Also overwrite the atomic numbers

Change-Id: I6d3d87bc7cfbdcdee0d2011ad0da72545750bf12
Use atomic numbers in the perception for common elements

Change-Id: I4919024f1fba96911201d3d38d3b47ed9240ca91
Pass around atom numbers instead of IAtom objects

Change-Id: Ie55f3b33a71fc8f8fbc62ae08eda4adf5e6b3234