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.

User Guide

• Installation
• Quick Start Guide
• Command-Line Interface
• Analysis Parameters Guide
• PDB Structure Fixing
• License

Developer Guide

• API Reference
• Development Guide
• Algorithm & Calculation Logic

Quick Start

Install HBAT

pip install hbat

Recommended: For fixing missing Hydrogen Atoms, install PDBFixer (preferred over OpenBabel). See PDB Structure Fixing for details.

pip install git+https://github.com/abhishektiwari/hbat.git

If you installed HBAT from PyPI, you can also install PDBFixer using,

pip install git+https://github.com/openmm/pdbfixer.git

See complete installation instructions in Installation.

Basic usage

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

See full CLI options Command-Line Interface.

Features

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

• Cooperativity Detection: Identifies chains of cooperative molecular interactions

• Structure Enhancement: Automated PDB fixing with OpenBabel and PDBFixer integration

• 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

Indices and tables

• Index

• Module Index

• Search Page