Metadata-Version: 2.1
Name: dgbg
Version: 0.0.2
Summary: Docking grid box generator for Autodock4 and Vina
Home-page: UNKNOWN
Author: Usman Jamshed
Author-email: jamshedu@berkeley.edu
License: MIT
Download-URL: https://github.com/ujamshed/dgbg/archive/refs/tags/0.0.2.tar.gz
Keywords: core package
Platform: UNKNOWN
Classifier: Development Status :: 5 - Production/Stable
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3
Classifier: Operating System :: OS Independent
Description-Content-Type: text/markdown
License-File: LICENSE

# Docking Grid Box Generator (DGBG)

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

## Preview

![screenshot](result.gif)

## Table of contents

- [Demo-Preview](#demo-preview)
- [Table of contents](#table-of-contents)
- [Installation](#installation)
- [Usage](#usage)
- [Development](#development)
- [Acknowledgements](#acknowledgements)
- [License](#license)


## Installation
[(Back to top)](#table-of-contents)

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

```pip install dgbg```

## Usage
[(Back to top)](#table-of-contents)

```python
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
[(Back to top)](#table-of-contents)

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
[(Back to top)](#table-of-contents)

1. Git Clone Repository
```git clone git@github.com: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](https://numpy.org/)
- [Pandas](https://pandas.pydata.org/)
- [MDTraj](https://www.mdtraj.org/1.9.8.dev0/index.html)
- [nglview](https://github.com/nglviewer/nglview)

## License
[(Back to top)](#table-of-contents)

[MIT](https://opensource.org/licenses/MIT)


