This script can accept SMILES-string as input, either from a .smi-file or as a string. The script will then "charge" the input SMILES according to the chosen pH-value and range, producing either an output file or return a string with the charged structure. This script was originally written by prof. Ruth Brenk (University of Bergen), and was adapted to work with RDKit and .csv-files.
We offer no guarantees that this script will work with all or any valid SMILES-structures. We acknowledge the existence of a lot of spaghetti code within this script, and its dire need of refactoring.
if input file is named input.smi, output will by default saved in a file called output.smi:
charger_RDKit_moldesc.py -i ./csvs/input.smi -r 1.0 -p 4 -o
if input is string, and ouput should be printed:
charger_rdkit_moldesc.py -str CCN -R 1.0 - p 4 -o
Expected output: CC[NH3+], CCN