feat: reportEnzymeUsage input and output

- use fluxes from usageData
- give protein pool in usageReport instead of printing to command window

src/geckomat/utilities/reportEnzymeUsage.m

@@ -1,10 +1,10 @@
-function usageReport = topEnzymeUsage(ecModel, usageData, highCapUsage, topAbsUsage)
+function usageReport = reportEnzymeUsage(ecModel, usageData, highCapUsage, topAbsUsage)
 % reportEnzymeUsage
 %   Summarizes the results from enzymeUsage.
 %
 %  Input:
 %   ecModel         a GECKO3 ecModel
-%   usageData       output from reportEnzymeUsage
+%   usageData       output from enzymeUsage
 %   highCapUsage    minimum ratio of enzyme capacity usage to be considered
 %                   as high usage (Optional, default 0.9, refering to a 
 %                   minimum of 90% capacity usage)
@@ -64,12 +64,7 @@
 % Calculate the protein pool flux from the 'prot_pool_exchange' reaction
 protPoolExchangeFlux = -ecModel.lb(strcmp(ecModel.rxns,'prot_pool_exchange'));
 
-% Obtain the fluxes
-sol = solveLP(ecModel);
-if isempty(sol.x)
-    error('No solution found.');
-end
-fluxValues = sol.x;
+fluxValues = usageData.fluxes;
 
 % Sum fluxes for all 'usage_prot_' reactions, excluding the 'usage_prot_standard'
 usageProtIndices = startsWith(ecModel.rxns, 'usage_prot_') & ...
@@ -81,10 +76,6 @@
 % Define the new protein pool as the sum of prot_pool_exchange flux and total usage_prot fluxes
 protPool = (protPoolExchangeFlux + totalUsageProtFlux)/100;
 
-fprintf('Total Protein Pool Flux: %f\n', protPoolExchangeFlux);
-fprintf('total UsageProt Flux: %f\n', totalUsageProtFlux);
-
-
 for i=1:numel(topEnzyme)
     [rxns, kcat, idx, rxnNames, grRules] = getReactionsFromEnzyme(ecModel,topEnzyme{i});
     rxnNumber = numel(rxns);
@@ -98,5 +89,7 @@
     topUsage.rxnNames(end+1:end+rxnNumber,1)    = rxnNames;
     topUsage.grRules(end+1:end+rxnNumber,1)     = grRules;
 end
-usageReport.topAbsUsage = struct2table(topUsage);
+usageReport.topAbsUsage     = struct2table(topUsage);
+usageReport.totalProtPool   = protPoolExchangeFlux;
+usageReport.totalUsageFlux  = totalUsageProtFlux;
 end