HBAT Documentation

HBAT Documentation#

GitHub Release GitHub Actions Test Workflow Status https://img.shields.io/pypi/v/hbat https://img.shields.io/pypi/wheel/hbat https://img.shields.io/pypi/pyversions/hbat?logo=python&logoColor=white https://img.shields.io/github/last-commit/abhishektiwari/hbat/main PyPI - Status Conda Version https://img.shields.io/github/license/abhishektiwari/hbat GitHub Downloads (all assets, all releases) SourceForge Downloads PyPI Downloads Codecov Coverage Cited by Google Scholar Socket CodeFactor

Welcome to HBAT (Hydrogen Bond Analysis Tool) documentation!

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.

HBAT GUI

User Guide

Developer Guide

Quick Start#

Install HBAT#

pip install hbat

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

See complete installation instructions in Installation.

Basic usage#

hbat input.pdb                                                   # Show results in terminal
hbat input.pdb -o results.csv                                    # Save results to CSV file (default)
hbat input.pdb -o results.json  --fix-pdb                        # Apply PDB fixing and Save results to JSON file
hbat input.pdb -o results.json  --fix-pdb  --fix-method=pdbfixer # Apply PDB fixing using PdbFixer and Save results to JSON file

See full CLI options Command-Line Interface.

Features#

  • Comprehensive Analysis: Detects hydrogen bonds, halogen bonds, and X-H…π interactions

  • Cooperativity Detection: Identifies chains of cooperative molecular interactions

  • Structure Enhancement: Automated PDB fixing with OpenBabel and PDBFixer integration

  • Flexible Parameters: Customizable analysis parameters for different research needs

  • Multiple Output Formats: Support for CSV (default), JSON, and formatted text output with automated file generation for each interaction type

  • GUI Interface: User-friendly graphical interface for interactive analysis

  • Command Line Tool: Scriptable CLI for batch processing and automation

Cooperativity chain visualization

Cite HBAT#

@article{tiwari2023hbat,
    title={HBAT: A Python Package for Automated Hydrogen Bond Analysis in Macromolecular Structures},
    author={Tiwari, Abhishek and others},
    journal={Journal of Open Research Software},
    volume={11},
    number={1},
    pages={1-8},
    year={2023},
    publisher={Ubiquity Press}
}

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

Indices and tables#

Contents