ueit said:
For a hydrogen atom we assume the electron and nucleus to be point charges
Well, technically speaking, the Hydrogen atom is treated as a system with Hamiltonian (I'll write it in Cartesians and their conjugate momenta since they are the usual canonical variables in the electrostatic case, although it'd be more concise in spherical polar co-ordinates):
[tex]
\hat{H}(<br />
\hat{x}_1, <br />
\hat{p_x}_1, <br />
\hat{y}_1, <br />
\hat{p_y}_1, <br />
\hat{z}_1, <br />
\hat{p_z}_1, <br />
\hat{x}_2, <br />
\hat{p_x}_2, <br />
\hat{y}_2, <br />
\hat{p_y}_2, <br />
\hat{z}_2, <br />
\hat{p_z}_2) =[/tex]
[tex]
\frac{\hat{p_x}_1^2+<br />
\hat{p_y}_1^2+<br />
\hat{p_z}_1^2}<br />
{2m_1}+<br />
\frac{\hat{p_x}_2^2+<br />
\hat{p_y}_2^2+<br />
\hat{p_z}_2^2}<br />
{2m_2}-<br />
\frac{1}{4\pi\epsilon_0}<br />
\frac{e^2}<br />
{\sqrt{<br />
(\hat{x}_1 - \hat{x}_2)^2+<br />
(\hat{y}_1 - \hat{y}_2)^2+<br />
(\hat{z}_1 - \hat{z}_2)^2}}[/tex]
You haven't assumed anything of the system apart from the fact that it has the above Hamiltonian. To get to that expression, you might use some classical physics of point particles and the Coulombic interaction between charged particles. However, note that the quantum mechanics of the system starts here, at the Hamiltonian.
You haven't assumed anything more, specifically, you haven't talked about particles - you've talked about systems. I'm not being pedantic: in QFT, you don't deal with particles directly, you deal with oscillating fields, where particles happen to emerge.
P.S. You usually eliminate 6 of the variables by transforming to so-called "centre-of-mass" and "relative" co-ordinates, and while this has physical content in this case, it didn't have to.