findTransRxns.m

function [transRxns,nonTransRxns,transRxnsBool] = findTransRxns(model,inclExc, ... 
    rxnInds,inclObjAsExc,irrevFlag)
%findTransRxns identify all transport reactions in a model, which are
%defined as reactions involved with metabolites in more than 1 compartment
%
% [transRxns,nonTransRxns] = findTransRxns(model,inclExc,rxnInds)
%
%INPUT
% model             COBRA model structure
%
%OPTIONAL INPUT
% inclExc           include exchange reactions as transport?
%                   (Default = false)
% rxnInds           indices of reactions to test for transport activity.
%                   (default = test all columns of model.S)
% inclObjAsExc      include objective as an exchange reaction? this is
%                   passed to findExcRxns. (default = false)
% irrevFlag         is model irreversible? this is passed to findExcRxns.
%                   (default=false)
%
%OUTPUT
% transRxns         transport reactions in rxnInds
% nonTransRxns      non-transport reactions in rxnInds
%
% right now, this function only works with models the compartments [c],
% [p], and [e]. Jeff Orth, 8/31/07
% 
% modified the function to work with arbitrary compartments, to accept 
% rxnInds, & to use findExcRxns. Jonathan Dreyfuss, 10/9/12
%
% modified to also output a boolean vector version of transRxns. Thierry
% Mondeel, 07/15/15

if nargin < 2
    inclExc = false;
end
if nargin < 3
    rxnInds = 1:size(model.S, 2);
end
if nargin < 4
    inclObjAsExc = false;
end
if nargin < 5
    irrevFlag = false;
end

if inclExc
    % findExcRxns returns boolean vector
    isExc0 = findExcRxns(model,inclObjAsExc,irrevFlag);
    % subset to rxnInds
    isExc = isExc0(rxnInds);
else
    isExc=zeros(length(rxnInds), 1);
end

% initialize isNonexchangeTransport rxns vector
isNonexchTrans = zeros(length(rxnInds), 1);
% get compartment symbols for each metabolite
[baseMetNames,compSymbols]=arrayfun(@parseMetNames, model.mets);
for i = 1:length(rxnInds)
    rxnIndTmp=rxnInds(i);
    % get compartment symbols for each rxn
    compSymbolsTmp=compSymbols(model.S(:,rxnIndTmp)~=0);
    % if there's more than 1 compartment involved, it's a transport rxn
    if length(unique(compSymbolsTmp))>1
        isNonexchTrans(i) = 1;
    end
end

% get rxn abbreviations for all rxns in rxnInds
rxnAbbrevs=model.rxns(rxnInds);
% if inclExc==1, exchange rxns will have isExc==1, and should be counted as
% transport rxns; else, all isExc will be 0.
transRxnsBool = isNonexchTrans==1 | isExc==1;
transRxns = rxnAbbrevs(transRxnsBool);
nonTransRxns = setdiff(rxnAbbrevs, transRxns);