modelSetting.m

function [model2,targetRID,extype] = modelSetting(model,targetMet)
% modelSetting is a function of gDel_minRN that adds an auxiliary
% exchange reaction for the target metabolite when there is no
% original corresponding exchange reaction.
%
% function [model2,targetRID,extype] = modelSetting(model,targetMet)
%
%INPUTS
%model     COBRA model structure containing the following required fields to perform gDel_minRN.
%   rxns                    Rxns in the model
%   mets                    Metabolites in the model
%   genes               Genes in the model
%   grRules            Gene-protein-reaction relations in the model
%   S                       Stoichiometric matrix (sparse)
%   b                       RHS of Sv = b (usually zeros)
%   c                       Objective coefficients
%   lb                      Lower bounds for fluxes
%   ub                      Upper bounds for fluxes
%   rev                     Reversibility of fluxes
% targetMet   target metabolites
%                           (e.g.,  'btn_c')
%
%OUTPUTS
% model2        the model that has the exchange reaction of the target metabolite
% targetRID     ID of the exchange reaction of the target metabolite
% extype          indicates that an auxiliary exchange reaction was added.
%                       1,2: there was the corresponding exchange reaction.
%                        3: An auxiliary exchange reaction was added.
%
%  Apr. 22, 2021   Takeyuki TAMURA
%
target=findMetIDs(model,targetMet);
m=size(model.mets,1);
n=size(model.rxns,1);
if isempty(find(strcmp(model.rxns,strcat('EX_',targetMet))))==0
    targetRID=find(strcmp(model.rxns,strcat('EX_',targetMet)));
    model2=model;
    extype=1;
elseif isempty(find(strcmp(model.rxns,strcat('DM_',targetMet))))==0
    targetRID=find(strcmp(model.rxns,strcat('DM_',targetMet)));
    model2=model;
    extype=2;
else
    [model2,rxnIDexists]=addReaction(model,'Transport',{targetMet},[-1]);
    m=size(model2.mets,1);
    n=size(model2.rxns,1);
    model2.S(target,n)=-1;
    model2.ub(n)=999999;
    model2.lb(n)=0;
    model2.rev(n)=0;
    targetRID=n;
    extype=3;
end
%save('modelSetting.mat');
end