Unofficial PubChem MCP Server

Instructions

Implementation Reference

• src/index.ts:882-905 (handler)

  The core handler function for the 'get_compound_info' tool. Validates input using isValidCidArgs, fetches compound data from PubChem REST API by CID in specified format (default JSON), and returns the response as text content.

  private async handleGetCompoundInfo(args: any) {
    if (!isValidCidArgs(args)) {
      throw new McpError(ErrorCode.InvalidParams, 'Invalid CID arguments');
    }
  
    try {
      const format = args.format || 'json';
      const response = await this.apiClient.get(`/compound/cid/${args.cid}/${format === 'json' ? 'JSON' : format}`);
  
      return {
        content: [
          {
            type: 'text',
            text: format === 'json' ? JSON.stringify(response.data, null, 2) : String(response.data),
          },
        ],
      };
    } catch (error) {
      throw new McpError(
        ErrorCode.InternalError,
        `Failed to get compound info: ${error instanceof Error ? error.message : 'Unknown error'}`
      );
    }
  }

• src/index.ts:383-394 (schema)

  Tool definition in ListTools response, including name, description, and input schema for validation (cid required, format optional).

  {
    name: 'get_compound_info',
    description: 'Get detailed information for a specific compound by PubChem CID',
    inputSchema: {
      type: 'object',
      properties: {
        cid: { type: ['number', 'string'], description: 'PubChem Compound ID (CID)' },
        format: { type: 'string', enum: ['json', 'sdf', 'xml', 'asnt', 'asnb'], description: 'Output format (default: json)' },
      },
      required: ['cid'],
    },
  },

• src/index.ts:742-743 (registration)

  Switch case in CallToolRequest handler that routes 'get_compound_info' tool calls to the handleGetCompoundInfo method.

  case 'get_compound_info':
    return await this.handleGetCompoundInfo(args);

• src/index.ts:66-74 (helper)

  Type guard function validating input arguments for get_compound_info tool, matching the input schema.

    args: any
  ): args is { cid: number | string; format?: string } => {
    return (
      typeof args === 'object' &&
      args !== null &&
      (typeof args.cid === 'number' || typeof args.cid === 'string') &&
      (args.format === undefined || ['json', 'sdf', 'xml', 'asnt', 'asnb'].includes(args.format))
    );
  };