findTransRxns

PURPOSE ^

findTransRxns identify all transport reactions in a model

SYNOPSIS ^

function [transRxns,nonTransRxns] = findTransRxns(model,inclExc)

DESCRIPTION ^

findTransRxns identify all transport reactions in a model

 [transRxns,nonTransRxns] = findTransRxns(model,inclExc)

INPUT
 model             COBRA model structure

OPTIONAL INPUT
 inclExc           include exchange reactions as transport?
                   (Default = false)

OUTPUT
 transRxns         all transport reactions in the model
 nonTransRxns      all non-transport reactions in the model

 right now, this function only works with models the compartments [c],
 [p], and [e]

 Jeff Orth  8/31/07

CROSS-REFERENCE INFORMATION ^

This function calls: This function is called by:

SOURCE CODE ^

0001 function [transRxns,nonTransRxns] = findTransRxns(model,inclExc)
0002 %findTransRxns identify all transport reactions in a model
0003 %
0004 % [transRxns,nonTransRxns] = findTransRxns(model,inclExc)
0005 %
0006 %INPUT
0007 % model             COBRA model structure
0008 %
0009 %OPTIONAL INPUT
0010 % inclExc           include exchange reactions as transport?
0011 %                   (Default = false)
0012 %
0013 %OUTPUT
0014 % transRxns         all transport reactions in the model
0015 % nonTransRxns      all non-transport reactions in the model
0016 %
0017 % right now, this function only works with models the compartments [c],
0018 % [p], and [e]
0019 %
0020 % Jeff Orth  8/31/07
0021 
0022 if nargin < 2
0023     inclExc = false;
0024 end
0025 
0026 isTrans = zeros(1,length(model.rxns));
0027 
0028 for i = 1:length(model.rxns)
0029     mets = model.mets(find(model.S(:,i)));
0030     cMets = regexp(mets,'\[c\]');
0031     hasCs = ~isempty([cMets{:}]);
0032     pMets = regexp(mets,'\[p\]');
0033     hasPs = ~isempty([pMets{:}]);
0034     eMets = regexp(mets,'\[e\]');
0035     hasEs = ~isempty([eMets{:}]);
0036     
0037     if (sum([hasCs,hasPs,hasEs]) > 1) || hasEs&&inclExc
0038         isTrans(i) = 1;
0039     end
0040 end
0041 
0042 transRxns = model.rxns(isTrans==1);
0043 nonTransRxns = model.rxns(isTrans==0);
0044 
0045 
0046

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