PubChem MCP Server

Instructions

Implementation Reference

• src/index.ts:1012-1014 (handler)

  The handler function for the 'substructure_search' tool. It is a placeholder implementation that returns a message indicating it is not yet implemented.

  private async handleSubstructureSearch(args: any) {
    return { content: [{ type: 'text', text: JSON.stringify({ message: 'Substructure search not yet implemented', args }, null, 2) }] };
  }

• src/index.ts:454-465 (schema)

  The tool schema definition including name, description, and input schema for 'substructure_search'.

  {
    name: 'substructure_search',
    description: 'Find compounds containing a specific substructure',
    inputSchema: {
      type: 'object',
      properties: {
        smiles: { type: 'string', description: 'SMILES string of the substructure query' },
        max_records: { type: 'number', description: 'Maximum number of results (1-10000, default: 100)', minimum: 1, maximum: 10000 },
      },
      required: ['smiles'],
    },
  },

• src/index.ts:756-757 (registration)

  The switch case in the request handler that dispatches calls to the 'substructure_search' handler function.

  case 'substructure_search':
    return await this.handleSubstructureSearch(args);