If you have set distance constraints on the hydrogen bonds you want, but the constraints are not obeyed, there are three possibilities:
1) the constraint isn’t set right and Rosetta is ignoring it (or its scorefunction weight is zero)
2) the constraint scorefunction weight (probably atom_pair_constraint) is too small, and Rosetta isn’t obeying it strongly enough
3) Rosetta thinks the hydrogen bonds cannot form for some conformational reason
For digging into the hbondset – if you want some output other than the human-readable show() function, look in the C++ at the HBondSet class (src/core/scoring/hbonds/HBondSet.hh) – I don’t know what information you want so I’m hoping what you need may be there. Notice HBondSet is a read-only object – you can’t tell it where the hbonds you want should be, it tells you where the hbonds you already have are.