Hydrogen Bond Analysis Tool (HBAT) v2

A Python package to automate the analysis of potential hydrogen bonds and similar type of weak interactions like halogen bonds and non-canonical interactions in macromolecular structures, available in Brookhaven Protein Database (PDB) file format. HBAT uses a geometric approach to identify potential hydrogen bonds by analyzing distance and angular criteria between donor-hydrogen-acceptor triplets.

Background

HBAT v2 is a modern Python re-implementation of the original Perl-based tool developed by Abhishek Tiwari and Sunil Kumar Panigrahi.

Features

• Comprehensive Analysis: Detect and analyze potential hydrogen bonds, halogen bonds, and X-H...π interactions
• Dual Interface: Both graphical (tkinter) and command-line interfaces
• Advanced Visualization: Choice between NetworkX/matplotlib and GraphViz renderers for cooperativity chain visualization
• High-Quality Graphics: Export visualizations to PNG, SVG, PDF with configurable resolution
• Interactive GUI: Scrollable visualizations with dynamic layout switching and engine selection
• Parameter Presets: Built-in presets for different structure types (high-resolution, NMR, membrane proteins, etc.)
• Flexible Parameters: Customizable distance cutoffs, angle thresholds, and analysis modes.
• Multiple Output Formats: Text, CSV, and JSON export options
• Fast Processing: Optimized algorithms for efficient analysis of large structures
• Cross-Platform: Works on Windows, macOS, and Linux.

Please review HBAT documentation for more details.

Supported Interactions

1. Hydrogen Bonds: O-H...O, N-H...O, N-H...N, and other X-H...Y interactions
2. Halogen Bonds: C-X...Y interactions (X = F, Cl, Br, I; Y = N, O, S)
3. X-H...π Interactions: Hydrogen bonds to aromatic ring systems

Please review HBAT documentation for more details.

Installation

Option 1: Install from PyPI (Recommended)

bash pip install hbat

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

Option 2: Install from Source

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

Alternatively,

bash 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: bash sudo apt-get update sudo apt-get install graphviz

On macOS (using Homebrew): bash 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:

bash 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:

bash hbat input.pdb

Output Format Options

HBAT supports multiple output formats with automatic detection based on file extension:

```bash

Single file outputs (format auto-detected from extension)

hbat input.pdb -o results.txt # Text format hbat input.pdb -o results.csv # CSV format (single file with all data) hbat input.pdb -o results.json # JSON format (single file with all data)

Multiple file outputs (separate files per interaction type)

hbat input.pdb --csv results # Creates resultshbonds.csv, resultsxbonds.csv, etc. hbat input.pdb --json results # Creates resultshbonds.json, resultsxbonds.json, etc. ```

With custom parameters:

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

List Available Presets

bash hbat --list-presets

Use a specific preset

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

Use preset with custom overrides

bash 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, .csv, .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: --hb-distance HBDISTANCE Hydrogen bond H...A distance cutoff in Å (default: 3.5) --hb-angle HBANGLE Hydrogen bond D-H...A angle cutoff in degrees (default: 120) --da-distance DADISTANCE Donor-acceptor distance cutoff in Å (default: 4.0) --xb-distance XBDISTANCE Halogen bond X...A distance cutoff in Å (default: 4.0) --xb-angle XBANGLE Halogen bond C-X...A angle cutoff in degrees (default: 120) --pi-distance PIDISTANCE π interaction H...π distance cutoff in Å (default: 4.5) --pi-angle PIANGLE π interaction D-H...π angle cutoff in degrees (default: 90) --covalent-factor COVALENTFACTOR Covalent bond detection factor (default: 1.2) --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 ```

License

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

Citation

If you use HBAT in your research, please cite:

@software{tiwari2025hbat, author = {Tiwari, Abhishek}, title = {HBAT: Hydrogen Bond Analysis Tool}, version = {v2}, year = {2025}, url = {https://github.com/abhishektiwari/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} }

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