HBAT 2 (Hydrogen Bond Analysis Tool 2)

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

GitHub Release GitHub Actions Test Workflow Status PyPI Version PyPI Wheel Python Versions Last Commit PyPI - Status Conda Version License GitHub Downloads (all assets, all releases) SourceForge Downloads PyPI Downloads Codecov Coverage Socket CodeFactor HBAT 1.0/1.1 DOI Scholar Citations Arxiv Paper ChemRxiv Paper HBAT 2.0 Scholar Citations
HBAT Desktop

HBAT Desktop (Mac, Windows, Linux).#

HBAT Web

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

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

  • Hydrogen bond network (potential cooperativity/anticooperativity chains and water-mediated hydrogen bond networks) visualization using NetworkX/matplotlib and GraphViz

  • Export hydrogen bond network 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 2#

@article{tiwari_2026_hbat_arxiv,
   author       = {Tiwari, Abhishek},
   title        = {HBAT 2: A Python Package to analyse Hydrogen Bonds and Other Non-covalent Interactions in Macromolecular Structures},
   year         = 2026,
   publisher    = {arXiv},
   doi          = {10.48550/arXiv.2602.17712},
   url.         = {https://arxiv.org/abs/2602.17712},
}

Tiwari, A. (2026). HBAT 2: A Python Package to analyse Hydrogen Bonds and Other Non-covalent Interactions in Macromolecular Structures. arXiv. https://doi.org/10.48550/arXiv.2602.17712

@article{tiwari_2026_hbat_chemrxiv,
   author = {Abhishek Tiwari },
   title = {HBAT 2: A Python Package to Analyse Hydrogen Bonds and Other Non-covalent Interactions in Macromolecular Structures},
   publisher = {ChemRxiv},
   year = {2026},
   doi = {10.26434/chemrxiv.15000141/v1},
   URL = {https://chemrxiv.org/doi/abs/10.26434/chemrxiv.15000141/v1},
   eprint = {https://chemrxiv.org/doi/pdf/10.26434/chemrxiv.15000141/v1},
}

Tiwari, A. (2026). HBAT 2: A Python Package to analyse Hydrogen Bonds and Other Non-covalent Interactions in Macromolecular Structures. ChemRxiv. https://chemrxiv.org/doi/abs/10.26434/chemrxiv.15000141/v1

Cite HBAT 1.0 and 1.1#

@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

User Guide

Developer Guide

Indices and tables#