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I don’t know the answer to 1 – the organization of this code is a mystery to me. It ought to be in AbrelaxApplication.cc somewhere.
As for 2 – no, it does not use a superposition, it uses raw coordinates. This seems silly so it’s probably because it was very tough to do it any other way. The problem is likely to be that the constraints are managed as very abstract – they’re part of the scorefunction and part of the pose, but not a class that you usually interact with directly. I’d guess they couldn’t figure out a good way to pass in the necessary companion data to perform the superposition in a reliable way. (It may have turned out to be too slow as well – performing the superposition every time the constraint is evalulated would be a huge hit).
I believe most users use AtomPairConstraints instead of CoordinateConstraints; these constrain atoms relative to one another and thus don’t need superposition. They may work better in your case? There is also a BindingSite constraint which does something similar but is meant for interfaces.