C++ Species::setInitialConcentration方法代码示例

//.........这里部分代码省略.........

  //---------------------------------------------------------------------------
  //
  // 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. 
  //

//.........这里部分代码省略.........


  //---------------------------------------------------------------------------
  //
  // 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. 
  //
  //---------------------------------------------------------------------------

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
//.........这里部分代码省略.........

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");
//.........这里部分代码省略.........

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();
//.........这里部分代码省略.........