only update molecule when the flag is set to True
only update molecule when the flag is set to True

nickvandewiele/RMG-Py,nyee/RMG-Py,nickvandewiele/RMG-Py,chatelak/RMG-Py,nyee/RMG-Py,pierrelb/RMG-Py,pierrelb/RMG-Py,chatelak/RMG-Py