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");
}
