Docking Grid Box Generator (DGBG)

Python module to automatically generate a grid box around a ligand present in a pdb file.

Preview

Table of contents

• Demo-Preview
• Table of contents
• Installation
• Usage
• Development
• Acknowledgements
• License

Installation

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To use this project, pip install the module on your device using the command below:

pip install dgbg

Usage

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from dgbg import dgbg

box = dgbg.binding_box('ex_file_path.pdb')

ligand_data = box.get_ligand_data('ligand_ID', 'chain_ID')

centroid, box_size = box.create_box(spacing=0.375, padding=np.array([0, 0, 0]))

# Visualize using the following commands in Jupyter Notebook.

result = box.show_result(centroid, box_size)

result

Examples

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1. General example use case.

2. Adjusting grid box after generation.

3. Integration with DeepChem and its docking functionality.

4. Integration with AutoDock Vina.

5. Multiple identical ligands on the same protein chain.

Development

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1. Git Clone Repository git clone [email protected]:ujamshed/dgbg.git

2. Create Virtual Environment python3 -m venv .venv

3. Activate Virtual Environment source .venv/bin/activate

4. Install Project Dependencies pip install -r requirements.txt

Acknowledgements

This software uses the following open source packages:

• NumPy
• Pandas
• MDTraj
• nglview

License

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MIT