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ChemSpace Copilot

LLM-powered agent system for GTM-based chemical space analysis

ChemSpace Copilot is a multi-agent system powered by the Agno framework. The default runtime team coordinates seven specialized AI agents for ChEMBL bioactivity download, unified GTM workflows, downstream chemoinformatics, report generation, small-molecule generation, peptide generation, and retrosynthetic planning. A separate robustness evaluation agent is available for analyzing prompt-robustness test outputs. The GTM engine is provided by chemographykit.

Features

  • 7 Runtime Agents + 1 Evaluation Agent — ChEMBL data download, unified GTM operations, chemoinformatics analysis, report generation, small-molecule generation, peptide WAE workflows, retrosynthetic planning, and robustness evaluation
  • Generative Topographic Mapping — Dimensionality reduction and visualization of chemical space via chemographykit
  • Molecular and Peptide Generation — LSTM autoencoder-based small-molecule generation plus peptide WAE generation, interpolation, and GTM-guided targeting
  • S3/MinIO Integration — Session-scoped cloud storage with local filesystem fallback
  • Chainlit Interface — WebSocket-based real-time chat with password authentication, file upload, and inline molecule rendering
  • Agentic Memory — SQLite-backed agentic state and recent session history shared across agent workflows
  • Robustness Testing — Framework for validating prompt variation handling with semantic similarity scoring

Architecture

┌─────────────────────────────────────────┐
│  UI Layer (Chainlit)                    │  Real-time chat interface
├─────────────────────────────────────────┤
│  Agent Orchestration (teams.py)         │  Multi-agent coordination
├─────────────────────────────────────────┤
│  Specialized Agents (factories.py)      │  7 runtime agents + 1 evaluation agent
├─────────────────────────────────────────┤
│  Tools + Storage (toolkits + S3)        │  Domain logic & persistence
└─────────────────────────────────────────┘

Quick Start

Get started with the Installation Guide or the Docker Deployment Guide.