/**
*
* Creates an SBML model represented in "7.2 Example involving units"
* in the SBML Level 2 Version 4 Specification.
*
*/
SBMLDocument* createExampleInvolvingUnits()
{
const unsigned int level = Level;
const unsigned int version = Version;
//---------------------------------------------------------------------------
//
// Creates an SBMLDocument object
//
//---------------------------------------------------------------------------
SBMLDocument* sbmlDoc = new SBMLDocument(level,version);
// Adds the namespace for XHTML to the SBMLDocument object. We need this
// because we will add notes to the model. (By default, the SBML document
// created by SBMLDocument only declares the SBML XML namespace.)
sbmlDoc->getNamespaces()->add("http://www.w3.org/1999/xhtml", "xhtml");
//---------------------------------------------------------------------------
//
// Creates a Model object inside the SBMLDocument object.
//
//---------------------------------------------------------------------------
Model* model = sbmlDoc->createModel();
model->setId("unitsExample");
//---------------------------------------------------------------------------
//
// Creates UnitDefinition objects inside the Model object.
//
//---------------------------------------------------------------------------
// Temporary pointers (reused more than once below).
UnitDefinition* unitdef;
Unit *unit;
//---------------------------------------------------------------------------
// (UnitDefinition1) Creates an UnitDefinition object ("substance").
//
// This has the effect of redefining the default unit of subtance for the
// whole model.
//---------------------------------------------------------------------------
unitdef = model->createUnitDefinition();
unitdef->setId("substance");
// Creates an Unit inside the UnitDefinition object
unit = unitdef->createUnit();
unit->setKind(UNIT_KIND_MOLE);
unit->setScale(-3);
//--------------------------------------------------------------------------------
// (UnitDefinition2) Creates an UnitDefinition object ("mmls")
//--------------------------------------------------------------------------------
// Note that we can reuse the pointers 'unitdef' and 'unit' because the
// actual UnitDefinition object (along with the Unit objects within it)
// is already attached to the Model object.
unitdef = model->createUnitDefinition();
unitdef->setId("mmls");
// Creates an Unit inside the UnitDefinition object ("mmls")
unit = unitdef->createUnit();
unit->setKind(UNIT_KIND_MOLE);
unit->setScale(-3);
// Creates an Unit inside the UnitDefinition object ("mmls")
unit = unitdef->createUnit();
unit->setKind(UNIT_KIND_LITRE);
unit->setExponent(-1);
// Creates an Unit inside the UnitDefinition object ("mmls")
unit = unitdef->createUnit();
unit->setKind(UNIT_KIND_SECOND);
unit->setExponent(-1);
//--------------------------------------------------------------------------------
// (UnitDefinition3) Creates an UnitDefinition object ("mml")
//--------------------------------------------------------------------------------
unitdef = model->createUnitDefinition();
unitdef->setId("mml");
// Creates an Unit inside the UnitDefinition object ("mml")
unit = unitdef->createUnit();
unit->setKind(UNIT_KIND_MOLE);
unit->setScale(-3);
// Creates an Unit inside the UnitDefinition object ("mml")
unit = unitdef->createUnit();
unit->setKind(UNIT_KIND_LITRE);
unit->setExponent(-1);
//---------------------------------------------------------------------------
//
// Creates a Compartment object inside the Model object.
//
//---------------------------------------------------------------------------
Compartment* comp;
const string compName = "cell";
// Creates a Compartment object ("cell")
comp = model->createCompartment();
comp->setId(compName);
// Sets the "size" attribute of the Compartment object.
//
// The units of this Compartment object is the default SBML
// units of volume (litre), and thus we don't have to explicitly invoke
// setUnits("litre") function to set the default units.
//
comp->setSize(1);
//---------------------------------------------------------------------------
//
// Creates Species objects inside the Model object.
//
//---------------------------------------------------------------------------
// Temporary pointer (reused more than once below).
Species *sp;
//---------------------------------------------------------------------------
// (Species1) Creates a Species object ("x0")
//---------------------------------------------------------------------------
sp = model->createSpecies();
sp->setId("x0");
// Sets the "compartment" attribute of the Species object to identify the
// compartnet in which the Species object located.
sp->setCompartment(compName);
// Sets the "initialConcentration" attribute of the Species object.
//
// The units of this Species object is determined by two attributes of this
// Species object ("substanceUnits" and "hasOnlySubstanceUnits") and the
// "spatialDimensions" attribute of the Compartment object ("cytosol") in which
// this species object is located.
// Since the default values are used for "substanceUnits" (substance (mole))
// and "hasOnlySubstanceUnits" (false) and the value of "spatialDimension" (3)
// is greater than 0, the units of this Species object is moles/liters .
//
sp->setInitialConcentration(1);
//---------------------------------------------------------------------------
// (Species2) Creates a Species object ("x1")
//---------------------------------------------------------------------------
sp = model->createSpecies();
sp->setId("x1");
sp->setCompartment(compName);
sp->setInitialConcentration(1);
//---------------------------------------------------------------------------
// (Species3) Creates a Species object ("s1")
//---------------------------------------------------------------------------
sp = model->createSpecies();
sp->setCompartment(compName);
sp->setId("s1");
sp->setInitialConcentration(1);
//---------------------------------------------------------------------------
// (Species4) Creates a Species object ("s2")
//---------------------------------------------------------------------------
sp = model->createSpecies();
sp->setCompartment(compName);
sp->setId("s2");
sp->setInitialConcentration(1);
//---------------------------------------------------------------------------
//
// Creates global Parameter objects inside the Model object.
//
//---------------------------------------------------------------------------
Parameter* para;
// Creates a Parameter ("vm")
para = model->createParameter();
para->setId("vm");
para->setValue(2);
para->setUnits("mmls");
// Creates a Parameter ("km")
para = model->createParameter();
para->setId("km");
para->setValue(2);
para->setUnits("mml");
//---------------------------------------------------------------------------
//
// Creates Reaction objects inside the Model object.
//
//---------------------------------------------------------------------------
// Temporary pointers.
Reaction* reaction;
SpeciesReference* spr;
KineticLaw* kl;
//---------------------------------------------------------------------------
// (Reaction1) Creates a Reaction object ("v1").
//---------------------------------------------------------------------------
reaction = model->createReaction();
reaction->setId("v1");
//---------------------------------------------------------------------------
// Creates Reactant objects inside the Reaction object ("v1").
//---------------------------------------------------------------------------
// (Reactant1) Creates a Reactant object that references Species "x0"
// in the model.
spr = reaction->createReactant();
spr->setSpecies("x0");
//---------------------------------------------------------------------------
// Creates a Product object inside the Reaction object ("v1").
//---------------------------------------------------------------------------
// Creates a Product object that references Species "s1" in the model.
spr = reaction->createProduct();
spr->setSpecies("s1");
//---------------------------------------------------------------------------
// Creates a KineticLaw object inside the Reaction object ("v1").
//---------------------------------------------------------------------------
kl = reaction->createKineticLaw();
// Creates a <notes> element in the KineticLaw object.
// Here we illustrate how to do it using a literal string. This requires
// known the required syntax of XHTML and the requirements for SBML <notes>
// elements. Later below, we show how to create notes using objects instead
// of strings.
string notesString = "<xhtml:p> ((vm * s1)/(km + s1)) * cell </xhtml:p>";
kl->setNotes(notesString);
//---------------------------------------------------------------------------
// Creates an ASTNode object which represents the following KineticLaw object.
//
// <math xmlns=\"http://www.w3.org/1998/Math/MathML\">
// <apply>
// <times/>
// <apply>
// <divide/>
// <apply>
// <times/>
// <ci> vm </ci>
// <ci> s1 </ci>
// </apply>
// <apply>
// <plus/>
// <ci> km </ci>
// <ci> s1 </ci>
// </apply>
// </apply>
// <ci> cell </ci>
// </apply>
// </math>
//---------------------------------------------------------------------------
//
// In the following code, ASTNode objects, which construct an ASTNode tree
// of the above math, are created and added in the order of preorder traversal
// of the tree (i.e. the order corresponds to the nested structure of the above
// MathML elements), and thus the following code maybe a bit more efficient but
// maybe a bit difficult to read.
//
ASTNode* astMath = new ASTNode(AST_TIMES);
astMath->addChild(new ASTNode(AST_DIVIDE));
ASTNode* astDivide = astMath->getLeftChild();
astDivide->addChild(new ASTNode(AST_TIMES));
ASTNode* astTimes = astDivide->getLeftChild();
astTimes->addChild(new ASTNode(AST_NAME));
astTimes->getLeftChild()->setName("vm");
astTimes->addChild(new ASTNode(AST_NAME));
astTimes->getRightChild()->setName("s1");
astDivide->addChild(new ASTNode(AST_PLUS));
ASTNode* astPlus = astDivide->getRightChild();
astPlus->addChild(new ASTNode(AST_NAME));
astPlus->getLeftChild()->setName("km");
astPlus->addChild(new ASTNode(AST_NAME));
astPlus->getRightChild()->setName("s1");
astMath->addChild(new ASTNode(AST_NAME));
astMath->getRightChild()->setName("cell");
//---------------------------------------------
//
// set the Math element
//
//------------------------------------------------
kl->setMath(astMath);
delete astMath;
//---------------------------------------------------------------------------
// (Reaction2) Creates a Reaction object ("v2").
//---------------------------------------------------------------------------
reaction = model->createReaction();
reaction->setId("v2");
//---------------------------------------------------------------------------
// Creates Reactant objects inside the Reaction object ("v2").
//---------------------------------------------------------------------------
// (Reactant2) Creates a Reactant object that references Species "s1"
// in the model.
spr = reaction->createReactant();
spr->setSpecies("s1");
//---------------------------------------------------------------------------
// Creates a Product object inside the Reaction object ("v2").
//---------------------------------------------------------------------------
// Creates a Product object that references Species "s2" in the model.
spr = reaction->createProduct();
spr->setSpecies("s2");
//---------------------------------------------------------------------------
// Creates a KineticLaw object inside the Reaction object ("v2").
//---------------------------------------------------------------------------
kl = reaction->createKineticLaw();
// Sets a notes (by XMLNode) to the KineticLaw object.
//
// The following code is an alternative to using setNotes(const string&).
// The equivalent code would be like this:
//
// notesString = "<xhtml:p>((vm * s2)/(km + s2))*cell</xhtml:p>";
// kl->setNotes(notesString);
// Creates an XMLNode of start element (<xhtml:p>) without attributes.
XMLNode notesXMLNode(XMLTriple("p", "", "xhtml"), XMLAttributes());
// Adds a text element to the start element.
notesXMLNode.addChild(XMLNode(" ((vm * s2)/(km + s2)) * cell "));
// Adds it to the kineticLaw object.
kl->setNotes(¬esXMLNode);
//---------------------------------------------------------------------------
// Sets a math (ASTNode object) to the KineticLaw object.
//---------------------------------------------------------------------------
// To create mathematical expressions, one would typically construct
// an ASTNode tree as the above example code which creates a math of another
// KineticLaw object. Here, to save some space and illustrate another approach
// of doing it, we will write out the formula in MathML form and then use a
// libSBML convenience function to create the ASTNode tree for us.
// (This is a bit dangerous; it's very easy to make mistakes when writing MathML
// by hand, so in a real program, we would not really want to do it this way.)
string mathXMLString = "<math xmlns=\"http://www.w3.org/1998/Math/MathML\">"
" <apply>"
" <times/>"
" <apply>"
" <divide/>"
" <apply>"
" <times/>"
" <ci> vm </ci>"
" <ci> s2 </ci>"
" </apply>"
" <apply>"
" <plus/>"
" <ci> km </ci>"
" <ci> s2 </ci>"
" </apply>"
" </apply>"
" <ci> cell </ci>"
" </apply>"
"</math>";
astMath = readMathMLFromString(mathXMLString.c_str());
kl->setMath(astMath);
delete astMath;
//---------------------------------------------------------------------------
// (Reaction3) Creates a Reaction object ("v3").
//---------------------------------------------------------------------------
reaction = model->createReaction();
reaction->setId("v3");
//---------------------------------------------------------------------------
// Creates Reactant objects inside the Reaction object ("v3").
//---------------------------------------------------------------------------
// (Reactant2) Creates a Reactant object that references Species "s2"
// in the model.
spr = reaction->createReactant();
spr->setSpecies("s2");
//---------------------------------------------------------------------------
// Creates a Product object inside the Reaction object ("v3").
//---------------------------------------------------------------------------
// Creates a Product object that references Species "x1" in the model.
spr = reaction->createProduct();
spr->setSpecies("x1");
//---------------------------------------------------------------------------
// Creates a KineticLaw object inside the Reaction object ("v3").
//---------------------------------------------------------------------------
kl = reaction->createKineticLaw();
// Sets a notes (by string) to the KineticLaw object.
notesString = "<xhtml:p> ((vm * x1)/(km + x1)) * cell </xhtml:p>";
kl->setNotes(notesString);
//---------------------------------------------------------------------------
// Sets a math (ASTNode object) to the KineticLaw object.
//---------------------------------------------------------------------------
mathXMLString = "<math xmlns=\"http://www.w3.org/1998/Math/MathML\">"
" <apply>"
" <times/>"
" <apply>"
" <divide/>"
" <apply>"
" <times/>"
" <ci> vm </ci>"
" <ci> x1 </ci>"
" </apply>"
" <apply>"
" <plus/>"
" <ci> km </ci>"
" <ci> x1 </ci>"
" </apply>"
" </apply>"
" <ci> cell </ci>"
" </apply>"
"</math>";
astMath = readMathMLFromString(mathXMLString.c_str());
kl->setMath(astMath);
delete astMath;
// Returns the created SBMLDocument object.
// The returned object must be explicitly deleted by the caller,
// otherwise memory leak will happen.
return sbmlDoc;
}
/**
*
* Creates an SBML model represented in "7.8 Example involving function definitions"
* in the SBML Level 2 Version 4 Specification.
*
*/
SBMLDocument* createExampleInvolvingFunctionDefinitions()
{
const unsigned int level = Level;
const unsigned int version = Version;
//---------------------------------------------------------------------------
//
// Creates an SBMLDocument object
//
//---------------------------------------------------------------------------
SBMLDocument* sbmlDoc = new SBMLDocument(level,version);
//---------------------------------------------------------------------------
//
// Creates a Model object inside the SBMLDocument object.
//
//---------------------------------------------------------------------------
Model* model = sbmlDoc->createModel();
model->setId("functionExample");
//---------------------------------------------------------------------------
//
// Creates a FunctionDefinition object inside the Model object.
//
//---------------------------------------------------------------------------
FunctionDefinition* fdef = model->createFunctionDefinition();
fdef->setId("f");
// Sets a math (ASTNode object) to the FunctionDefinition object.
string mathXMLString = "<math xmlns=\"http://www.w3.org/1998/Math/MathML\">"
" <lambda>"
" <bvar>"
" <ci> x </ci>"
" </bvar>"
" <apply>"
" <times/>"
" <ci> x </ci>"
" <cn> 2 </cn>"
" </apply>"
" </lambda>"
"</math>";
ASTNode* astMath = readMathMLFromString(mathXMLString.c_str());
fdef->setMath(astMath);
delete astMath;
//---------------------------------------------------------------------------
//
// Creates a Compartment object inside the Model object.
//
//---------------------------------------------------------------------------
Compartment* comp;
const string compName = "compartmentOne";
// Creates a Compartment object ("compartmentOne")
comp = model->createCompartment();
comp->setId(compName);
// Sets the "size" attribute of the Compartment object.
//
// The units of this Compartment object is the default SBML
// units of volume (litre), and thus we don't have to explicitly invoke
// setUnits("litre") function to set the default units.
//
comp->setSize(1);
//---------------------------------------------------------------------------
//
// Creates Species objects inside the Model object.
//
//---------------------------------------------------------------------------
Species* sp;
//---------------------------------------------------------------------------
// (Species1) Creates a Species object ("S1")
//---------------------------------------------------------------------------
sp = model->createSpecies();
sp->setId("S1");
// Sets the "compartment" attribute of the Species object to identify the
// compartnet in which the Species object located.
sp->setCompartment(compName);
// Sets the "initialConcentration" attribute of the Species object.
//
// The units of this Species object is determined by two attributes of this
// Species object ("substanceUnits" and "hasOnlySubstanceUnits") and the
// "spatialDimension" attribute of the Compartment object ("cytosol") in which
// this species object located.
// Since the default values are used for "substanceUnits" (substance (mole))
// and "hasOnlySubstanceUnits" (false) and the value of "spatialDimension" (3)
// is greater than 0, the units of this Species object is mole/litre .
//
sp->setInitialConcentration(1);
//---------------------------------------------------------------------------
// (Species2) Creates a Species object ("S2")
//---------------------------------------------------------------------------
sp = model->createSpecies();
sp->setId("S2");
sp->setCompartment(compName);
sp->setInitialConcentration(0);
//---------------------------------------------------------------------------
//
// Creates a global Parameter object inside the Model object.
//
//---------------------------------------------------------------------------
Parameter* para;
// Creates a Parameter ("t")
para = model->createParameter();
para->setId("t");
para->setValue(1);
para->setUnits("second");
//---------------------------------------------------------------------------
//
// Creates Reaction objects inside the Model object.
//
//---------------------------------------------------------------------------
// Temporary pointers.
Reaction* reaction;
SpeciesReference* spr;
KineticLaw* kl;
//---------------------------------------------------------------------------
// (Reaction1) Creates a Reaction object ("reaction_1").
//---------------------------------------------------------------------------
reaction = model->createReaction();
reaction->setId("reaction_1");
reaction->setReversible(false);
//---------------------------------------------------------------------------
// Creates Reactant objects inside the Reaction object ("reaction_1").
//---------------------------------------------------------------------------
// (Reactant1) Creates a Reactant object that references Species "S1"
// in the model.
spr = reaction->createReactant();
spr->setSpecies("S1");
//---------------------------------------------------------------------------
// Creates a Product object inside the Reaction object ("reaction_1").
//---------------------------------------------------------------------------
// Creates a Product object that references Species "S2" in the model.
spr = reaction->createProduct();
spr->setSpecies("S2");
//---------------------------------------------------------------------------
// Creates a KineticLaw object inside the Reaction object ("reaction_1").
//---------------------------------------------------------------------------
kl = reaction->createKineticLaw();
//---------------------------------------------------------------------------
// Sets a math (ASTNode object) to the KineticLaw object.
//---------------------------------------------------------------------------
mathXMLString = "<math xmlns=\"http://www.w3.org/1998/Math/MathML\">"
" <apply>"
" <divide/>"
" <apply>"
" <times/>"
" <apply>"
" <ci> f </ci>"
" <ci> S1 </ci>"
" </apply>"
" <ci> compartmentOne </ci>"
" </apply>"
" <ci> t </ci>"
" </apply>"
"</math>";
astMath = readMathMLFromString(mathXMLString.c_str());
kl->setMath(astMath);
delete astMath;
// Returns the created SBMLDocument object.
// The returned object must be explicitly deleted by the caller,
// otherwise memory leak will happen.
return sbmlDoc;
}
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;
}
}
}
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;
}
LIBSBML_CPP_NAMESPACE_USE
int main(int argc,char** argv){
//
// Creates an SBMLNamespaces object with the given SBML level, version
// package name, package version.
//
// (NOTE) By defualt, the name of package (i.e. "groups") will be used
// if the arugment for the prefix is missing or empty. Thus the argument
// for the prefix can be added as follows:
//
// SBMLNamespaces sbmlns(3,1,"groups",1,"GROUP");
//
SBMLNamespaces sbmlns(3,1,"groups",1);
//
// (NOTES) The above code creating an SBMLNamespaces object can be replaced
// with one of the following other styles.
//
// (1) Creates an SBMLNamespace object with a SBML core namespace and then
// adds a groups package namespace to the object.
//
// SBMLNamespaces sbmlns(3,1);
// sbmlns.addPkgNamespace("groups",1);
//
// OR
//
// SBMLNamespaces sbmlns(3,1);
// sbmlns.addNamespace(GroupsExtension::XmlnsL3V1V1,"groups");
//
// (2) Creates a GroupsPkgNamespaces object (SBMLNamespace derived class for
// groups package. The class is basically used for createing an SBase derived
// objects defined in the groups package) with the given SBML level, version,
// and package version
//
// GroupsPkgNamespaces sbmlns(3,1,1);
//
// create the document
SBMLDocument *document = new SBMLDocument(&sbmlns);
// create the Model
Model* model=document->createModel();
// create the Compartment
Compartment* compartment = model->createCompartment();
compartment->setId("cytosol");
compartment->setConstant(true);
compartment=model->createCompartment();
compartment->setId("mitochon");
compartment->setConstant(true);
// create the Species
Species* species = model->createSpecies();
species->setId("ATPc");
species->setCompartment("cytosol");
species->setInitialConcentration(1);
species->setHasOnlySubstanceUnits(false);
species->setBoundaryCondition(false);
species->setConstant(false);
species = model->createSpecies();
species->setId("ATPm");
species->setCompartment("mitochon");
species->setInitialConcentration(2);
species->setHasOnlySubstanceUnits(false);
species->setBoundaryCondition(false);
species->setConstant(false);
// create the Groups
//
// Get a GroupsModelPlugin object plugged in the model object.
//
// The type of the returned value of SBase::getPlugin() function is SBasePlugin*, and
// thus the value needs to be casted for the corresponding derived class.
//
GroupsModelPlugin* mplugin = static_cast<GroupsModelPlugin*>(model->getPlugin("groups"));
//
// Creates a Group object via GroupsModelPlugin object.
//
Group* group = mplugin->createGroup();
group->setId("ATP");
group->setKind(GROUP_KIND_CLASSIFICATION);
group->setSBOTerm("SBO:0000252");
Member* member = group->createMember();
member->setIdRef("ATPc");
member = group->createMember();
member->setIdRef("ATPm");
writeSBML(document,"groups_example1.xml");
delete document;
}