UniChemicals MCP Server

中文版 (Chinese Version)

🔬 Introduction

An MCP (Model Context Protocol) server for multi-database chemistry queries, combining PubChem (via PubChemPy) and CAS Common Chemistry (official API, API-key authenticated).

What does it do? This server acts as a bridge between AI assistants (like Claude, Cursor, Trae) and public chemistry databases. By integrating this MCP server, your AI assistant gains the ability to autonomously search, retrieve, and analyze chemical compounds from PubChem (millions of freely accessible records) and CAS Common Chemistry (substance summaries, full details, properties and molfiles) directly within your chat or development environment.

Why use it? Instead of manually browsing PubChem or CAS websites to find molecular formulas, weights, structures (SMILES/InChI), synonyms, 3D conformers or molfiles, you can simply ask your AI assistant.

Data sources: PubChem data is fetched in real time from PubChem's official REST services (PUG REST / PUG-View); CAS data is fetched from the CAS Common Chemistry API (https://commonchemistry.cas.org/api). This server keeps no local cache or database.

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🚀 Installation & Configuration

You can use this server directly via uvx without manual installation.

CAS Common Chemistry API key (required for cas_* tools)

To use the cas_* tools you need a CAS Common Chemistry API token. Create a .env file in the directory you launch the server from (or export the variable in your environment):

CAS_COMMON_CHEMISTRY_API_KEY=your_api_key_here

See .env.example for the template. The PubChem tools (pubchem_*) do not require any key.

MCP client configuration

Add the following to your MCP client configuration (e.g., Cherry Studio MCP Servers import, or claude_desktop_config.json). A ready-to-use file is provided at mcp-client-example.json:

{
  "mcpServers": {
    "unichemicals": {
      "command": "uvx",
      "args": [
        "--refresh",
        "pubchempy-mcp-server"
      ],
      "env": {
        "CAS_COMMON_CHEMISTRY_API_KEY": "your_api_key_here"
      }
    }
  }
}

• Replace your_api_key_here with your real CAS Common Chemistry API token (the same value as CAS_COMMON_CHEMISTRY_API_KEY in .env). The cas_* tools read the key from this environment variable.
• The env block is supported by Cherry Studio and most modern MCP clients. If your client does not support env, set the same variable in your OS/user environment instead.
• Remove the env block if you only need the PubChem tools (pubchem_*).

Note: The --refresh flag ensures you always pull the latest version from PyPI.

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🛠️ Available Tools (API Reference)

This server exposes 51 semantic tools — 40 pubchem_* tools and 11 cas_* tools — each named as {database}_{action}_{entity}_by_{identifier} so the source database (pubchem / cas), the action (search / get / resolve), the entity and the search key are always explicit.

CAS Common Chemistry tools (cas_*)

Powered by the official CAS Common Chemistry API (/search, /detail, /export), authenticated with X-Api-Key.

Search substances (cas_search_substance_by_*)

All search tools share the /search endpoint; each accepts offset (default 0) and size (1–100, default 10) for pagination. Searches are case-insensitive.

• cas_search_substance_by_name: name search, supports a trailing wildcard (e.g. car*).
• cas_search_substance_by_casrn: CAS Registry Number (with or without dashes, e.g. 50-00-0).
• cas_search_substance_by_smiles: SMILES (canonical or isomeric).
• cas_search_substance_by_inchi: InChI (with or without the InChI= prefix).
• cas_search_substance_by_inchikey: InChIKey (the InChIKey= prefix is added automatically — required by the API in practice).

Substance details (cas_get_substance_by_*)

• cas_get_substance_by_casrn: full details by CAS RN (URI, names, InChI/InChIKey, canonical SMILES, molecular formula/mass, experimental properties + citations, synonyms, replaced RNs, SVG images).
• cas_get_substance_by_uri: same details by the exact uri returned by the API (e.g. substance/pt/50000).

Molfile export (cas_get_molfile_by_*)

• cas_get_molfile_by_uri: V2000 molfile text by URI (/export).
• cas_get_molfile_by_casrn: convenience — resolves the URI via /detail first, then exports the molfile.

Convenience extractors (cas_get_*_by_casrn)

• cas_get_properties_by_casrn: experimental properties and property citations extracted from /detail.
• cas_get_image_by_casrn: structure images (SVG) extracted from /detail.

Data policy: CAS Common Chemistry data is provided by CAS (American Chemical Society) under its own terms; see the CAS Common Chemistry website for access conditions. This server only reflects API capabilities available with your key.

1. Compound Search (pubchem_search_compound_by_*)

Retrieve standardized compound records from the PubChem database.

• Tools:
  • pubchem_search_compound_by_cid
  • pubchem_search_compound_by_name
  • pubchem_search_compound_by_smiles
  • pubchem_search_compound_by_sdf
  • pubchem_search_compound_by_inchi
  • pubchem_search_compound_by_inchikey
  • pubchem_search_compound_by_formula
  • pubchem_search_compound_by_cids (batch: pass a list of CIDs)
• Arguments:
  • identifier: The search query (int for cid, str for others).
  • searchtype (Optional): Advanced search type (substructure, superstructure, similarity).
  • cids (for the batch tool): A list of CIDs (at most 100 per request).

2. Substance Search (pubchem_search_substance_by_*)

Retrieve raw, unstandardized substance records as originally deposited to PubChem.

• Tools:
  • pubchem_search_substance_by_sid
  • pubchem_search_substance_by_name
  • pubchem_search_substance_by_sourceid (requires sourceid and source_name)

3. Assay Search (pubchem_search_assay_by_aid)

Retrieve bioassay (biological activity) records.

• Tools:
  • pubchem_search_assay_by_aid

4. Properties Retrieval (pubchem_get_property_by_*)

Efficiently retrieve specific chemical properties in batch without downloading the entire compound record.

• Tools:
  • pubchem_get_property_by_cid, name, smiles, sdf, inchi, inchikey, formula
  • pubchem_get_property_by_cids (batch: pass a list of CIDs)
• Arguments:
  • properties: A list of desired properties (e.g., ['MolecularFormula', 'MolecularWeight', 'InChI', 'CanonicalSMILES', 'IsomericSMILES', 'XLogP']).
  • identifier: The search query.
  • cids (for the batch tool): A list of CIDs (at most 100 per request).

5. Synonyms & Aliases (pubchem_get_synonym_by_*)

Fetch all known aliases, systematic names, and trade names for a given chemical.

• Tools:
  • pubchem_get_synonym_by_cid, name, smiles, sdf, inchi, inchikey, formula

6. Identifier Resolution (pubchem_resolve_*_by_*)

Convert between different chemical identifiers (e.g., finding the CID for a specific name or SMILES).

• Tools:
  • pubchem_resolve_cid_by_name, smiles, inchi, inchikey, formula
  • pubchem_resolve_sid_by_cid, name
  • pubchem_resolve_aid_by_cid, name

7. 3D Structure & Descriptors (pubchem_get_*_by_cid)

Retrieve 3D conformers, computed descriptors, and atom/bond topology for a single compound.

• Tools:
  • pubchem_get_conformer_by_cid: 3D coordinates (note: not every compound has 3D data).
  • pubchem_get_descriptor_by_cid: computed descriptors (MolecularWeight, XLogP, TPSA, HBondDonorCount, etc.); accepts an optional properties list, defaults to the standard set.
  • pubchem_get_structure_by_cid: atom/bond topology (elements, coordinates, bond orders).
  • pubchem_get_spectrum_by_cid: spectral data (1H/13C NMR, GC-MS, MS-MS, LC-MS, IR, FTIR, ATR-IR, UV, Raman) via PubChem PUG-View; not every compound has spectra.

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💻 Local Development

If you want to contribute or run from source:

# Clone the repository
git clone https://github.com/yourusername/pubchem-mcp-server.git
cd pubchem-mcp-server

# Build and run using uv
uv build
uv run pubchempy-mcp-server

📜 License

This project is licensed under the AGPL-3.0 License with an additional Commercial Use Restriction clause.

• Copyleft: the AGPL-3.0 license is infectious — any derivative work or networked service based on this project must be released under the same license terms.
• Commercial use: any commercial use requires a separate commercial license from the author. Without such authorization, commercial use is prohibited.

See the LICENSE file for details.

🙏 Acknowledgments

This project is built upon and serves as an MCP wrapper for the excellent PubChemPy library created by mcs07. We extend our deepest gratitude to the original author and contributors of PubChemPy for providing such a robust Python interface to the PubChem PUG REST API.