PubChem MCP Server

Instructions

Implementation Reference

• src/index.ts:958-979 (handler)

  The main handler function that validates the input CID, calls the PubChem API to retrieve synonyms, and returns the JSON response as text content.

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

• src/index.ts:431-437 (schema)

  Input schema definition for the tool, specifying that 'cid' is required as a number or string.

  inputSchema: {
    type: 'object',
    properties: {
      cid: { type: ['number', 'string'], description: 'PubChem Compound ID (CID)' },
    },
    required: ['cid'],
  },

• src/index.ts:428-438 (registration)

  Tool registration in the tools list provided to MCP server.setRequestHandler(ListToolsRequestSchema), including name, description, and schema.

  {
    name: 'get_compound_synonyms',
    description: 'Get all names and synonyms for a compound',
    inputSchema: {
      type: 'object',
      properties: {
        cid: { type: ['number', 'string'], description: 'PubChem Compound ID (CID)' },
      },
      required: ['cid'],
    },
  },

• src/index.ts:750-751 (registration)

  Dispatcher case in the CallToolRequestSchema handler that routes calls to the specific handler function.

  case 'get_compound_synonyms':
    return await this.handleGetCompoundSynonyms(args);

• src/index.ts:65-74 (helper)

  Type guard function used for input validation in the handler, checking for valid 'cid' (number or string). Note: format check is extra but harmless.

  const isValidCidArgs = (
    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))
    );
  };