fix/rxnConfidenceScores

[BenjaSanchez]

Main improvements in this PR:

Remade function for defining confidence scores, which fixed 38 scores (most of them from pseudoreactions)

I hereby confirm that I have:

• [X] Tested my code with all requirements for running the model
• [X] Selected devel as a target branch (top left drop-down menu)
• [X] If needed, asked first in the Gitter chat room about this PR

[edkerk]

To avoid confusion, you might want to modify the commented text in the addConfidenceScores, to make clear that scores are positive:

% Reactions with pubmedID and with gene information -3 --> % Reactions with pubmedID and with gene information: 3

[BenjaSanchez]

@edkerk thanks for the feedback, I included it in the latest commit :)