END_TEST START_TEST(test_FbcExtension_create_and_write_new_geneassociation ) { FbcPkgNamespaces *sbmlns = new FbcPkgNamespaces(3, 1, 2); // create the document SBMLDocument document(sbmlns); document.setConsistencyChecks(LIBSBML_CAT_UNITS_CONSISTENCY, false); document.setConsistencyChecks(LIBSBML_CAT_MODELING_PRACTICE, false); // create the Model Model* model = document.createModel(); // create the Compartment Compartment* compartment = model->createCompartment(); compartment->setId("compartment"); compartment->setConstant(true); compartment->setSize(1); // create the Species Species* species = model->createSpecies(); species->setId("Node1"); species->setCompartment("compartment"); species->setBoundaryCondition(false); species = model->createSpecies(); species->setId("Node2"); species->setCompartment("compartment"); species->setBoundaryCondition(false); Reaction* reaction = model->createReaction(); reaction->setId("J0"); reaction->setReversible(false); SpeciesReference* reactant = reaction->createReactant(); reactant->setSpecies("Node0"); reactant->setStoichiometry(1); SpeciesReference* product = reaction->createProduct(); product->setSpecies("Node1"); product->setStoichiometry(1); // use fbc FbcModelPlugin* mplugin = static_cast<FbcModelPlugin*>(model->getPlugin("fbc")); fail_unless(mplugin != NULL); FluxBound* bound = mplugin->createFluxBound(); bound->setId("bound1"); bound->setReaction("J0"); bound->setOperation("equal"); bound->setValue(10); Objective* objective = mplugin->createObjective(); objective->setId("obj1"); objective->setType("maximize"); FluxObjective* fluxObjective = objective->createFluxObjective(); fluxObjective->setReaction("J0"); fluxObjective->setCoefficient(1); FbcReactionPlugin* rplug = dynamic_cast<FbcReactionPlugin*>(reaction->getPlugin("fbc")); fail_unless(rplug != NULL); GeneProductAssociation * ga = rplug->createGeneProductAssociation(); ga->setId("ga1"); ga->setAssociation("MG_077 AND MG_321 AND MG_080 AND MG_078 AND MG_079"); fail_unless(ga->getAssociation() != NULL); fail_unless(mplugin->getNumGeneProducts() == 5); ga->setAssociation("MG_077 AND MG_321 AND MG_080 AND MG_078 AND MG_079"); fail_unless(ga->getAssociation() != NULL); fail_unless(mplugin->getNumGeneProducts() == 5); delete sbmlns; }
void Module::CreateSBMLModel() { Model* sbmlmod = m_sbml.createModel(); sbmlmod->setId(m_modulename); sbmlmod->setName(m_modulename); sbmlmod->setNotes("<body xmlns=\"http://www.w3.org/1999/xhtml\"><p> Originally created by libAntimony " VERSION_STRING " (using libSBML " LIBSBML_DOTTED_VERSION ") </p></body>"); char cc = g_registry.GetCC(); //User-defined functions for (size_t uf=0; uf<g_registry.GetNumUserFunctions(); uf++) { const UserFunction* userfunction = g_registry.GetNthUserFunction(uf); assert(userfunction != NULL); FunctionDefinition* fd = sbmlmod->createFunctionDefinition(); fd->setId(userfunction->GetModuleName()); ASTNode* math = parseStringToASTNode(userfunction->ToSBMLString()); fd->setMath(math); delete math; } //Compartments Compartment* defaultCompartment = sbmlmod->createCompartment(); defaultCompartment->setId(DEFAULTCOMP); defaultCompartment->setConstant(true); defaultCompartment->setSize(1); defaultCompartment->setSBOTerm(410); //The 'implicit compartment' size_t numcomps = GetNumVariablesOfType(allCompartments); for (size_t comp=0; comp<numcomps; comp++) { const Variable* compartment = GetNthVariableOfType(allCompartments, comp); Compartment* sbmlcomp = sbmlmod->createCompartment(); sbmlcomp->setId(compartment->GetNameDelimitedBy(cc)); if (compartment->GetDisplayName() != "") { sbmlcomp->setName(compartment->GetDisplayName()); } sbmlcomp->setConstant(compartment->GetIsConst()); formula_type ftype = compartment->GetFormulaType(); assert (ftype == formulaINITIAL || ftype==formulaASSIGNMENT || ftype==formulaRATE); if (ftype != formulaINITIAL) { sbmlcomp->setConstant(false); } const Formula* formula = compartment->GetFormula(); if (formula->IsDouble()) { sbmlcomp->setSize(atof(formula->ToSBMLString().c_str())); } SetAssignmentFor(sbmlmod, compartment); } //Species size_t numspecies = GetNumVariablesOfType(allSpecies); for (size_t spec=0; spec < numspecies; spec++) { const Variable* species = GetNthVariableOfType(allSpecies, spec); Species* sbmlspecies = sbmlmod->createSpecies(); sbmlspecies->setId(species->GetNameDelimitedBy(cc)); if (species->GetDisplayName() != "") { sbmlspecies->setName(species->GetDisplayName()); } sbmlspecies->setConstant(false); //There's no need to try to distinguish between const and var for species. if (species->GetIsConst()) { sbmlspecies->setBoundaryCondition(true); } else { sbmlspecies->setBoundaryCondition(false); } const Variable* compartment = species->GetCompartment(); if (compartment == NULL) { sbmlspecies->setCompartment(defaultCompartment->getId()); } else { sbmlspecies->setCompartment(compartment->GetNameDelimitedBy(cc)); } const Formula* formula = species->GetFormula(); if (formula->IsDouble()) { sbmlspecies->setInitialConcentration(atof(formula->ToSBMLString().c_str())); } else if (formula->IsAmountIn(species->GetCompartment())) { sbmlspecies->setInitialAmount(formula->ToAmount()); } SetAssignmentFor(sbmlmod, species); } //Formulas size_t numforms = GetNumVariablesOfType(allFormulas); for (size_t form=0; form < numforms; form++) { const Variable* formvar = GetNthVariableOfType(allFormulas, form); const Formula* formula = formvar->GetFormula(); Parameter* param = sbmlmod->createParameter(); param->setId(formvar->GetNameDelimitedBy(cc)); if (formvar->GetDisplayName() != "") { param->setName(formvar->GetDisplayName()); } param->setConstant(formvar->GetIsConst()); if (formula->IsDouble()) { param->setValue(atof(formula->ToSBMLString().c_str())); } SetAssignmentFor(sbmlmod, formvar); formula_type ftype = formvar->GetFormulaType(); assert (ftype == formulaINITIAL || ftype==formulaASSIGNMENT || ftype==formulaRATE); if (ftype != formulaINITIAL) { param->setConstant(false); } } //Reactions size_t numrxns = GetNumVariablesOfType(allReactions); for (size_t rxn=0; rxn < numrxns; rxn++) { const Variable* rxnvar = GetNthVariableOfType(allReactions, rxn); const AntimonyReaction* reaction = rxnvar->GetReaction(); if (reaction->IsEmpty()) { continue; //Reactions that involve no species are illegal in SBML. } Reaction* sbmlrxn = sbmlmod->createReaction(); sbmlrxn->setId(rxnvar->GetNameDelimitedBy(cc)); if (rxnvar->GetDisplayName() != "") { sbmlrxn->setName(rxnvar->GetDisplayName()); } if (reaction->GetType() == rdBecomes) { sbmlrxn->setReversible(true); } else { assert(reaction->GetType() == rdBecomesIrreversibly); sbmlrxn->setReversible(false); } const Formula* formula = reaction->GetFormula(); string formstring = formula->ToSBMLString(rxnvar->GetStrandVars()); if (!formula->IsEmpty()) { KineticLaw* kl = sbmlmod->createKineticLaw(); ASTNode* math = parseStringToASTNode(formstring); kl->setMath(math); delete math; } const ReactantList* left = reaction->GetLeft(); for (size_t lnum=0; lnum<left->Size(); lnum++) { const Variable* nthleft = left->GetNthReactant(lnum); double nthstoich = left->GetStoichiometryFor(lnum); SpeciesReference* sr = sbmlmod->createReactant(); sr->setSpecies(nthleft->GetNameDelimitedBy(cc)); sr->setStoichiometry(nthstoich); } const ReactantList* right = reaction->GetRight(); for (size_t rnum=0; rnum<right->Size(); rnum++) { const Variable* nthright = right->GetNthReactant(rnum); double nthstoich = right->GetStoichiometryFor(rnum); SpeciesReference* sr = sbmlmod->createProduct(); sr->setSpecies(nthright->GetNameDelimitedBy(cc)); sr->setStoichiometry(nthstoich); } //Find 'modifiers' and add them. vector<const Variable*> subvars = formula->GetVariablesFrom(formstring, m_modulename); for (size_t v=0; v<subvars.size(); v++) { if (subvars[v] != NULL && subvars[v]->GetType() == varSpeciesUndef) { if (left->GetStoichiometryFor(subvars[v]) == 0 && right->GetStoichiometryFor(subvars[v]) == 0) { ModifierSpeciesReference* msr = sbmlmod->createModifier(); msr->setSpecies(subvars[v]->GetNameDelimitedBy(cc)); } } } } //Events size_t numevents = GetNumVariablesOfType(allEvents); for (size_t ev=0; ev < numevents; ev++) { const Variable* eventvar = GetNthVariableOfType(allEvents, ev); const AntimonyEvent* event = eventvar->GetEvent(); Event* sbmlevent = sbmlmod->createEvent(); sbmlevent->setId(eventvar->GetNameDelimitedBy(cc)); if (eventvar->GetDisplayName() != "") { sbmlevent->setName(eventvar->GetDisplayName()); } Trigger* trig = sbmlevent->createTrigger(); ASTNode* ASTtrig = parseStringToASTNode(event->GetTrigger()->ToSBMLString()); trig->setMath(ASTtrig); delete ASTtrig; const Formula* delay = event->GetDelay(); if (!delay->IsEmpty()) { ASTtrig = parseStringToASTNode(delay->ToSBMLString()); Delay* sbmldelay = sbmlevent->createDelay(); sbmldelay->setMath(ASTtrig); delete ASTtrig; } long numasnts = static_cast<long>(event->GetNumAssignments()); for (long asnt=numasnts-1; asnt>=0; asnt--) { //events are stored in reverse order. Don't ask... EventAssignment* sbmlasnt = sbmlmod->createEventAssignment(); sbmlasnt->setVariable(event->GetNthAssignmentVariableName(asnt, cc)); ASTNode* ASTasnt = parseStringToASTNode(event->GetNthAssignmentFormulaString(asnt, '_', true)); sbmlasnt->setMath(ASTasnt); delete ASTasnt; } } //Interactions size_t numinteractions = GetNumVariablesOfType(allInteractions); for (size_t irxn=0; irxn<numinteractions; irxn++) { const Variable* arxnvar = GetNthVariableOfType(allInteractions, irxn); const AntimonyReaction* arxn = arxnvar->GetReaction(); Reaction* rxn = sbmlmod->getReaction(arxn->GetRight()->GetNthReactant(0)->GetNameDelimitedBy(cc)); if (rxn != NULL) { for (size_t interactor=0; interactor<arxn->GetLeft()->Size(); interactor++) { ModifierSpeciesReference* msr = rxn->createModifier(); msr->setSpecies(arxn->GetLeft()->GetNthReactant(interactor)->GetNameDelimitedBy(cc)); msr->setName(arxnvar->GetNameDelimitedBy(cc)); } } } //Unknown variables (turn into parameters) size_t numunknown = GetNumVariablesOfType(allUnknown); for (size_t form=0; form < numunknown; form++) { const Variable* formvar = GetNthVariableOfType(allUnknown, form); Parameter* param = sbmlmod->createParameter(); param->setId(formvar->GetNameDelimitedBy(cc)); if (formvar->GetDisplayName() != "") { param->setName(formvar->GetDisplayName()); } switch(formvar->GetConstType()) { case constVAR: param->setConstant(true); break; case constCONST: param->setConstant(false); break; case constDEFAULT: break; } } }
END_TEST START_TEST(test_FbcExtension_create_and_write_L3V1V1) { FbcPkgNamespaces *sbmlns = new FbcPkgNamespaces(3, 1, 1); // create the document SBMLDocument *document = new SBMLDocument(sbmlns); delete sbmlns; // create the Model Model* model = document->createModel(); // create the Compartment Compartment* compartment = model->createCompartment(); compartment->setId("compartment"); compartment->setConstant(true); compartment->setSize(1); // create the Species Species* species = model->createSpecies(); species->setId("Node1"); species->setCompartment("compartment"); species->setBoundaryCondition(false); species = model->createSpecies(); species->setId("Node2"); species->setCompartment("compartment"); species->setBoundaryCondition(false); Reaction* reaction = model->createReaction(); reaction->setId("J0"); reaction->setReversible(false); SpeciesReference* reactant = reaction->createReactant(); reactant->setSpecies("Node0"); reactant->setStoichiometry(1); SpeciesReference* product = reaction->createProduct(); product->setSpecies("Node1"); product->setStoichiometry(1); // use fbc FbcModelPlugin* mplugin = static_cast<FbcModelPlugin*>(model->getPlugin("fbc")); fail_unless(mplugin != NULL); FluxBound* bound = mplugin->createFluxBound(); bound->setId("bound1"); bound->setReaction("J0"); bound->setOperation("equal"); bound->setValue(10); Objective* objective = mplugin->createObjective(); objective->setId("obj1"); objective->setType("maximize"); FluxObjective* fluxObjective = objective->createFluxObjective(); fluxObjective->setReaction("J0"); fluxObjective->setCoefficient(1); string s1 = writeSBMLToStdString(document); // check clone() SBMLDocument* document2 = document->clone(); string s2 = writeSBMLToStdString(document2); fail_unless(s1 == s2); // check operator= Model m = *(document->getModel()); document2->setModel(&m); s2 = writeSBMLToStdString(document2); fail_unless(s1 == s2); delete document2; delete document; }
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; }
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 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) { 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; }