Revert "Merge pull request #372 from HossFir/update-reportEnzymeUsage"

This reverts commit cc8e449, reversing changes made to 883b40d.
SysBioChalmers · May 27, 2024 · 94efe9e · 94efe9e
1 parent cb54747
commit 94efe9e
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Showing 2 changed files with 2 additions and 19 deletions.
diff --git a/src/geckomat/utilities/enzymeUsage.m b/src/geckomat/utilities/enzymeUsage.m
@@ -26,7 +26,6 @@
 %               absUsage    vector of absolute enzyme usages
 %               UB          vector of enzyme exchange reaction upper bounds
 %               protID      string array of matching protein IDs
-%               fluxes      vector of fluxes, copy of input fluxes
 %
 % Usage:
 %   usageData = enzymeUsage(ecModel,fluxes,zero)
@@ -43,7 +42,6 @@
 usageData.LB          = ecModel.lb(rxnIdx);
 usageData.absUsage    = abs(fluxes(rxnIdx));
 usageData.capUsage    = abs(usageData.absUsage./usageData.LB);
-usageData.fluxes      = fluxes;
 
 if ~zero
     nonzero               = usageData.absUsage<0;

diff --git a/src/geckomat/utilities/reportEnzymeUsage.m b/src/geckomat/utilities/reportEnzymeUsage.m
@@ -61,20 +61,7 @@
 topUsage.rxnNames   = {};
 topUsage.grRules    = {};
 
-% Calculate the protein pool flux from the 'prot_pool_exchange' reaction
-protPoolExchangeFlux = -ecModel.lb(strcmp(ecModel.rxns,'prot_pool_exchange'));
-
-fluxValues = usageData.fluxes;
-
-% Sum fluxes for all 'usage_prot_' reactions, excluding the 'usage_prot_standard'
-usageProtIndices = startsWith(ecModel.rxns, 'usage_prot_') & ...
-                   ~contains(ecModel.rxns, 'standard');
-
-% Sum the absolute values of the usage fluxes
-totalUsageProtFlux = sum(abs(fluxValues(usageProtIndices)));
-
-% Define the new protein pool as the sum of prot_pool_exchange flux and total usage_prot fluxes
-protPool = (protPoolExchangeFlux + totalUsageProtFlux)/100;
+protPool = -ecModel.lb(strcmp(ecModel.rxns,'prot_pool_exchange'))/100;
 
 for i=1:numel(topEnzyme)
     [rxns, kcat, idx, rxnNames, grRules] = getReactionsFromEnzyme(ecModel,topEnzyme{i});
@@ -89,7 +76,5 @@
     topUsage.rxnNames(end+1:end+rxnNumber,1)    = rxnNames;
     topUsage.grRules(end+1:end+rxnNumber,1)     = grRules;
 end
-usageReport.topAbsUsage     = struct2table(topUsage);
-usageReport.totalProtPool   = protPoolExchangeFlux;
-usageReport.totalUsageFlux  = totalUsageProtFlux;
+usageReport.topAbsUsage = struct2table(topUsage);
 end