Add pKa and hydrophobicity to amino acid

[aukeheerdink]

In regard to issue #65

Made a small beginning to implement this issue but @douweschulte mentioned that you (@di-hardt) might have some code laying around that is similar to what I'm trying to do. Do you have something by any chance? Or some ideas on how to implement this? @douweschulte is already thinking about how to mold this into a trait (with IdentifiedPeptides).

My current idea is to make a separate module with these static tables and the pka function would work as a table lookup function basically. I would implement something similar for the hydrophobicity.

[douweschulte]

The trait proposed here allows for implementing the pKa basic behaviour for any pKa source and for any AminoAcid type. This should be generic enough for it to work for most use cases. I have some questions on how this should handle modifications, right now it takes a list of SimpleModification (so no ambiguous or cross-linked stuff), which to my mind indicates side chain modifications which would mean that terminal modifications are not taken into account properly.

@di-hardt I remember something about triplet or even quadruplet lookup tables for pKa values, should we think about some structure to allow that?

Then some more things that need to be done are more documentation, placing this into a separate file, and the implementation for the peptide_pKa. Additionally I am not overly happy about how all the names turned out, the normal casing pKa does not look best in all places. Any thoughts on this would be appreciated.

[di-hardt]

Hey everyone,
found my code finally. So it started as a reimplementation of an online Thermo tool to calculate the hydrophobicity of peptides. I still want to use it for my peptide database MaCPepDB. The underlaying JS script is a bit strange on first look. I figured out there are 3 different methods implemented to calcualte the hydrophobicity. All published/proposed by Krokhin et al. I started reimplementing everyone of them: https://github.com/di-hardt/omicstools/blob/feature-krokhin-hydrophibicity/src/chemistry/amino_acid/hydrophobicity/krokhin_hydrophobicity.rs
"Method 3" is probably the one used for the Thermo tool, but at the time I had actual time to work on this, I couldn't find the correction factors for the hydrophobicity clusters, which are the triplet and quaduples I mentioned to @douweschulte. They were not findable in the publication.
Luckily I found it a few month ago in the Skyline codebase here but never finished the reimplementaton.