embedding_example_1_sbml_make_model

0001 function [model_name, kinetic_models,network,network_CoHid,me_options] = embedding_example_1_sbml_make_model(kinetic_sbml_file,network_sbml_file,position_file,matlab_file)
0002 
0003 eval(default('matlab_file','[]'));
0004 
0005 model_name = 'embedding_example_1_sbml';
0006 
0007 % --------------------------------------------------------------------------------
0008 % Use kinetic model and network
0009 % made by embedding_example_1_sbml_make_networks
0010 
0011 kinetic_model                   = network_sbml_import(kinetic_sbml_file);
0012 kinetic_model.compartment_sizes = 1;
0013 
0014 network                         = network_sbml_import(network_sbml_file);
0015 network.compartment_sizes       = 1;
0016 
0017 % rearrange graphics
0018 
0019 if 0,
0020   netgraph_edit_positions(network, position_file,0);
0021 end
0022 
0023 % id fields for mapping the models
0024 % (these are the default values; an empty struct would also work in this case)
0025 
0026 id.metabolites_network        =  'metabolites';
0027 id.metabolites_kinetic_models = {'metabolites'};
0028 id.reactions_network          =  'actions';
0029 id.reactions_kinetic_models   = {'actions'};
0030 
0031 fba_constraints               = fba_default_options(network);
0032 fba_constraints.zv            = [0 0 1 1]';
0033 
0034 % ------------------------------------------------------
0035 
0036 me_options                      = struct;
0037 me_options.id                   = id;
0038 me_options.fba_constraints      = fba_constraints;
0039 me_options.arrowsize            = 0.1;
0040 me_options.squaresize           = 0.1;
0041 me_options.text_offset          = [0.05,0.02];
0042 me_options.arrowvaluesmax       = 1.2;
0043 me_options.legendFontsize       = 12;
0044 me_options.position_file        = position_file;
0045 me_options.enforce_stationarity = 0;
0046 
0047 me_options.c_init               = [0.01 0.01 0.01 0.01 1]';
0048 me_options.Tmax                 = 5; 
0049 
0050 kinetic_models = {kinetic_model};
0051 
0052 network_CoHid  = network;
0053 
0054 if length(matlab_file),
0055   save(matlab_file,'kinetic_models','network','network_CoHid','me_options');
0056 end