chem-deg 0.2.2

Chemical Degradation Simulation

Chemical Degradation Reaction

This repository provides a framework for simulating and analyzing chemical degradation pathways of organic compounds. It leverages the RDKit cheminformatics library to predict degradation products based on a set of predefined reaction rules and allows for the kinetic modeling of these degradation processes.

Reaction Libraries have been sourced from the EPA's Chemical Transformation Simulator.

Dependencies

• Python (>=3.12)
• RDKit (>=2024.9.6)
• NetworkX (>=3.4)
• Matplotlib (>=3.10)
• Seaborn (>=0.13)
• Pandas (>=2.2)
• SciPy (>=1.15)

Installation

Create and active virtual environment

python3 -m venv chem_deg
source chem_deg/bin/activate

Clone and install the repository

git clone [e-mail]:davidkuter/chem_deg.git
pip install -e .

Usage

from chem_deg import simulate_degradation

# Simulate degradation starting from a SMILES string
smiles = "CCC(=O)N(c1ccccc1)C1(C(=O)OC)CCN(CCC(=O)OC)CC1"
df_results = simulate_degradation(
    compound=smiles,    # The compound to simulate degradation of
    ph=5,               # The pH to simulate degradation kinetics of
    max_generation=2,   # The maximum number of degradation steps to simulate.
    plot_degradation=True,  # If `True`, generates a visualization of the degradation graph (saved as `degradation_graph.png`).
    plot_kinetics=True,     # If `True`, generates a plot of the degradation kinetics (saved as `degradation_kinetics.png`).
    time_log=True,      # If `True`, uses a logarithmic time scale for the kinetics simulation.
)

Development

To install development dependencies:

pip install -e ".[dev]"

Running Tests

pytest

License

This project is licensed under the Creative Commons Attribution-NonCommercial 4.0 International License - see the LICENSE file for details.

For commercial use, please contact David Kuter.