END_TEST
START_TEST (test_WriteL3SBML_Reaction_compartment)
{
const char* expected = "<reaction id=\"r\" reversible=\"false\""
" fast=\"true\" compartment=\"c\"/>";
const char* expected1 = "<reaction id=\"r\" reversible=\"false\""
" fast=\"true\"/>";
Reaction *r = D->createModel()->createReaction();
r->setId("r");
r->setReversible(false);
r->setFast(true);
r->setCompartment("c");
char* sbml = r->toSBML();
fail_unless( equals(expected, sbml) );
safe_free(sbml);
r->unsetCompartment();
sbml = r->toSBML();
fail_unless( equals(expected1, sbml) );
safe_free(sbml);
}
END_TEST
START_TEST (test_WriteL3SBML_Reaction_full)
{
const char* expected =
"<reaction id=\"v1\" reversible=\"true\" fast=\"false\">\n"
" <listOfReactants>\n"
" <speciesReference species=\"x0\"/>\n"
" </listOfReactants>\n"
" <listOfProducts>\n"
" <speciesReference species=\"s1\"/>\n"
" </listOfProducts>\n"
" <listOfModifiers>\n"
" <modifierSpeciesReference species=\"m1\"/>\n"
" </listOfModifiers>\n"
" <kineticLaw>\n"
" <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n"
" <apply>\n"
" <divide/>\n"
" <apply>\n"
" <times/>\n"
" <ci> vm </ci>\n"
" <ci> s1 </ci>\n"
" </apply>\n"
" <apply>\n"
" <plus/>\n"
" <ci> km </ci>\n"
" <ci> s1 </ci>\n"
" </apply>\n"
" </apply>\n"
" </math>\n"
" </kineticLaw>\n"
"</reaction>";
D->createModel();
Reaction* r = D->getModel()->createReaction();
r->setId("v1");
r->setReversible(true);
r->setFast(false);
r->createReactant()->setSpecies("x0");
r->createProduct ()->setSpecies("s1");
r->createModifier()->setSpecies("m1");
r->createKineticLaw()->setFormula("(vm * s1)/(km + s1)");
char* sbml = r->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;
}
void writeSpatialSBML() {
/*
// SBMLNamespaces of SBML Level 3 Version 1 with Spatial Version 1
SBMLNamespaces sbmlns(3,1,"spatial",1);
// SpatialPkgNamespaces spatialns(3,1,1);
// add Required Elements package namespace
sbmlns.addPkgNamespace("req", 1);
*/
// SBMLNamespaces of SBML Level 3 Version 1 with 'req' Version 1
// then add 'spatial' package namespace.
RequiredElementsPkgNamespaces sbmlns(3,1,1);
sbmlns.addPkgNamespace("spatial",1);
// create the L3V1 document with spatial package
SBMLDocument document(&sbmlns);
// set 'required' attribute on document for 'spatial' and 'req' packages to 'T'??
SBMLDocumentPlugin* dplugin;
dplugin = static_cast<SBMLDocumentPlugin*>(document.getPlugin("spatial"));
dplugin->setRequired(true);
dplugin = static_cast<SBMLDocumentPlugin*>(document.getPlugin("req"));
dplugin->setRequired(true);
// create the Model
Model *model = document.createModel();
model-> setId("trial_spatial");
model-> setName("trial_spatial");
// create the Compartments
Compartment* compartment = model->createCompartment();
compartment->setId("cytosol");
compartment->setConstant(true);
// create the Species
Species* species1 = model->createSpecies();
species1->setId("ATPc");
species1->setCompartment("cytosol");
species1->setInitialConcentration(1.0);
species1->setHasOnlySubstanceUnits(false);
species1->setBoundaryCondition(false);
species1->setConstant(false);
// spatial package extension to species.
// required elements package extention to parameter
RequiredElementsSBasePlugin* reqplugin;
reqplugin = static_cast<RequiredElementsSBasePlugin*>(species1->getPlugin("req"));
reqplugin->setMathOverridden("spatial");
reqplugin->setCoreHasAlternateMath(true);
SpatialSpeciesRxnPlugin* srplugin;
srplugin = static_cast<SpatialSpeciesRxnPlugin*>(species1->getPlugin("spatial"));
srplugin->setIsSpatial(true);
// add parameter for diff coeff of species1
Parameter* paramSp = model->createParameter();
paramSp->setId(species1->getId()+"_dc");
paramSp->setValue(1.0);
// required elements package extention to parameter
reqplugin = static_cast<RequiredElementsSBasePlugin*>(paramSp->getPlugin("req"));
reqplugin->setMathOverridden("spatial");
reqplugin->setCoreHasAlternateMath(true);
// spatial package extension to parameter.
SpatialParameterPlugin* pplugin;
pplugin = static_cast<SpatialParameterPlugin*>(paramSp->getPlugin("spatial"));
DiffusionCoefficient* diffCoeff = pplugin->getDiffusionCoefficient();
diffCoeff->setVariable(species1->getId());
diffCoeff->setCoordinateIndex(0);
// add parameter for adv coeff of species1
paramSp = model->createParameter();
paramSp->setId(species1->getId()+"_ac");
paramSp->setValue(1.5);
// required elements package extention to parameter
reqplugin = static_cast<RequiredElementsSBasePlugin*>(paramSp->getPlugin("req"));
reqplugin->setMathOverridden("spatial");
reqplugin->setCoreHasAlternateMath(true);
// spatial package extension to parameter.
pplugin = static_cast<SpatialParameterPlugin*>(paramSp->getPlugin("spatial"));
AdvectionCoefficient* advCoeff = pplugin->getAdvectionCoefficient();
advCoeff->setVariable(species1->getId());
advCoeff->setCoordinateIndex(0);
// add parameter for boundary condition of species1
paramSp = model->createParameter();
paramSp->setId(species1->getId()+"_bc");
paramSp->setValue(2.0);
// required elements package extention to parameter
reqplugin = static_cast<RequiredElementsSBasePlugin*>(paramSp->getPlugin("req"));
reqplugin->setMathOverridden("spatial");
reqplugin->setCoreHasAlternateMath(true);
// spatial package extension to parameter.
pplugin = static_cast<SpatialParameterPlugin*>(paramSp->getPlugin("spatial"));
BoundaryCondition* boundCon = pplugin->getBoundaryCondition();
boundCon->setVariable(species1->getId());
boundCon->setType("value");
boundCon->setCoordinateBoundary("Xmin");
Species* species2 = model->createSpecies();
species2->setId("ADPc");
species2->setCompartment("cytosol");
species2->setInitialConcentration(1);
species2->setHasOnlySubstanceUnits(false);
species2->setBoundaryCondition(false);
species2->setConstant(false);
srplugin = static_cast<SpatialSpeciesRxnPlugin*>(species2->getPlugin("spatial"));
srplugin->setIsSpatial(true);
/* // create a parameter
Parameter* param = model->createParameter();
param->setId("k_1");
param->setValue(0.24);
param->setConstant(true);
// create an assignment rule
AssignmentRule* assignRule = model->createAssignmentRule();
assignRule->setVariable(species1->getId());
assignRule->setFormula("species2+k_1");
*/
/*
reqplugin = static_cast<RequiredElementsSBasePlugin*>(assignRule->getPlugin("req"));
reqplugin->setMathOverridden("spatial");
reqplugin->setCoreHasAlternateMath(false);
*/
Reaction* reaction = model->createReaction();
reaction->setId("rxn1");
reaction->setReversible(false);
reaction->setFast(false);
reaction->setCompartment("cytosol");
srplugin = static_cast<SpatialSpeciesRxnPlugin*>(reaction->getPlugin("spatial"));
srplugin->setIsLocal(true);
//
// Get a SpatialModelPlugin 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.
//
SpatialModelPlugin* mplugin;
mplugin = static_cast<SpatialModelPlugin*>(model->getPlugin("spatial"));
//
// Creates a geometry object via SpatialModelPlugin object.
//
Geometry* geometry = mplugin->getGeometry();
geometry->setCoordinateSystem("XYZ");
CoordinateComponent* coordX = geometry->createCoordinateComponent();
coordX->setSpatialId("coordComp1");
coordX->setComponentType("cartesian");
coordX->setSbmlUnit("umeter");
coordX->setIndex(1);
BoundaryMin* minX = coordX->createBoundaryMin();
minX->setSpatialId("Xmin");
minX->setValue(0.0);
BoundaryMax* maxX = coordX->createBoundaryMax();
maxX->setSpatialId("Xmax");
maxX->setValue(10.0);
Parameter* paramX = model->createParameter();
paramX->setId("x");
paramX->setValue(8.0);
// required elements package extention to parameter
// RequiredElementsSBasePlugin* reqplugin;
reqplugin = static_cast<RequiredElementsSBasePlugin*>(paramX->getPlugin("req"));
reqplugin->setMathOverridden("spatial");
reqplugin->setCoreHasAlternateMath(true);
// spatial package extension to parameter.
// SpatialParameterPlugin* pplugin;
pplugin = static_cast<SpatialParameterPlugin*>(paramX->getPlugin("spatial"));
SpatialSymbolReference* spSymRef = pplugin->getSpatialSymbolReference();
spSymRef->setSpatialId(coordX->getSpatialId());
spSymRef->setType(coordX->getElementName());
DomainType* domainType = geometry->createDomainType();
domainType->setSpatialId("dtype1");
domainType->setSpatialDimensions(3);
// Spatial package extension to compartment (mapping compartment with domainType)
// required elements package extention to compartment
reqplugin = static_cast<RequiredElementsSBasePlugin*>(compartment->getPlugin("req"));
reqplugin->setMathOverridden("spatial");
reqplugin->setCoreHasAlternateMath(true);
SpatialCompartmentPlugin* cplugin;
cplugin = static_cast<SpatialCompartmentPlugin*>(compartment->getPlugin("spatial"));
CompartmentMapping* compMapping = cplugin->getCompartmentMapping();
compMapping->setSpatialId("compMap1");
compMapping->setCompartment(compartment->getId());
compMapping->setDomainType(domainType->getSpatialId());
compMapping->setUnitSize(1.0);
Domain* domain = geometry->createDomain();
domain->setSpatialId("domain1");
domain->setDomainType("dtype1");
domain->setImplicit(false);
domain->setShapeId("circle");
InteriorPoint* internalPt1 = domain->createInteriorPoint();
internalPt1->setCoord1(1.0);
domain = geometry->createDomain();
domain->setSpatialId("domain2");
domain->setDomainType("dtype1");
domain->setImplicit(false);
domain->setShapeId("square");
InteriorPoint* internalPt2 = domain->createInteriorPoint();
internalPt2->setCoord1(5.0);
AdjacentDomains* adjDomain = geometry->createAdjacentDomains();
adjDomain->setSpatialId("adjDomain1");
adjDomain->setDomain1("domain1");
adjDomain->setDomain2("domain2");
AnalyticGeometry* analyticGeom = geometry->createAnalyticGeometry();
analyticGeom->setSpatialId("analyticGeom1");
AnalyticVolume* analyticVol = analyticGeom->createAnalyticVolume();
analyticVol->setSpatialId("analyticVol1");
analyticVol->setDomainType(domainType->getSpatialId());
analyticVol->setFunctionType("squareFn");
analyticVol->setOrdinal(1);
const char* mathMLStr = "<math xmlns=\"http://www.w3.org/1998/Math/MathML\"><apply xmlns=\"\"><plus /><apply><times /><ci>x</ci><ci>x</ci></apply><apply><minus /><cn>1.0</cn></apply></apply></math>";
ASTNode* mathNode = readMathMLFromString(mathMLStr);
analyticVol->setMath(mathNode);
SampledFieldGeometry* sfg = geometry->createSampledFieldGeometry();
sfg->setSpatialId("sampledFieldGeom1");
SampledField* sampledField = sfg->createSampledField();
sampledField->setSpatialId("sampledField1");
sampledField->setNumSamples1(4);
sampledField->setNumSamples2(4);
sampledField->setNumSamples3(2);
sampledField->setDataType("double");
sampledField->setInterpolationType("linear");
sampledField->setEncoding("encoding1");
//int samples[5] = {1, 2, 3, 4, 5};
int samples[32] = {
// z=0
0,0,0,0,
0,1,1,0,
0,1,1,0,
0,0,0,0,
// z=1
0,0,0,0,
0,1,1,0,
0,1,1,0,
0,0,0,0
};
ImageData* id = sampledField->createImageData();
id->setDataType("compressed");
id->setSamples(samples, 32);
SampledVolume* sampledVol = sfg->createSampledVolume();
sampledVol->setSpatialId("sv_1");
sampledVol->setDomainType(domainType->getSpatialId());
sampledVol->setSampledValue(128.0);
sampledVol->setMinValue(0.0);
sampledVol->setMaxValue(255.0);
ParametricGeometry* pg = geometry->createParametricGeometry();
pg->setSpatialId("parametricGeom1");
ParametricObject* paramObj = pg->createParametricObject();
paramObj->setSpatialId("po_1");
paramObj->setDomain(domain->getSpatialId());
paramObj->setPolygonType("hexagon");
int ptIndices[5] = {1, 2, 3, 4, 5};
PolygonObject* po = paramObj->createPolygonObject();
po->setPointIndices(ptIndices, 5);
SpatialPoint* spPt = pg->createSpatialPoint();
spPt->setSpatialId("sp_1");
spPt->setDomain(domain->getSpatialId());
spPt->setCoord1(1);
spPt->setCoord2(2);
spPt->setCoord3(3);
CSGeometry* csg = geometry->createCSGeometry();
csg->setSpatialId("csGeom1");
CSGObject* csgObj = csg->createCSGObject();
csgObj->setSpatialId("csg_csgo_1");
csgObj->setDomainType(domainType->getSpatialId());
csgObj->setOrdinal(1);
CSGScale* scale = csgObj->createCSGScale();
scale->setScaleX(2.0);
scale->setScaleY(3.0);
scale->setScaleZ(4.0);
CSGPrimitive* prim1 = scale->createCSGPrimitive();
prim1->setPrimitiveType("SOLID_SPHERE");
csgObj = csg->createCSGObject();
csgObj->setSpatialId("csg_csgo_2");
csgObj->setDomainType(domainType->getSpatialId());
CSGSetOperator* setUnion = csgObj->createCSGSetOperator();
setUnion->setOperationType("UNION");
/* CSGPrimitive* prim = setUnion->createCSGPrimitive();
prim->setPrimitiveType("SOLID_SPHERE");
CSGPrimitive* prim2 = setUnion->createCSGPrimitive();
prim2->setPrimitiveType("SOLID_CONE");
*/
CSGPrimitive* prim2 = new CSGPrimitive(3,1,1);
prim2->setSpatialId("cone0");
prim2->setPrimitiveType("SOLID_CONE");
CSGTranslation* translatedCone = new CSGTranslation(3,1,1);
translatedCone->setSpatialId("translation0");
translatedCone->setTranslateX(2.0);
translatedCone->setTranslateY(2.0);
translatedCone->setTranslateZ(2.0);
translatedCone->setChild(prim2);
int n = setUnion->addCSGNodeChild(translatedCone);
CSGPrimitive* prim3 = new CSGPrimitive(3,1,1);
prim3->setSpatialId("sphere0");
prim3->setPrimitiveType("SOLID_SPHERE");
n = setUnion->addCSGNodeChild(prim3);
writeSBML(&document, "spatial_example0.xml");
}
void writeSpatialSBML()
{
// SBMLNamespaces of SBML Level 3 Version 1 with 'req' Version 1
// then add 'spatial' package namespace.
SpatialPkgNamespaces sbmlns(3,1,1);
// create the L3V1 document with spatial package
SBMLDocument document(&sbmlns);
// set 'required' attribute on document for 'spatial' and 'req' packages to 'T'??
SBMLDocumentPlugin* dplugin;
dplugin = static_cast<SBMLDocumentPlugin*>(document.getPlugin("spatial"));
dplugin->setRequired(true);
// create the Model
Model *model = document.createModel();
model-> setId("trial_spatial");
model-> setName("trial_spatial");
// create the Compartments
Compartment* compartment = model->createCompartment();
compartment->setId("cytosol");
compartment->setConstant(true);
// create the Species
Species* species1 = model->createSpecies();
species1->setId("ATPc");
species1->setCompartment("cytosol");
species1->setInitialConcentration(1.0);
species1->setHasOnlySubstanceUnits(false);
species1->setBoundaryCondition(false);
species1->setConstant(false);
// spatial package extension to species.
SpatialSpeciesPlugin* srplugin;
srplugin = static_cast<SpatialSpeciesPlugin*>(species1->getPlugin("spatial"));
srplugin->setIsSpatial(true);
// add parameter for diff coeff of species1
Parameter* paramSp = model->createParameter();
paramSp->setId(species1->getId()+"_dc");
paramSp->setValue(1.0);
// spatial package extension to parameter.
SpatialParameterPlugin* pplugin;
pplugin = static_cast<SpatialParameterPlugin*>(paramSp->getPlugin("spatial"));
DiffusionCoefficient* diffCoeff = pplugin->createDiffusionCoefficient();
diffCoeff->setVariable(species1->getId());
diffCoeff->setType(SPATIAL_DIFFUSIONKIND_ANISOTROPIC);
CoordinateReference* coordRef = diffCoeff->createCoordinateReference();
coordRef->setCoordinate(SPATIAL_COORDINATEKIND_CARTESIAN_X);
// add parameter for adv coeff of species1
paramSp = model->createParameter();
paramSp->setId(species1->getId()+"_ac");
paramSp->setValue(1.5);
// spatial package extension to parameter.
pplugin = static_cast<SpatialParameterPlugin*>(paramSp->getPlugin("spatial"));
AdvectionCoefficient* advCoeff = pplugin->createAdvectionCoefficient();
advCoeff->setVariable(species1->getId());
advCoeff->setCoordinate(SPATIAL_COORDINATEKIND_CARTESIAN_X);
// add parameter for boundary condition of species1
paramSp = model->createParameter();
paramSp->setId(species1->getId()+"_bc");
paramSp->setValue(2.0);
// spatial package extension to parameter.
pplugin = static_cast<SpatialParameterPlugin*>(paramSp->getPlugin("spatial"));
BoundaryCondition* boundCon = pplugin->createBoundaryCondition();
boundCon->setVariable(species1->getId());
boundCon->setType(SPATIAL_BOUNDARYKIND_DIRICHLET);
boundCon->setCoordinateBoundary("Xmin");
Species* species2 = model->createSpecies();
species2->setId("ADPc");
species2->setCompartment("cytosol");
species2->setInitialConcentration(1);
species2->setHasOnlySubstanceUnits(false);
species2->setBoundaryCondition(false);
species2->setConstant(false);
srplugin = static_cast<SpatialSpeciesPlugin*>(species2->getPlugin("spatial"));
srplugin->setIsSpatial(true);
Reaction* reaction = model->createReaction();
reaction->setId("rxn1");
reaction->setReversible(false);
reaction->setFast(false);
reaction->setCompartment("cytosol");
SpatialReactionPlugin* rplugin = static_cast<SpatialReactionPlugin*>(reaction->getPlugin("spatial"));
rplugin->setIsLocal(true);
//
// Get a SpatialModelPlugin 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.
//
SpatialModelPlugin* mplugin;
mplugin = static_cast<SpatialModelPlugin*>(model->getPlugin("spatial"));
//
// Creates a geometry object via SpatialModelPlugin object.
//
Geometry* geometry = mplugin->createGeometry();
geometry->setCoordinateSystem(SPATIAL_GEOMETRYKIND_CARTESIAN);
CoordinateComponent* coordX = geometry->createCoordinateComponent();
coordX->setId("coordComp1");
coordX->setType(SPATIAL_COORDINATEKIND_CARTESIAN_X);
coordX->setUnit("umeter");
Boundary* minX = coordX->createBoundaryMin();
minX->setId("Xmin");
minX->setValue(0.0);
Boundary* maxX = coordX->createBoundaryMax();
maxX->setId("Xmax");
maxX->setValue(10.0);
Parameter* paramX = model->createParameter();
paramX->setId("x");
paramX->setValue(8.0);
// spatial package extension to parameter.
// SpatialParameterPlugin* pplugin;
pplugin = static_cast<SpatialParameterPlugin*>(paramX->getPlugin("spatial"));
SpatialSymbolReference* spSymRef = pplugin->createSpatialSymbolReference();
spSymRef->setSpatialRef(coordX->getId());
DomainType* domainType = geometry->createDomainType();
domainType->setId("dtype1");
domainType->setSpatialDimension(3);
// Spatial package extension to compartment (mapping compartment with domainType)
SpatialCompartmentPlugin* cplugin;
cplugin = static_cast<SpatialCompartmentPlugin*>(compartment->getPlugin("spatial"));
CompartmentMapping* compMapping = cplugin->createCompartmentMapping();
compMapping->setId("compMap1");
compMapping->setDomainType(domainType->getId());
compMapping->setUnitSize(1.0);
Domain* domain = geometry->createDomain();
domain->setId("domain1");
domain->setDomainType("dtype1");
InteriorPoint* internalPt1 = domain->createInteriorPoint();
internalPt1->setCoord1(1.0);
domain = geometry->createDomain();
domain->setId("domain2");
domain->setDomainType("dtype1");
InteriorPoint* internalPt2 = domain->createInteriorPoint();
internalPt2->setCoord1(5.0);
AdjacentDomains* adjDomain = geometry->createAdjacentDomains();
adjDomain->setId("adjDomain1");
adjDomain->setDomain1("domain1");
adjDomain->setDomain2("domain2");
AnalyticGeometry* analyticGeom = geometry->createAnalyticGeometry();
analyticGeom->setId("analyticGeom1");
AnalyticVolume* analyticVol = analyticGeom->createAnalyticVolume();
analyticVol->setId("analyticVol1");
analyticVol->setDomainType(domainType->getId());
analyticVol->setFunctionType(SPATIAL_FUNCTIONKIND_LAYERED);
analyticVol->setOrdinal(1);
const char* mathMLStr = "<math xmlns=\"http://www.w3.org/1998/Math/MathML\"><apply xmlns=\"\"><plus /><apply><times /><ci>x</ci><ci>x</ci></apply><apply><minus /><cn>1.0</cn></apply></apply></math>";
ASTNode* mathNode = readMathMLFromString(mathMLStr);
analyticVol->setMath(mathNode);
SampledFieldGeometry* sfg = geometry->createSampledFieldGeometry();
sfg->setId("sampledFieldGeom1");
SampledField* sampledField = sfg->createSampledField();
sampledField->setId("sampledField1");
sampledField->setNumSamples1(4);
sampledField->setNumSamples2(4);
sampledField->setNumSamples3(2);
sampledField->setDataType("double");
sampledField->setInterpolationType("linear");
sampledField->setEncoding("encoding1");
//int samples[5] = {1, 2, 3, 4, 5};
int samples[32] = {
// z=0
0,0,0,0,
0,1,1,0,
0,1,1,0,
0,0,0,0,
// z=1
0,0,0,0,
0,1,1,0,
0,1,1,0,
0,0,0,0
};
ImageData* id = sampledField->createImageData();
id->setDataType("uint8");
id->setSamples(samples, 32);
SampledVolume* sampledVol = sfg->createSampledVolume();
sampledVol->setId("sv_1");
sampledVol->setDomainType(domainType->getId());
sampledVol->setSampledValue(128.0);
sampledVol->setMinValue(0.0);
sampledVol->setMaxValue(255.0);
writeSBML(&document, "spatial_example2.xml");
}
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;
}