getcarbonnum

 getcarbonnum
   Gets carbon numbers matching the model.

 Input:
   model           ecModel that was generated by makeEcModel, or loaded from
                   an earlier run. Not compatible with ecModels generated by
                   earlier GECKO versions (pre 3.0).
   exrxn           Exchange reaction to use for counting
 Output:
   model           ecModel

0001 function [CarbonNum,EXfors,changedmets] = getcarbonnum(model,exrxn)
0002 % getcarbonnum
0003 %   Gets carbon numbers matching the model.
0004 %
0005 % Input:
0006 %   model           ecModel that was generated by makeEcModel, or loaded from
0007 %                   an earlier run. Not compatible with ecModels generated by
0008 %                   earlier GECKO versions (pre 3.0).
0009 %   exrxn           Exchange reaction to use for counting
0010 % Output:
0011 %   model           ecModel
0012 %
0013 
0014 % exrxn must be an exchange rxn and only contain one mets in the equation
0015 [~,idx] = ismember(exrxn,model.rxns);
0016 EXmets = model.S(:,idx);
0017 % find all exchange mets
0018 EXmetsIdx = zeros(length(exrxn),1);
0019 for k = 1:length(EXmets(1,:))
0020     EXmetsIdx(k) = find(EXmets(:,k)); %
0021 end
0022 EXfors = model.metFormulas(EXmetsIdx);
0023 [Ematrix, elements] = getElementalComposition(EXfors,{'C'});
0024 Ematrix = Ematrix(:,1);
0025 changedmets = exrxn(isnan(Ematrix));
0026 Ematrix(isnan(Ematrix)) = 1;
0027 CarbonNum = Ematrix';
0028 end