/**
* Save the gene network to an SBML file. If the argument is null, use the network id.
* @param filename URL to the file describing the network to load
* @throws IOException
*/
void GeneNetwork::writeSBML(const char *filename) {
ofstream data_file(filename);
if (!data_file.is_open()) {
std::cerr << "Failed to open file " << filename << std::endl;
exit(1);
}
data_file.close();
::logging::log::emit<Info>() << "Writing file " << filename <<
::logging::log::endl;
SBMLDocument *sbmlDoc = new SBMLDocument(3, 1);
Model *model = sbmlDoc->createModel();
model->setId(id_);
//model.getNotes ().add (comment_); // save network description
int size = getSize();
Compartment *comp = model->createCompartment();
comp->setId("cell");
comp->setSize(1);
std::vector<Species*> all_sp;
Species *sp;
for (int s=0; s < size; s++) { // save gene as species
// species[s] = new Species(nodeIds_.get(s), nodeIds_.get(s));
sp = model->createSpecies();
sp->setCompartment("cell");
sp->setId((nodes_.at(s)).getLabel());
all_sp.push_back(sp);
//species[s].setInitialAmount(?); // maybe save the wild-type steady state?
//model.addSpecies(species[s]);
}
// create the void species
sp = model->createSpecies();
sp->setCompartment("cell");
sp->setId("_void_");
sp->setInitialAmount(0);
sp->setBoundaryCondition(true);
sp->setConstant(true);
all_sp.push_back(sp);
//model.addSpecies(species[size]);
// SET SYNTHESIS AND DEGRADATION REACTIONS FOR EVERY GENE
for (int i=0; i<size; i++) {
//::logging::log::emit<Info>() << ::logging::log::dec << i <<
//::logging::log::endl;
// the ID of gene i
// String currentGeneID = nodeIds_.get(i);
string currentGeneID = (nodes_.at(i)).getLabel();
// The modifiers (regulators) of gene i
std::vector<std::string> inputGenes = (nodes_.at(i)).getInputGenes();
// SYNTHESIS REACTION
std::string reactionId = currentGeneID + "_synthesis";
Reaction *reaction = model->createReaction();
KineticLaw *kineticLaw = reaction->createKineticLaw();
SpeciesReference *spr;
ModifierSpeciesReference *msr;
reaction->setId(reactionId);
reaction->setReversible (false);
spr = reaction->createReactant();
spr->setSpecies(sp->getId());
spr = reaction->createProduct();
spr->setSpecies((all_sp.at(i))->getId());
std::stringstream ss;
ss << inputGenes.size();
//::logging::log::emit<Debug>() << "node = " << nodes_.at(i).getLabel().c_str() << " #inputs = " << ss.str().c_str() << ::logging::log::endl;
for (unsigned int r=0; r<inputGenes.size(); r++) {// set gene modifiers
// reaction.addModifier(species[inputIndexes.get(r)]);
//log.log(Level.INFO, "i = " + size);
msr = reaction->createModifier();
msr->setSpecies((all_sp.at(getIndexOfNode(inputGenes.at(r))))->getId());
}
//std::vector<RegulatoryModule> modules = (nodes_.at(i)).getRegulatoryModules();
//log.log(Level.INFO, "size = " + modules.size());
std::map<std::string, double> *params = new std::map<std::string, double>();
(nodes_.at(i)).compileParameters(*params);
//char buf[256];
//sprintf(buf, "%f", nodes_.at(i).getDelta());
//::logging::log::emit<Info>() << buf << ::logging::log::endl;
//::logging::log::emit<Info>() << ::logging::log::dec << nodes_.at(i).getAlpha().size() <<
// ::logging::log::endl;
Parameter *para;
// save gene parameters (note, the first param is the degradation rate)
std::map<std::string, double>::iterator p = params->begin();
//p++;
for (; p!=params->end(); p++) {
//if (p == params->begin()) {
// p++;
// continue;
//}
//::logging::log::emit<Info>() << p->first.c_str() <<
// ::logging::log::endl;
if (p->first != "delta") {
para = kineticLaw->createParameter();
para->setId(p->first);
para->setValue(p->second);
}
}
reaction->setKineticLaw(kineticLaw);
model->addReaction(reaction);
// DEGRADATION REACTION
reaction = model->createReaction();
kineticLaw = reaction->createKineticLaw();
reactionId = currentGeneID + "_degradation";
reaction->setId(reactionId);
reaction->setReversible(false);
spr = reaction->createReactant();
spr->setSpecies((all_sp.at(i))->getId());
spr = reaction->createProduct();
spr->setSpecies(sp->getId());
para = kineticLaw->createParameter();
std::map<std::string,double>::iterator it = params->find("delta");
para->setId(it->first);
para->setValue(it->second);
reaction->setKineticLaw (kineticLaw);
model->addReaction (reaction);
}
// PRINT FILE
SBMLWriter sbmlWriter;
sbmlWriter.writeSBML(sbmlDoc, filename);
delete sbmlDoc;
}
END_TEST
START_TEST(test_FbcExtension_create_and_write_new_geneassociation
)
{
FbcPkgNamespaces *sbmlns = new FbcPkgNamespaces(3, 1, 2);
// create the document
SBMLDocument document(sbmlns);
document.setConsistencyChecks(LIBSBML_CAT_UNITS_CONSISTENCY, false);
document.setConsistencyChecks(LIBSBML_CAT_MODELING_PRACTICE, false);
// create the Model
Model* model = document.createModel();
// create the Compartment
Compartment* compartment = model->createCompartment();
compartment->setId("compartment");
compartment->setConstant(true);
compartment->setSize(1);
// create the Species
Species* species = model->createSpecies();
species->setId("Node1");
species->setCompartment("compartment");
species->setBoundaryCondition(false);
species = model->createSpecies();
species->setId("Node2");
species->setCompartment("compartment");
species->setBoundaryCondition(false);
Reaction* reaction = model->createReaction();
reaction->setId("J0");
reaction->setReversible(false);
SpeciesReference* reactant = reaction->createReactant();
reactant->setSpecies("Node0");
reactant->setStoichiometry(1);
SpeciesReference* product = reaction->createProduct();
product->setSpecies("Node1");
product->setStoichiometry(1);
// use fbc
FbcModelPlugin* mplugin = static_cast<FbcModelPlugin*>(model->getPlugin("fbc"));
fail_unless(mplugin != NULL);
FluxBound* bound = mplugin->createFluxBound();
bound->setId("bound1");
bound->setReaction("J0");
bound->setOperation("equal");
bound->setValue(10);
Objective* objective = mplugin->createObjective();
objective->setId("obj1");
objective->setType("maximize");
FluxObjective* fluxObjective = objective->createFluxObjective();
fluxObjective->setReaction("J0");
fluxObjective->setCoefficient(1);
FbcReactionPlugin* rplug = dynamic_cast<FbcReactionPlugin*>(reaction->getPlugin("fbc"));
fail_unless(rplug != NULL);
GeneProductAssociation * ga = rplug->createGeneProductAssociation();
ga->setId("ga1");
ga->setAssociation("MG_077 AND MG_321 AND MG_080 AND MG_078 AND MG_079");
fail_unless(ga->getAssociation() != NULL);
fail_unless(mplugin->getNumGeneProducts() == 5);
ga->setAssociation("MG_077 AND MG_321 AND MG_080 AND MG_078 AND MG_079");
fail_unless(ga->getAssociation() != NULL);
fail_unless(mplugin->getNumGeneProducts() == 5);
delete sbmlns;
}
END_TEST
START_TEST(test_FbcExtension_create_and_write_L3V1V1)
{
FbcPkgNamespaces *sbmlns = new FbcPkgNamespaces(3, 1, 1);
// create the document
SBMLDocument *document = new SBMLDocument(sbmlns);
delete sbmlns;
// create the Model
Model* model = document->createModel();
// create the Compartment
Compartment* compartment = model->createCompartment();
compartment->setId("compartment");
compartment->setConstant(true);
compartment->setSize(1);
// create the Species
Species* species = model->createSpecies();
species->setId("Node1");
species->setCompartment("compartment");
species->setBoundaryCondition(false);
species = model->createSpecies();
species->setId("Node2");
species->setCompartment("compartment");
species->setBoundaryCondition(false);
Reaction* reaction = model->createReaction();
reaction->setId("J0");
reaction->setReversible(false);
SpeciesReference* reactant = reaction->createReactant();
reactant->setSpecies("Node0");
reactant->setStoichiometry(1);
SpeciesReference* product = reaction->createProduct();
product->setSpecies("Node1");
product->setStoichiometry(1);
// use fbc
FbcModelPlugin* mplugin = static_cast<FbcModelPlugin*>(model->getPlugin("fbc"));
fail_unless(mplugin != NULL);
FluxBound* bound = mplugin->createFluxBound();
bound->setId("bound1");
bound->setReaction("J0");
bound->setOperation("equal");
bound->setValue(10);
Objective* objective = mplugin->createObjective();
objective->setId("obj1");
objective->setType("maximize");
FluxObjective* fluxObjective = objective->createFluxObjective();
fluxObjective->setReaction("J0");
fluxObjective->setCoefficient(1);
string s1 = writeSBMLToStdString(document);
// check clone()
SBMLDocument* document2 = document->clone();
string s2 = writeSBMLToStdString(document2);
fail_unless(s1 == s2);
// check operator=
Model m = *(document->getModel());
document2->setModel(&m);
s2 = writeSBMLToStdString(document2);
fail_unless(s1 == s2);
delete document2;
delete document;
}
LIBSBML_CPP_NAMESPACE_USE
int main(int argc,char** argv)
{
DynPkgNamespaces sbmlns;
sbmlns.addPackageNamespace("comp", 1, "comp");
// create the document
SBMLDocument *document = new SBMLDocument(&sbmlns);
document->setPackageRequired("dyn", true);
document->setPackageRequired("comp", true);
// create the Model
Model* model=document->createModel();
model->setId("grid2x2");
// create the Compartment
Compartment* compartment = model->createCompartment();
compartment->setId("Loc1");
compartment->setConstant(false);
compartment->setSize(1);
compartment->setSpatialDimensions(2.0);
DynCompartmentPlugin* cplugin =
static_cast<DynCompartmentPlugin*>(compartment->getPlugin("dyn"));
SpatialComponent* component = cplugin->createSpatialComponent();
component->setSpatialIndex(DYN_SPATIALKIND_CARTESIANX);
component->setVariable("q1_X");
component = cplugin->createSpatialComponent();
component->setSpatialIndex(DYN_SPATIALKIND_CARTESIANY);
component->setVariable("q1_Y");
CompSBasePlugin* compPlugin =
static_cast<CompSBasePlugin*>(compartment->getPlugin("comp"));
ReplacedElement* relement = compPlugin->createReplacedElement();
relement->setIdRef("C");
relement->setSubmodelRef("GRID_1_1_cell");
compartment = model->createCompartment();
compartment->setId("Loc2");
compartment->setConstant(false);
compartment->setSize(1);
compartment->setSpatialDimensions(2.0);
cplugin =
static_cast<DynCompartmentPlugin*>(compartment->getPlugin("dyn"));
component = cplugin->createSpatialComponent();
component->setSpatialIndex(DYN_SPATIALKIND_CARTESIANX);
component->setVariable("q2_X");
component = cplugin->createSpatialComponent();
component->setSpatialIndex(DYN_SPATIALKIND_CARTESIANY);
component->setVariable("q2_Y");
compPlugin =
static_cast<CompSBasePlugin*>(compartment->getPlugin("comp"));
relement = compPlugin->createReplacedElement();
relement->setIdRef("C");
relement->setSubmodelRef("GRID_1_2_cell");
compartment = model->createCompartment();
compartment->setId("Loc3");
compartment->setConstant(false);
compartment->setSize(1);
compartment->setSpatialDimensions(2.0);
cplugin =
static_cast<DynCompartmentPlugin*>(compartment->getPlugin("dyn"));
component = cplugin->createSpatialComponent();
component->setSpatialIndex(DYN_SPATIALKIND_CARTESIANX);
component->setVariable("q3_X");
component = cplugin->createSpatialComponent();
component->setSpatialIndex(DYN_SPATIALKIND_CARTESIANY);
component->setVariable("q3_Y");
compPlugin =
static_cast<CompSBasePlugin*>(compartment->getPlugin("comp"));
relement = compPlugin->createReplacedElement();
relement->setIdRef("C");
relement->setSubmodelRef("GRID_2_1_cell");
compartment = model->createCompartment();
compartment->setId("Loc4");
compartment->setConstant(false);
compartment->setSize(1);
compartment->setSpatialDimensions(2.0);
cplugin =
static_cast<DynCompartmentPlugin*>(compartment->getPlugin("dyn"));
component = cplugin->createSpatialComponent();
component->setSpatialIndex(DYN_SPATIALKIND_CARTESIANX);
component->setVariable("q4_X");
component = cplugin->createSpatialComponent();
component->setSpatialIndex(DYN_SPATIALKIND_CARTESIANY);
component->setVariable("q4_Y");
compPlugin =
static_cast<CompSBasePlugin*>(compartment->getPlugin("comp"));
relement = compPlugin->createReplacedElement();
relement->setIdRef("C");
relement->setSubmodelRef("GRID_2_2_cell");
// create Parameters
Parameter* param = model->createParameter();
param->initDefaults();
param->setId("q1_X");
param->setValue(1);
param = model->createParameter();
param->initDefaults();
param->setId("q1_Y");
param->setValue(1);
param = model->createParameter();
param->initDefaults();
param->setId("q2_X");
param->setValue(2);
param = model->createParameter();
param->initDefaults();
param->setId("q2_Y");
param->setValue(1);
param = model->createParameter();
param->initDefaults();
param->setId("q3_X");
param->setValue(1);
param = model->createParameter();
param->initDefaults();
param->setId("q3_Y");
param->setValue(2);
param = model->createParameter();
param->initDefaults();
param->setId("q4_X");
param->setValue(2);
param = model->createParameter();
param->initDefaults();
param->setId("q4_Y");
param->setValue(2);
// create SubModels
CompModelPlugin* mplugin =
static_cast<CompModelPlugin*>(model->getPlugin("comp"));
Submodel* submodel = mplugin->createSubmodel();
submodel->setId("GRID_1_1_cell");
submodel->setModelRef("Cell");
submodel = mplugin->createSubmodel();
submodel->setId("GRID_1_2_cell");
submodel->setModelRef("Cell");
submodel = mplugin->createSubmodel();
submodel->setId("GRID_2_1_cell");
submodel->setModelRef("Cell");
submodel = mplugin->createSubmodel();
submodel->setId("GRID_2_2_cell");
submodel->setModelRef("Cell");
// create the ModelDefinition
CompSBMLDocumentPlugin* dplugin =
static_cast<CompSBMLDocumentPlugin*>(document->getPlugin("comp"));
ModelDefinition* mdef = dplugin->createModelDefinition();
mdef->setId("Cell");
compartment = mdef->createCompartment();
compartment->initDefaults();
compartment->setId("C");
compartment->setSpatialDimensions(2.0);
compartment->setSize(1.0);
Species* species = mdef->createSpecies();
species->setId("R");
species->setCompartment("C");
species->setHasOnlySubstanceUnits(false);
species->setBoundaryCondition(false);
species->setConstant(false);
species = mdef->createSpecies();
species->setId("S");
species->setCompartment("C");
species->setHasOnlySubstanceUnits(false);
species->setBoundaryCondition(false);
species->setConstant(false);
Reaction* reaction = mdef->createReaction();
reaction->setId("Degradation_R");
reaction->setReversible(false);
reaction->setFast(false);
reaction->setCompartment("C");
SpeciesReference* reactant = reaction->createReactant();
reactant->setSpecies("R");
reactant->setStoichiometry(1);
reactant->setConstant(true);
reaction = mdef->createReaction();
reaction->setId("Degradation_S");
reaction->setReversible(false);
reaction->setFast(false);
reaction->setCompartment("C");
reactant = reaction->createReactant();
reactant->setSpecies("S");
reactant->setStoichiometry(1);
reactant->setConstant(true);
document->checkConsistency();
Event* event = mdef->createEvent();
event->setId("event0");
event->setUseValuesFromTriggerTime(false);
DynEventPlugin* eplugin =
static_cast<DynEventPlugin*>(event->getPlugin("dyn"));
eplugin->setApplyToAll(true);
eplugin->setCboTerm("http://cbo.biocomplexity.indiana.edu/svn/cbo/trunk/CBO_1_0.owl#CellDivision");
Trigger* trigger = event->createTrigger();
trigger->setInitialValue(false);
trigger->setPersistent(false);
trigger->setMath(SBML_parseFormula("true"));
if (document->getNumErrors(LIBSBML_SEV_ERROR) > 0)
document->printErrors();
writeSBML(document,"dyn_example2.xml");
delete document;
}
LIBSBML_CPP_NAMESPACE_USE
int main(int argc,char** argv)
{
DynPkgNamespaces sbmlns;
// create the document
SBMLDocument *document = new SBMLDocument(&sbmlns);
document->setPackageRequired("dyn", true);
// create the Model
Model* model=document->createModel();
model->setId("singleCell");
// create the Compartment
Compartment* compartment = model->createCompartment();
compartment->setId("Extracellular");
compartment->setConstant(true);
compartment->setSize(8000000);
compartment->setSpatialDimensions(3.0);
compartment = model->createCompartment();
compartment->setId("PlasmaMembrane");
compartment->setConstant(true);
compartment->setSize(314);
compartment->setSpatialDimensions(2.0);
compartment = model->createCompartment();
compartment->setId("Cytosol");
compartment->setConstant(true);
compartment->setSize(523);
compartment->setSpatialDimensions(3.0);
// create the Species
Species* species = model->createSpecies();
species->setId("C_EC");
species->setCompartment("Extracellular");
species->setBoundaryCondition(false);
species->setConstant(false);
species->setHasOnlySubstanceUnits(false);
species = model->createSpecies();
species->setId("RTR_M");
species->setCompartment("PlasmaMembrane");
species->setBoundaryCondition(false);
species->setConstant(false);
species->setHasOnlySubstanceUnits(false);
species = model->createSpecies();
species->setId("RCC_M");
species->setCompartment("PlasmaMembrane");
species->setBoundaryCondition(false);
species->setConstant(false);
species->setHasOnlySubstanceUnits(false);
species = model->createSpecies();
species->setId("A_C");
species->setCompartment("Cytosol");
species->setBoundaryCondition(false);
species->setConstant(false);
species->setHasOnlySubstanceUnits(false);
species = model->createSpecies();
species->setId("AA_C");
species->setCompartment("Cytosol");
species->setBoundaryCondition(false);
species->setConstant(false);
species->setHasOnlySubstanceUnits(false);
species = model->createSpecies();
species->setId("T");
species->setCompartment("Cytosol");
species->setBoundaryCondition(false);
species->setConstant(false);
species->setInitialConcentration(10);
species->setHasOnlySubstanceUnits(false);
species = model->createSpecies();
species->setId("S");
species->setCompartment("Cytosol");
species->setBoundaryCondition(false);
species->setConstant(false);
species->setInitialConcentration(5);
species->setHasOnlySubstanceUnits(false);
// create the Reactions
Reaction* reaction = model->createReaction();
reaction->setId("r1");
reaction->setReversible(true);
reaction->setFast(false);
reaction->setCompartment("Extracellular");
SpeciesReference* reactant = reaction->createReactant();
reactant->setSpecies("RTR_M");
reactant->setStoichiometry(1);
reactant->setConstant(true);
reactant = reaction->createReactant();
reactant->setSpecies("C_EC");
reactant->setStoichiometry(1);
reactant->setConstant(true);
SpeciesReference* product = reaction->createProduct();
product->setSpecies("RCC_M");
product->setStoichiometry(1);
product->setConstant(true);
reaction = model->createReaction();
reaction->setId("r2");
reaction->setReversible(true);
reaction->setFast(false);
reaction->setCompartment("Cytosol");
reactant = reaction->createReactant();
reactant->setSpecies("A_C");
reactant->setStoichiometry(1);
reactant->setConstant(true);
product = reaction->createProduct();
product->setSpecies("AA_C");
product->setStoichiometry(1);
product->setConstant(true);
SimpleSpeciesReference* modifier = reaction->createModifier();
modifier->setSpecies("RCC_M");
// Create Event
Event* event = model->createEvent();
event->setUseValuesFromTriggerTime(true);
Trigger* trigger = event->createTrigger();
trigger->setInitialValue(false);
trigger->setPersistent(true);
trigger->setMath(SBML_parseFormula("lt(AA_C, T)"));
//
// Get a DynEventPlugin object plugged in the event object.
//
// The type of the returned value of SBase::getPlugin() function is
// SBasePlugin*, and thus the value needs to be casted for the
// corresponding derived class.
//
DynEventPlugin* eplugin
= static_cast<DynEventPlugin*>(event->getPlugin("dyn"));
eplugin->setApplyToAll(true);
eplugin->setCboTerm("http://cbo.biocomplexity.indiana.edu/svn/cbo/trunk/CBO_1_0.owl#CellDeath");
event = model->createEvent();
event->setUseValuesFromTriggerTime(true);
trigger = event->createTrigger();
trigger->setInitialValue(false);
trigger->setPersistent(true);
trigger->setMath(SBML_parseFormula("lt(AA_C, S)"));
eplugin = static_cast<DynEventPlugin*>(event->getPlugin("dyn"));
eplugin->setApplyToAll(true);
eplugin->setCboTerm("http://cbo.biocomplexity.indiana.edu/svn/cbo/trunk/CBO_1_0.owl#CellDevision");
document->checkConsistency();
if (document->getNumErrors(LIBSBML_SEV_ERROR) > 0)
document->printErrors();
writeSBML(document,"dyn_example1.xml");
delete document;
}
LIBSBML_CPP_NAMESPACE_USE
int main(int argc,char** argv)
{
SBMLNamespaces sbmlns(3,1,"fbc",1);
// create the document
SBMLDocument *document = new SBMLDocument(&sbmlns);
document->setPackageRequired("fbc", false);
// create the Model
Model* model=document->createModel();
// create the Compartment
Compartment* compartment = model->createCompartment();
compartment->setId("compartment");
compartment->setConstant(true);
compartment->setSize(1);
// create the Species
Species* species = model->createSpecies();
species->setId("Node1");
species->setCompartment("compartment");
species->setBoundaryCondition(false);
species->setConstant(false);
species->setHasOnlySubstanceUnits(false);
species = model->createSpecies();
species->setId("Node2");
species->setCompartment("compartment");
species->setBoundaryCondition(false);
species->setConstant(false);
species->setHasOnlySubstanceUnits(false);
species = model->createSpecies();
species->setId("Node3");
species->setCompartment("compartment");
species->setBoundaryCondition(false);
species->setConstant(false);
species->setHasOnlySubstanceUnits(false);
species = model->createSpecies();
species->setId("Node4");
species->setCompartment("compartment");
species->setBoundaryCondition(false);
species->setConstant(false);
species->setHasOnlySubstanceUnits(false);
species = model->createSpecies();
species->setId("Node5");
species->setCompartment("compartment");
species->setBoundaryCondition(false);
species->setConstant(false);
species->setHasOnlySubstanceUnits(false);
species = model->createSpecies();
species->setId("Node6");
species->setCompartment("compartment");
species->setBoundaryCondition(false);
species->setConstant(false);
species->setHasOnlySubstanceUnits(false);
species = model->createSpecies();
species->setId("Node7");
species->setCompartment("compartment");
species->setBoundaryCondition(false);
species->setConstant(false);
species->setHasOnlySubstanceUnits(false);
species = model->createSpecies();
species->setId("Node8");
species->setCompartment("compartment");
species->setBoundaryCondition(false);
species->setConstant(false);
species->setHasOnlySubstanceUnits(false);
species = model->createSpecies();
species->setId("Node0");
species->setCompartment("compartment");
species->setBoundaryCondition(true);
species->setConstant(false);
species->setHasOnlySubstanceUnits(false);
species = model->createSpecies();
species->setId("Node9");
species->setCompartment("compartment");
species->setBoundaryCondition(true);
species->setConstant(false);
species->setHasOnlySubstanceUnits(false);
Reaction* reaction = model->createReaction();
reaction->setId("J0");
reaction->setReversible(false);
reaction->setFast(false);
SpeciesReference* reactant = reaction->createReactant();
reactant->setSpecies("Node0");
reactant->setStoichiometry(1);
reactant->setConstant(true);
SpeciesReference* product = reaction->createProduct();
product->setSpecies("Node1");
product->setStoichiometry(1);
product->setConstant(true);
reaction = model->createReaction();
reaction->setId("J1");
reaction->setReversible(false);
reaction->setFast(false);
reactant = reaction->createReactant();
reactant->setSpecies("Node1");
reactant->setStoichiometry(1);
reactant->setConstant(true);
product = reaction->createProduct();
product->setSpecies("Node2");
product->setStoichiometry(1);
product->setConstant(true);
reaction = model->createReaction();
reaction->setId("J2");
reaction->setReversible(false);
reaction->setFast(false);
reactant = reaction->createReactant();
reactant->setSpecies("Node2");
reactant->setStoichiometry(1);
reactant->setConstant(true);
product = reaction->createProduct();
product->setSpecies("Node3");
product->setStoichiometry(1);
product->setConstant(true);
reaction = model->createReaction();
reaction->setId("J3");
reaction->setReversible(false);
reaction->setFast(false);
reactant = reaction->createReactant();
reactant->setSpecies("Node1");
reactant->setStoichiometry(1);
reactant->setConstant(true);
product = reaction->createProduct();
product->setSpecies("Node4");
product->setStoichiometry(1);
product->setConstant(true);
reaction = model->createReaction();
reaction->setId("J4");
reaction->setReversible(false);
reaction->setFast(false);
reactant = reaction->createReactant();
reactant->setSpecies("Node4");
reactant->setStoichiometry(1);
reactant->setConstant(true);
product = reaction->createProduct();
product->setSpecies("Node3");
product->setStoichiometry(1);
product->setConstant(true);
reaction = model->createReaction();
reaction->setId("J5");
reaction->setReversible(false);
reaction->setFast(false);
reactant = reaction->createReactant();
reactant->setSpecies("Node3");
reactant->setStoichiometry(1);
reactant->setConstant(true);
product = reaction->createProduct();
product->setSpecies("Node5");
product->setStoichiometry(1);
product->setConstant(true);
reaction = model->createReaction();
reaction->setId("J6");
reaction->setReversible(false);
reaction->setFast(false);
reactant = reaction->createReactant();
reactant->setSpecies("Node5");
reactant->setStoichiometry(1);
reactant->setConstant(true);
product = reaction->createProduct();
product->setSpecies("Node6");
product->setStoichiometry(1);
product->setConstant(true);
reaction = model->createReaction();
reaction->setId("J7");
reaction->setReversible(false);
reaction->setFast(false);
reactant = reaction->createReactant();
reactant->setSpecies("Node6");
reactant->setStoichiometry(1);
reactant->setConstant(true);
product = reaction->createProduct();
product->setSpecies("Node7");
product->setStoichiometry(1);
product->setConstant(true);
reaction = model->createReaction();
reaction->setId("J8");
reaction->setReversible(false);
reaction->setFast(false);
reactant = reaction->createReactant();
reactant->setSpecies("Node5");
reactant->setStoichiometry(1);
reactant->setConstant(true);
product = reaction->createProduct();
product->setSpecies("Node8");
product->setStoichiometry(1);
product->setConstant(true);
reaction = model->createReaction();
reaction->setId("J9");
reaction->setReversible(false);
reaction->setFast(false);
reactant = reaction->createReactant();
reactant->setSpecies("Node8");
reactant->setStoichiometry(1);
reactant->setConstant(true);
product = reaction->createProduct();
product->setSpecies("Node7");
product->setStoichiometry(1);
product->setConstant(true);
reaction = model->createReaction();
reaction->setId("J10");
reaction->setReversible(false);
reaction->setFast(false);
reactant = reaction->createReactant();
reactant->setSpecies("Node7");
reactant->setStoichiometry(1);
reactant->setConstant(true);
product = reaction->createProduct();
product->setSpecies("Node9");
product->setStoichiometry(1);
product->setConstant(true);
//
// Get a FbcModelPlugin object plugged in the model object.
//
// The type of the returned value of SBase::getPlugin() function is
// SBasePlugin*, and thus the value needs to be casted for the
// corresponding derived class.
//
FbcModelPlugin* mplugin
= static_cast<FbcModelPlugin*>(model->getPlugin("fbc"));
FluxBound* bound= mplugin->createFluxBound();
bound->setId("bound1");
bound->setReaction("J0");
bound->setOperation("equal");
bound->setValue(10);
Objective* objective = mplugin->createObjective();
objective->setId("obj1");
objective->setType("maximize");
// mark obj1 as active objective
mplugin->setActiveObjectiveId("obj1");
FluxObjective* fluxObjective = objective->createFluxObjective();
fluxObjective->setReaction("J8");
fluxObjective->setCoefficient(1);
writeSBML(document,"fbc_example1.xml");
delete document;
}