i have no idea what to do

Spoiler alert for my game below

ok so the atomizer feature needs a new mechanic I'm thinking a challenges mechanic where the game gets temperarly harder but if you beat the challange you get a reward I have no clue how to execute this is why I have been inactive for months now and I just cant figure out a way to execute this what should I do basically I need a system that counts how many protons, neutrons, and electrons, the player has and they need to construct a specific atom to start a challenge for instance a hydrogen challenge needs 1 proton/electron