Convert molecule to a class

[uppittu11]

Created molecules class that can be loaded and loaded and saved to JSON files. Also propagated these changes to modules that use `Molecules.

[codecov[bot]]

Codecov Report

Merging #41 into master will increase coverage by 12.83%. The diff coverage is 91.33%.

@@             Coverage Diff             @@
##           master      #41       +/-   ##
===========================================
+ Coverage   33.09%   45.92%   +12.83%     
===========================================
  Files          14       14               
  Lines         420      540      +120     
===========================================
+ Hits          139      248      +109     
- Misses        281      292       +11

Impacted Files	Coverage Δ
analysis/tests/conf_test.py	50% <ø> (ø)	:arrow_up:
analysis/tests/test_molecules.py	100% <100%> (ø)	:arrow_up:
analysis/molecules/molecules.py	89.9% <88.42%> (-10.1%)	:arrow_down: