Substituent Replacement

This codebase is an adaptation of the Pat Walter's blog on using the "R-Group Replacement Database" published by Takeuchi et al. By supplying a molecule and it's core scaffold, the code will produce a series of derivatives in which R-groups have been substituted based on transformations in the "R-Group Replacement Database"

Requirements

python3.8
RDKit 2021-03-5

Installation Instructions

1. Create a virtual environment

python -m venv env_name

2. Install RDKit

RDKit can be easily installed via Cyclica's rdkit-installer. Install RDKit as follows:

git clone https://github.com/cyclica/rdkit-installer.git

./rdkit-installer/install-rdkit python=3.8 --release=Release_2021_03_5 /path/to/install/dir

3. Install Substituent Replacement

git clone https://github.com/davidkuter/substituent_replacement.git

cd substituent_replacement

pip install -r requirements.txt
pip install -e .

Usage

An example script can be found in contrib/example/run_script. Required inputs are:

target_smiles: SMILES of the molecule you want to perform substituent replacement on

core_smarts: SMARTS pattern of the core structure.

out_folder: Path to where results will be stored

level: The number of layers to be used from the R-Group Replacement Database

Currently, the output is a tsv file with information about the derivatives and a folder containing SVGs of the parent and derivatives.