HBAT Documentation

HBAT Documentation#

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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 in macromolecular structures, available in Protein Data Bank (PDB) file format. HBAT uses a geometric approach to identify molecular interactions by analyzing distance and angular criteria.

Supported Interaction Types:

  • Hydrogen Bonds: Classical N-H···O, O-H···O, and weak C-H···O interactions

  • Halogen Bonds: C-X···A interactions (X = Cl, Br, I)

  • π Interactions: X-H···π interactions with aromatic rings (Phe, Tyr, Trp, His)

  • π-π Stacking: Aromatic ring-ring interactions (parallel, T-shaped, offset)

  • Carbonyl Interactions: n→π* interactions between carbonyl groups

  • n-π Interactions: Lone pair interactions with aromatic π systems

HBAT GUI

User Guide

Developer Guide

Quick Start#

Install HBAT#

pip install hbat

Run HBAT Command-Line Interface (CLI) using hbat or launch HBAT GUI using hbat-gui.

See complete installation instructions in Installation.

Basic usage#

hbat input.pdb                                                   # Show results in terminal
hbat input.pdb -o results.csv                                    # Save results to CSV file (default)
hbat input.pdb -o results.json  --fix-pdb                        # Apply PDB fixing and Save results to JSON file
hbat input.pdb -o results.json  --fix-pdb  --fix-method=pdbfixer # Apply PDB fixing using PdbFixer and Save results to JSON file

See full CLI options Command-Line Interface.

Features#

  • Comprehensive Interaction Detection: Hydrogen bonds, halogen bonds, π interactions, π-π stacking, carbonyl interactions, and n-π interactions

  • Automated PDB Fixing: Integration with OpenBabel and PDBFixer for structure preparation

  • Multiple Interfaces: Graphical (tkinter), command-line, and programming interfaces

  • Batch Processing: CLI/API for automation and large-scale analysis

  • Cooperativity Analysis: Chain visualization using NetworkX/matplotlib and GraphViz

  • Flexible Export: PNG, SVG, PDF visualizations; CSV, JSON, text data formats

  • Built-in Presets: Optimized parameters for high-resolution, NMR, membrane proteins, etc.

  • Customizable Parameters: Adjustable distance cutoffs, angle thresholds, and analysis modes

  • High Performance: NumPy-vectorized algorithms for efficient large structure analysis

  • Cross-Platform: Works on Windows, macOS, and Linux

Cooperativity chain visualization

Cite HBAT#

@article{tiwari2007hbat,
   author = {Tiwari, Abhishek and Panigrahi, Sunil Kumar},
   doi = {10.3233/ISI-2007-00337},
   journal = {In Silico Biology},
   month = dec,
   number = {6},
   title = {{HBAT: A Complete Package for Analysing Strong and Weak Hydrogen Bonds in Macromolecular Crystal Structures}},
   volume = {7},
   year = {2007}
}

Tiwari, A., & Panigrahi, S. K. (2007). HBAT: A Complete Package for Analysing Strong and Weak Hydrogen Bonds in Macromolecular Crystal Structures. In Silico Biology, 7(6). https://doi.org/10.3233/ISI-2007-00337

Indices and tables#

Contents