VinaScreen

VinaScreen.py is a Python script designed to automate the docking of multiple ligands using AutoDock Vina. It processes ligand files in a specified directory, runs docking simulations, extracts the best binding affinity scores, and writes the results to a CSV file. This script also saves debug logs and console outputs for reference.

Features

• Automated Docking: Dock multiple ligands against a single receptor.
• Customizable Grid Box: Prompts the user to input grid box coordinates and sizes, making it adaptable to various proteins.
• Result Extraction: Automatically extracts the best binding affinity and saves it in a CSV file.
• Logging: Generates a debug log and a console output file for tracking docking progress and potential errors.

Prerequisites

Before running VinaScreen.py, ensure you have:

• Smina or AutoDock Vina installed and in your system path.
• Python 3.x.
• Necessary Python libraries: argparse, os, subprocess, csv, and re.

Installation

1. Clone this repository:

   git clone https://github.com/yboulaamane/VinaScreen.git
   cd VinaScreen

2. Ensure Smina or AutoDock Vina is installed and accessible in your system path.

3. Make the script executable:

   chmod +x VinaScreen.py

Setting Up the Docking Folder

To start, create a docking folder structured as follows:

• Place a receptor file named receptor.pdbqt in the root of the docking folder.
• Create a ligands/ subfolder containing all ligand files in .pdbqt format.

Your directory structure should look like this:

docking/
├── receptor.pdbqt
└── ligands/
    ├── ligand1.pdbqt
    ├── ligand2.pdbqt
    └── ...

Usage

Run VinaScreen.py and follow the prompts for grid box settings:

python VinaScreen.py

When prompted, enter the grid box center coordinates and sizes for AutoDock Vina:

• center_x, center_y, center_z: Coordinates of the grid box center.
• size_x, size_y, size_z: Dimensions of the grid box in Ångstroms.

The script will process each ligand in the ligands/ folder and output results to:

• docking_scores.csv: A CSV file with ligand names and binding affinities.
• docked_ligands/: A directory containing the docked ligand files.
• debug_log.txt: A log file capturing debug messages.
• docking_console_output.txt: A text file with console outputs for each docking.

Output

The docking_scores.csv file will have columns:

• Ligand: Name of the ligand.
• Best Affinity: The best binding affinity (in kcal/mol) obtained for each ligand.

Contributing

Feel free to submit issues or pull requests for improvements or bug fixes. Contributions are welcome!

License

This project is licensed under the MIT License. See the LICENSE file for more information.