Пример #1
0
/*
 * Subclasses should override this method to write out their contained
 * SBML objects as XML elements.  Be sure to call your parents
 * implementation of this method as well.
 */
void
SpeciesReference::writeElements (XMLOutputStream& stream) const
{
  if ( mNotes != NULL ) stream << *mNotes;
  SpeciesReference * sr = const_cast <SpeciesReference *> (this);
  sr->syncAnnotation();
  if ( mAnnotation != NULL ) stream << *mAnnotation;

  if (getLevel() == 2)
  {
    if (mStoichiometryMath || mDenominator != 1)
    {
      if (mStoichiometryMath != NULL) 
      {
        mStoichiometryMath->write(stream);
      }
      else
      {
        ASTNode node;
        node.setValue(static_cast<long>(mStoichiometry), mDenominator);

        stream.startElement("stoichiometryMath");
        writeMathML(&node, stream);
        stream.endElement("stoichiometryMath");
      }
    }
  }

  //
  // (EXTENSION)
  //
  SBase::writeExtensionElements(stream);

}
// #######################################################################
SpeciesReference* SBML_formatter::species2SpeciesReference(const Species* species, const Reaction* rxn, string addToSpeciesID){
  string value = species->getId(); 
  
  SpeciesReference* SR = new SpeciesReference(species->getLevel(), species->getVersion());
  
  value = species->getId();

  if (addToSpeciesID != ""){
    // sets the species name, as 
    value.append(addToSpeciesID);
  }
  
  SR->setSpecies(value);
  
  SR->setStoichiometry(1);
  SR->setId((value.append("_ref_")).append(dtostr(unique)));
  value.clear();
  value.append(species->getId());
  SR->setName((value.append("_in_rxn_")).append(rxn->getId()));
  // unique is a static variable which allows anything that needs a modelwide unique value to get
  // one;
  unique++;

  return SR;
}
END_TEST


START_TEST ( test_Reaction_parent_NULL )
{
    SBMLDocument *d = new SBMLDocument();
    Model *m = d->createModel();
    Reaction *c = m->createReaction();
    SpeciesReference *sr = c->createReactant();
    KineticLaw *kl = c->createKineticLaw();

    fail_unless(c->getAncestorOfType(SBML_MODEL) == m);
    fail_unless (c->getSBMLDocument() == d);
    fail_unless(sr->getAncestorOfType(SBML_REACTION) == c);
    fail_unless(kl->getAncestorOfType(SBML_REACTION) == c);

    Reaction *c1 = c->clone();
    delete d;

    fail_unless(c1->getAncestorOfType(SBML_MODEL) == NULL);
    fail_unless(c1->getParentSBMLObject() == NULL);
    fail_unless (c1->getSBMLDocument() == NULL);

    SpeciesReference *sr1 = c1->getReactant(0);
    fail_unless(sr1->getAncestorOfType(SBML_MODEL) == NULL);
    fail_unless(sr1->getAncestorOfType(SBML_REACTION) == c1);
    fail_unless (sr1->getSBMLDocument() == NULL);

    fail_unless(c1->getKineticLaw()->getAncestorOfType(SBML_MODEL) == NULL);
    fail_unless(c1->getKineticLaw()->getAncestorOfType(SBML_REACTION) == c1);
    fail_unless (c1->getKineticLaw()->getSBMLDocument() == NULL);


    delete c1;
}
Пример #4
0
int StoichiometryMath::removeFromParentAndDelete()
{
  SBase* parent = getParentSBMLObject();
  if (parent==NULL) return LIBSBML_OPERATION_FAILED;
  SpeciesReference* parentSR = static_cast<SpeciesReference*>(parent);
  if (parentSR == NULL) return LIBSBML_OPERATION_FAILED;
  return parentSR->unsetStoichiometryMath();
}
Пример #5
0
bool variesIn(string id, ListOfSpeciesReferences* srs,  const map<string, vector<double> >& results)
{
  if (variesIn(id, results)) return true;
  for (unsigned long sr=0; sr<srs->size(); sr++) {
    SpeciesReference* spref = static_cast<SpeciesReference*>(srs->get(sr));
    if (spref->getSpecies() == id) return true;
  }
  return false;
}
Пример #6
0
END_TEST

START_TEST ( test_SpeciesReference )
{
  SpeciesReference* sr = new SpeciesReference(2, 4);
  
  fail_unless (sr->hasRequiredElements());

  delete sr;
}
END_TEST


START_TEST ( test_SpeciesReference_Reactant_parent_create )
{
    Reaction *r = new Reaction(2, 4);
    SpeciesReference *sr = r->createReactant();

    ListOf *lo = r->getListOfReactants();

    fail_unless(lo == r->getReactant(0)->getParentSBMLObject());
    fail_unless(lo == sr->getParentSBMLObject());
    fail_unless(r == lo->getParentSBMLObject());
}
END_TEST

START_TEST ( test_SpeciesReference )
{
  SpeciesReference* sr = new SpeciesReference(2, 4);
  
  fail_unless (!(sr->hasRequiredAttributes()));

  sr->setSpecies("sr");

  fail_unless (sr->hasRequiredAttributes());

  delete sr;
}
END_TEST


START_TEST ( test_SpeciesReference_Product_parent_create_model )
{
    Model *m = new Model(2, 4);
    Reaction *r = m->createReaction();
    SpeciesReference *sr = m->createProduct();

    ListOf *lo = r->getListOfProducts();

    fail_unless(lo == r->getProduct(0)->getParentSBMLObject());
    fail_unless(lo == sr->getParentSBMLObject());
    fail_unless(r == lo->getParentSBMLObject());
}
Пример #10
0
void
createParameterAsRateRule(Model &m, SpeciesReference &sr, Rule &rr, 
                          unsigned int idCount)
{
  char newid[15];
  std::string id;

  // create parameter as variable of rate rule 
  // and use stoichiometryMath to point to this
  sprintf(newid, "parameterId_%u", idCount);
  id.assign(newid);

  Parameter *p = m.createParameter();
  p->setId(id);
  p->setConstant(false);

  rr.setVariable(id);
  
  StoichiometryMath *sm = sr.createStoichiometryMath();
  if (sm != NULL)
  {
    ASTNode *ast = SBML_parseFormula(id.c_str());
    sm->setMath(ast);
  }
}
END_TEST


START_TEST ( test_StoichiometryMath_parent_add )
{
    StoichiometryMath *m = new StoichiometryMath(2, 4);
    SpeciesReference *sr = new SpeciesReference(2, 4);

    sr->setStoichiometryMath(m);

    delete m;

    fail_unless(sr == sr->getStoichiometryMath()->getParentSBMLObject());

    delete sr;
}
Пример #12
0
/*
 * Copy constructor. Creates a copy of this SpeciesReference.
 */
SpeciesReference::SpeciesReference (const SpeciesReference& orig) :
   SimpleSpeciesReference( orig                )
 , mStoichiometryMath    ( NULL                   )
{
  if (&orig == NULL)
  {
    throw SBMLConstructorException("Null argument to copy constructor");
  }
  else
  {
    mStoichiometry = orig.mStoichiometry ;
    mDenominator = orig.mDenominator   ;
    mConstant = orig.mConstant;
    mIsSetConstant = orig.mIsSetConstant;
    mIsSetStoichiometry = orig.mIsSetStoichiometry;
    mExplicitlySetStoichiometry = orig.mExplicitlySetStoichiometry;
    mExplicitlySetDenominator = orig.mExplicitlySetDenominator;

    if (orig.mStoichiometryMath != NULL)
    {
      mStoichiometryMath = new StoichiometryMath(*orig.getStoichiometryMath());
    mStoichiometryMath->connectToParent(this);
    }
  }
}
Пример #13
0
END_TEST


START_TEST (test_WriteL3SBML_SpeciesReference)
{
  const char* expected = "<speciesReference species=\"s\""
    " stoichiometry=\"3\" constant=\"true\"/>";


  SpeciesReference *sr = D->createModel()->createReaction()->createReactant();
  sr->setSpecies("s");
  sr->setStoichiometry(3);
  sr->setConstant(true);

  char* sbml = sr->toSBML();
  fail_unless( equals(expected, sbml) );
  safe_free(sbml);
}
END_TEST


START_TEST ( test_SpeciesReference_Reactant_parent_add )
{
    SpeciesReference *sr = new SpeciesReference(2, 4);
    Reaction *r = new Reaction(2, 4);

    sr->setSpecies("s");
    r->addReactant(sr);

    delete sr;

    ListOf *lo = r->getListOfReactants();

    fail_unless(lo == r->getReactant(0)->getParentSBMLObject());
    fail_unless(r == lo->getParentSBMLObject());
}
Пример #15
0
std::string fixMissingStoich(const std::string sbml) {
    SBMLDocument *doc = NULL;

    try {
        doc =  readSBMLFromString (sbml.c_str());

        Model *m = doc->getModel();

        for (int j = 0; j<m->getNumReactions(); ++j) {
            Reaction* r = m->getReaction(j);
            if (!r)
                throw std::runtime_error("No reaction");

            // check stoich defined on reactants / products
            for (int k = 0; k<r->getNumReactants(); ++k) {
                SpeciesReference* s = r->getReactant(k);
                if (!isStoichDefined(s))
                    if (s->setStoichiometry(1.) != LIBSBML_OPERATION_SUCCESS)
                        throw std::runtime_error("Unable to set stoichiometry");
            }

            for (int k = 0; k<r->getNumProducts(); ++k) {
                SpeciesReference* s = r->getProduct(k);
                if (!isStoichDefined(s))
                    if (s->setStoichiometry(1.) != LIBSBML_OPERATION_SUCCESS)
                        throw std::runtime_error("Unable to set stoichiometry");
            }

            // modifiers have no stoichiometry
        }

    } catch(...) {
        delete doc;
        throw;
    }

    SBMLWriter writer;

    char* sbml_cstr = writer.writeSBMLToString(doc);
    delete doc;
    std::string result(sbml_cstr);
    free(sbml_cstr);
    return result;
}
Пример #16
0
void
useStoichMath(Model & m, SpeciesReference &sr, bool isRule)
{
  // use stoichiometryMath instead
  StoichiometryMath *sm = sr.createStoichiometryMath();
  if (sm != NULL)
  {
    if (isRule == true)
    {
      sm->setMath(m.getRule(sr.getId())->getMath());
      m.removeRule(sr.getId());
    }
    else
    {
      sm->setMath(m.getInitialAssignment(sr.getId())->getMath());
      m.removeInitialAssignment(sr.getId());
    }
  }
}
Пример #17
0
/*
 * Copy constructor. Creates a copy of this SpeciesReference.
 */
SpeciesReference::SpeciesReference (const SpeciesReference& orig)
 : SimpleSpeciesReference( orig                )
 , mStoichiometry        ( orig.mStoichiometry )
 , mDenominator          ( orig.mDenominator   )
 , mStoichiometryMath    ( NULL                )
 , mConstant             ( orig.mConstant)
 , mIsSetConstant        ( orig.mIsSetConstant)
 , mIsSetStoichiometry   ( orig.mIsSetStoichiometry)
 , mExplicitlySetStoichiometry ( orig.mExplicitlySetStoichiometry)
 , mExplicitlySetDenominator   ( orig.mExplicitlySetDenominator)
{
  if (orig.mStoichiometryMath != NULL)
  {
    mStoichiometryMath = new StoichiometryMath(*orig.getStoichiometryMath());
    mStoichiometryMath->connectToParent(this);
  }
}
Пример #18
0
void
createNoValueStoichMath(Model & m, SpeciesReference & sr, unsigned int idCount)
{
  char newid[15];
  std::string id;

  // no stoichiometry and no id to set the stoichiometry
  // replace with stoichiometryMath using a parameter with no value

  sprintf(newid, "parameterId_%u", idCount);
  id.assign(newid);

  Parameter *p = m.createParameter();
  p->setId(id);
  p->setConstant(false);

  StoichiometryMath *sm = sr.createStoichiometryMath();
  if (sm != NULL)
  {
    ASTNode *ast = SBML_parseFormula(id.c_str());
    sm->setMath(ast);
  }
}
Пример #19
0
void dealWithAssigningL1Stoichiometry(Model & m, bool l2)
{
  //char newid[15];
  std::string id;

  for (unsigned int i = 0; i < m.getNumReactions(); i++)
  {
    Reaction *r = m.getReaction(i);
    unsigned int j;

    for (j = 0; j < r->getNumReactants(); j++)
    {
      SpeciesReference *sr = r->getReactant(j);
      // we do not get here unless the stoichiometryMath is an integer
      // or a rational 
      if (l2 == true && sr->isSetStoichiometryMath() == true)
      {
        const ASTNode* ast = sr->getStoichiometryMath()->getMath();
        if (ast->isInteger())
        {
          int num = ast->getInteger();
          sr->setStoichiometry(num);
          sr->setDenominator(1);
        }
        else
        {
          int num = ast->getNumerator();
          int denom = ast->getDenominator();
          sr->setStoichiometry(num);
          sr->setDenominator(denom);
        }
        sr->unsetStoichiometryMath();
      }
      else
      {
        sr->setStoichiometry(sr->getStoichiometry());
        sr->setDenominator(1);
      }
    }
    for (j = 0; j < r->getNumProducts(); j++)
    {
      SpeciesReference *sr = r->getProduct(j);
      // we do not get here unless the stoichiometryMath is an integer
      // or a rational 
      if (l2 == true && sr->isSetStoichiometryMath() == true)
      {
        const ASTNode* ast = sr->getStoichiometryMath()->getMath();
        if (ast->isInteger())
        {
          int num = ast->getInteger();
          sr->setStoichiometry(num);
          sr->setDenominator(1);
        }
        else
        {
          int num = ast->getNumerator();
          int denom = ast->getDenominator();
          sr->setStoichiometry(num);
          sr->setDenominator(denom);
        }
        sr->unsetStoichiometryMath();
      }
      else
      {
        sr->setStoichiometry(sr->getStoichiometry());
        sr->setDenominator(1);
      }
    }
  }
}
Пример #20
0
void dealWithL1Stoichiometry(Model & m, bool l2)
{
  unsigned int idCount = 0;
  char newid[15];
  std::string id;

  for (unsigned int i = 0; i < m.getNumReactions(); i++)
  {
    Reaction *r = m.getReaction(i);
    unsigned int j;

    for (j = 0; j < r->getNumReactants(); j++)
    {
      SpeciesReference *sr = r->getReactant(j);
      if (sr->getDenominator() != 1)
      {
        long stoich = static_cast<long>(sr->getStoichiometry());
        int denom = sr->getDenominator();
        ASTNode *node = new ASTNode();
        node->setValue(stoich, denom);   
        if (l2 == true)
        {
          StoichiometryMath * sm = sr->createStoichiometryMath();
          sm->setMath(node);
        }
        else
        {
          sprintf(newid, "speciesRefId_%u", idCount);
          id.assign(newid);
          idCount++;
          sr->setId(id);
          InitialAssignment * ar = m.createInitialAssignment();
          ar->setSymbol(id);
          ar->setMath(node);
          sr->unsetStoichiometry();
        }
      }
    }
    for (j = 0; j < r->getNumProducts(); j++)
    {
      SpeciesReference *sr = r->getProduct(j);
      if (sr->getDenominator() != 1)
      {
        long stoich = static_cast<long>(sr->getStoichiometry());
        int denom = sr->getDenominator();
        ASTNode *node = new ASTNode();
        node->setValue(stoich, denom);   
        if (l2 == true)
        {
          StoichiometryMath * sm = sr->createStoichiometryMath();
          sm->setMath(node);
        }
        else
        {
          sprintf(newid, "speciesRefId_%u", idCount);
          id.assign(newid);
          idCount++;
          sr->setId(id);
          InitialAssignment * ar = m.createInitialAssignment();
          ar->setSymbol(id);
          ar->setMath(node);
          sr->unsetStoichiometry();
        }
      }
    }
  }
}
Пример #21
0
void
Model::dealWithStoichiometry()
{
  unsigned int idCount = 0;
  for (unsigned int i = 0; i < getNumReactions(); i++)
  {
    Reaction *r = getReaction(i);
    unsigned int j;

    for (j = 0; j < r->getNumReactants(); j++)
    {
      SpeciesReference *sr = r->getReactant(j);
      if (sr->isSetStoichiometry() == false)
      {
        if (sr->isSetId() == false)
        {
          createNoValueStoichMath(*this, *sr, idCount);
          idCount++;
        }
        else
        {
          // id is set it could be used by initialAssignment
          // used by rule
          // not used
          if (getInitialAssignment(sr->getId()) != NULL)
          {
            useStoichMath(*this, *sr, false);
          }
          else if (getRule(sr->getId()) != NULL)
          {
            //assignmentRule
            if (getRule(sr->getId())->getTypeCode() == SBML_ASSIGNMENT_RULE)
            {  
              useStoichMath(*this, *sr, true);
            }
            else if (getRule(sr->getId())->getTypeCode() == SBML_RATE_RULE)
            {
              createParameterAsRateRule(*this, *sr, *(getRule(sr->getId())), idCount);
              idCount++;
            }
          }
          else
          {
            createNoValueStoichMath(*this, *sr, idCount);
            idCount++;
          }
        }
      }
      else
      {
        // stoichiometry is set
        if (sr->isSetId())
        {
          // id is set it could be used by initialAssignment
          // used by rule
          // not used
          if (getInitialAssignment(sr->getId()) != NULL)
          {
            useStoichMath(*this, *sr, false);
          }
          else if (getRule(sr->getId()) != NULL)
          {
            //assignmentRule
            if (getRule(sr->getId())->getTypeCode() == SBML_ASSIGNMENT_RULE)
            {            
              useStoichMath(*this, *sr, true);
            }
            else if (getRule(sr->getId())->getTypeCode() == SBML_RATE_RULE)
            {
              createParameterAsRateRule(*this, *sr, *(getRule(sr->getId())), idCount);
              idCount++;
            }
          }
        }
        // no id set - do not need to do anything
      }
    }
    for (j = 0; j < r->getNumProducts(); j++)
    {
      SpeciesReference *sr = r->getProduct(j);
      if (sr->isSetStoichiometry() == false)
      {
        if (sr->isSetId() == false)
        {
          createNoValueStoichMath(*this, *sr, idCount);
          idCount++;
        }
        else
        {
          // id is set it could be used by initialAssignment
          // used by rule
          // not used
          if (getInitialAssignment(sr->getId()) != NULL)
          {
            useStoichMath(*this, *sr, false);
          }
          else if (getRule(sr->getId()) != NULL)
          {
            //assignmentRule
            if (getRule(sr->getId())->getTypeCode() == SBML_ASSIGNMENT_RULE)
            {  
              useStoichMath(*this, *sr, true);
            }
            else if (getRule(sr->getId())->getTypeCode() == SBML_RATE_RULE)
            {
              createParameterAsRateRule(*this, *sr, *(getRule(sr->getId())), idCount);
              idCount++;
            }
          }
          else
          {
            createNoValueStoichMath(*this, *sr, idCount);
            idCount++;
          }
        }
      }
      else
      {
        // stoichiometry is set
        if (sr->isSetId())
        {
          // id is set it could be used by initialAssignment
          // used by rule
          // not used
          if (getInitialAssignment(sr->getId()) != NULL)
          {
            useStoichMath(*this, *sr, false);
          }
          else if (getRule(sr->getId()) != NULL)
          {
            //assignmentRule
            if (getRule(sr->getId())->getTypeCode() == SBML_ASSIGNMENT_RULE)
            {            
              useStoichMath(*this, *sr, true);
            }
            else if (getRule(sr->getId())->getTypeCode() == SBML_RATE_RULE)
            {
              createParameterAsRateRule(*this, *sr, *(getRule(sr->getId())), idCount);
              idCount++;
            }
          }
        }
        // no id set - do not need to do anything
      }
    }
  }
}
/**
 *
 * 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;

}
Пример #23
0
int
main (int argc, char* argv[])
{
  if (argc != 2)
  {
    cout << endl << "Usage: printNotes filename" << endl << endl;
    return 1;
  }

  unsigned int i,j;
  const char* filename   = argv[1];
  SBMLDocument* document;
  SBMLReader reader;

  document = reader.readSBML(filename);

  unsigned int errors = document->getNumErrors();

  cout << endl;
  cout << "filename: " << filename << endl;
  cout << endl;

  if(errors > 0)
  {
    document->printErrors(cerr);
    delete document;

    return errors;
  }

  /* Model */

  Model* m = document->getModel();
  printNotes(m);

  for(i=0; i < m->getNumReactions(); i++)
  {
    Reaction* re = m->getReaction(i);
    printNotes(re);

    /* SpeciesReference (Reacatant) */

    for(j=0; j < re->getNumReactants(); j++)
    {
      SpeciesReference* rt = re->getReactant(j);
      if (rt->isSetNotes()) cout << "   ";
      printNotes(rt, (rt->isSetSpecies() ? rt->getSpecies() : std::string("")) );
    }

    /* SpeciesReference (Product) */

    for(j=0; j < re->getNumProducts(); j++)
    {
      SpeciesReference* rt = re->getProduct(j);
      if (rt->isSetNotes()) cout << "   ";
      printNotes(rt, (rt->isSetSpecies() ? rt->getSpecies() : std::string("")) );
    }

    /* ModifierSpeciesReference (Modifier) */

    for(j=0; j < re->getNumModifiers(); j++)
    {
      ModifierSpeciesReference* md = re->getModifier(j);
      if (md->isSetNotes()) cout << "   ";
      printNotes(md, (md->isSetSpecies() ? md->getSpecies() : std::string("")) );
    }

    /* Kineticlaw */

    if(re->isSetKineticLaw())
    {
      KineticLaw* kl = re->getKineticLaw();
      if (kl->isSetNotes()) cout << "   ";
      printNotes(kl);

      /* Parameter */

      for(j=0; j < kl->getNumParameters(); j++)
      {
        Parameter* pa = kl->getParameter(j);
        if (pa->isSetNotes()) cout << "      ";
        printNotes(pa);
      }
    }

  }

  /* Species */

  for(i=0; i < m->getNumSpecies(); i++)
  {
    Species* sp = m->getSpecies(i);
    printNotes(sp);
  }

  /* Compartment */

  for(i=0; i < m->getNumCompartments(); i++)
  {
    Compartment* sp = m->getCompartment(i);
    printNotes(sp);
  }

  /* FunctionDefinition */

  for(i=0; i < m->getNumFunctionDefinitions(); i++)
  {
    FunctionDefinition* sp = m->getFunctionDefinition(i);
    printNotes(sp);
  }

  /* UnitDefinition */

  for(i=0; i < m->getNumUnitDefinitions(); i++)
  {
    UnitDefinition* sp = m->getUnitDefinition(i);
    printNotes(sp);
  }

  /* Parameter */

  for(i=0; i < m->getNumParameters(); i++)
  {
    Parameter* sp = m->getParameter(i);
    printNotes(sp);
  }

  /* Rule */

  for(i=0; i < m->getNumRules(); i++)
  {
    Rule* sp = m->getRule(i);
    printNotes(sp);
  }

  /* InitialAssignment */

  for(i=0; i < m->getNumInitialAssignments(); i++)
  {
    InitialAssignment* sp = m->getInitialAssignment(i);
    printNotes(sp);
  }

  /* Event */

  for(i=0; i < m->getNumEvents(); i++)
  {
    Event* sp = m->getEvent(i);
    printNotes(sp);

    /* Trigger */

    if(sp->isSetTrigger())
    {
      const Trigger* tg = sp->getTrigger();
      if (tg->isSetNotes()) cout << "   ";
      printNotes(const_cast<Trigger*>(tg));
    }

    /* Delay */

    if(sp->isSetDelay())
    {
      const Delay* dl = sp->getDelay();
      if (dl->isSetNotes()) cout << "   ";
      printNotes(const_cast<Delay*>(dl));
    }

    /* EventAssignment */

    for(j=0; j < sp->getNumEventAssignments(); j++)
    {
      EventAssignment* ea = sp->getEventAssignment(j);
      if (ea->isSetNotes()) cout << "   ";
      printNotes(ea);
    }
  }

  /* SpeciesType */

  for(i=0; i < m->getNumSpeciesTypes(); i++)
  {
    SpeciesType* sp = m->getSpeciesType(i);
    printNotes(sp);
  }

  /* Constraint */

  for(i=0; i < m->getNumConstraints(); i++)
  {
    Constraint* sp = m->getConstraint(i);
    printNotes(sp);
  }

  delete document;
  return errors;
}
Пример #24
0
void
Model::convertStoichiometryMath()
{
  unsigned int n, j;
  Reaction * r;
  SpeciesReference *sr;
  unsigned int idCount = 0;
  char newid[15];
  std::string id;

  for (n = 0; n < getNumReactions(); n++)
  {
    r = getReaction(n);
    for (j = 0; j < r->getNumReactants(); j++)
    {
      sr = r->getReactant(j);
      if (sr->isSetStoichiometryMath())
      {
        if (!sr->isSetId())
        {
          sprintf(newid, "generatedId_%u", idCount);
          id.assign(newid);
          sr->setId(id);
          idCount++;
        }
        else
        {
          id = sr->getId();
        }
        sr->setConstant(false);

        AssignmentRule * ar = createAssignmentRule();
        ar->setVariable(id);
        if (sr->getStoichiometryMath()->isSetMath())
        {
          ar->setMath(sr->getStoichiometryMath()->getMath());
        }
      }
    }
    for (j = 0; j < r->getNumProducts(); j++)
    {
      sr = r->getProduct(j);
      if (sr->isSetStoichiometryMath())
      {
        if (!sr->isSetId())
        {
          sprintf(newid, "generatedId_%u", idCount);
          id.assign(newid);
          sr->setId(id);
          idCount++;
        }
        else
        {
          id = sr->getId();
        }

        sr->setConstant(false);
        AssignmentRule * ar = createAssignmentRule();
        ar->setVariable(id);
        if (sr->getStoichiometryMath()->isSetMath())
        {
          ar->setMath(sr->getStoichiometryMath()->getMath());
        }
      }
    }
  }
}
Пример #25
0
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;
}
Пример #26
0
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);
      }
    }
  }

}
/**
 *
 * 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;
}
Пример #28
0
/**
 * Save the gene network to an SBML file. If the argument is null, use the network id.
 * @param filename URL to the file describing the network to load
 * @throws IOException
 */
void GeneNetwork::writeSBML(const char *filename) {
			
	ofstream data_file(filename); 
    if (!data_file.is_open()) {
        std::cerr << "Failed to open file " << filename << std::endl;
        exit(1);
    }
    data_file.close();
			
	::logging::log::emit<Info>() << "Writing file " << filename <<
		::logging::log::endl;
	
	SBMLDocument *sbmlDoc = new SBMLDocument(3, 1);

	Model *model = sbmlDoc->createModel();
	model->setId(id_);
	//model.getNotes ().add (comment_); // save network description
	
	int size = getSize();
	
	Compartment *comp = model->createCompartment();
  	comp->setId("cell");
	comp->setSize(1);

	std::vector<Species*> all_sp;
	Species *sp;

	for (int s=0; s < size; s++) { // save gene as species
//			species[s] = new Species(nodeIds_.get(s), nodeIds_.get(s));
		sp = model->createSpecies();
  		sp->setCompartment("cell");
  		sp->setId((nodes_.at(s)).getLabel());
  		all_sp.push_back(sp);
		//species[s].setInitialAmount(?); // maybe save the wild-type steady state?
		//model.addSpecies(species[s]);
	}
	
	// create the void species
	sp = model->createSpecies();
  	sp->setCompartment("cell");
  	sp->setId("_void_");
	sp->setInitialAmount(0);
	sp->setBoundaryCondition(true);
	sp->setConstant(true);
	all_sp.push_back(sp);
	//model.addSpecies(species[size]);


	// SET SYNTHESIS AND DEGRADATION REACTIONS FOR EVERY GENE
	for (int i=0; i<size; i++) {
		//::logging::log::emit<Info>() << ::logging::log::dec << i <<
		//::logging::log::endl;
		
		// the ID of gene i
//			String currentGeneID = nodeIds_.get(i);
		string currentGeneID = (nodes_.at(i)).getLabel();
		// The modifiers (regulators) of gene i
		std::vector<std::string> inputGenes = (nodes_.at(i)).getInputGenes();
		
		// SYNTHESIS REACTION
		std::string reactionId = currentGeneID + "_synthesis";
		Reaction *reaction = model->createReaction();
		KineticLaw *kineticLaw = reaction->createKineticLaw();
		SpeciesReference *spr;
		ModifierSpeciesReference *msr;
		reaction->setId(reactionId);
		reaction->setReversible (false);
		spr = reaction->createReactant();
  		spr->setSpecies(sp->getId());
  		spr = reaction->createProduct();
  		spr->setSpecies((all_sp.at(i))->getId());
		
		std::stringstream ss;
		ss << inputGenes.size();
		//::logging::log::emit<Debug>() << "node = " << nodes_.at(i).getLabel().c_str() << " #inputs = " << ss.str().c_str() << ::logging::log::endl;
		
		for (unsigned int r=0; r<inputGenes.size(); r++) {// set gene modifiers
//				reaction.addModifier(species[inputIndexes.get(r)]);
			//log.log(Level.INFO, "i = " + size);
			msr = reaction->createModifier();
			msr->setSpecies((all_sp.at(getIndexOfNode(inputGenes.at(r))))->getId());
		}

		//std::vector<RegulatoryModule> modules = (nodes_.at(i)).getRegulatoryModules();
		//log.log(Level.INFO, "size = " + modules.size());
		std::map<std::string, double> *params = new std::map<std::string, double>();
		(nodes_.at(i)).compileParameters(*params);
		
		//char buf[256];
		//sprintf(buf, "%f", nodes_.at(i).getDelta());
		//::logging::log::emit<Info>() << buf << ::logging::log::endl;
		//::logging::log::emit<Info>() << ::logging::log::dec << nodes_.at(i).getAlpha().size() <<
		//		::logging::log::endl;
		
		Parameter *para;
		// save gene parameters (note, the first param is the degradation rate)
		std::map<std::string, double>::iterator p = params->begin();
		//p++;
		for (; p!=params->end(); p++) {
			//if (p == params->begin()) {
			//	p++;
			//	continue;
			//}
			//::logging::log::emit<Info>() << p->first.c_str() <<
			//	::logging::log::endl;
			if (p->first != "delta") {
				para = kineticLaw->createParameter();
				para->setId(p->first);
				para->setValue(p->second);
			}
		}
		reaction->setKineticLaw(kineticLaw);
		model->addReaction(reaction);

		// DEGRADATION REACTION
		reaction = model->createReaction();
		kineticLaw = reaction->createKineticLaw();
		reactionId = currentGeneID + "_degradation";
		reaction->setId(reactionId);
		reaction->setReversible(false);
		spr = reaction->createReactant();
  		spr->setSpecies((all_sp.at(i))->getId());
  		spr = reaction->createProduct();
  		spr->setSpecies(sp->getId());

		para = kineticLaw->createParameter();
		std::map<std::string,double>::iterator it = params->find("delta");
		para->setId(it->first);
		para->setValue(it->second);
		
		reaction->setKineticLaw (kineticLaw);
		model->addReaction (reaction);
	}
	
	// PRINT FILE
	SBMLWriter sbmlWriter;
	sbmlWriter.writeSBML(sbmlDoc, filename);
	
	delete sbmlDoc;
}
/**
 *
 * 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(&notesXMLNode);

  //---------------------------------------------------------------------------
  // 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;

}
Пример #30
0
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;
}