Refactor code to allow for scoring

[rvhonorato]

This PR refactors the code to allow for the scoring workflow.

[codecov-commenter]

Codecov Report

Merging #199 (47636fa) into main (bde6e6e) will decrease coverage by 0.41%.
The diff coverage is 9.83%.

@@            Coverage Diff             @@
##             main     #199      +/-   ##
==========================================
- Coverage   40.00%   39.58%   -0.42%     
==========================================
  Files          42       42              
  Lines        2405     2425      +20     
==========================================
- Hits          962      960       -2     
- Misses       1443     1465      +22     

Impacted Files	Coverage Δ
src/haddock/libs/libcns.py	23.68% <0.00%> (-1.67%)	⬇️
src/haddock/modules/scoring/emscoring/__init__.py	25.42% <11.42%> (-3.39%)	⬇️
src/haddock/libs/libpdb.py	26.66% <16.66%> (-0.79%)	⬇️
src/haddock/libs/libontology.py	35.36% <20.00%> (-0.89%)	⬇️

---

Continue to review full report at Codecov.

Legend - Click here to learn more
Δ = absolute <relative> (impact), ø = not affected, ? = missing data
Powered by Codecov. Last update bde6e6e...47636fa. Read the comment docs.