Update ProtPool Calculation by Including usage_prot_ Reaction Fluxes

[HossFir]

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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.