medchemfilters

Overview

medchemfilters is a Python-based utility designed to streamline virtual screening in drug discovery. It features MCFilter, a comprehensive module for calculating molecular properties and filtering compounds according to well-established pharmaceutical guidelines such as Ro5, Pfizer, and GSK rules.

Installation

To install and set up medchemfilters, follow these steps:

1. Clone the repository:

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

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 medchemfilters.ADMET.filters import MCFilter

# Initialize MCFilter with default settings
filter = MCFilter()

# Calculate molecular descriptors for a 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: A single SMILES string or the path to a CSV file containing SMILES strings.
• -c, --smiles_column: Specifies the column name in the CSV that contains SMILES strings (default: smiles).
• -o, --output: Specifies the output file path for processed results. If not provided, results will be displayed in the terminal.
• -j, --jobs: The number of parallel jobs for processing (default: 1).
• -v, --verbose: Sets the verbosity level of the output (default: 0, silent).

Requirements

Python 3.9 or higher is required. All dependencies are listed in the requirements.txt file.

License

medchemfilters is open-source software licensed under the MIT License. See the LICENSE file for more details.