MultiRxnsLib

 MultiRxnsLib
 generates shared multi-step reactions among all models saved
 in Bigg2Kegg folder. This list is used in both function UniModel and
 MultiRxns
 
 O. Jamialahmadi
 TMU, Chem. Eng. Dept., Biotech. Group 
 Jan. 2015

0001 function MultiRxnsLib
0002 % MultiRxnsLib
0003 % generates shared multi-step reactions among all models saved
0004 % in Bigg2Kegg folder. This list is used in both function UniModel and
0005 % MultiRxns
0006 %
0007 % O. Jamialahmadi
0008 % TMU, Chem. Eng. Dept., Biotech. Group
0009 % Jan. 2015
0010 
0011 Pth1 = which ('Bigg2Kegg.m');
0012 tind = find(Pth1=='\',1,'last');
0013 Pth = Pth1(1:tind-1);
0014 Pth2 = fullfile(Pth,'BiGG2KEGG\*.mat');
0015 Pth3 = fullfile(Pth,'BiGG2KEGG');
0016 BMatfiles = dir(Pth2);
0017 BNames = cell(numel(BMatfiles)-2,1);
0018 ct1 = 1;
0019 for ct = 1:numel(BMatfiles)
0020     if ~strcmp(BMatfiles(ct).name,'BiGG2KEGG_HMRbased-RECON1.mat') && ...
0021             ~strcmp(BMatfiles(ct).name,'Multirxns.mat')
0022         BNames{ct1} = BMatfiles(ct).name;
0023         ct1 = ct1 + 1;
0024     end
0025 end
0026 BM = ({}); NotBM = ({}); NotKM = ({});
0027 for count =1:numel(BNames)
0028     load(fullfile(Pth3,BNames{count}))
0029     B=B2Kegg.B;K=B2Kegg.K;
0030     MltLoci = find(ismember(B,'MULTIR'));
0031     NotBM1 = B(1:MltLoci-1); NotKM1 = K(1:MltLoci-1);
0032     BM1 = B(MltLoci+1:end); 
0033     NonOverlp = ~ismember(BM1,BM);
0034     BM1 = BM1(NonOverlp);
0035     [NotBM1,NotKM1] = Rxnfinder(BM1,NotBM1,NotKM1);
0036     Len = numel(BM)+1:numel(BM1)+numel(BM);
0037     clear B2Kegg
0038     BM(Len) = BM1; 
0039     if ~isempty(NotBM1)
0040         Len1 = numel(NotBM)+1:numel(NotBM1)+numel(NotBM);
0041         NotBM(Len1) = NotBM1; NotKM(Len1) = NotKM1;
0042     end
0043 end
0044 [ParentRxn,ChildRxns] = MultiRxns(NotKM);
0045 Multirxns.P = ParentRxn; Multirxns.C = ChildRxns;
0046 save ([Pth3,'\Multirxns.mat'],'Multirxns')
0047 clear
0048 disp('Multi Reactions Library has been generated successfully!')
0049 %--------------------------------------------------------------------------
0050 function [NotBM,NotKM] =  Rxnfinder(BM1,NotBM1,NotKM1)
0051 count = 1; NotBM = ({}); NotKM = ({});
0052 while numel(BM1)
0053     Tfind = find(ismember(BM1,BM1{1}));
0054     Tfind1 = find(ismember(NotBM1,BM1{Tfind(1)}));
0055     for ct = 1:numel(Tfind1)
0056         NotBM{count} = NotBM1{Tfind1(ct)};
0057         NotKM{count} = NotKM1{Tfind1(ct)};
0058         count = count + 1;
0059     end
0060     BM1(Tfind) = [];
0061 end