SDF_Redundancy_Eliminator

SDF_Redundancy_Eliminator is a Python3 code to:

1. Generate canonical SMILES for each of the compounds in an .SD/.SDF compound library,
2. Detect redundant ligands/structural isomers in the library,
3. Generate unique and redundant name lists and, optionally,
4. Move redundant ligands/structural isomers to a separate file to produce a library of unique compounds.

Prerequisites/Dependencies

• Python3
• RDKit

Installation of dependencies

• RDKit

On Linux or OS X, there are multiple options:

Option 1: Install RDKit with Conda if you have conda installed

Create a python3 environment (tested with python versions 3.8 and 3.7)

conda create -n py38_rdkit python=3.8

Install RDkit with pip using

pip install rdkit

or

pip install rdkit-pypi

Option 2: Install RDKit from repositories

On Ubuntu, you may run

sudo apt-get install python3-rdkit librdkit1 rdkit-data

or run

pip3 install rdkit

Option 3: Build from Source

On Windows

You may follow the instructions here, or here

How to Use SDF_Redundancy_Eliminator

1. Create a folder and copy in your .SD/.SDF compound library
2. Copy RedundancyEliminator.py into the same directory
3. Run the code and it will walk you through the steps:

python3 RedundancyEliminator.py

Features

• Generates canonical SMILES for the compounds in the library if they are not annotated with SMILES strings
• Produces another copy of the library with SMILES string annotation
• Interactively walks the user through the steps

Citation

If you use this code in your work, kindly cite it as:

Yekeen, A. A. (2022). SDF_Redundancy_Eliminator: A python code to remove redundant ligands in a .SD/.SDF compound library. https://github.com/abeebyekeen/SDF_Redundancy_Eliminator, DOI: https://doi.org/10.5281/zenodo.7049711