vsutils 0.0.1

Utility for reaction modeling using graph grammar

VSUtils

Introduction

VSUtils is a Python-based utility designed for facilitating virtual screening processes in the realm of drug discovery. This tool incorporates MCFilter, a powerful module that offers extensive molecular property calculations and filtering capabilities based on established pharmaceutical rules such as Ro5, Pfizer, and GSK, among others.

Installation

To set up VSUtils for use, follow these steps:

1. Clone the repository:

   git clone https://github.com/your-username/VSUtils.git
   cd VSUtils
   

2. Install required Python packages:

   pip install -r requirements.txt
   

Usage

In a Jupyter Notebook

For interactive use, such as in a Jupyter notebook, follow this example to utilize the MCFilter:

from vsutils.ADMET.filters import MCFilter

# Initialize the MCFilter with default settings
filter = MCFilter()

# Calculate descriptors for a single SMILES string
smiles = "CCO"
results = filter.calculate_des(smiles)
print(results)

Command-Line Interface

MCFilter can also be executed from the command line to process either individual SMILES strings or batches from a CSV file:

• Processing a Single SMILES String:

  python main.py "CCO"
  

• Processing SMILES from a CSV File:

  python main.py path/to/input.csv --smiles_column column_name --output path/to/output.csv
  

Command-Line Options

• input: Input SMILES string or path to a CSV file containing SMILES strings.
• -c, --smiles_column: Specifies the column name in the CSV that contains the SMILES strings. Default is 'smiles'.
• -o, --output: Specifies the path for the output CSV file. If not provided, results will be printed to the console.
• -j, --jobs: Number of parallel jobs to run for processing. Default is 1.
• -v, --verbose: Verbosity level of output. Default is 0 (silent).

Requirements

This utility requires Python 3.9 or later. All dependencies are listed in requirements.txt.

License

VSUtils is open-source software licensed under the MIT License - see the License.