PubChem Chemical Safety MCP Server

Instructions

Implementation Reference

• pubchem_mcp/mcp_server.py:21-69 (handler)

  The main handler function for the `get_compound_info` tool in the MCP server. It manages cache checking, PubChem API interaction via `PubChemClient`, and result parsing.

  @app.tool()
  async def get_compound_info(ctx: Context, name: str) -> Dict[str, Any]:
      """
      获取化合物基础信息
      
      Args:
          name: 化合物名称
          
      Returns:
          包含CID、分子式、分子量等基础信息的字典
      """
      try:
          # 初始化缓存服务
          cache_service = CacheService()
          await cache_service.initialize()
          
          # 检查缓存
          cached_data = await cache_service.get_compound_info(name)
          if cached_data:
              await cache_service.close()
              return cached_data
          
          # 从PubChem获取数据
          async with PubChemClient() as client:
              # 获取CID
              cid = await client.get_compound_cid(name)
              if not cid:
                  await cache_service.close()
                  return {"name": name, "error": "Compound not found"}
              
              # 获取基础信息
              compound_data = await client.get_compound_by_name(name)
              
              if "error" in compound_data:
                  await cache_service.close()
                  return {"name": name, "error": compound_data["error"]}
              
              # 解析数据
              info = _parse_compound_data(name, cid, compound_data)
              
              # 缓存结果
              await cache_service.set_compound_info(name, info.model_dump())
              await cache_service.close()
              
              return info.model_dump()
              
      except Exception as e:
          logger.error(f"Error getting compound info for {name}: {e}")
          return {"name": name, "error": str(e)}

• pubchem_mcp/mcp_server.py:21-21 (registration)

  The `get_compound_info` tool is registered here using the `@app.tool()` decorator from the `FastMCP` framework.

  @app.tool()

• pubchem_mcp/mcp_server.py:156-177 (helper)

  A helper function `_parse_compound_data` used by `get_compound_info` to transform raw PubChem API responses into the structured `CompoundInfo` model.

  def _parse_compound_data(name: str, cid: int, data: Dict[str, Any]) -> CompoundInfo:
      """解析化合物数据"""
      try:
          properties = data.get("PropertyTable", {}).get("Properties", [])
          if not properties:
              return CompoundInfo(name=name, cid=cid)
          
          props = properties[0]
          
          return CompoundInfo(
              cid=cid,
              name=name,
              molecular_formula=props.get("MolecularFormula"),
              molecular_weight=props.get("MolecularWeight"),
              iupac_name=props.get("IUPACName"),
              smiles=props.get("IsomericSMILES"),
              inchi_key=props.get("InChIKey"),
              synonyms=[]  # 需要额外API调用获取
          )
      except Exception as e:
          logger.error(f"Error parsing compound data: {e}")
          return CompoundInfo(name=name, cid=cid)