Basically you take the quantum field of the quark-gluon to the proton and neutron and superimpose those fields (interference/resonance/amplification) with the electron fields to find the quantum (probability) field of the atom. Use Hydrogen first, then Helium and on up to get the quantum wave pattern of each element. Then move to small molecules, Hydrogen gas, H2O, etc to get the quantum wave (probability) patterns of the small molecules. Each time testing to see if the results are accurate or not with known data; throwing out mistakes and following the ones that work.