HBAT (Hydrogen Bond Analysis Tool) v2

HBAT (Hydrogen Bond Analysis Tool) v2#

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

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Background#

HBAT v2 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 v2#

  • 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.

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

User Guide

Developer Guide

Indices and tables#

Contents