You are spot on, 10ms internal time for 100000 molecules, 60ms with the "stack on top": https://www.chemeo.com/similar?smiles=CCCCO https://www.chemeo.com/simil

You are spot on, 10ms internal time for 100000 molecules, 60ms with the "stack on top": https://www.chemeo.com/similar?smiles=CCCCO https://www.chemeo.com/similar?smiles=CCCCO It is using a manually coded, most likely not that efficient, with popcnt.