separated .rst documentation of dihedral PCA and hydrogen-bonds

separated .rst documentation of dihedral PCA and hydrogen-bonds

The section of the reference manual on hydrogen-bonds was included
in dihedral-pca.rst. This hindered insertion of a section on an
analysis method related to PCA right after the dihedral PCA section.

Change-Id: I4d7c88624a12fc516cb63465098060fc871cc987