free_descriptors.py

A python script for generating descriptors from a directory of .mol files

Prerequisites

This script requires the RDKit and Mordred packages to be installed. This is best done with conda: conda install -c rdkit -c mordred_descriptors mordred rdkit

Usage

Invoke on a folder with .mol files to get rdkit descriptors in a CSV minimum example:

python ./free_descriptors.py -i /path/to/molfiles -o output_name

will read all .mol files in /path/to/molfiles and create output_name.csv inside the same folder.

Options

Several options exist to compute additional descriptors:

• fragments: -f or --fragments flag
• MACCS keys: -M or --MACCS flag
• ECFP6 fingerprints: -E or --ECFP6 flag
• Mordred descriptors: -m or --mordred flag
• Macrocycle descriptors: -c or --macrocycle flag Optional descriptors have a tendency to take a long time to compute and to fail on some molecules. Be sure to check output files.

Thanks and Acknowledgements

• This script is a modification of the rdkit_descriptors.py script by Petr Škoda
• This script also includes code from Phyo Phyo Kyaw Zin article