Merge pull request #66 from SysBioChalmers/feat/yeastCompatibility

Feat/yeast compatibility
SysBioChalmers · Jan 7, 2019 · 0b14cc3 · 0b14cc3
2 parents af55d8c + d0c91ec
commit 0b14cc3
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Showing 4 changed files with 35 additions and 24 deletions.
diff --git a/geckomat/change_model/addEnzymesToRxn.m b/geckomat/change_model/addEnzymesToRxn.m
@@ -43,7 +43,7 @@
 rxnToAdd.mets         = [metS,newMets,metP];
 rxnToAdd.stoichCoeffs = [coeffsS,-kvalues.^-1,coeffsP];
 if ismember(newRxnName{1},model.rxns)
-    model = changeRxns(model,newRxnName(1),rxnToAdd,1,comp);
+    model = changeRxns(model,newRxnName(1),rxnToAdd,1,comp,true);
 else    
     rxnToAdd.rxns     = newRxnName(1);
     rxnToAdd.rxnNames = newRxnName(2);

diff --git a/geckomat/change_model/manualModifications.m b/geckomat/change_model/manualModifications.m
@@ -62,20 +62,19 @@
             for k = 1:length(prot_set)
                 model.S(int_pos(k),i) = 0;
             end
-            %If some proteins where not present previously, add them:
-            newMets = uniprots{j};
+            %Add new protein stoich. coeffs to rxn:
+            kvalues = kcats(j)./stoich{j};
+            rxnID   = model.rxns{i};
+            newMets = strcat('prot_',uniprots{j});
+            rxnName = model.rxnNames{i};
             grRule  = protGenes{j};
+            model   = addEnzymesToRxn(model,kvalues,rxnID,newMets,{rxnID,rxnName},grRule);
+            %If some proteins where not present previously, add them:
             for k = 1:length(uniprots{j})
                 if sum(strcmp(model.enzymes,uniprots{j}{k})) == 0
                     model = addProtein(model,uniprots{j}{k},kegg,swissprot);
                 end
-                newMets{k} = ['prot_' newMets{k}];     
             end
-            %Add new protein stoich. coeffs to rxn:
-            kvalues = kcats(j)./stoich{j};
-            rxnID   = model.rxns{i};
-            rxnName = model.rxnNames{i};
-            model   = addEnzymesToRxn(model,kvalues,rxnID,newMets,{rxnID,rxnName},grRule);
         end
     end
     %Update int_pos:

diff --git a/geckomat/limit_proteins/scaleBioMass.m b/geckomat/limit_proteins/scaleBioMass.m
@@ -60,11 +60,13 @@
 
 rxnName = [metName ' pseudoreaction'];
 rxnPos  = strcmp(model.rxnNames,rxnName);
-for i = 1:length(model.mets)
-    S_ir   = model.S(i,rxnPos);
-    isProd = strcmp(model.metNames{i},metName);
-    if S_ir ~= 0 && ~isProd
-        model.S(i,rxnPos) = f*S_ir;
+if sum(rxnPos) == 1
+    for i = 1:length(model.mets)
+        S_ir   = model.S(i,rxnPos);
+        isProd = strcmp(model.metNames{i},metName);
+        if S_ir ~= 0 && ~isProd
+            model.S(i,rxnPos) = f*S_ir;
+        end
     end
 end
 

diff --git a/models/saveECmodel.m b/models/saveECmodel.m
@@ -39,16 +39,16 @@
     %Transform model back to COBRA for saving purposes:
     model_cobra = ravenCobraWrapper(model);
     %Remove fields from COBRA model (temporal):
-    model_cobra = rmfield(model_cobra,'metCharges');
-    model_cobra = rmfield(model_cobra,'metChEBIID');
-    model_cobra = rmfield(model_cobra,'metKEGGID');
-    model_cobra = rmfield(model_cobra,'metSBOTerms');
-    model_cobra = rmfield(model_cobra,'rxnConfidenceScores');
-    model_cobra = rmfield(model_cobra,'rxnECNumbers');
-    model_cobra = rmfield(model_cobra,'rxnKEGGID');
-    model_cobra = rmfield(model_cobra,'rxnReferences');
-    model_cobra = rmfield(model_cobra,'subSystems');
-    model_cobra = rmfield(model_cobra,'rxnSBOTerms');
+    model_cobra = takeOutField(model_cobra,'metCharges');
+    model_cobra = takeOutField(model_cobra,'metChEBIID');
+    model_cobra = takeOutField(model_cobra,'metKEGGID');
+    model_cobra = takeOutField(model_cobra,'metSBOTerms');
+    model_cobra = takeOutField(model_cobra,'rxnConfidenceScores');
+    model_cobra = takeOutField(model_cobra,'rxnECNumbers');
+    model_cobra = takeOutField(model_cobra,'rxnKEGGID');
+    model_cobra = takeOutField(model_cobra,'rxnReferences');
+    model_cobra = takeOutField(model_cobra,'subSystems');
+    model_cobra = takeOutField(model_cobra,'rxnSBOTerms');
     %Save model as sbml and text:
     writeCbModel(model_cobra,'sbml',[file_name '.xml']);
     writeCbModel(model_cobra,'text',[file_name '.txt']);
@@ -81,3 +81,13 @@
 end
 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+function model = takeOutField(model,field)
+
+if isfield(model,field)
+    model = rmfield(model,field);
+end
+
+end
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%