HBAT Documentation

Welcome to HBAT (Hydrogen Bond Analysis Tool) documentation!

A Python package to automate the analysis of potential hydrogen bonds and similar type of weak interactions like halogen bonds and non-canonical interactions in macromolecular structures, available in Brookhaven Protein Database (PDB) file format. HBAT uses a geometric approach to identify potential hydrogen bonds by analyzing distance and angular criteria between donor-hydrogen-acceptor triplets.

Contents:

• Installation
  • Requirements
  • Installation Methods
  • Verification
• Quick Start Guide
  • Basic Usage
  • Next Steps
• Command-Line Interface
  • Basic Usage
  • Command-Line Options
  • Examples
  • Output Formats
  • Exit Codes
  • Integration with Scripts
• Analysis Parameters Guide
  • Overview
  • Hydrogen Bond Parameters
  • Halogen Bond Parameters
  • π Interaction Parameters
  • General Analysis Parameters
  • Parameter Tuning Guidelines
  • Common Use Cases
  • Parameter Presets
  • Command Line Usage
  • Literature References
• API Reference
  • Core Modules
  • Command Line Interface
  • Graphical User Interface
  • Constants and Utilities
  • API Usage Examples
• Development Guide
  • Quick Start
  • Project Structure
  • Development Workflow
  • Core Components
  • Adding New Features
  • Testing Guidelines
  • Performance Considerations
  • Contributing
  • License
• Algorithm & Calculation Logic
  • 1. Algorithm Overview
  • 2. Core Calculation Steps
  • 3. Geometric Validation Process
  • 4. Key Parameters and Defaults
  • 5. Covalent Bond Detection
  • 6. Vector Mathematics
  • 7. Analysis Flow
  • 8. Output Structure
  • 9. Additional Features
• License

Features

• Comprehensive Analysis: Detects hydrogen bonds, halogen bonds, and X-H…π interactions

• Cooperativity Detection: Identifies chains of cooperative molecular interactions

• Flexible Parameters: Customizable analysis parameters for different research needs

• Multiple Output Formats: Support for CSV, JSON, and formatted text output

• GUI Interface: User-friendly graphical interface for interactive analysis

• Command Line Tool: Scriptable CLI for batch processing and automation

Quick Start

Install HBAT:

pip install hbat

Basic usage:

hbat input.pdb                          # Basic analysis
hbat input.pdb -o results.txt           # Save results to file

See full CLI options Command-Line Interface.

Indices and tables

• Index

• Module Index

• Search Page