API Reference

This section contains the complete API documentation for HBAT.

Core Package

• Module Overview
  • Molecular Interaction Analyzer
  • Molecular Interaction Data Structures
  • Core Data Structures
  • PDB File Parser
  • PDB Structure Fixer
  • Vecctor Support
• Main Analysis Engine
  • Molecular Interaction Analyzer
• Interaction Data Structures
  • Molecular Interaction Classes
• PDB Structure Handling
  • PDB File Parser
  • Molecular Data Structures
• PDB Structure Enhancement
  • PDB Structure Fixer
• 3D Vector Mathematics
  • NumPy Vector Operations
  • Utility Functions
• Legacy Compatibility
  • Analysis Module (Backward Compatibility)
• Performance Notes

CCD Package

• CCD Package
  • Module Overview
• Key Components
  • Usage Example
  • Data Storage

Command Line Interface

• Main CLI Module
  • ProgressBar
  • create_parser()
  • get_example_presets_directory()
  • list_available_presets()
  • load_preset_file()
  • resolve_preset_path()
  • load_parameters_from_args()
  • print_progress()
  • print_error()
  • validate_input_file()
  • format_results_text()
  • export_to_json()
  • detect_output_format()
  • export_to_csv_files()
  • export_to_json_files()
  • export_to_csv()
  • run_analysis()
  • main()

Graphical User Interface

• Graphical User Interface
  • Core Components
• Main Window
  • MainWindow
  • Dialog Components
• Geometry Cutoffs Dialog
  • GeometryCutoffsDialog
• Preset Manager Dialog
  • PresetManagerDialog
• PDB Fixing Dialog
  • PDBFixingDialog
• Results Panel
  • ResultsPanel
• Chain Visualization
  • ChainVisualizationWindow
  • Visualization System
• Visualization Renderer Protocol
  • VisualizationRenderer
  • BaseVisualizationRenderer
  • RendererFactory
• GraphViz Renderer
  • GraphVizRenderer
• Matplotlib Renderer
  • MatplotlibRenderer
• Export Manager
  • ExportManager
  • ExportDialog
  • show_quick_export_dialog()
• GraphViz Preferences Dialog
  • GraphVizPreferencesDialog
  • show_graphviz_preferences()

Constants

• Constants
• Modules
  • Analysis Parameters
  • Atomic Data
  • PDB Structure Constants
  • Miscellaneous Constants
  • Application Metadata

Utilities

• Utilities
• Overview
• Modules
  • Atom Utilities
  • GraphViz Utilities
• Module Summary
• Key Features
• Usage Examples
• Migration Notes

API Usage Examples

• API Usage Examples
• Basic Analysis
  • Simple Hydrogen Bond Analysis
  • Advanced Parameter Customization
  • Multi-Type Interaction Analysis
• Batch Processing
  • Processing Multiple Structures
  • Comparative Analysis
• Data Export and Visualization
  • Detailed CSV Export
  • JSON Export with Metadata
• Specialized Analysis Tasks
  • Drug-Target Interaction Analysis
  • Membrane Protein Analysis
• Integration with Other Tools
  • Using with Pandas for Analysis