):

{
  "mcpServers": {
    "pubchem": {
      "command": "C:\\path\\to\\pubchem-mcp\\.venv\\Scripts\\python.exe",
      "args": ["C:\\path\\to\\pubchem-mcp\\pcp_mcp.py"]
    }
  }
}

You can also start it directly with python pcp_mcp.py.

Usage

Properties: call query_pubchem with {"compound_name": "aspirin"}.
Structure image: call img with {"compound_name": "aspirin"}.

Notes

Pass compound names in English; translate them before calling the tools if needed.
Internet access to PubChem is required. A name may match multiple compounds.
Image display depends on the MCP client; img also returns browser-ready URLs.
PubChem data should be independently verified before safety-critical, medical, or regulatory use.

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