Unofficial PubChem MCP Server

Instructions

Implementation Reference

• src/index.ts:1152-1154 (handler)

  The primary handler function implementing the 'search_by_target' tool logic. It is a placeholder that returns a 'not yet implemented' message with the input arguments.

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

• src/index.ts:612-623 (registration)

  Registration of the 'search_by_target' tool in the ListToolsRequestSchema handler, including its name, description, and input schema definition.

  {
    name: 'search_by_target',
    description: 'Find compounds tested against a specific biological target',
    inputSchema: {
      type: 'object',
      properties: {
        target: { type: 'string', description: 'Target name (gene, protein, or pathway)' },
        activity_type: { type: 'string', description: 'Type of activity (e.g., IC50, EC50, Ki)' },
        max_records: { type: 'number', description: 'Maximum number of results (1-1000, default: 100)', minimum: 1, maximum: 1000 },
      },
      required: ['target'],
    },

• src/index.ts:615-623 (schema)

  The input schema defining the expected parameters for the 'search_by_target' tool.

  inputSchema: {
    type: 'object',
    properties: {
      target: { type: 'string', description: 'Target name (gene, protein, or pathway)' },
      activity_type: { type: 'string', description: 'Type of activity (e.g., IC50, EC50, Ki)' },
      max_records: { type: 'number', description: 'Maximum number of results (1-1000, default: 100)', minimum: 1, maximum: 1000 },
    },
    required: ['target'],
  },

• src/index.ts:786-787 (registration)

  Dispatch case in the CallToolRequestSchema handler that routes calls to the 'search_by_target' tool to its handler function.

  case 'search_by_target':
    return await this.handleSearchByTarget(args);