Docking Script (dock.py)

Overview

This Python script performs molecular docking using the dockstring library. It processes input SMILES strings from a CSV file, performs docking, and outputs the docking scores to a CSV file. The script also includes an option to convert SMILES strings to their canonical form using RDKit.

Requirements

• Python 3.6 or later
• dockstring
• pandas
• tqdm
• rdkit
• openbabel

Installation

1. Install the necessary Python packages:

   pip install dockstring pandas tqdm rdkit

2. Install Open Babel:

   sudo apt-get install openbabel

Usage

The script can be run from the command line with the following options:

python dock.py --input_csv <path/to/input.csv> --smiles_column <SMILES_column_name> --mol2_path <path/to/mol2file.mol2> --output_path <path/to/output.csv> [options]

Required Arguments

• --input_csv: URL or path to the input CSV file containing the SMILES strings.
• --smiles_column: Column name in the CSV file that contains the SMILES strings.
• --mol2_path: Path to the mol2 file of the target protein.
• --output_path: Path to the output CSV file where the docking results will be saved.

Optional Arguments

• --docking_dir: Directory name/path where docking files will be stored (default: dockdir).
• --mol_name: Name of the molecule (default: mol).
• --conf_path: Path to the configuration file (_conf.txt) containing the center and box sizes.
• --center_coords: Center coordinates for the docking box (X Y Z). Required if --conf_path is not provided.
• --box_sizes: Box sizes for docking (X Y Z). Required if --conf_path is not provided.
• --canonicalize: Flag to convert SMILES to canonical SMILES.

Examples

Using center coordinates and box sizes:

python dock.py --input_csv path/to/your/input.csv --smiles_column SMILES --mol2_path path/to/mol2file.mol2 --output_path path/to/output.csv --center_coords 68.0658 -5.1678 -54.97 --box_sizes 98.194 95.5592 116.24 --canonicalize

Using a configuration file:

python dock.py --input_csv path/to/your/input.csv --smiles_column SMILES --mol2_path path/to/mol2file.mol2 --conf_path path/to/conf.txt --output_path path/to/output.csv --canonicalize

Format for _conf.txt File

If you choose to use a configuration file for the docking box parameters, the _conf.txt file should have the following format:

center_x = <center_x_value>
center_y = <center_y_value>
center_z = <center_z_value>

size_x = <size_x_value>
size_y = <size_y_value>
size_z = <size_z_value>

For example:

center_x = 68.0658
center_y = -5.1678
center_z = -54.97

size_x = 98.194
size_y = 95.5592
size_z = 116.24

Notes

• Ensure that the input CSV file contains the correct column name for SMILES strings.
• If using the --canonicalize flag, RDKit will be used to convert SMILES strings to their canonical form.
• If the configuration file (_conf.txt) is not provided, the script requires the center coordinates and box sizes to be specified.

License

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

Acknowledgments

• Dockstring
• RDKit
• Open Babel

Feel free to reach out with any questions or issues regarding the script. Happy docking!