Identify Conserved Moieties

tutorial_initConservedMoietyPaths
projectDir = '~/work/sbgCloud/programExperimental/projects/tracerBased'
dataDir = '~/work/sbgCloud/programExperimental/projects/tracerBased/data/'
softwareDir = '~/work/sbgCloud/programExperimental/projects/tracerBased/software/'
visDataDir = '~/work/sbgCloud/programExperimental/projects/tracerBased/data/visualisation/'
resultsDir = '~/work/sbgCloud/programExperimental/projects/tracerBased/results/iDopaNeuro1_ConservedMoieties/'
rxnfileDir = '~/work/sbgCloud/code/fork-ctf/rxns/atomMapped'
if ~recompute || isequal(modelName,'iDopaNeuro1')
    load([resultsDir modelName '_arm.mat'])
    return
end

1.2.3. Conserved moieties

With the atom mappings we obtained, we can compute the conserved moieties for the iDopaNeuro metabolic network using the atom transition network and the COBRA function identifyConservedMoieties.

switch modelName
    case 'DAS'
        load('DAS.mat')
    otherwise
        load([dataDir modelName '.mat'])
end
load([resultsDir modelName '_dATM.mat'])
options.sanityChecks=0;
[arm, moietyFormulae] = identifyConservedMoieties(model, dATM, options);
save([resultsDir modelName '_arm.mat'],'arm', 'moietyFormulae','options')