END_TEST
START_TEST (test_WriteL3SBML_Species_conversionFactor)
{
const char* expected =
"<species id=\"Ca2\" compartment=\"cell\""
" hasOnlySubstanceUnits=\"false\""
" boundaryCondition=\"true\" constant=\"true\""
" conversionFactor=\"p\"/>";
const char* expected1 =
"<species id=\"Ca2\" compartment=\"cell\""
" hasOnlySubstanceUnits=\"false\""
" boundaryCondition=\"true\" constant=\"true\"/>";
Species *s = D->createModel()->createSpecies();
s->setId("Ca2");
s->setCompartment("cell");
s->setBoundaryCondition(true);
s->setHasOnlySubstanceUnits(false);
s->setConstant(true);
s->setConversionFactor("p");
char* sbml = s->toSBML();
fail_unless( equals(expected, sbml) );
safe_free(sbml);
s->unsetConversionFactor();
sbml = s->toSBML();
fail_unless( equals(expected1, sbml) );
safe_free(sbml);
}
END_TEST
START_TEST (test_WriteL3SBML_Species)
{
const char* expected =
"<species id=\"Ca2\" compartment=\"cell\" initialAmount=\"0.7\""
" substanceUnits=\"mole\" hasOnlySubstanceUnits=\"false\""
" boundaryCondition=\"true\" constant=\"true\"/>";
Species *s = D->createModel()->createSpecies();
s->setId("Ca2");
s->setCompartment("cell");
s->setInitialAmount(0.7);
s->setUnits("mole");
s->setBoundaryCondition(true);
s->setHasOnlySubstanceUnits(false);
s->setConstant(true);
char* sbml = s->toSBML();
fail_unless( equals(expected, sbml) );
safe_free(sbml);
}
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;
}
void
Model::assignRequiredValues()
{
// when converting to L3 some attributes which have default values in L1/L2
// but are required in L3 are not present or set
unsigned int i, n;
if (getNumUnitDefinitions() > 0)
{
for (i = 0; i < getNumUnitDefinitions(); i++)
{
for (n = 0; n < getUnitDefinition(i)->getNumUnits(); n++)
{
Unit *u = getUnitDefinition(i)->getUnit(n);
if (!u->isSetExponent())
u->setExponent(1.0);
if (!u->isSetScale())
u->setScale(0);
if (!u->isSetMultiplier())
u->setMultiplier(1.0);
}
}
}
if (getNumCompartments() > 0)
{
for (i = 0; i < getNumCompartments(); i++)
{
Compartment *c = getCompartment(i);
c->setConstant(c->getConstant());
}
}
if (getNumSpecies() > 0)
{
for (i = 0; i < getNumSpecies(); i++)
{
Species * s = getSpecies(i);
s->setBoundaryCondition(s->getBoundaryCondition());
s->setHasOnlySubstanceUnits(s->getHasOnlySubstanceUnits());
s->setConstant(s->getConstant());
}
}
if (getNumParameters() > 0)
{
for (i = 0; i < getNumParameters(); i++)
{
Parameter * p = getParameter(i);
p->setConstant(p->getConstant());
}
}
if (getNumReactions() > 0)
{
for (i = 0; i < getNumReactions(); i++)
{
Reaction * r = getReaction(i);
r->setFast(r->getFast());
r->setReversible(r->getReversible());
if (r->getNumReactants() > 0)
{
for (n = 0; n < r->getNumReactants(); n++)
{
SpeciesReference *sr = r->getReactant(n);
if (sr->isSetStoichiometryMath())
{
sr->setConstant(false);
}
else
{
sr->setConstant(true);
}
}
}
if (r->getNumProducts() > 0)
{
for (n = 0; n < r->getNumProducts(); n++)
{
SpeciesReference *sr = r->getProduct(n);
if (sr->isSetStoichiometryMath())
{
sr->setConstant(false);
}
else
{
sr->setConstant(true);
}
}
}
}
}
if (getNumEvents() > 0)
{
for (i = 0; i < getNumEvents(); i++)
{
Event * e = getEvent(i);
e->setUseValuesFromTriggerTime(e->getUseValuesFromTriggerTime());
if (e->isSetTrigger())
{
Trigger *t = e->getTrigger();
t->setPersistent(true);
t->setInitialValue(true);
}
}
}
}
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;
}
int main(int argc,char** argv)
{
int retval = 0;
SBMLNamespaces sbmlns(3,1,"comp",1);
// create the document
SBMLDocument *document = new SBMLDocument(&sbmlns);
//Define the external model definitions
CompSBMLDocumentPlugin* compdoc
= static_cast<CompSBMLDocumentPlugin*>(document->getPlugin("comp"));
compdoc->setRequired(true);
ExternalModelDefinition* extmod = compdoc->createExternalModelDefinition();
extmod->setId("ExtMod1");
extmod->setSource("enzyme_model.xml");
extmod->setModelRef("enzyme");
// create the main Model
Model* model=document->createModel();
// Set the submodels
CompModelPlugin* mplugin = static_cast<CompModelPlugin*>(model->getPlugin("comp"));
Submodel* submod1 = mplugin->createSubmodel();
submod1->setId("A");
submod1->setModelRef("ExtMod1");
Submodel* submod2 = mplugin->createSubmodel();
submod2->setId("B");
submod2->setModelRef("ExtMod1");
// create a replacement compartment
Compartment* comp=model->createCompartment();
comp->setSpatialDimensions((unsigned int)3);
comp->setConstant(true);
comp->setId("comp");
comp->setSize(1L);
//Tell the model that this compartment replaces both of the inside ones.
CompSBasePlugin* compartplug = static_cast<CompSBasePlugin*>(comp->getPlugin("comp"));
ReplacedElement re;
re.setIdRef("comp");
re.setSubmodelRef("A");
compartplug->addReplacedElement(&re);
re.setSubmodelRef("B");
compartplug->addReplacedElement(&re);
// create a replacement species
Species* spec = model->createSpecies();
spec->setCompartment("comp");
spec->setHasOnlySubstanceUnits(false);
spec->setConstant(false);
spec->setBoundaryCondition(false);
spec->setId("S");
//Tell the model that this species replaces both of the inside ones.
CompSBasePlugin* spp = static_cast<CompSBasePlugin*>(spec->getPlugin("comp"));
re.setIdRef("S");
re.setSubmodelRef("A");
spp->addReplacedElement(&re);
re.setSubmodelRef("B");
spp->addReplacedElement(&re);
writeSBMLToFile(document,"eg-import-external.xml");
writeSBMLToFile(document,"spec_example2.xml");
delete document;
document = readSBMLFromFile("spec_example2.xml");
if (document == NULL)
{
cout << "Error reading back in file." << endl;
retval = -1;
}
else
{
document->setConsistencyChecks(LIBSBML_CAT_UNITS_CONSISTENCY, false);
document->checkConsistency();
if (document->getErrorLog()->getNumFailsWithSeverity(2) > 0
|| document->getErrorLog()->getNumFailsWithSeverity(3) > 0)
{
stringstream errorstream;
document->printErrors(errorstream);
cout << "Errors encoutered when round-tripping SBML file: \n"
<< errorstream.str() << endl;
retval = -1;
}
writeSBMLToFile(document, "spec_example2_rt.xml");
delete document;
}
#ifdef WIN32
if (retval != 0)
{
cout << "(Press any key to exit.)" << endl;
_getch();
}
#endif
return retval;
}
LIBSBML_CPP_NAMESPACE_USE
int
main (int argc, char* argv[])
{
SBMLNamespaces sbmlns(3,1,"multi",1);
// create the document
SBMLDocument *document = new SBMLDocument(&sbmlns);
// set the required attribute to true
MultiSBMLDocumentPlugin * docPlug =
static_cast<MultiSBMLDocumentPlugin*>(document->getPlugin("multi"));
docPlug->setRequired(true);
// create the Model
Model* model=document->createModel();
// create the compartments
Compartment * c = model->createCompartment();
c->setId("membrane");
c->setConstant(true);
// set the multi attribute isType via the compartmentPlugin
MultiCompartmentPlugin * compPlug =
static_cast<MultiCompartmentPlugin*>(c->getPlugin("multi"));
compPlug->setIsType(true);
// create the speciesTypes
MultiModelPlugin * modelPlug =
static_cast<MultiModelPlugin*>(model->getPlugin("multi"));
MultiSpeciesType * st = modelPlug->createMultiSpeciesType();
st->setId("stX");
st->setCompartment("membrane");
// create species
Species *s = model->createSpecies();
s->setId("s1");
s->setCompartment("membrane");
s->setBoundaryCondition(false);
s->setHasOnlySubstanceUnits(false);
s->setConstant(false);
// set the multi attribute speciesType via the compartmentPlugin
MultiSpeciesPlugin * spPlug =
static_cast<MultiSpeciesPlugin*>(s->getPlugin("multi"));
spPlug->setSpeciesType("stX");
// create species feature
SpeciesFeature *sf = spPlug->createSpeciesFeature();
sf->setSpeciesFeatureType("a");
sf->setOccur(1);
sf->setComponent("b");
SpeciesFeatureValue *sfv = sf->createSpeciesFeatureValue();
sfv->setValue("c");
// create a subListOfSpeciesFeatures
SubListOfSpeciesFeatures* subloSF = spPlug->createSubListOfSpeciesFeatures();
subloSF->setRelation(Relation_fromString("and"));
// add speciesFeatures to the subList
SpeciesFeature *sf1 = new SpeciesFeature(3, 1, 1);
sf1->setSpeciesFeatureType("a1");
sf1->setOccur(1);
sf1->setComponent("b1");
SpeciesFeatureValue *sfv1 = sf1->createSpeciesFeatureValue();
sfv1->setValue("c1");
subloSF->appendAndOwn(sf1);
sf1 = new SpeciesFeature(3, 1, 1);
sf1->setSpeciesFeatureType("a2");
sf1->setOccur(1);
sf1->setComponent("b2");
sfv1 = sf1->createSpeciesFeatureValue();
sfv1->setValue("c2");
subloSF->appendAndOwn(sf1);
// create a second subListOfSpeciesfeatures
subloSF = spPlug->createSubListOfSpeciesFeatures();
subloSF->setRelation(Relation_fromString("or"));
sf1 = new SpeciesFeature(3, 1, 1);
sf1->setSpeciesFeatureType("a3");
sf1->setOccur(1);
sf1->setComponent("b3");
sfv1 = sf1->createSpeciesFeatureValue();
sfv1->setValue("c3");
subloSF->appendAndOwn(sf1);
sf1 = new SpeciesFeature(3, 1, 1);
sf1->setSpeciesFeatureType("a4");
sf1->setOccur(1);
sf1->setComponent("b4");
sfv1 = sf1->createSpeciesFeatureValue();
sfv1->setValue("c4");
subloSF->appendAndOwn(sf1);
writeSBML(document,"multi_example3.xml");
delete document;
return 0;
}
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){
//
// 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;
}
