fix: exportModel valid libSBML output

SysBioChalmers · May 21, 2024 · d390475 · d390475
1 parent 191c89b
commit d390475
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Showing 7 changed files with 804 additions and 810 deletions.
diff --git a/doc/core/getAllowedBounds.html b/doc/core/getAllowedBounds.html
@@ -118,28 +118,29 @@ <h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" sr
 0049     tmpModel = model;
 0050     tmpModel.c = c;
 0051 
-0052     <span class="comment">% Get minimal flux</span>
-0053     tmpModel.c(rxns(i)) = -1;
-0054     solMin = solveLP(tmpModel);
-0055     <span class="keyword">if</span> ~isempty(solMin.f)
-0056         minFluxes(i) = solMin.x(rxns(i));
+0052     <span class="comment">% Get maximal flux</span>
+0053     tmpModel.c(rxns(i)) = 1;
+0054     [solMax,hsSol]=solveLP(tmpModel);
+0055     <span class="keyword">if</span> ~isempty(solMax.f)
+0056         maxFluxes(i) = solMax.x(rxns(i));
 0057     <span class="keyword">else</span>
-0058         minFluxes(i) = NaN;
+0058         maxFluxes(i) = NaN;
 0059     <span class="keyword">end</span>
 0060 
-0061     <span class="comment">% Get maximal flux</span>
-0062     tmpModel.c(rxns(i)) = 1;
-0063     solMax=solveLP(tmpModel);
-0064     exitFlags(i,:) = [solMin.stat solMax.stat];
-0065     <span class="keyword">if</span> ~isempty(solMax.f)
-0066         maxFluxes(i) = solMax.x(rxns(i));
-0067     <span class="keyword">else</span>
-0068         maxFluxes(i) = NaN;
-0069     <span class="keyword">end</span>
-0070 <span class="keyword">end</span>
-0071 <span class="comment">% Reset original Parallel setting</span>
-0072 ps.Pool.AutoCreate = oldPoolAutoCreateSetting;
-0073 <span class="keyword">end</span></pre></div>
+0061     <span class="comment">% Get minimal flux</span>
+0062     tmpModel.c(rxns(i)) = -1;
+0063     solMin = solveLP(tmpModel,[],[],hsSol);
+0064     <span class="keyword">if</span> ~isempty(solMin.f)
+0065         minFluxes(i) = solMin.x(rxns(i));
+0066     <span class="keyword">else</span>
+0067         minFluxes(i) = NaN;
+0068     <span class="keyword">end</span>
+0069     exitFlags(i,:) = [solMin.stat solMax.stat];
+0070 
+0071 <span class="keyword">end</span>
+0072 <span class="comment">% Reset original Parallel setting</span>
+0073 ps.Pool.AutoCreate = oldPoolAutoCreateSetting;
+0074 <span class="keyword">end</span></pre></div>
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diff --git a/doc/core/getGenesFromGrRules.html b/doc/core/getGenesFromGrRules.html
@@ -120,7 +120,7 @@ <h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" sr
 0054 
 0055 <span class="comment">% construct new gene list</span>
 0056 nonEmpty = ~cellfun(@isempty,rxnGenes);
-0057 genes = unique([rxnGenes{nonEmpty}]');
+0057 genes = unique(transpose([rxnGenes{nonEmpty}]));
 0058 genes(cellfun(@isempty,genes)) = [];
 0059 
 0060 <span class="keyword">if</span> ~isempty(originalGenes)

diff --git a/doc/core/haveFlux.html b/doc/core/haveFlux.html
@@ -120,25 +120,28 @@ <h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" sr
 0058 <span class="comment">%Loop through and maximize then minimize each rxn if it does not already</span>
 0059 <span class="comment">%have a flux</span>
 0060 Z=zeros(numel(smallModel.c),1);
-0061 hsSolOut=[];
-0062 <span class="keyword">for</span> i=[1 -1]
-0063     <span class="keyword">for</span> j=1:numel(J)
-0064         <span class="keyword">if</span> J(j)==false
-0065             <span class="comment">%Only minimize for reversible reactions</span>
-0066             <span class="keyword">if</span> i==1 || smallModel.rev(mixIndexes(j))~=0
-0067                 smallModel.c=Z;
-0068                 smallModel.c(mixIndexes(j))=i;
-0069                 [sol, hsSolOut]=solveLP(smallModel,0,[],hsSolOut);
-0070                 <span class="keyword">if</span> any(sol.x)
-0071                     J(abs(sol.x(mixIndexes))&gt;cutOff)=true;
-0072                 <span class="keyword">end</span>
-0073             <span class="keyword">end</span>
-0074         <span class="keyword">end</span>
-0075     <span class="keyword">end</span>
-0076 <span class="keyword">end</span>
-0077 
-0078 I=ismember(rxns,smallModel.rxns(mixIndexes(J)));
-0079 <span class="keyword">end</span></pre></div>
+0061 tryMin = find(J == false);
+0062 isRev = smallModel.rev
+0063 
+0064 parfor 
+0065 <span class="keyword">for</span> i=[1 -1]
+0066     <span class="keyword">for</span> j=1:numel(J)
+0067         <span class="keyword">if</span> J(j)==false
+0068             <span class="comment">%Only minimize for reversible reactions</span>
+0069             <span class="keyword">if</span> i==1 || smallModel.rev(mixIndexes(j))~=0
+0070                 smallModel.c=Z;
+0071                 smallModel.c(mixIndexes(j))=i;
+0072                 sol=solveLP(smallModel,0);
+0073                 <span class="keyword">if</span> any(sol.x)
+0074                     J(abs(sol.x(mixIndexes))&gt;cutOff)=true;
+0075                 <span class="keyword">end</span>
+0076             <span class="keyword">end</span>
+0077         <span class="keyword">end</span>
+0078     <span class="keyword">end</span>
+0079 <span class="keyword">end</span>
+0080 
+0081 I=ismember(rxns,smallModel.rxns(mixIndexes(J)));
+0082 <span class="keyword">end</span></pre></div>
 <hr><address>Generated by <strong><a href="http://www.artefact.tk/software/matlab/m2html/" title="Matlab Documentation in HTML">m2html</a></strong> &copy; 2005</address>
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