API Usage Examples

API Usage Examples#

HBAT 2 provides interactive Jupyter notebooks demonstrating various features and use cases with 3D molecular visualizations.

Example Notebooks#

The following notebooks are available in the notebooks/ directory:

Notebook

Description

Open in Colab

01_analyze_6rsa_with_visualization.ipynb

Comprehensive analysis of 6RSA (Ribonuclease A) structure including hydrogen bonds, cooperativity chains, and 3D visualization with py3Dmol

Open In Colab

02_halogen_bonds_4x21.ipynb

Halogen bond detection and visualization in 4X21 crystal structure, demonstrating C-X···A interactions with interactive 3D views

Open In Colab

03_pdbfixer_vs_openbabel_comparison.ipynb

Comparing PDBFixer vs OpenBabel for hydrogen addition, analyzing determinism and hydrogen bond count variations

Open In Colab
Hydrogen Bonds in PDB Entry 4x21

Hydrogen Bonds in PDB Entry 4x21#

Prerequisites#

To run the notebooks locally, install the required dependencies:

pip install hbat py3Dmol pandas jupyter graphviz

Note: The graphviz Python package also requires the Graphviz system software:

  • Ubuntu/Debian: sudo apt-get install graphviz

  • macOS: brew install graphviz

  • Windows: Download from graphviz.org

Running the Notebooks#

Using Jupyter Notebook#

jupyter notebook

Navigate to the notebooks directory and open the desired notebook.

Using JupyterLab#

jupyter lab

Using VS Code#

  1. Open the notebook file in VS Code

  2. Select the Python kernel

  3. Run cells interactively

Using Google Colab#

Click the “Open in Colab” badge next to any notebook in the table above to run it directly in your browser without any local installation.

Data Files#

The notebooks use example PDB files from the example_pdb_files/ directory:

  • 6rsa.pdb - Ribonuclease A structure (hydrogen bonds, π interactions)

  • 4x21.pdb - Crystal structure with halogen bonds

Additional Resources#

Contents