Answer from @matteo-ferla, converted from comment:

If command line interface is more suitable for you, you may consider OpenBabel, which can predict Gasteiger charges, protonate at pH 7, accept a smi file of multiple SMILES or a multi-entry sdf file and can output in PDQBT format, but is not quite the same as the python script allows merging and various settings. But to use the script iteratively (a horrendous thing to do as it loads up the python kernel each time) check out how to loop files via bash