Species Database::fillSpecie()
{
Species s;
this->query.first();
this->record = this->query.record();
s.setId(this->query.value(this->record.indexOf("id")));
s.setName(this->query.value(this->record.indexOf("name")));
return s;
}
QList<Species> Database::getAllSpecies()
{
QList<Species> species;
this->query.prepare("Select * FROM Species ORDER BY Species.name;");
if(!this->query.exec()){
this->showError(this->query.lastError());
return species;
}
while(this->query.next()){
Species s;
s.setId(this->query.value(0));
s.setName(this->query.value(1));
species.push_back(s);
}
return species;
}
/**
*
* Creates an SBML model represented in "7.1 A Simple example application of SBML"
* in the SBML Level 2 Version 4 Specification.
*
*/
SBMLDocument* createExampleEnzymaticReaction()
{
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("EnzymaticReaction");
//---------------------------------------------------------------------------
//
// Creates UnitDefinition objects inside the Model object.
//
//---------------------------------------------------------------------------
// Temporary pointers (reused more than once below).
UnitDefinition* unitdef;
Unit* unit;
//---------------------------------------------------------------------------
// (UnitDefinition1) Creates an UnitDefinition object ("per_second")
//---------------------------------------------------------------------------
unitdef = model->createUnitDefinition();
unitdef->setId("per_second");
// Creates an Unit inside the UnitDefinition object
unit = unitdef->createUnit();
unit->setKind(UNIT_KIND_SECOND);
unit->setExponent(-1);
//--------------------------------------------------------------------------------
// (UnitDefinition2) Creates an UnitDefinition object ("litre_per_mole_per_second")
//--------------------------------------------------------------------------------
// 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("litre_per_mole_per_second");
// Creates an Unit inside the UnitDefinition object ("litre_per_mole_per_second")
unit = unitdef->createUnit();
unit->setKind(UNIT_KIND_MOLE);
unit->setExponent(-1);
// Creates an Unit inside the UnitDefinition object ("litre_per_mole_per_second")
unit = unitdef->createUnit();
unit->setKind(UNIT_KIND_LITRE);
unit->setExponent(1);
// Creates an Unit inside the UnitDefinition object ("litre_per_mole_per_second")
unit = unitdef->createUnit();
unit->setKind(UNIT_KIND_SECOND);
unit->setExponent(-1);
//---------------------------------------------------------------------------
//
// Creates a Compartment object inside the Model object.
//
//---------------------------------------------------------------------------
Compartment* comp;
const string compName = "cytosol";
// Creates a Compartment object ("cytosol")
comp = model->createCompartment();
comp->setId(compName);
// Sets the "size" attribute of the Compartment object.
//
// We are not setting the units on the compartment size explicitly, so
// the units of this Compartment object will be the default SBML units of
// volume, which are liters.
//
comp->setSize(1e-14);
//---------------------------------------------------------------------------
//
// Creates Species objects inside the Model object.
//
//---------------------------------------------------------------------------
// Temporary pointer (reused more than once below).
Species *sp;
//---------------------------------------------------------------------------
// (Species1) Creates a Species object ("ES")
//---------------------------------------------------------------------------
// Create the Species objects inside the Model object.
sp = model->createSpecies();
sp->setId("ES");
sp->setName("ES");
// Sets the "compartment" attribute of the Species object to identify the
// compartment in which the Species object is located.
sp->setCompartment(compName);
// Sets the "initialAmount" attribute of the Species object.
//
// In SBML, the units of a Species object's initial quantity are
// determined by two attributes, "substanceUnits" and
// "hasOnlySubstanceUnits", and the "spatialDimensions" attribute
// of the Compartment object ("cytosol") in which the species
// object is located. Here, we are using the default values for
// "substanceUnits" (which is "mole") and "hasOnlySubstanceUnits"
// (which is "false"). The compartment in which the species is
// located uses volume units of liters, so the units of these
// species (when the species appear in numerical formulas in the
// model) will be moles/liters.
//
sp->setInitialAmount(0);
//---------------------------------------------------------------------------
// (Species2) Creates a Species object ("P")
//---------------------------------------------------------------------------
sp = model->createSpecies();
sp->setCompartment(compName);
sp->setId("P");
sp->setName("P");
sp->setInitialAmount(0);
//---------------------------------------------------------------------------
// (Species3) Creates a Species object ("S")
//---------------------------------------------------------------------------
sp = model->createSpecies();
sp->setCompartment(compName);
sp->setId("S");
sp->setName("S");
sp->setInitialAmount(1e-20);
//---------------------------------------------------------------------------
// (Species4) Creates a Species object ("E")
//---------------------------------------------------------------------------
sp = model->createSpecies();
sp->setCompartment(compName);
sp->setId("E");
sp->setName("E");
sp->setInitialAmount(5e-21);
//---------------------------------------------------------------------------
//
// Creates Reaction objects inside the Model object.
//
//---------------------------------------------------------------------------
// Temporary pointers.
Reaction* reaction;
SpeciesReference* spr;
KineticLaw* kl;
//---------------------------------------------------------------------------
// (Reaction1) Creates a Reaction object ("veq").
//---------------------------------------------------------------------------
reaction = model->createReaction();
reaction->setId("veq");
// (Reactant1) Creates a Reactant object that references Species "E"
// in the model. The object will be created within the reaction in the
// SBML <listOfReactants>.
spr = reaction->createReactant();
spr->setSpecies("E");
// (Reactant2) Creates a Reactant object that references Species "S"
// in the model.
spr = reaction->createReactant();
spr->setSpecies("S");
//---------------------------------------------------------------------------
// (Product1) Creates a Product object that references Species "ES" in
// the model.
//---------------------------------------------------------------------------
spr = reaction->createProduct();
spr->setSpecies("ES");
//---------------------------------------------------------------------------
// Creates a KineticLaw object inside the Reaction object ("veq").
//---------------------------------------------------------------------------
kl = reaction->createKineticLaw();
//---------------------------------------------------------------------------
// Creates an ASTNode object which represents the following math of the
// KineticLaw.
//
// <math xmlns="http://www.w3.org/1998/Math/MathML">
// <apply>
// <times/>
// <ci> cytosol </ci>
// <apply>
// <minus/>
// <apply>
// <times/>
// <ci> kon </ci>
// <ci> E </ci>
// <ci> S </ci>
// </apply>
// <apply>
// <times/>
// <ci> koff </ci>
// <ci> ES </ci>
// </apply>
// </apply>
// </apply>
// </math>
//
//---------------------------------------------------------------------------
//------------------------------------------
//
// create nodes representing the variables
//
//------------------------------------------
ASTNode* astCytosol = new ASTNode(AST_NAME);
astCytosol->setName("cytosol");
ASTNode* astKon = new ASTNode(AST_NAME);
astKon->setName("kon");
ASTNode* astKoff = new ASTNode(AST_NAME);
astKoff->setName("koff");
ASTNode* astE = new ASTNode(AST_NAME);
astE->setName("E");
ASTNode* astS = new ASTNode(AST_NAME);
astS->setName("S");
ASTNode* astES = new ASTNode(AST_NAME);
astES->setName("ES");
//--------------------------------------------
//
// create node representing
// <apply>
// <times/>
// <ci> koff </ci>
// <ci> ES </ci>
// </apply>
//
//--------------------------------------------
ASTNode *astTimes1 = new ASTNode(AST_TIMES);
astTimes1->addChild(astKoff);
astTimes1->addChild(astES);
//--------------------------------------------
//
// create node representing
// <apply>
// <times/>
// <ci> kon </ci>
// <ci> E </ci>
// <ci> S </ci>
// </apply>
//
//
// (NOTES)
//
// Since there is a restriction with an ASTNode of "<times/>" operation
// such that the ASTNode is a binary class and thus only two operands can
// be directly added, the following code in this comment block is invalid
// because the code directly adds three <ci> ASTNodes to <times/> ASTNode.
//
// ASTNode *astTimes = new ASTNode(AST_TIMES);
// astTimes->addChild(astKon);
// astTimes->addChild(astE);
// astTimes->addChild(astS);
//
// The following valid code after this comment block creates the ASTNode
// as a binary tree.
//
// Please see "Converting between ASTs and text strings" described
// at http://sbml.org/Software/libSBML/docs/cpp-api/class_a_s_t_node.html
// for the detailed information.
//
//--------------------------------------------
ASTNode *astTimes2 = new ASTNode(AST_TIMES);
astTimes2->addChild(astE);
astTimes2->addChild(astS);
ASTNode *astTimes = new ASTNode(AST_TIMES);
astTimes->addChild(astKon);
astTimes->addChild(astTimes2);
//--------------------------------------------
//
// create node representing
// <apply>
// <minus/>
// <apply>
// <times/>
// <ci> kon </ci>
// <ci> E </ci>
// <ci> S </ci>
// </apply>
// <apply>
// <times/>
// <ci> koff </ci>
// <ci> ES </ci>
// </apply>
// </apply>
//
//--------------------------------------------
ASTNode *astMinus = new ASTNode(AST_MINUS);
astMinus->addChild(astTimes);
astMinus->addChild(astTimes1);
//--------------------------------------------
//
// create node representing
// <apply>
// <times/>
// <ci> cytosol </ci>
// <apply>
// <minus/>
// <apply>
// <times/>
// <ci> kon </ci>
// <ci> E </ci>
// <ci> S </ci>
// </apply>
// <apply>
// <times/>
// <ci> koff </ci>
// <ci> ES </ci>
// </apply>
// </apply>
// </apply>
//
//--------------------------------------------
ASTNode* astMath = new ASTNode(AST_TIMES);
astMath->addChild(astCytosol);
astMath->addChild(astMinus);
//---------------------------------------------
//
// set the Math element
//
//------------------------------------------------
kl->setMath(astMath);
// KineticLaw::setMath(const ASTNode*) sets the math of the KineticLaw object
// to a copy of the given ASTNode, and thus basically the caller should delete
// the original ASTNode object if the caller has the ownership of the object to
// avoid memory leak.
delete astMath;
//---------------------------------------------------------------------------
// Creates local Parameter objects inside the KineticLaw object.
//---------------------------------------------------------------------------
// Creates a Parameter ("kon")
Parameter* para = kl->createParameter();
para->setId("kon");
para->setValue(1000000);
para->setUnits("litre_per_mole_per_second");
// Creates a Parameter ("koff")
para = kl->createParameter();
para->setId("koff");
para->setValue(0.2);
para->setUnits("per_second");
//---------------------------------------------------------------------------
// (Reaction2) Creates a Reaction object ("vcat") .
//---------------------------------------------------------------------------
reaction = model->createReaction();
reaction->setId("vcat");
reaction->setReversible(false);
//---------------------------------------------------------------------------
// Creates Reactant objects inside the Reaction object ("vcat").
//---------------------------------------------------------------------------
// (Reactant1) Creates a Reactant object that references Species "ES" in the
// model.
spr = reaction->createReactant();
spr->setSpecies("ES");
//---------------------------------------------------------------------------
// Creates a Product object inside the Reaction object ("vcat").
//---------------------------------------------------------------------------
// (Product1) Creates a Product object that references Species "E" in the model.
spr = reaction->createProduct();
spr->setSpecies("E");
// (Product2) Creates a Product object that references Species "P" in the model.
spr = reaction->createProduct();
spr->setSpecies("P");
//---------------------------------------------------------------------------
// Creates a KineticLaw object inside the Reaction object ("vcat").
//---------------------------------------------------------------------------
kl = reaction->createKineticLaw();
//---------------------------------------------------------------------------
// 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/>"
" <ci> cytosol </ci>"
" <ci> kcat </ci>"
" <ci> ES </ci>"
" </apply>"
"</math>";
astMath = readMathMLFromString(mathXMLString.c_str());
kl->setMath(astMath);
delete astMath;
//---------------------------------------------------------------------------
// Creates local Parameter objects inside the KineticLaw object.
//---------------------------------------------------------------------------
// Creates a Parameter ("kcat")
para = kl->createParameter();
para->setId("kcat");
para->setValue(0.1);
para->setUnits("per_second");
// Returns the created SBMLDocument object.
// The returned object must be explicitly deleted by the caller,
// otherwise a 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;
}
}
}
