Agent System¶

The system uses a Factory Pattern + Registry for agent creation.

Location: src/cs_copilot/agents/

Key Files¶

factories.py — 8 factory classes (7 runtime agents plus the robustness evaluation agent)
registry.py — Dynamic agent registry with auto-discovery
teams.py — Multi-agent team coordination using the Agno framework
prompts.py — Agent instructions and system prompts

Runtime Team Agents¶

Agent	Role
ChEMBL Downloader	Downloads and filters bioactivity data from the ChEMBL database
GTM Agent	Unified GTM workflows: build, load, density, activity, projection, and GTM sampling support
Chemoinformatician	Downstream chemoinformatics analysis including scaffold, similarity, clustering, and SAR workflows
Report Generator	Formats analysis outputs into reports and visual artifacts
Autoencoder	Small-molecule generation via LSTM autoencoders, including standalone and GTM-guided modes
Peptide WAE	Peptide generation, latent-space GTM workflows, and DBAASP-backed peptide activity landscapes
SynPlanner	Retrosynthetic planning and route visualization for target molecules

Separate Evaluation Agent¶

Agent	Role
Robustness Evaluation	Analyzes robustness test runs, score distributions, failures, and trends

Adding a New Agent¶

Create a factory in src/cs_copilot/agents/factories.py:

class MyNewAgentFactory(BaseAgentFactory):
    def create_agent(self, model, **kwargs):
        config = AgentConfig(
            name="my_new_agent",
            description="What this agent does",
            instructions="Detailed instructions here",
            tools=[MyToolkit(), ...],
            model=model,
            **kwargs
        )
        return self._create_agent(config)

The registry auto-discovers it via AgentRegistry.auto_register()
Add to the team in teams.py if needed