austin-mroz/tanimoto_extraction

Simple extraction of a subset of molecules using Tanimoto similarity metric

Author:	Austin Mroz

Overview

tanimoto extraction is a simple script to extract a subset of molecules using the Tanimoto similarity metric

Set-up and installation

To run this extraction, follow these steps:

1. Ensure that all of the relevant packages are installed. This is most easily accomplished using `Anaconda`_ .. _Anaconda:https://www.anaconda.com/products/distribution

2. Create a new conda environment by executing

   $ conda create --name tanimoto_extraction

   $ conda activate tanimoto_extraction

3. Install the necessary python packages by executing

   $ conda install -c conda-forge ase pandas numpy

   $ conda install -c rdkit rdkit

4. Clone the repository

   $ git clone https://github.com/austin-mroz/tanimoto_extraction/

5. Run the extraction code by

   $ python extract_by_tanimoto.py /path/to/csv/smiles.txt num2extract

Where /path/to/csv/smiles.txt is the path to your text file containing the smiles strings and num2extract is the number of molecular systems you want to extract from your bulk dataset

For example, (to run the example script)

$ python extract_by_tanimoto.py example/example_chem_set.csv 23