Water bridge 2nd Order implementation

[talagayev]

Changes made:

• Addition of code for 2nd Order water bridges
• Implementation of input variable order

we would need to see if we make the order input then in the Fingerprint class and have a default, currently being 1
that the user can then input in the Fingerprint class.

As for the higher water bridge orders we would need to see how we do the recognition of interactions within the
water-water analysis multiple times. Maybe through some looping like some step wise matching

[codecov]

Codecov Report

Attention: Patch coverage is 97.72727% with 3 lines in your changes missing coverage. Please review.

Project coverage is 94.72%. Comparing base (72e4854) to head (2066772).
Report is 1 commits behind head on water_bridge.

Files with missing lines	Patch %	Lines
prolif/fingerprint.py	93.33%	2 Missing ⚠️
prolif/interactions/base.py	94.73%	1 Missing ⚠️

Additional details and impacted files

@@               Coverage Diff                @@
##           water_bridge     #230      +/-   ##
================================================
+ Coverage         94.50%   94.72%   +0.21%     
================================================
  Files                21       22       +1     
  Lines              1548     1650     +102     
================================================
+ Hits               1463     1563     +100     
- Misses               85       87       +2     

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[cbouy]

I moved the code to a new module to make things clearer, it was getting quite daunting in the fingerprint.py file.

I also simplified the code a bit since there was a bit too much repetition in the metadata part to my liking.

Next is getting in a less "for-loop" approach to implementing each higher order and finding something more generalisable. Most likely using networkx to build the actual water network and then finding all shortest paths of length <order> in the graph that go from <ligand residue> to <protein residue>. Let's see if I have time to do that before the new year

[talagayev]

I moved the code to a new module to make things clearer, it was getting quite daunting in the fingerprint.py file.

I also simplified the code a bit since there was a bit too much repetition in the metadata part to my liking.

Next is getting in a less "for-loop" approach to implementing each higher order and finding something more generalisable. Most likely using networkx to build the actual water network and then finding all shortest paths of length in the graph that go from to . Let's see if I have time to do that before the new year

Ah nice, true it gets a little bit overwhelming with the metadata.

Ah, somehow I didn't think about the networkx option. I would probably be on holidays till the new year, but would be
able to take a look from January 2nd to assist :)