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 from Protein Data Bank (PDB). HBAT supports both .pdb and .cif (mmCIF) file formats and 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

  • Water Bridges: Water-mediated hydrogen bond networks connecting protein/ligand residues

  • Ligand Interactions: Comprehensive detection of all interaction types between ligands and protein/nucleic acid residues

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 PyMoL
Visualizing interactions using PyMoL

Visualizing interactions with HBAT Web using D3MOl and PyMOL (PDB Entry 6RSA)#

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, n-π interactions, water bridges, and ligand 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

  • Ligand interaction analysis with residue-specific visualization and filtering

  • Water bridge detection and analysis with bridge path visualization

  • 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

  • 3D visualization of interactions using 3Dmol.js in Jupyter notebooks and HBAT web interface

  • Export and visualize interactions in PyMOL from HBAT web interface

  • 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#