Enhance FragmentationMatchScore with additional metrics

[PMSeitzer]

Including (but not limited to), modified cosine score, neutral loss match score, and the updated cosine score.

This can be used very generally, and updated in the GUI, but was originally devised as a part of #543, #546, and associated mass_spec case https://github.com/calico/mass_spec/issues/752

[PMSeitzer]

Return to this after starting mass_spc case https://github.com/calico/mass_spec/issues/752

[PMSeitzer]

Implement spectral entropy score

paper:
https://www.nature.com/articles/s41592-021-01331-z

source code:
https://github.com/YuanyueLi/SpectralEntropy/blob/master/spectral_entropy/spectral_entropy.py#L26-L28

scipy.stats.entropy:
https://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.entropy.html

[PMSeitzer]

more information about various spectral scoring approaches:
https://www.biorxiv.org/content/biorxiv/early/2022/06/02/2022.06.01.494370.full.pdf

[PMSeitzer]

Modified cosine score, as it is explained in the original manuscript (https://www.pnas.org/doi/abs/10.1073/pnas.1203689109):

Vector similarities are calculated for every possible pair of spectra with a
minimum of six matching fragment ions (i.e., peaks) with similarity
determined by using a modified cosine calculation that takes into
account the relative intensities of the fragment ions as well as the
precursor m/z difference between the paired spectra

This has come to mean something more specific:

Two peaks are considered a potential match if their m/z ratios lie within the given ‘tolerance’, or if their m/z ratios lie within the tolerance once a mass-shift is applied. The mass shift is simply the difference in precursor-m/z between the two spectra.

So, a peak may match another peak after a mass-shift is applied.

See this implementation:
https://github.com/matchms/matchms/blob/master/matchms/similarity/ModifiedCosine.py#L109-L129

It looks like they are matching to both the m/z and NL m/z of an observed spectrum (where NL m/z = precursorMz - fragMz).

[PMSeitzer]

Inspired by ASMS 2024, re-opening this case. Introduced now in modified cosine score, flash entropy, kullback-leibler divergence, Jansen-Shanon divergence, etc.

[PMSeitzer]

spectral entropy python:
https://github.com/YuanyueLi/SpectralEntropy