getExchangeRxns

 getExchangeRxns
   Retrieves the exchange reactions from a model

   model               a model structure
   reactionType        retrieve all reactions ('both'), only production
                       ('out'), or only consumption ('in') (opt, default
                       'both')

   exchangeRxns        cell array with the IDs of the exchange reactions
   exchangeRxnsIndexes vector with the indexes of the exchange reactions

   Exchange reactions are defined as reactions which involve only products
   or only reactants. If the unconstrained field is present, then that is
   used instead.

   Usage: [exchangeRxns,exchangeRxnsIndexes]=getExchangeRxns(model,reactionType)

0001 function [exchangeRxns, exchangeRxnsIndexes]=getExchangeRxns(model,reactionType)
0002 % getExchangeRxns
0003 %   Retrieves the exchange reactions from a model
0004 %
0005 %   model               a model structure
0006 %   reactionType        retrieve all reactions ('both'), only production
0007 %                       ('out'), or only consumption ('in') (opt, default
0008 %                       'both')
0009 %
0010 %   exchangeRxns        cell array with the IDs of the exchange reactions
0011 %   exchangeRxnsIndexes vector with the indexes of the exchange reactions
0012 %
0013 %   Exchange reactions are defined as reactions which involve only products
0014 %   or only reactants. If the unconstrained field is present, then that is
0015 %   used instead.
0016 %
0017 %   Usage: [exchangeRxns,exchangeRxnsIndexes]=getExchangeRxns(model,reactionType)
0018 
0019 if nargin<2
0020     reactionType='both';
0021 else
0022     reactionType=char(reactionType);
0023 end
0024 
0025 hasNoProducts=sparse(numel(model.rxns),1);
0026 hasNoReactants=sparse(numel(model.rxns),1);
0027 
0028 if isfield(model,'unconstrained')
0029     if strcmpi(reactionType,'both') || strcmpi(reactionType,'out')
0030         [~, I]=find(model.S(model.unconstrained~=0,:)>0);
0031         hasNoProducts(I)=true;
0032     end
0033     if strcmpi(reactionType,'both') || strcmpi(reactionType,'in')
0034         [~, I]=find(model.S(model.unconstrained~=0,:)<0);
0035         hasNoReactants(I)=true;
0036     end
0037 else
0038     if strcmpi(reactionType,'both') || strcmpi(reactionType,'out')
0039         hasNoProducts=sum((model.S>0))==0;
0040     end
0041     if strcmpi(reactionType,'both') || strcmpi(reactionType,'in')
0042         hasNoReactants=sum((model.S<0))==0;
0043     end
0044 end
0045 exchangeRxnsIndexes=find(hasNoProducts(:) | hasNoReactants(:));
0046 exchangeRxns=model.rxns(exchangeRxnsIndexes);
0047 end