model_embedding_kinetics_combined2flat

0001 function nn = model_embedding_kinetics_combined2flat(network_combined)
0002 
0003 kk = network_combined.kinetics;
0004 
0005 % kinetics type must be 'embedded_kinetic_models'
0006 
0007 if ~strcmp(kk.type, 'embedded_kinetic_models'),
0008   error('Wrong kinetics type');
0009 end
0010 
0011 % all metabolite names must match
0012 
0013 for it = 1:length(kk.mapping_metabolites),
0014    map = kk.mapping_metabolites{it};
0015    met_kinetic_model = kk.kinetic_models{it}.metabolites;
0016    met_network_model = network_combined.metabolites(map);
0017    if ~prod(double(strcmp(met_kinetic_model, met_network_model))),
0018      error('Metabolite IDs do not match between network model and embedded kinetic model');
0019    end
0020 end
0021 
0022 % convert network kinetics to type 'kinetic_strings'
0023 
0024 kk.kinetics_network = kinetics_convert_to_strings(network_combined,kk.kinetics_network);
0025 
0026 % convert kinetic submodel kinetics to type 'kinetic_strings'
0027 
0028 for it = 1:length(kk.kinetic_models),
0029    kk.kinetic_models{it}.kinetics = kinetics_convert_to_strings(kk.kinetic_models{it}, kk.kinetic_models{it}.kinetics);
0030   if length(kk.kinetic_models{it}.kinetics.parameters),
0031     error('Cannot convert kinetics with global parameters');
0032   end
0033 end
0034 
0035 % make new kinetics field for entire model
0036 % first insert 'kinetic_strings' type kinetics for entire network ..
0037 
0038 kkk.type             = 'kinetic_strings';
0039 kkk.reactions        = kk.kinetics_network.reactions;
0040 kkk.parameters       = {};
0041 kkk.parameter_values = [];
0042 
0043 % .. then insert rate laws from submodels
0044 
0045 for it = 1:length(kk.kinetic_models),
0046   ind_reactions = kk.mapping_reactions{it};
0047   my_rate_laws  = kk.kinetic_models{it}.kinetics.reactions;
0048   my_enzyme_adjustments = kk.enzyme_adjustment{1};
0049   %% don't forget to adjust enzyme levels!!
0050   for itt = 1:length( my_rate_laws),
0051    my_rate_laws{itt}.string = sprintf('EnzymeAdjustment * ( %s )', my_rate_laws{itt}.string);
0052    my_rate_laws{itt}.parameters = [my_rate_laws{itt}.parameters; 'EnzymeAdjustment'];
0053    my_rate_laws{itt}.parameter_values = [my_rate_laws{itt}.parameter_values; my_enzyme_adjustments(itt)];
0054   end
0055   kkk.reactions(ind_reactions) = my_rate_laws;
0056 end
0057 
0058 nn = network_combined;
0059 nn.kinetics = kkk;