Skip to content

API Reference

This section provides comprehensive API documentation for DeepCritical's core modules and components.

Core Modules

Agents API

Complete documentation for the agent system including specialized agents, orchestrators, and workflow management.

→ Agents API Documentation

  • AgentType - Agent type enumeration
  • AgentDependencies - Agent configuration and dependencies
  • BaseAgent - Abstract base class for all agents
  • AgentOrchestrator - Multi-agent coordination
  • CodeExecutionAgent - Code execution and improvement
  • CodeGenerationAgent - Natural language to code conversion
  • CodeImprovementAgent - Error analysis and code enhancement

Tools API

Documentation for the tool ecosystem, registry system, and execution framework.

→ Tools API Documentation

  • ToolRunner - Abstract base class for tools
  • ToolSpec - Tool specification and metadata
  • ToolRegistry - Global tool registry and management
  • ExecutionResult - Tool execution results
  • ToolRequest/ToolResponse - Tool communication interfaces

Data Types

Agent Framework Types

Core types for agent communication and state management.

→ Agent Framework Types

  • AgentRunResponse - Agent execution response
  • ChatMessage - Message format for agent communication
  • Role - Message roles (user, assistant, system)
  • Content - Message content types
  • TextContent - Text message content

Research Types

Types for research workflows and data structures.

→ Research Types

  • ResearchState - Main research workflow state
  • ResearchOutcome - Research execution results
  • StepResult - Individual step execution results
  • ExecutionHistory - Workflow execution tracking

Configuration API

Hydra Configuration

Configuration management and validation system.

→ Configuration API

  • Configuration file structure
  • Environment variable integration
  • Configuration validation
  • Dynamic configuration composition

Tool Categories

Knowledge Query Tools

Tools for information retrieval and knowledge querying.

→ Knowledge Query Tools

Sequence Analysis Tools

Bioinformatics tools for sequence analysis and processing.

→ Sequence Analysis Tools

Structure Prediction Tools

Molecular structure prediction and modeling tools.

→ Structure Prediction Tools

Molecular Docking Tools

Drug-target interaction and docking simulation tools.

→ Molecular Docking Tools

De Novo Design Tools

Novel molecule design and generation tools.

→ De Novo Design Tools

Function Prediction Tools

Protein function annotation and prediction tools.

→ Function Prediction Tools

Specialized APIs

Bioinformatics Integration

APIs for bioinformatics data sources and integration.

→ Bioinformatics API

RAG System API

Retrieval-augmented generation system interfaces.

→ RAG API

Search Integration API

Web search and content processing APIs.

→ Search API

MCP Server Framework

MCP Server Base Classes

Base classes for Model Context Protocol server implementations.

→ MCP Server Base Classes

  • MCPServerBase - Enhanced base class with Pydantic AI integration
  • @mcp_tool - Custom decorator for Pydantic AI tool creation
  • MCPServerConfig - Server configuration management

Available MCP Servers

29 pre-built bioinformatics MCP servers with containerized deployment.

→ Available MCP Servers

Development APIs

Testing Framework

APIs for comprehensive testing and validation.

→ Testing API

CI/CD Integration

APIs for continuous integration and deployment.

→ CI/CD API