LIBSBML_CPP_NAMESPACE_USE
int main(int argc,char** argv)
{
if (argc != 2)
{
std::cout << "Usage: example1\n";
return 1;
}
//
// Creates an SBMLNamespaces object with the given SBML level, version
// package name, package version.
//
// (NOTE) By defualt, the name of package (i.e. "qual") will be used
// if the arugment for the prefix is missing or empty. Thus the argument
// for the prefix can be added as follows:
//
// SBMLNamespaces sbmlns(3,1,"qual",1,"QUAL");
//
SBMLNamespaces sbmlns(3,1,"qual",1);
//
// (NOTES) The above code creating an SBMLNamespaces object can be replaced
// with one of the following other styles.
//
// (1) Creates an SBMLNamespace object with a SBML core namespace and then
// adds a qual package namespace to the object.
//
// SBMLNamespaces sbmlns(3,1);
// sbmlns.addPkgNamespace("qual",1);
//
// OR
//
// SBMLNamespaces sbmlns(3,1);
// sbmlns.addNamespace(QualExtension::XmlnsL3V1V1,"qual");
//
// (2) Creates a QualPkgNamespaces object (SBMLNamespace derived class for
// qual package. The class is basically used for createing an SBase
// derived objects defined in the qual package) with the given SBML
// level, version, and package version
//
// QualPkgNamespaces sbmlns(3,1,1);
//
// create the document
SBMLDocument *document = new SBMLDocument(&sbmlns);
// mark qual as required
document->setPackageRequired("qual", true);
// create the Model
Model* model=document->createModel();
// create the Compartment
Compartment* compartment = model->createCompartment();
compartment->setId("c");
compartment->setConstant(true);
//
// Get a QualModelPlugin 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.
//
QualModelPlugin* mplugin
= static_cast<QualModelPlugin*>(model->getPlugin("qual"));
// create the QualitativeSpecies
QualitativeSpecies* qs = mplugin->createQualitativeSpecies();
qs->setId("s1");
qs->setCompartment("c");
qs->setConstant(false);
qs->setInitialLevel(1);
qs->setMaxLevel(4);
qs->setName("sss");
// create the Transition
Transition* t = mplugin->createTransition();
t->setId("d");
t->setSBOTerm(1);
Input* i = t->createInput();
i->setId("RD");
i->setQualitativeSpecies("s1");
i->setTransitionEffect(INPUT_TRANSITION_EFFECT_NONE);
i->setSign(INPUT_SIGN_NEGATIVE);
i->setThresholdLevel(2);
i->setName("aa");
Output* o = t->createOutput();
o->setId("wd");
o->setQualitativeSpecies("s1");
o->setTransitionEffect(OUTPUT_TRANSITION_EFFECT_PRODUCTION);
o->setOutputLevel(2);
o->setName("aa");
DefaultTerm* dt = t->createDefaultTerm();
dt->setResultLevel(2) ;
FunctionTerm* ft = t->createFunctionTerm();
ASTNode* math = SBML_parseL3Formula("geq(s1, 2)");
ft->setResultLevel(1);
ft->setMath(math);
writeSBML(document,"qual_example1.xml");
delete document;
return 0;
}
LIBSBML_CPP_NAMESPACE_USE
int main(int argc, char** argv)
{
//
// Creates an SBMLNamespaces object with the given SBML level, version
// package name.
//
SBMLNamespaces sbmlns(2, 3);
sbmlns.addNamespace(LayoutExtension::getXmlnsL2(), "layout");
// (NOTES) The above code creating an SBMLNamespaces object can be replaced
// with the following other style.
//
// (2) Creates a LayoutPkgNamespaces object (SBMLNamespace derived class
// for layout package. The class is basically used for createing an
// SBase derived objects belonging to the layout package) with the
// given SBML level, version. (Package version is not required by
// Layout extension of SBML Level 2)
//
// LayoutPkgNamespaces sbmlns(2, 3);
//
// create the document
SBMLDocument *document = new SBMLDocument(&sbmlns);
// create the Model
Model* model = document->createModel();
model->setId("TestModel_with_modifiers");
document->setModel(model);
// create the Layout
LayoutPkgNamespaces layoutns(2, 3);
LayoutModelPlugin* mplugin
= static_cast<LayoutModelPlugin*>(model->getPlugin("layout"));
Layout* layout = mplugin->createLayout();
layout->setId("Layout_1");
Dimensions dim(&layoutns, 400.0, 230.0);
layout->setDimensions(&dim);
// create the Compartment
Compartment* compartment = model->createCompartment();
compartment->setId("Yeast");
// create the CompartmentGlyph
CompartmentGlyph* compartmentGlyph = layout->createCompartmentGlyph();
compartmentGlyph->setId("CompartmentGlyph_1");
compartmentGlyph->setCompartmentId(compartment->getId());
BoundingBox bb(&layoutns, "bb1", 5, 5, 390, 220);
compartmentGlyph->setBoundingBox(&bb);
// create the Species, SpeciesGlyphs and associated TextGlyphs
// Glucose
Species* species_Gluc = model->createSpecies();
species_Gluc->setId("Glucose");
species_Gluc->setCompartment(compartment->getId());
SpeciesGlyph* glyph_Gluc = layout->createSpeciesGlyph();
glyph_Gluc->setId("SpeciesGlyph_Glucose");
glyph_Gluc->setSpeciesId(species_Gluc->getId());
bb = BoundingBox(&layoutns, "bb2", 105, 20, 130, 20);
glyph_Gluc->setBoundingBox(&bb);
TextGlyph* tGlyph = layout->createTextGlyph();
tGlyph->setId("TextGlyph_Glucose");
bb = BoundingBox(&layoutns, "bbA", 115, 20, 110, 20);
tGlyph->setBoundingBox(&bb);
tGlyph->setOriginOfTextId(species_Gluc->getId());
tGlyph->setGraphicalObjectId(glyph_Gluc->getId());
// Glucose-6-phosphate
Species* species_G6P = model->createSpecies();
species_G6P->setId("Glucose_hyphen_6_hyphen_phosphate");
species_G6P->setCompartment(compartment->getId());
SpeciesGlyph* glyph_G6P = layout->createSpeciesGlyph();
glyph_G6P->setId("SpeciesGlyph_G6P");
glyph_G6P->setSpeciesId(species_G6P->getId());
bb = BoundingBox(&layoutns, "bb5", 50, 190, 270, 20);
glyph_G6P->setBoundingBox(&bb);
tGlyph = layout->createTextGlyph();
tGlyph->setId("TextGlyph_G6P");
bb = BoundingBox(&layoutns, "bbD", 60, 190, 250, 20);
tGlyph->setBoundingBox(&bb);
tGlyph->setOriginOfTextId(species_G6P->getId());
tGlyph->setGraphicalObjectId(glyph_G6P->getId());
// ATP
Species* species_ATP = model->createSpecies();
species_ATP->setId("ATP");
species_ATP->setCompartment(compartment->getId());
SpeciesGlyph* glyph_ATP = layout->createSpeciesGlyph();
glyph_ATP->setId("SpeciesGlyph_ATP");
glyph_ATP->setSpeciesId(species_ATP->getId());
bb = BoundingBox(&layoutns, "bb3", 270, 70, 80, 20);
glyph_ATP->setBoundingBox(&bb);
tGlyph = layout->createTextGlyph();
tGlyph->setId("TextGlyph_ATP");
bb = BoundingBox(&layoutns, "bbB", 280, 70, 60, 20);
tGlyph->setBoundingBox(&bb);
tGlyph->setOriginOfTextId(species_ATP->getId());
tGlyph->setGraphicalObjectId(glyph_ATP->getId());
// ADP
Species* species_ADP = model->createSpecies();
species_ADP->setId("ADP");
species_ADP->setCompartment(compartment->getId());
SpeciesGlyph* glyph_ADP = layout->createSpeciesGlyph();
glyph_ADP->setId("glyph_ADP");
glyph_ADP->setSpeciesId(species_ADP->getId());
bb = BoundingBox(&layoutns, "bb4", 270, 140, 80, 20);
glyph_ADP->setBoundingBox(&bb);
tGlyph = layout->createTextGlyph();
tGlyph->setId("TextGlyph_ADP");
bb = BoundingBox(&layoutns, "bbC", 280, 140, 60, 20);
tGlyph->setBoundingBox(&bb);
tGlyph->setOriginOfTextId(species_ADP->getId());
tGlyph->setGraphicalObjectId(glyph_ADP->getId());
// Phosphate
Species* species_Pi = model->createSpecies();
species_Pi->setId("Pi");
species_Pi->setCompartment(compartment->getId());
SpeciesGlyph* glyph_Pi = layout->createSpeciesGlyph();
glyph_Pi->setId("SpeciesGlyph_Pi");
glyph_Pi->setSpeciesId(species_Pi->getId());
bb = BoundingBox(&layoutns, "bb6", 50, 100, 60, 20);
glyph_Pi->setBoundingBox(&bb);
tGlyph = layout->createTextGlyph();
tGlyph->setId("TextGlyph_PI");
bb = BoundingBox(&layoutns, "bbE", 60, 100, 40, 20);
tGlyph->setBoundingBox(&bb);
tGlyph->setOriginOfTextId(species_Pi->getId());
tGlyph->setGraphicalObjectId(glyph_Pi->getId());
// create the Reaction
Reaction* reaction_Hexokinase = model->createReaction();
reaction_Hexokinase->setId("Hexokinase");
reaction_Hexokinase->setReversible(false);
ReactionGlyph* glyph_Hexokinase = layout->createReactionGlyph();
glyph_Hexokinase->setId("glyph_Hexokinase");
glyph_Hexokinase->setReactionId(reaction_Hexokinase->getId());
Curve* curve_Hexokinase = glyph_Hexokinase->getCurve();
LineSegment* ls = curve_Hexokinase->createLineSegment();
Point p(&layoutns, 170, 100);
ls->setStart(&p);
p = Point(&layoutns, 170, 130);
ls->setEnd(&p);
// create the species reference for glucose
SpeciesReference* reference_Gluc = reaction_Hexokinase->createReactant();
reference_Gluc->setSpecies(species_Gluc->getId());
reference_Gluc->setId("SpeciesReference_Glucose");
// create species reference glyph for glucose
SpeciesReferenceGlyph* speciesReferenceGlyph
= glyph_Hexokinase->createSpeciesReferenceGlyph();
speciesReferenceGlyph->setId("SpeciesReferenceGlyph_Glucose");
speciesReferenceGlyph->setSpeciesGlyphId(glyph_Gluc->getId());
speciesReferenceGlyph->setSpeciesReferenceId(reference_Gluc->getId());
speciesReferenceGlyph->setRole(SPECIES_ROLE_SUBSTRATE);
ls = speciesReferenceGlyph->createLineSegment();
p = Point(&layoutns, 170, 100);
ls->setStart(&p);
p = Point(&layoutns, 170, 50);
ls->setEnd(&p);
// create species reference for ATP
SpeciesReference* reference_ATP
= reaction_Hexokinase->createReactant();
reference_ATP->setSpecies(species_ATP->getId());
reference_ATP->setId("SpeciesReference_ATP");
// create the species reference glyph for ATP
speciesReferenceGlyph = glyph_Hexokinase->createSpeciesReferenceGlyph();
speciesReferenceGlyph->setId("SpeciesReferenceGlyph_ATP");
speciesReferenceGlyph->setSpeciesGlyphId(glyph_ATP->getId());
speciesReferenceGlyph->setSpeciesReferenceId(reference_ATP->getId());
speciesReferenceGlyph->setRole(SPECIES_ROLE_SIDESUBSTRATE);
CubicBezier* cb = speciesReferenceGlyph->createCubicBezier();
p = Point(&layoutns, 170, 100);
cb->setStart(&p);
p = Point(&layoutns, 170, 80);
cb->setBasePoint1(&p);
p = Point(&layoutns, 170, 80);
cb->setBasePoint2(&p);
p = Point(&layoutns, 260, 80);
cb->setEnd(&p);
// create species reference for G6P
SpeciesReference* reference_G6P = reaction_Hexokinase->createProduct();
reference_G6P->setSpecies(species_G6P->getId());
reference_G6P->setId("SpeciesReference_G6P");
// create species reference for G6P as product
speciesReferenceGlyph = glyph_Hexokinase->createSpeciesReferenceGlyph();
speciesReferenceGlyph->setId("SpeciesReferenceGlyph_G6P_1");
speciesReferenceGlyph->setSpeciesGlyphId(glyph_G6P->getId());
speciesReferenceGlyph->setSpeciesReferenceId(reference_G6P->getId());
speciesReferenceGlyph->setRole(SPECIES_ROLE_PRODUCT);
ls = speciesReferenceGlyph->createLineSegment();
p = Point(&layoutns, 170, 130);
ls->setStart(&p);
p = Point(&layoutns, 170, 180);
ls->setEnd(&p);
// create species reference for ADP
SpeciesReference* reference_ADP = reaction_Hexokinase->createProduct();
reference_ADP->setSpecies(species_ADP->getId());
reference_ADP->setId("SpeciesReference_ADP");
// create the species reference glyph for ADP
speciesReferenceGlyph = glyph_Hexokinase->createSpeciesReferenceGlyph();
speciesReferenceGlyph->setId("SpeciesReferenceGlyph_ADP");
speciesReferenceGlyph->setSpeciesGlyphId(glyph_ADP->getId());
speciesReferenceGlyph->setSpeciesReferenceId(reference_ADP->getId());
speciesReferenceGlyph->setRole(SPECIES_ROLE_SIDEPRODUCT);
cb = speciesReferenceGlyph->createCubicBezier();
p = Point(&layoutns, 170, 130);
cb->setStart(&p);
p = Point(&layoutns, 170, 150);
cb->setBasePoint1(&p);
p = Point(&layoutns, 170, 150);
cb->setBasePoint2(&p);
p = Point(&layoutns, 260, 150);
cb->setEnd(&p);
// create modifier species reference for glucose-6-phosphate
ModifierSpeciesReference* reference_G6P_2
= reaction_Hexokinase->createModifier();
reference_G6P_2->setSpecies(species_G6P->getId());
reference_G6P_2->setId("ModifierSpeciesReference_G6P");
reaction_Hexokinase->addModifier(reference_G6P_2);
// create species reference glyph for G6P as a modifier
speciesReferenceGlyph = glyph_Hexokinase->createSpeciesReferenceGlyph();
speciesReferenceGlyph->setId("SpeciesReferenceGlyph_G6P_2");
speciesReferenceGlyph->setSpeciesReferenceId(reference_G6P_2->getId());
speciesReferenceGlyph->setSpeciesGlyphId(glyph_G6P->getId());
speciesReferenceGlyph->setRole(SPECIES_ROLE_INHIBITOR);
cb = speciesReferenceGlyph->createCubicBezier();
p = Point(&layoutns, 45, 200);
cb->setStart(&p);
p = Point(&layoutns, 0, 200);
cb->setBasePoint1(&p);
p = Point(&layoutns, 0, 120);
cb->setBasePoint2(&p);
p = Point(&layoutns, 165, 120);
cb->setEnd(&p);
// create modifier species reference for phosphate
ModifierSpeciesReference* reference_Pi = reaction_Hexokinase->createModifier();
reference_Pi->setSpecies(species_Pi->getId());
reference_Pi->setId("ModifierSpeciesReference_Pi");
reaction_Hexokinase->addModifier(reference_Pi);
// create the species reference glyph for Phosphate
speciesReferenceGlyph = glyph_Hexokinase->createSpeciesReferenceGlyph();
speciesReferenceGlyph->setId("SpeciesReferenceGlyph_PI");
speciesReferenceGlyph->setSpeciesReferenceId(reference_Pi->getId());
speciesReferenceGlyph->setSpeciesGlyphId(glyph_Pi->getId());
speciesReferenceGlyph->setRole(SPECIES_ROLE_ACTIVATOR);
cb = speciesReferenceGlyph->createCubicBezier();
p = Point(&layoutns, 115, 110);
cb->setStart(&p);
p = Point(&layoutns, 140, 110);
cb->setBasePoint1(&p);
p = Point(&layoutns, 140, 110);
cb->setBasePoint2(&p);
p = Point(&layoutns, 165, 110);
cb->setEnd(&p);
// write model to file
writeSBML(document, "layout_example3_L2.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;
}
LIBSBML_CPP_NAMESPACE_USE
int main(int argc,char** argv){
//
// Creates an SBMLNamespaces object with the given SBML level, version
// package name, package version.
//
// (NOTE) By defualt, the name of package (i.e. "groups") will be used
// if the arugment for the prefix is missing or empty. Thus the argument
// for the prefix can be added as follows:
//
// SBMLNamespaces sbmlns(3,1,"groups",1,"GROUP");
//
SBMLNamespaces sbmlns(3,1,"groups",1);
//
// (NOTES) The above code creating an SBMLNamespaces object can be replaced
// with one of the following other styles.
//
// (1) Creates an SBMLNamespace object with a SBML core namespace and then
// adds a groups package namespace to the object.
//
// SBMLNamespaces sbmlns(3,1);
// sbmlns.addPkgNamespace("groups",1);
//
// OR
//
// SBMLNamespaces sbmlns(3,1);
// sbmlns.addNamespace(GroupsExtension::XmlnsL3V1V1,"groups");
//
// (2) Creates a GroupsPkgNamespaces object (SBMLNamespace derived class for
// groups package. The class is basically used for createing an SBase derived
// objects defined in the groups package) with the given SBML level, version,
// and package version
//
// GroupsPkgNamespaces sbmlns(3,1,1);
//
// create the document
SBMLDocument *document = new SBMLDocument(&sbmlns);
// create the Model
Model* model=document->createModel();
// create the Compartment
Compartment* compartment = model->createCompartment();
compartment->setId("cytosol");
compartment->setConstant(true);
compartment=model->createCompartment();
compartment->setId("mitochon");
compartment->setConstant(true);
// create the Species
Species* species = model->createSpecies();
species->setId("ATPc");
species->setCompartment("cytosol");
species->setInitialConcentration(1);
species->setHasOnlySubstanceUnits(false);
species->setBoundaryCondition(false);
species->setConstant(false);
species = model->createSpecies();
species->setId("ATPm");
species->setCompartment("mitochon");
species->setInitialConcentration(2);
species->setHasOnlySubstanceUnits(false);
species->setBoundaryCondition(false);
species->setConstant(false);
// create the Groups
//
// Get a GroupsModelPlugin 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.
//
GroupsModelPlugin* mplugin = static_cast<GroupsModelPlugin*>(model->getPlugin("groups"));
//
// Creates a Group object via GroupsModelPlugin object.
//
Group* group = mplugin->createGroup();
group->setId("ATP");
group->setKind(GROUP_KIND_CLASSIFICATION);
group->setSBOTerm("SBO:0000252");
Member* member = group->createMember();
member->setIdRef("ATPc");
member = group->createMember();
member->setIdRef("ATPm");
writeSBML(document,"groups_example1.xml");
delete document;
}
