Apply image shifting by fragment

[hannahbaumann]

When two chains of a protein have the same segid, the PBC are not handled correctly during alignment since they would appear as one segment. This PR switches to use the protein.fragments instead. For fragments to be recognized correctly, we first need to guess the bonds in the protein.
Having the large fragments now makes unwrap() very slow which is fragment based.

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 98.27%. Comparing base (d09c786) to head (3fd980b).

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #124      +/-   ##
==========================================
+ Coverage   98.26%   98.27%   +0.01%     
==========================================
  Files           9        9              
  Lines         461      465       +4     
==========================================
+ Hits          453      457       +4     
  Misses          8        8              

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[hannahbaumann]

This now makes the alignment very very slow. Unwrap loops over the fragments and before (when there was no bond information), there were a lot of fragments that were very small.