closeModel

 closeModel
   Adds boundary metabolites and their participation in exchange
   reactions.

   model                 a model structure

   closedModel           an updated closedModel structure

   Usage: closedModel=closeModel(model)

0001 function closedModel=closeModel(model)
0002 % closeModel
0003 %   Adds boundary metabolites and their participation in exchange
0004 %   reactions.
0005 %
0006 %   model                 a model structure
0007 %
0008 %   closedModel           an updated closedModel structure
0009 %
0010 %   Usage: closedModel=closeModel(model)
0011 
0012 closedModel=model;
0013 
0014 closedModel.comps{numel(closedModel.comps)+1}='b';
0015 closedModel.compNames{numel(closedModel.compNames)+1}='boundary';
0016 if isfield(closedModel,'compMiriams')
0017     closedModel.compMiriams{numel(closedModel.compMiriams)+1}=[];
0018 end;
0019 closedModel.unconstrained=zeros(numel(closedModel.mets),1);
0020 
0021 for i=1:numel(closedModel.rxns)
0022     if sum(abs(closedModel.S(:,i)))==1
0023         closedModel.mets{numel(closedModel.mets)+1}=strcat(closedModel.mets{find(closedModel.S(:,i))},'_b');
0024         if isfield(closedModel,'metNames')
0025             closedModel.metNames{numel(closedModel.metNames)+1}=closedModel.metNames{find(closedModel.S(:,i))};
0026         end;
0027         closedModel.metComps(numel(closedModel.metComps)+1)=numel(closedModel.comps);
0028         if isfield(closedModel,'inchis')
0029             closedModel.inchis{numel(closedModel.inchis)+1}=closedModel.inchis{find(closedModel.S(:,i))};
0030         end;
0031         if isfield(closedModel,'metSmiles')
0032             closedModel.metSmiles{numel(closedModel.metSmiles)+1}=closedModel.metSmiles{find(closedModel.S(:,i))};
0033         end;
0034         if isfield(closedModel,'metFormulas')
0035             closedModel.metFormulas{numel(closedModel.metFormulas)+1}=closedModel.metFormulas{find(closedModel.S(:,i))};
0036         end;
0037         if isfield(closedModel,'metMiriams')
0038             closedModel.metMiriams{numel(closedModel.metMiriams)+1}=closedModel.metMiriams{find(closedModel.S(:,i))};
0039         end;
0040         if isfield(closedModel,'metFrom')
0041             closedModel.metFrom{numel(closedModel.metFrom)+1}='';
0042         end;
0043         if isfield(closedModel,'metCharges')
0044             closedModel.metCharges(numel(closedModel.metCharges)+1)=closedModel.metCharges(find(closedModel.S(:,i)));
0045         end;
0046         if isfield(closedModel,'metDeltaG')
0047             closedModel.metDeltaG(numel(closedModel.metDeltaG)+1)=closedModel.metDeltaG(find(closedModel.S(:,i)));
0048         end;
0049         closedModel.unconstrained(numel(closedModel.unconstrained)+1)=1;
0050         closedModel.b(numel(closedModel.b)+1)=0;
0051         closedModel.S=[closedModel.S;sparse(1,size(closedModel.S,2))];
0052         if sum(closedModel.S(:,i))==1
0053             closedModel.S(numel(closedModel.mets),i)=-1;
0054         else
0055             closedModel.S(numel(closedModel.mets),i)=1;
0056         end;
0057     end;
0058 end;
0059 
0060 end