removeReactions

 removeReactions
   Deletes a set of reactions from a model

 Input:
   model             a model structure
   rxnsToRemove      either a cell array of reaction IDs, a logical vector
                     with the same number of elements as reactions in the
                     model, or a vector of indexes to remove
   removeUnusedMets  remove metabolites that are no longer in use
                     (optional, default false)
   removeUnusedGenes remove genes that are no longer in use (optional,
                     default false)
   removeUnusedComps remove compartments that are no longer in use
                     (optional, default false)

 Output:
   reducedModel      an updated model structure

 Usage: reducedModel = removeReactions(model, rxnsToRemove, removeUnusedMets,...
                           removeUnusedGenes, removeUnusedComps)

0001 function reducedModel=removeReactions(model,rxnsToRemove,removeUnusedMets,removeUnusedGenes,removeUnusedComps)
0002 % removeReactions
0003 %   Deletes a set of reactions from a model
0004 %
0005 % Input:
0006 %   model             a model structure
0007 %   rxnsToRemove      either a cell array of reaction IDs, a logical vector
0008 %                     with the same number of elements as reactions in the
0009 %                     model, or a vector of indexes to remove
0010 %   removeUnusedMets  remove metabolites that are no longer in use
0011 %                     (optional, default false)
0012 %   removeUnusedGenes remove genes that are no longer in use (optional,
0013 %                     default false)
0014 %   removeUnusedComps remove compartments that are no longer in use
0015 %                     (optional, default false)
0016 %
0017 % Output:
0018 %   reducedModel      an updated model structure
0019 %
0020 % Usage: reducedModel = removeReactions(model, rxnsToRemove, removeUnusedMets,...
0021 %                           removeUnusedGenes, removeUnusedComps)
0022 
0023 if nargin<3
0024     removeUnusedMets=false;
0025 end
0026 if nargin<4
0027     removeUnusedGenes=false;
0028 end
0029 if nargin<5
0030     removeUnusedComps=false;
0031 end
0032 if ~islogical(rxnsToRemove) && ~isnumeric(rxnsToRemove)
0033     rxnsToRemove=convertCharArray(rxnsToRemove);
0034 end
0035 
0036 reducedModel=model;
0037 
0038 if ~isempty(rxnsToRemove) || removeUnusedMets || removeUnusedGenes
0039     indexesToDelete=getIndexes(model,rxnsToRemove,'rxns');
0040     
0041     %Remove reactions
0042     if ~isempty(indexesToDelete)
0043         reducedModel.rxns(indexesToDelete)=[];
0044         if isfield(reducedModel,'lb')
0045             reducedModel.lb(indexesToDelete)=[];
0046         end
0047         if isfield(reducedModel,'ub')
0048             reducedModel.ub(indexesToDelete)=[];
0049         end
0050         if isfield(reducedModel,'rev')
0051             reducedModel.rev(indexesToDelete)=[];
0052         end
0053         if isfield(reducedModel,'c')
0054             reducedModel.c(indexesToDelete)=[];
0055         end
0056         if isfield(reducedModel,'S')
0057             reducedModel.S(:,indexesToDelete)=[];
0058         end
0059         if isfield(reducedModel,'rxnNames')
0060             reducedModel.rxnNames(indexesToDelete)=[];
0061         end
0062         if isfield(reducedModel,'rxnGeneMat')
0063             reducedModel.rxnGeneMat(indexesToDelete,:)=[];
0064         end
0065         if isfield(reducedModel,'grRules')
0066             reducedModel.grRules(indexesToDelete,:)=[];
0067         end
0068         if isfield(reducedModel,'subSystems')
0069             reducedModel.subSystems(indexesToDelete,:)=[];
0070         end
0071         if isfield(reducedModel,'eccodes')
0072             reducedModel.eccodes(indexesToDelete,:)=[];
0073         end
0074         if isfield(reducedModel,'equations')
0075             reducedModel.equations(indexesToDelete,:)=[];
0076         end
0077         if isfield(reducedModel,'rxnMiriams')
0078             reducedModel.rxnMiriams(indexesToDelete,:)=[];
0079         end
0080         if isfield(reducedModel,'rxnComps')
0081             reducedModel.rxnComps(indexesToDelete,:)=[];
0082         end
0083         if isfield(reducedModel,'rxnFrom')
0084             reducedModel.rxnFrom(indexesToDelete,:)=[];
0085         end
0086         if isfield(reducedModel,'rxnScores')
0087             reducedModel.rxnScores(indexesToDelete,:)=[];
0088         end
0089         if isfield(reducedModel,'rxnNotes')
0090             reducedModel.rxnNotes(indexesToDelete,:)=[];
0091         end
0092         if isfield(reducedModel,'rxnReferences')
0093             reducedModel.rxnReferences(indexesToDelete,:)=[];
0094         end
0095         if isfield(reducedModel,'rxnConfidenceScores')
0096             reducedModel.rxnConfidenceScores(indexesToDelete,:)=[];
0097         end
0098         if isfield(reducedModel,'rxnDeltaG')
0099             reducedModel.rxnDeltaG(indexesToDelete,:)=[];
0100         end
0101         if isfield(reducedModel,'pwys')
0102             reducedModel.pwys(indexesToDelete,:)=[];
0103         end
0104         if isfield(reducedModel,'spontaneous')
0105             reducedModel.spontaneous(indexesToDelete)=[];
0106         end
0107     end
0108     
0109     %Remove unused metabolites
0110     if removeUnusedMets==true
0111         if isfield(reducedModel,'S')
0112             [usedMets, ~]=find(reducedModel.S);
0113             unUsedMets=true(numel(reducedModel.mets),1);
0114             unUsedMets(usedMets)=false;
0115             reducedModel=removeMets(reducedModel,unUsedMets,false,false,false,removeUnusedComps);
0116         end
0117     end
0118     
0119     %Remove unused genes
0120     if removeUnusedGenes==true && isfield(reducedModel,'rxnGeneMat')
0121         %Find all genes that are not used
0122         [~, b]=find(reducedModel.rxnGeneMat);
0123         toKeep=false(numel(reducedModel.genes),1);
0124         toKeep(b)=true;
0125         
0126         reducedModel.genes=reducedModel.genes(toKeep);
0127         reducedModel.rxnGeneMat=reducedModel.rxnGeneMat(:,toKeep);
0128         
0129         if isfield(reducedModel,'geneShortNames')
0130             reducedModel.geneShortNames=reducedModel.geneShortNames(toKeep);
0131         end
0132 
0133         if isfield(reducedModel,'proteins')
0134             reducedModel.proteins=reducedModel.proteins(toKeep);
0135         end
0136         
0137         if isfield(reducedModel,'geneMiriams')
0138             reducedModel.geneMiriams=reducedModel.geneMiriams(toKeep);
0139         end
0140         
0141         if isfield(reducedModel,'geneFrom')
0142             reducedModel.geneFrom=reducedModel.geneFrom(toKeep);
0143         end
0144         
0145         if isfield(reducedModel,'geneComps')
0146             reducedModel.geneComps=reducedModel.geneComps(toKeep);
0147         end
0148     end
0149 else
0150     reducedModel=model;
0151 end
0152 end