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 2 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

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.

Please review HBAT documentation for more details.

Installation

Option 1: Install from PyPI (Recommended)

pip install hbat

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

Option 2: Install from Source

git clone https://github.com/abhishektiwari/hbat.git
cd hbat
pip install -e .

Alternatively,

pip install git+https://github.com/abhishektiwari/hbat.git

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

Option 3: Install from Conda

conda install -c hbat hbat

Requirements

System Requirements

• Python: 3.9 or higher
• tkinter: tkinter is included with Python standard library on most systems. However, on Mac install Python and tkinter using brew.

brew install python python3-tk

• GraphViz (Optional): Required for advanced cooperativity chain visualization with high-quality graph rendering. HBAT will automatically fall back to NetworkX/matplotlib visualization if GraphViz is not available.

Install GraphViz:

On Ubuntu/Debian:

sudo apt-get update
sudo apt-get install graphviz

On macOS (using Homebrew):

brew install graphviz

On Windows:

• Download and install from GraphViz official website
• Or using Chocolatey: choco install graphviz
• Or using conda: conda install -c conda-forge graphviz

Note: After installing GraphViz, restart your terminal/command prompt before running HBAT to ensure the GraphViz executables are available in your PATH.

Usage

Graphical Interface

Launch the GUI application:

hbat-gui

The GUI provides,

• File browser for loading PDB files
• Parameter configuration panels
• Tabbed results display
• Export and visualization options

Command-Line Interface

Basic usage:

hbat input.pdb

Output Format Options

HBAT supports multiple output formats:

# No output flag - displays results to console
hbat input.pdb                    # Display results to console

# Single file outputs (format auto-detected from extension)
hbat input.pdb -o results.txt     # Text format (human-readable summary + details)
hbat input.pdb -o results.json    # JSON format (single file with all interactions)

# Multiple file outputs (separate files per interaction type)
hbat input.pdb --csv results      # Creates results_h_bonds.csv, results_x_bonds.csv, etc.
hbat input.pdb --json results     # Creates results_h_bonds.json, results_x_bonds.json, etc.

With custom parameters:

hbat input.pdb -o results.txt --hb-distance 3.0 --mode local

List Available Presets

hbat --list-presets

Use a specific preset

hbat protein.pdb --preset high_resolution
hbat membrane_protein.pdb --preset membrane_proteins

Use preset with custom overrides

hbat protein.pdb --preset drug_design_strict --hb-distance 3.0 --verbose

CLI Options

positional arguments:
  input                 Input PDB file

optional arguments:
  -h, --help            show this help message and exit
  -o OUTPUT, --output OUTPUT
                        Output file (format auto-detected from extension: .txt, .json)
  --json JSON           Export to multiple JSON files (base name for files)
  --csv CSV             Export to multiple CSV files (base name for files)

Preset Options:
  --preset PRESET       Load parameters from preset file (.hbat or .json)
  --list-presets        List available example presets and exit

Analysis Parameters:
  Hydrogen Bond Parameters:
  --hb-distance HB_DISTANCE
                        Hydrogen bond H...A distance cutoff in Å (default: 2.5)
  --hb-angle HB_ANGLE   Hydrogen bond D-H...A angle cutoff in degrees (default: 120)
  --da-distance DA_DISTANCE
                        Donor-acceptor distance cutoff in Å (default: 3.5)

  Halogen Bond Parameters:
  --xb-distance XB_DISTANCE
                        Halogen bond X...A distance cutoff in Å (default: 3.9)
  --xb-angle XB_ANGLE   Halogen bond C-X...A angle cutoff in degrees (default: 150)

  π Interaction Parameters:
  --pi-distance PI_DISTANCE
                        π interaction H...π distance cutoff in Å (default: 3.5)
  --pi-angle PI_ANGLE   π interaction D-H...π angle cutoff in degrees (default: 110)

  π-π Stacking Parameters:
  --pi-pi-distance PI_PI_DISTANCE
                        π-π centroid-to-centroid distance cutoff in Å (default: 3.8)
  --pi-pi-parallel-angle PI_PI_PARALLEL_ANGLE
                        Maximum angle for parallel π-π stacking in degrees (default: 30.0)
  --pi-pi-tshaped-angle-min PI_PI_TSHAPED_ANGLE_MIN
                        Minimum angle for T-shaped π-π stacking in degrees (default: 60.0)
  --pi-pi-tshaped-angle-max PI_PI_TSHAPED_ANGLE_MAX
                        Maximum angle for T-shaped π-π stacking in degrees (default: 90.0)
  --pi-pi-offset PI_PI_OFFSET
                        Maximum lateral offset for parallel π-π stacking in Å (default: 2.0)

  Carbonyl Interaction Parameters (n→π*):
  --carbonyl-distance CARBONYL_DISTANCE
                        Carbonyl O···C distance cutoff in Å (default: 3.2)
  --carbonyl-angle-min CARBONYL_ANGLE_MIN
                        Minimum O···C=O angle for carbonyl interactions in degrees (default: 95.0)
  --carbonyl-angle-max CARBONYL_ANGLE_MAX
                        Maximum O···C=O angle for carbonyl interactions in degrees (default: 125.0)

  n→π* Interaction Parameters:
  --n-pi-distance N_PI_DISTANCE
                        Lone pair to π center distance cutoff in Å (default: 3.6)
  --n-pi-sulfur-distance N_PI_SULFUR_DISTANCE
                        Sulfur-specific distance cutoff in Å (default: 4.0)
  --n-pi-angle-min N_PI_ANGLE_MIN
                        Minimum angle to π plane in degrees (default: 0.0)
  --n-pi-angle-max N_PI_ANGLE_MAX
                        Maximum angle to π plane in degrees (default: 45.0)

  General Parameters:
  --covalent-factor COVALENT_FACTOR
                        Covalent bond detection factor (default: 0.85)
  --mode {complete,local}
                        Analysis mode: complete (all interactions) or local (intra-residue only)

Output Control:
  --verbose, -v         Verbose output with detailed progress
  --quiet, -q           Quiet mode with minimal output
  --summary-only        Output summary statistics only

Analysis Filters:
  --no-hydrogen-bonds   Skip hydrogen bond analysis
  --no-halogen-bonds    Skip halogen bond analysis
  --no-pi-interactions  Skip π interaction analysis
  --no-pi-pi-stacking   Skip π-π stacking analysis
  --no-carbonyl-interactions
                        Skip carbonyl n→π* interaction analysis
  --no-n-pi-interactions
                        Skip n→π* interaction analysis

Example Notebooks

Interactive Jupyter notebooks demonstrating HBAT usage with 3D visualizations using Py3DMol.

Notebook	Description	Colab
01_analyze_6rsa_with_visualization.ipynb	Hydrogen bond analysis of 6RSA (Ribonuclease A) with py3Dmol visualization
02_halogen_bonds_4x21.ipynb	Halogen bond detection and visualization in 4X21 structure
03_pdbfixer_vs_openbabel_comparison.ipynb	Comparing PDBFixer vs OpenBabel for hydrogen addition

See the notebooks directory for more details.

License

This project is licensed under the MIT License - see the LICENSE file for details.

Cite HBAT and HBAT 2

If you use HBAT or HBAT 2 in your research, please cite:

@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},
}

Contributing

See our contributing guide and development guide. At a high-level,

1. Fork the repository
2. Create a feature branch
3. Make your changes
4. Add tests if applicable
5. Submit a pull request