extractCompModel.m

function compModel = extractCompModel(model,compSymbol,intOnlyFlag)
%extractCompModel Create model for a cellular compartment
%
% compModel = extractCompModel(model,compSymbol,intOnlyFlag)
%
%INPUTS
% model         COBRA model structure
% compSymbol    Compartment symbol
%
%OPTIONAL INPUT
% intOnlyFlag   Include only non-transport reactions (Default = true)
%
%OUTPUT
% compModel     COBRA model for a cellular compartment
%
% Markus Herrgard 3/1/06

if (nargin < 3)
    intOnlyFlag = true;
end

[baseMetNames,compSymbols] = parseMetNames(model.mets);

selMets = strcmp(compSymbols,compSymbol);

if (sum(selMets) == 0)
    warning('Compartment symbol not found');
    compModel = [];
    return;
end

if (intOnlyFlag)

    % Include only non-transport reactions
    selRxns = (sum(model.S(selMets,:) ~= 0)' == sum(model.S ~= 0)') & any(model.S(selMets,:) ~= 0,1)';
    rxnList = model.rxns(selRxns);

else

    % Include transporters
    selRxns = any(model.S(selMets,:) ~= 0,1)';
    rxnList = model.rxns(selRxns);

end

% Extract subnetwork model
compModel = extractSubNetwork(model,rxnList);

if (isfield(compModel,'description'))
    compModel.description = [compModel.description ' Compartment:' compSymbol'];
end