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getRxnsInComp

PURPOSE ^

getRxnsInComp

SYNOPSIS ^

function [I rxnNames]=getRxnsInComp(model,comp,includePartial)

DESCRIPTION ^

 getRxnsInComp
   Gets the reactions in a specified compartment

   model           a model structure
   comp            string with the compartment id
   includePartial  true if reactions with metabolites in several
                   compartments (normally transport reactions) should
                   be included (opt, default false)

   I               boolean vector of the reactions
   rxnNames        the names of the reactions

   Usage: [I rxnNames]=getRxnsInComp(model,comp,includePartial)

   Rasmus Agren, 2013-08-01

CROSS-REFERENCE INFORMATION ^

This function calls: This function is called by:

SOURCE CODE ^

0001 function [I rxnNames]=getRxnsInComp(model,comp,includePartial)
0002 % getRxnsInComp
0003 %   Gets the reactions in a specified compartment
0004 %
0005 %   model           a model structure
0006 %   comp            string with the compartment id
0007 %   includePartial  true if reactions with metabolites in several
0008 %                   compartments (normally transport reactions) should
0009 %                   be included (opt, default false)
0010 %
0011 %   I               boolean vector of the reactions
0012 %   rxnNames        the names of the reactions
0013 %
0014 %   Usage: [I rxnNames]=getRxnsInComp(model,comp,includePartial)
0015 %
0016 %   Rasmus Agren, 2013-08-01
0017 %
0018 
0019 if ischar(comp)
0020     comp={comp};
0021 end
0022 if nargin<3
0023     includePartial=false;
0024 end
0025 
0026 J=find(ismember(upper(model.comps),upper(comp)));
0027 
0028 if numel(J)~=1
0029    dispEM(['No unique match to compartment "' comp{1} '"']); 
0030 end
0031 
0032 K=model.metComps==J; %Get all metabolites in the compartment
0033 
0034 S=model.S~=0;
0035 
0036 %Find the reactions which involve any of the mets
0037 [crap I]=find(S(K,:));
0038 I=unique(I);
0039 
0040 %Then remove the ones which also include metabolites in other comps
0041 if includePartial==false 
0042     I=I(sum(S(:,I))==sum(S(K,I)));
0043 end
0044 rxnNames=model.rxnNames(I);
0045 end

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