AI Agent Integration

codemol includes an AI agent system that lets users interact with molecular structures using natural language. The agent calls the same tool system as manual commands.

Key Idea

User: "show me the hydrogen bonds between the ligand and protein"

Agent internally calls:
  /interactions hbonds
  /rep sticks organic
  /labels smart ligand

Agent responds:
  "I found 4 hydrogen bonds between the ligand and surrounding residues..."

Sections

• Architecture — The run_agent loop and multi-round tool calling
• Agent Types — 7 specialist agents and the router system
• Tool Bridge — Schema generation and tool execution bridge