Not keeping the E-Z isomerism of the molecules

[arashsadri]

Gypsum-DL inputs and outputs.zip

I have observed that while converting smiles with one of the specific E-Z isomerisms to their 3D representations with various protomers and tautomers, both of the isomers are generated. I have attached the inputs and the outputs. I used this script for the conversion:

#!/usr/bin/env bash

File: compounds.sh

for compound in $(ls ./galbanicacidderivatives/)
do
./run_gypsum_dl.py --source ./galbanicacidderivatives/$compound --output_folder ./galbanicacidderivatives/${compound::-4}/ --job_manager serial --pka_precision 3 --min_ph 4 --max_ph 10 --max_variants_per_compound 100 --separate_output_files --use_durrant_lab_filters
done
echo "successfully finished"