HBAT 2 (Hydrogen Bond Analysis Tool 2)#

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 and C-X···π interactions with aromatic rings (Phe, Tyr, Trp, His, etc.)
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

Announcement

HBAT 2 Web Interface is Live! Try it out at hbat-web.abhishek-tiwari.com

https://img.shields.io/github/last-commit/abhishektiwari/hbat/main

https://img.shields.io/github/license/abhishektiwari/hbat

GitHub Downloads (all assets, all releases)

HBAT Web (https://hbat-web.abhishek-tiwari.com)#

Visualizing interactions using Jupyter notebook — Visualizing interactions using HBAT Web (Halogen Bond in PDB Entry 4x21).#

Cooperativity chain detection and visualization (PDB Entry 6RSA).#

Background#

HBAT 2 is a modern Python re-implementation of the original Perl-based tool developed by Abhishek Tiwari and Sunil Kumar Panigrahi. HBAT v1 can still be downloaded from SourceForge however Perl version is not maintained anymore.

Highlights of HBAT 2#

Detect and analyze potential hydrogen bonds, halogen bonds, π interactions, π-π stacking, carbonyl interactions, and n-π interactions
Automated PDB fixing with OpenBabel and PDBFixer integration
Support graphical (tkinter), command-line, and programming API interfaces
Use graphical interfaces for interactive analysis, CLI/API for batch processing and automation
Cooperativity chain visualization using NetworkX/matplotlib and GraphViz
Export cooperativity chain visualizations to PNG, SVG, PDF formats
Built-in presets for different structure types (high-resolution, NMR, membrane proteins, etc.)
Customizable distance cutoffs, angle thresholds, and analysis modes.
Multiple Output Formats: Text, CSV, and JSON export options
Optimized algorithms for efficient analysis of large structures
Cross-Platform: Works on Windows, macOS, and Linux.

Cite HBAT & HBAT 2#

@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}
}

@misc{tiwari_2025_17645321,
   author    = {Tiwari, Abhishek},
   title     = {HBAT 2: A Python Package to analyse Hydrogen Bonds and Other Non-covalent Interactions in Macromolecular Structures},
   month     = nov,
   year      = 2025,
   publisher = {Zenodo},
   doi       = {10.5281/zenodo.17645321},
   url       = {https://doi.org/10.5281/zenodo.17645321},
}

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

Tiwari, A. (2025). HBAT 2: A Python Package to analyse Hydrogen Bonds and Other Non-covalent Interactions in Macromolecular Structures. Zenodo. https://doi.org/10.5281/zenodo.17645321

User Guide

Developer Guide

HBAT 2 (Hydrogen Bond Analysis Tool 2)

Contents

HBAT 2 (Hydrogen Bond Analysis Tool 2)#

Background#

Highlights of HBAT 2#

Cite HBAT & HBAT 2#

Indices and tables#