Docking grid box generator for Autodock4 and Vina
Project description
Docking Grid Box Generator (DGBG)
Python module to automatically generate a grid box around a ligand present in a pdb file.
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Table of contents
Installation
To use this project, pip install the module on your device using the command below:
pip install dgbg
Usage
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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General example use case.
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Adjusting grid box after generation.
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Integration with DeepChem and its docking functionality.
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Integration with AutoDock Vina.
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Multiple identical ligands on the same protein chain.
Development
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Git Clone Repository
git clone git@github.com:ujamshed/dgbg.git
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Create Virtual Environment
python3 -m venv .venv
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Activate Virtual Environment
source .venv/bin/activate
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Install Project Dependencies
pip install -r requirements.txt
Acknowledgements
This software uses the following open source packages:
License
Project details
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