PubChem MCP Server

Instructions

Implementation Reference

• src/index.ts:958-979 (handler)

  Main execution logic for get_compound_synonyms tool: validates CID input, calls PubChem API for synonyms, returns JSON response.

  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:428-438 (schema)

  Tool registration entry including name, description, and input schema (requires 'cid' as number or string). Serves both registration and schema purposes.

  {
    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 CallToolRequestSchema handler that routes calls to the tool's handler function.

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

• src/index.ts:65-74 (helper)

  Type guard function for validating CID-based arguments, used in the handler for input validation.

  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))
    );
  };