fix: compliance with yeast-GEM

molecular formulas assigned to all backbones based on mass balances. A couple of other changes in the model format
SysBioChalmers · May 20, 2018 · 9368d42 · 9368d42
1 parent 2a8dc31
commit 9368d42
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Showing 2 changed files with 35 additions and 10 deletions.
diff --git a/models/SLIMEr.m b/models/SLIMEr.m
@@ -1,7 +1,7 @@
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 % model = SLIMEr(model,data,includeTails)
 %
-% Benjamín J. Sánchez. Last update: 2018-03-30
+% Benjamín J. Sánchez. Last update: 2018-05-20
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
 function model = SLIMEr(model,data,includeTails)
@@ -12,13 +12,19 @@
 for i = 1:length(metIDs)
     backName = getBackboneName(metNames{i});
     if ~isempty(backName)
-        if ~ismember(backName,model.metNames)
+        if ismember(backName,model.metNames)
+            if ~startsWith(backName,'ergosterol [')
+                model.metFormulas{strcmp(model.metNames,backName)} = '';
+            end
+        else
             model = addLipidSpecies(model,backName,'',false);
         end
         %Add transport rxn to cytoplasm for non cytoplasmic backbones:
         if ~contains(backName,'cytoplasm')
             cytoName = [backName(1:strfind(backName,'[')) 'cytoplasm]'];
-            if ~ismember(cytoName,model.metNames)
+            if ismember(cytoName,model.metNames)
+                model.metFormulas{strcmp(model.metNames,cytoName)} = '';
+            else
                 model = addLipidSpecies(model,cytoName,'',false);
             end
             backID    = model.mets(strcmp(model.metNames,backName));
@@ -53,12 +59,12 @@
 end
 
 %Create lipid pseudo-rxn for backbones:
-model = addLipidSpecies(model,'lipid - backbones [cytoplasm]','NA',includeTails);
+model = addLipidSpecies(model,'lipid - backbones [cytoplasm]','',includeTails);
 model = changeLipidComp(model,data.lipidData);
 
 %Create lipid pseudo-rxn for tails:
 if includeTails
-    model = addLipidSpecies(model,'lipid - tails [cytoplasm]','NA',includeTails);
+    model = addLipidSpecies(model,'lipid - tails [cytoplasm]','',includeTails);
     model = changeChainComp(model,data.chainData);
 end
 
@@ -121,8 +127,9 @@
 model.S(Hpos,bioRxn)   = +GAM;
 model.S(Ppos,bioRxn)   = +GAM;
 
-%Remove wrongly created field:
-model = rmfield(model,'grRules');
+%Correct some wrongly created fields:
+model   = rmfield(model,'grRules');
+model.S = full(model.S);
 
 end
 

diff --git a/models/addSLIMErxn.m b/models/addSLIMErxn.m
@@ -109,12 +109,30 @@
 tailCoeffs    = zeros(size(tailIDs));
 
 %Match to corresponding tail:
+prodFormulas = cell(size(tailsRxn));
 for i = 1:length(tailsRxn)
-    tailName   = [tailsRxn{i} ' chain [cytoplasm]'];
-    tailMatch  = strcmp(tailsModel,tailName);
-    tailCoeffs = tailCoeffs + tailMatch.*tailsMWs;
+    tailName        = [tailsRxn{i} ' chain [cytoplasm]'];
+    tailMatch       = strcmp(tailsModel,tailName);
+    tailCoeffs      = tailCoeffs + tailMatch.*tailsMWs;
+    prodFormulas{i} = tailsFormulas{tailMatch};
 end
 
+%Assign molecular formula to backbone by balancing out the SLIME rxns:
+backName     = [backName ' ['];
+formula      = '';
+elements     = {'C','H','N','O','P','S'};
+for j = 1:length(elements)
+    Nin  = getStoichFromFormula(specFormula, elements{j});
+    Nout = getStoichFromFormula(prodFormulas, elements{j});
+    diff = Nin - sum(Nout);
+    if diff == 1
+        formula = [formula elements{j}];
+    elseif diff > 1
+        formula = [formula elements{j} num2str(diff)];
+    end
+end
+model.metFormulas(startsWith(model.metNames,backName)) = {formula};
+
 %Create SLIME rxn (with same ID as previous ISA rxn but different name):
 model = addReaction(model,rxnID, ...
                     'reactionName', rxnName, ...