Crossover Operators for Molecular Graphs with an Application to Virtual Drug Screening

For more details, see here.

Structure

The main scripts to cut molecules and join molecular fragments can be found in the root directory.

Prerequisites

NOTE: This works relies on MongoDB and Gurobi. Additional licenses may be required.

Core developement was done on Python 3.11.5 The following Python packages are needed:

- networkx = 3.3
- Pebble = 5.0.7
- more-itertools = 10.3.0
- gurobipy = 11.0.3
- rdkit = 2023.9.1 
- tqdm = 4.66.1
- pymongo = 4.8.0
- matplotlib = 3.8.1
- numpy = 1.26.1
- pandas = 2.1.2

Usage

Prepare your data as a newline delimited SMILES textfile.

To use the cut-and-join algorithm:

1. edit the util.py to suit your MongoDB Installation.

2. run cut.py to generate fragments and save them to the DB

python cut.py <SMILES file>

3. run generate_SMARTS.py to save the SMARTS to the DB

python generate_SMARTS.py

4. run join.py to generate the recombinants and save them to the DB

python join.py