There is a reason for this – it is not a bug. The way the hydrogen bonds are calculated, storing those values on a per-residue basis requires a bunch of extra effort beyond just calculating the energies. In other words, the hydrogen bond energies are accurate, but storing them on a per-residue basis requires extra work (slowing the program down). So, they’re stored only on a whole-pose basis.
If you want to fix this, there’s a demonstration of how in the backrub app. You’ll need to do some coding of your own. You need to use the function decompose_bb_hb_into_pair_energies; look at backrub.cc line 263 for an example. In fixbb.cc, you’ll have to make a ScoreFunction, make an EnergyMethodOptions, use the function, and pass the ScoreFunction into the PackRotamersMover.
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