Update ProtPool Calculation by Including usage_prot_ Reaction Fluxes

[HossFir]

Description:

Issue: The original implementation of topEnzymeUsage function calculates protPool by only considering the prot_pool_exchange flux. However, this does not reflect the total enzymatic capacity used by the metabolic reactions, especially when proteomics data is integrated into the model.

Enhancement: The function has been enhanced to account for the fluxes of all usage_prot_ reactions, excluding the ones related to usage_prot_standard.

Changes:

1. Flux Calculation Integration: The function now includes a call to solveLP(ecModel) to calculate the flux distribution within the model.

2. Targeted Flux Summation: After obtaining the flux distribution, the function identifies all usage_prot_ reactions while filtering out any that include standard in their reaction IDs. Since this reaction was embedded into Protein_pool_exchange.

3. Adjusted protPool Definition: The protein pool (protPool) is redefined to be the sum of the prot_pool_exchange flux and the total usage fluxes.

[edkerk]

Nice work, I have a few suggested edits. Could you please give me the right to push to this by following these instructions?

[edkerk]

Suggested changes applied:

• instead of running solveLP in reportEnzymeUsage, use the same solution as provided in the usageData that is now output by enzymeUsage.
• instead of printing the total protein pool flux and total usageProt flux into the command window, have it as fields in the usageReport output structure.

@HossFir, can you check if this works for you? Should give the same results as your earlier code.

[HossFir]

@edkerk Thanks for your suggestions!

The results were somehow identical! I've attached two TopUsed Enzymes for you to review.

topAbsUsage_stage4_PH.xlsx topAbsUsage_stage4_PH2.xlsx

[edkerk]

This PR will be reverted, as the changes by #379 avoid this problem to occur. If kept, the new protein usage numbers would be too high, due to double counting vai the total protein usage and the protein specific usage reactions.