removed AtomsBegin/End, ResiduesBegin/End from entity

they added very little benefits and were in general very slow.
The call sites of AtomsBegin have been replaced by a triple
for loop, ResiduesBegin by a double for loop. While that adds
some typing overhead, it gives a speed up compared to the old
version. It also happens to fix a problem noticed by Niklaus.

the superposition code has also been refactored to reduce
redundancy and make it easier to read.