extractCompModel

PURPOSE ^

extractCompModel Create model for a cellular compartment

SYNOPSIS ^

function compModel = extractCompModel(model,compSymbol,intOnlyFlag)

DESCRIPTION ^

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

CROSS-REFERENCE INFORMATION ^

This function calls: This function is called by:

SOURCE CODE ^

0001 function compModel = extractCompModel(model,compSymbol,intOnlyFlag)
0002 %extractCompModel Create model for a cellular compartment
0003 %
0004 % compModel = extractCompModel(model,compSymbol,intOnlyFlag)
0005 %
0006 %INPUTS
0007 % model         COBRA model structure
0008 % compSymbol    Compartment symbol
0009 %
0010 %OPTIONAL INPUT
0011 % intOnlyFlag   Include only non-transport reactions (Default = true)
0012 %
0013 %OUTPUT
0014 % compModel     COBRA model for a cellular compartment
0015 %
0016 % Markus Herrgard 3/1/06
0017 
0018 if (nargin < 3)
0019     intOnlyFlag = true;
0020 end
0021 
0022 [baseMetNames,compSymbols] = parseMetNames(model.mets);
0023 
0024 selMets = strcmp(compSymbols,compSymbol);
0025 
0026 if (sum(selMets) == 0)
0027     warning('Compartment symbol not found');
0028     compModel = [];
0029     return;
0030 end
0031 
0032 if (intOnlyFlag)
0033 
0034     % Include only non-transport reactions
0035     selRxns = (sum(model.S(selMets,:) ~= 0)' == sum(model.S ~= 0)') & any(model.S(selMets,:) ~= 0,1)';
0036     rxnList = model.rxns(selRxns);
0037 
0038 else
0039 
0040     % Include transporters
0041     selRxns = any(model.S(selMets,:) ~= 0,1)';
0042     rxnList = model.rxns(selRxns);
0043 
0044 end
0045 
0046 % Extract subnetwork model
0047 compModel = extractSubNetwork(model,rxnList);
0048 
0049 if (isfield(compModel,'description'))
0050     compModel.description = [compModel.description ' Compartment:' compSymbol'];
0051 end

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