feat: additional model fields

INIT/getINITModel.m

@@ -391,6 +391,9 @@
 if isfield(model,'geneShortNames')
     model.geneShortNames(I)=[];
 end
+if isfield(model,'proteinNames')
+    model.proteinNames(I)=[];
+end
 if isfield(model,'geneMiriams')
     model.geneMiriams(I)=[];
 end

INIT/mergeLinear.m

@@ -29,6 +29,9 @@
 if isfield(reducedModel,'geneShortNames')
     reducedModel.geneShortNames={};
 end
+if isfield(reducedModel,'proteinNames')
+    reducedModel.proteinNames={};
+end
 if isfield(reducedModel,'geneMiriams')
     reducedModel.geneMiriams={};
 end

INIT/removeLowScoreGenes.m

@@ -119,6 +119,9 @@
 if isfield(newModel,'geneShortNames')
     newModel.geneShortNames(remInd) = [];
 end
+if isfield(newModel,'proteinNames')
+    newModel.proteinNames(remInd) = [];
+end
 if isfield(newModel,'geneMiriams')
     newModel.geneMiriams(remInd) = [];
 end

core/addGenesRaven.m

@@ -14,6 +14,8 @@
 %                               default '')
 %                geneMiriams    cell array with MIRIAM structures (optional,
 %                               default [])
+%                proteinNames   cell array of protein names associated to
+%                               each gene (optional, default '')
 %
 %   newModel     an updated model structure
 %
@@ -56,6 +58,9 @@
     if isfield(genesToAdd,'geneShortNames')
         genesToAdd.geneShortNames(I)=[];
     end
+    if isfield(genesToAdd,'proteinNames')
+        genesToAdd.proteinNames(I)=[];
+    end
     if isfield(genesToAdd,'geneMiriams')
         genesToAdd.geneMiriams(I)=[];
     end
@@ -81,6 +86,24 @@
         newModel.geneShortNames=[newModel.geneShortNames;filler];
     end
 end
+if isfield(genesToAdd,'proteinNames')
+    genesToAdd.proteinNames=convertCharArray(genesToAdd.proteinNames);
+    if numel(genesToAdd.proteinNames)~=nGenes
+        EM='genesToAdd.proteinNames must have the same number of elements as genesToAdd.genes';
+        dispEM(EM);
+    end
+    %Add empty field if it doesn't exist
+    if ~isfield(newModel,'proteinNames')
+        newModel.proteinNames=largeFiller;
+    end
+    newModel.proteinNames=[newModel.proteinNames;genesToAdd.proteinNames(:)];
+else
+    %Add empty strings if structure is in model
+    if isfield(newModel,'proteinNames')
+        newModel.proteinNames=[newModel.proteinNames;filler];
+    end
+end
+
 
 %Don't check the type of geneMiriams
 if isfield(genesToAdd,'geneMiriams')

core/deleteUnusedGenes.m

@@ -37,6 +37,10 @@
     reducedModel.geneShortNames=reducedModel.geneShortNames(toKeep);
 end
 
+if isfield(reducedModel,'proteinNames')
+    reducedModel.proteinNames=reducedModel.proteinNames(toKeep);
+end
+
 if isfield(reducedModel,'geneMiriams')
     reducedModel.geneMiriams=reducedModel.geneMiriams(toKeep);
 end

core/getModelFromHomology.m

@@ -107,14 +107,17 @@
 modelNames=cell(numel(models),1);
 for i=1:numel(models)
     modelNames{i}=models{i}.id;
-    %Gene short names and geneMiriams are often different between species,
-    %safer not to include them
+    %Gene short names, geneMiriams and proteins are often different
+    %between species, safer not to include them
     if isfield(models{i},'geneShortNames')
         models{i}=rmfield(models{i},'geneShortNames');
     end
     if isfield(models{i},'geneMiriams')
         models{i}=rmfield(models{i},'geneMiriams');
     end
+    if isfield(models{i},'proteinNames')
+        models{i}=rmfield(models{i},'proteinNames');
+    end
     %The geneFrom field also loses meaning if the genes are replaced by
     %orthologs
     if isfield(models{i},'geneFrom')

core/mergeModels.m

@@ -492,7 +492,11 @@
             if isfield(models{i},'geneShortNames')
                 model.geneShortNames=models{i}.geneShortNames;
             end
-
+
+            if isfield(models{i},'proteinNames')
+                model.proteinNames=models{i}.proteinNames;
+            end
+
             if isfield(models{i},'geneMiriams')
                 model.geneMiriams=models{i}.geneMiriams;
             end
@@ -530,7 +534,23 @@
                         model.geneShortNames=[model.geneShortNames;emptyGeneSN];
                     end
                 end
-
+
+                if isfield(models{i},'proteinNames')
+                    if isfield(model,'proteinNames')
+                        model.proteinNames=[model.proteinNames;models{i}.proteinNames(genesToAdd)];
+                    else
+                        emptyGeneSN=cell(numel(model.genes)-numel(genesToAdd),1);
+                        emptyGeneSN(:)={''};
+                        model.proteinNames=[emptyGeneSN;models{i}.proteinNames(genesToAdd)];
+                    end
+                else
+                    if isfield(model,'proteinNames')
+                        emptyGeneSN=cell(numel(genesToAdd),1);
+                        emptyGeneSN(:)={''};
+                        model.proteinNames=[model.proteinNames;emptyGeneSN];
+                    end
+                end
+
                 if isfield(models{i},'geneMiriams')
                     if isfield(model,'geneMiriams')
                         model.geneMiriams=[model.geneMiriams;models{i}.geneMiriams(genesToAdd)];

core/permuteModel.m

@@ -132,6 +132,9 @@
         if isfield(newModel,'geneShortNames')
             newModel.geneShortNames=newModel.geneShortNames(indexes);
         end
+        if isfield(newModel,'proteinNames')
+            newModel.proteinNames=newModel.proteinNames(indexes);
+        end
         if isfield(newModel,'rxnGeneMat')
             newModel.rxnGeneMat=newModel.rxnGeneMat(:,indexes);
         end

core/predictLocalization.m

@@ -199,6 +199,9 @@
     if isfield(model,'geneMiriams')
         model.geneMiriams=[model.geneMiriams;{[]}];
     end
+    if isfield(model,'proteinNames')
+        model.proteinNames=[model.proteinNames;{[]}];
+    end
     if isfield(model,'geneFrom')
         model.geneFrom=[model.geneFrom;{{'FAKE'}}];
     end
@@ -258,6 +261,9 @@
     if isfield(model,'geneShortNames')
         model.geneShortNames=[model.geneShortNames;{''}];
     end
+    if isfield(model,'proteinNames')
+        model.proteinNames=[model.proteinNames;{''}];
+    end
     if isfield(model,'geneFrom')
         model.geneFrom=[model.geneFrom;{'COMPLEX'}];
     end
@@ -759,6 +765,9 @@
 if isfield(outModel,'geneShortNames')
     outModel.geneShortNames(I)=[];
 end
+if isfield(outModel,'proteinNames')
+    outModel.proteinNames(I)=[];
+end
 outModel.rxnGeneMat(:,I)=[];
 
 %Fix grRules and reconstruct rxnGeneMat

core/removeReactions.m

@@ -129,6 +129,10 @@
         if isfield(reducedModel,'geneShortNames')
             reducedModel.geneShortNames=reducedModel.geneShortNames(toKeep);
         end
+
+        if isfield(reducedModel,'proteinNames')
+            reducedModel.proteinNames=reducedModel.proteinNames(toKeep);
+        end
 
         if isfield(reducedModel,'geneMiriams')
             reducedModel.geneMiriams=reducedModel.geneMiriams(toKeep);

core/simplifyModel.m

@@ -221,6 +221,9 @@
     if isfield(reducedModel,'geneShortNames')
         reducedModel.geneShortNames={};
     end
+    if isfield(reducedModel,'proteinNames')
+        reducedModel.proteinNames={};
+    end
     if isfield(reducedModel,'geneMiriams')
         reducedModel.geneMiriams={};
     end

doc/INIT/getINITModel.html

@@ -544,77 +544,80 @@ <h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" sr
 0391 <span class="keyword">if</span> isfield(model,<span class="string">'geneShortNames'</span>)
 0392     model.geneShortNames(I)=[];
 0393 <span class="keyword">end</span>
-0394 <span class="keyword">if</span> isfield(model,<span class="string">'geneMiriams'</span>)
-0395     model.geneMiriams(I)=[];
+0394 <span class="keyword">if</span> isfield(model,<span class="string">'proteinNames'</span>)
+0395     model.proteinNames(I)=[];
 0396 <span class="keyword">end</span>
-0397 <span class="keyword">if</span> isfield(model,<span class="string">'geneFrom'</span>)
-0398     model.geneFrom(I)=[];
+0397 <span class="keyword">if</span> isfield(model,<span class="string">'geneMiriams'</span>)
+0398     model.geneMiriams(I)=[];
 0399 <span class="keyword">end</span>
-0400 <span class="keyword">if</span> isfield(model,<span class="string">'geneComps'</span>)
-0401     model.geneComps(I)=[];
+0400 <span class="keyword">if</span> isfield(model,<span class="string">'geneFrom'</span>)
+0401     model.geneFrom(I)=[];
 0402 <span class="keyword">end</span>
-0403 
-0404 <span class="comment">%At this stage the model will contain some exchange reactions but probably</span>
-0405 <span class="comment">%not all (and maybe zero). This can be inconvenient, so all exchange</span>
-0406 <span class="comment">%reactions from the reference model are added, except for those which</span>
-0407 <span class="comment">%involve metabolites that are not in the model.</span>
-0408 
-0409 <span class="comment">%First delete and included exchange reactions in order to prevent the order</span>
-0410 <span class="comment">%from changing</span>
-0411 model=removeReactions(model,getExchangeRxns(model));
-0412 
-0413 <span class="comment">%Create a model with only the exchange reactions in refModel</span>
-0414 excModel=removeReactions(refModel,setdiff(refModel.rxns,getExchangeRxns(refModel)),true,true);
+0403 <span class="keyword">if</span> isfield(model,<span class="string">'geneComps'</span>)
+0404     model.geneComps(I)=[];
+0405 <span class="keyword">end</span>
+0406 
+0407 <span class="comment">%At this stage the model will contain some exchange reactions but probably</span>
+0408 <span class="comment">%not all (and maybe zero). This can be inconvenient, so all exchange</span>
+0409 <span class="comment">%reactions from the reference model are added, except for those which</span>
+0410 <span class="comment">%involve metabolites that are not in the model.</span>
+0411 
+0412 <span class="comment">%First delete and included exchange reactions in order to prevent the order</span>
+0413 <span class="comment">%from changing</span>
+0414 model=removeReactions(model,getExchangeRxns(model));
 0415 
-0416 <span class="comment">%Find the metabolites there which are not exchange metabolites and which do</span>
-0417 <span class="comment">%not exist in the output model</span>
-0418 I=~ismember(excModel.mets,model.mets) &amp; excModel.unconstrained==0;
-0419 
-0420 <span class="comment">%Then find those reactions and delete them</span>
-0421 [~, J]=find(excModel.S(I,:));
-0422 excModel=removeReactions(excModel,J,true,true);
-0423 
-0424 <span class="comment">%Merge with the output model</span>
-0425 model=mergeModels({model;excModel},<span class="string">'metNames'</span>);
-0426 model.id=<span class="string">'INITModel'</span>;
-0427 model.name=[<span class="string">'Automatically generated model for '</span> tissue];
-0428 <span class="keyword">if</span> any(celltype)
-0429     model.name=[model.name <span class="string">' - '</span> celltype];
-0430 <span class="keyword">end</span>
-0431 
-0432 <span class="keyword">if</span> printReport==true
-0433     <a href="#_sub1" class="code" title="subfunction [rxnS, geneS]=printScores(model,name,hpaData,arrayData,tissue,celltype)">printScores</a>(model,<span class="string">'Final model statistics'</span>,hpaData,arrayData,tissue,celltype);
-0434 <span class="keyword">end</span>
-0435 
-0436 <span class="comment">%Add information about essential reactions and reactions included for</span>
-0437 <span class="comment">%gap-filling and return a taskReport</span>
-0438 <span class="keyword">if</span> ~isempty(taskStructure)
-0439     I=find(taskReport.ok); <span class="comment">%Ignore failed tasks</span>
-0440     <span class="keyword">for</span> i=1:numel(I)
-0441         taskReport.essential{I(i),1}=cModel.rxns(essentialRxnMat(:,I(i)));
-0442         taskReport.gapfill{I(i),1}=refModelNoExc.rxns(addedRxnMat(:,i));
-0443     <span class="keyword">end</span>
-0444 <span class="keyword">else</span>
-0445     taskReport=[];
-0446 <span class="keyword">end</span>
-0447 
-0448 <span class="comment">%Fix grRules and reconstruct rxnGeneMat</span>
-0449 [grRules,rxnGeneMat] = standardizeGrRules(model,true);
-0450 model.grRules = grRules;
-0451 model.rxnGeneMat = rxnGeneMat;
-0452 <span class="keyword">end</span>
-0453 
-0454 <span class="comment">%This is for printing a summary of a model</span>
-0455 <a name="_sub1" href="#_subfunctions" class="code">function [rxnS, geneS]=printScores(model,name,hpaData,arrayData,tissue,celltype)</a>
-0456 [a, b]=scoreModel(model,hpaData,arrayData,tissue,celltype);
-0457 rxnS=mean(a);
-0458 geneS=mean(b(~isinf(b)));
-0459 fprintf([name <span class="string">':\n'</span>]);
-0460 fprintf([<span class="string">'\t'</span> num2str(numel(model.rxns)) <span class="string">' reactions, '</span> num2str(numel(model.genes)) <span class="string">' genes\n'</span>]);
-0461 fprintf([<span class="string">'\tMean reaction score: '</span> num2str(rxnS) <span class="string">'\n'</span>]);
-0462 fprintf([<span class="string">'\tMean gene score: '</span> num2str(geneS) <span class="string">'\n'</span>]);
-0463 fprintf([<span class="string">'\tReactions with positive scores: '</span> num2str(100*sum(a&gt;0)/numel(a)) <span class="string">'%%\n\n'</span>]);
-0464 <span class="keyword">end</span></pre></div>
+0416 <span class="comment">%Create a model with only the exchange reactions in refModel</span>
+0417 excModel=removeReactions(refModel,setdiff(refModel.rxns,getExchangeRxns(refModel)),true,true);
+0418 
+0419 <span class="comment">%Find the metabolites there which are not exchange metabolites and which do</span>
+0420 <span class="comment">%not exist in the output model</span>
+0421 I=~ismember(excModel.mets,model.mets) &amp; excModel.unconstrained==0;
+0422 
+0423 <span class="comment">%Then find those reactions and delete them</span>
+0424 [~, J]=find(excModel.S(I,:));
+0425 excModel=removeReactions(excModel,J,true,true);
+0426 
+0427 <span class="comment">%Merge with the output model</span>
+0428 model=mergeModels({model;excModel},<span class="string">'metNames'</span>);
+0429 model.id=<span class="string">'INITModel'</span>;
+0430 model.name=[<span class="string">'Automatically generated model for '</span> tissue];
+0431 <span class="keyword">if</span> any(celltype)
+0432     model.name=[model.name <span class="string">' - '</span> celltype];
+0433 <span class="keyword">end</span>
+0434 
+0435 <span class="keyword">if</span> printReport==true
+0436     <a href="#_sub1" class="code" title="subfunction [rxnS, geneS]=printScores(model,name,hpaData,arrayData,tissue,celltype)">printScores</a>(model,<span class="string">'Final model statistics'</span>,hpaData,arrayData,tissue,celltype);
+0437 <span class="keyword">end</span>
+0438 
+0439 <span class="comment">%Add information about essential reactions and reactions included for</span>
+0440 <span class="comment">%gap-filling and return a taskReport</span>
+0441 <span class="keyword">if</span> ~isempty(taskStructure)
+0442     I=find(taskReport.ok); <span class="comment">%Ignore failed tasks</span>
+0443     <span class="keyword">for</span> i=1:numel(I)
+0444         taskReport.essential{I(i),1}=cModel.rxns(essentialRxnMat(:,I(i)));
+0445         taskReport.gapfill{I(i),1}=refModelNoExc.rxns(addedRxnMat(:,i));
+0446     <span class="keyword">end</span>
+0447 <span class="keyword">else</span>
+0448     taskReport=[];
+0449 <span class="keyword">end</span>
+0450 
+0451 <span class="comment">%Fix grRules and reconstruct rxnGeneMat</span>
+0452 [grRules,rxnGeneMat] = standardizeGrRules(model,true);
+0453 model.grRules = grRules;
+0454 model.rxnGeneMat = rxnGeneMat;
+0455 <span class="keyword">end</span>
+0456 
+0457 <span class="comment">%This is for printing a summary of a model</span>
+0458 <a name="_sub1" href="#_subfunctions" class="code">function [rxnS, geneS]=printScores(model,name,hpaData,arrayData,tissue,celltype)</a>
+0459 [a, b]=scoreModel(model,hpaData,arrayData,tissue,celltype);
+0460 rxnS=mean(a);
+0461 geneS=mean(b(~isinf(b)));
+0462 fprintf([name <span class="string">':\n'</span>]);
+0463 fprintf([<span class="string">'\t'</span> num2str(numel(model.rxns)) <span class="string">' reactions, '</span> num2str(numel(model.genes)) <span class="string">' genes\n'</span>]);
+0464 fprintf([<span class="string">'\tMean reaction score: '</span> num2str(rxnS) <span class="string">'\n'</span>]);
+0465 fprintf([<span class="string">'\tMean gene score: '</span> num2str(geneS) <span class="string">'\n'</span>]);
+0466 fprintf([<span class="string">'\tReactions with positive scores: '</span> num2str(100*sum(a&gt;0)/numel(a)) <span class="string">'%%\n\n'</span>]);
+0467 <span class="keyword">end</span></pre></div>
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