fix: standardize all names of exchange reactions

[edkerk]

Main improvements in this PR:

Contributing towards #181, names of exchange reactions are not ambiguous and can therefore directly be defined by the metabolite that they exchange. In 1.8.1, 469/1658 exchange reactions had no name.

Instead of only filling in the empty exchange reaction names, I redefined it for all exchange reactions, for consistency, but from the diff it also becomes clear that this fixes some previously unnecessarily complex names

Code:

[~,exchRxns] = getExchangeRxns(humanGEM);
[rxnNames, ~] = find(humanGEM.S(:,exchRxns));
rxnNames= humanGEM.metNames(rxnNames);
rxnNames= append('Exchange of ',rxnNames);
humanGEM.rxnNames(exchRxns) = rxnNames;

Example of non-empty reaction name that was changed:

ID	Old name	New name
MAR01986	Exchange of [ (2R, 3S, 4R, 5R)-5- (2, 4-Dioxo-1, 2, 3, 4-Tetrahydropyrimidin-1-Yl)-3, 4-Dihydroxyoxolan-2-Yl]Methyl {[ (3R, 4S, 5S, 6R)-3, 4, 5-Trihydroxy-6- (Hydroxymethyl)Oxan-2-Yl Phosphonato]Oxy}Phosphonate	Exchange of UDP-glucose

I hereby confirm that I have:

• Tested my code on my own computer for running the model
• Selected develop as a target branch
• Any removed reactions and metabolites have been moved to the corresponding deprecated identifier lists

[mihai-sysbio]

Awesome!

Just to note that some of the previous reaction names contained morphological metadata ("in hepatic vein", "in lumen", "in bile"). Perhaps some of this could be moved to the rxnNotes field.

[feiranl]

LGTM!

[edkerk]

Awesome!

Just to note that some of the previous reaction names contained morphological metadata ("in hepatic vein", "in lumen", "in bile"). Perhaps some of this could be moved to the rxnNotes field.

This might have been defined as such when first generating the model, but this information is never used to define tissue-specific functions (this is based on (f)tINIT), and not consistently done for all exchange reactions. Also, there are no duplicate exchange reactions: there are no seperate exchange reactions for e.g. "glucose exchange in hepatic vein" and "glucose exchange in myocytes" (and this also should not be the case!). I see therefore no purpose for retaining such legacy phrases in some reaction names.