Unofficial PubChem MCP Server

Instructions

Implementation Reference

• src/index.ts:1207-1227 (handler)

  The core execution logic for the batch_compound_lookup tool. Validates input using isValidBatchArgs, processes up to 10 CIDs by fetching MolecularWeight, CanonicalSMILES, IUPACName from PubChem API, collects results with success/error status, and returns JSON-formatted batch results.

  private async handleBatchCompoundLookup(args: any) {
    if (!isValidBatchArgs(args)) {
      throw new McpError(ErrorCode.InvalidParams, 'Invalid batch arguments');
    }
  
    try {
      const results = [];
      for (const cid of args.cids.slice(0, 10)) {
        try {
          const response = await this.apiClient.get(`/compound/cid/${cid}/property/MolecularWeight,CanonicalSMILES,IUPACName/JSON`);
          results.push({ cid, data: response.data, success: true });
        } catch (error) {
          results.push({ cid, error: error instanceof Error ? error.message : 'Unknown error', success: false });
        }
      }
  
      return { content: [{ type: 'text', text: JSON.stringify({ batch_results: results }, null, 2) }] };
    } catch (error) {
      throw new McpError(ErrorCode.InternalError, `Batch lookup failed: ${error instanceof Error ? error.message : 'Unknown error'}`);
    }
  }

• src/index.ts:719-730 (registration)

  Registration of the batch_compound_lookup tool in the ListTools response, including name, description, and full input schema definition.

  {
    name: 'batch_compound_lookup',
    description: 'Process multiple compound IDs efficiently',
    inputSchema: {
      type: 'object',
      properties: {
        cids: { type: 'array', items: { type: 'number' }, description: 'Array of PubChem CIDs (1-200)', minItems: 1, maxItems: 200 },
        operation: { type: 'string', enum: ['property', 'synonyms', 'classification', 'description'], description: 'Operation to perform (default: property)' },
      },
      required: ['cids'],
    },
  },

• src/index.ts:722-728 (schema)

  JSON schema defining the input parameters for batch_compound_lookup: required array of CIDs (1-200 numbers), optional operation enum.

  inputSchema: {
    type: 'object',
    properties: {
      cids: { type: 'array', items: { type: 'number' }, description: 'Array of PubChem CIDs (1-200)', minItems: 1, maxItems: 200 },
      operation: { type: 'string', enum: ['property', 'synonyms', 'classification', 'description'], description: 'Operation to perform (default: property)' },
    },
    required: ['cids'],

• src/index.ts:89-101 (helper)

  Type guard and validation helper function for batch_compound_lookup arguments, checking cids array validity and operation enum.

  const isValidBatchArgs = (
    args: any
  ): args is { cids: number[]; operation?: string } => {
    return (
      typeof args === 'object' &&
      args !== null &&
      Array.isArray(args.cids) &&
      args.cids.length > 0 &&
      args.cids.length <= 200 &&
      args.cids.every((cid: any) => typeof cid === 'number' && cid > 0) &&
      (args.operation === undefined || ['property', 'synonyms', 'classification', 'description'].includes(args.operation))
    );
  };

• src/index.ts:808-809 (registration)

  Dispatch registration in the CallToolRequestSchema switch statement, routing calls to the handleBatchCompoundLookup method.

  case 'batch_compound_lookup':
    return await this.handleBatchCompoundLookup(args);