The HB score measures the quality of the hydrogen-bonding network.  I have a Fortran  program uploaded here in RG that can you can use to find all H bonds in a protein 3D structure.  From those results you can calculate the HB score (consult PubMed). Remember that an ideal HB is 2.8 Angs.  But one should also measure the van der Waals distances and assess their quality.  I also have a Fortran program uploaded here in RG that can find all VDWs in a protein structure. You can definitely use it to calculate some sort of VDW-score to augment the power of the HB score in assessing quality of protein 3D structures.  There are several ideal VDW distances (unlike the single ideal HB distance) depending on the atomic neighbors under consideration.