/*
* Converts a Watt Unit into the corresponding UnitDefinition
* consisting only of SI units.
* If the given unit does not have the correct kind, a NULL pointer is
* returned.
* It is up to the receiver to free the memory of the returned
* UnitDefinition.
* @param const Unit& unit
* @return UnitDefinition* result
*/
LIBSBML_EXTERN
UnitDefinition* UnitConversionFactory::convertWattToSI(const Unit& unit)
{
UnitKind_t uKind = unit.getKind();
if (uKind != UNIT_KIND_WATT) return NULL;
UnitDefinition* pUdef = new UnitDefinition(UnitConversionFactory::SBML_LEVEL, UnitConversionFactory::SBML_VERSION);
Unit* pU = new Unit(unit);
pU->setOffset(0.0);
pU->setKind(UNIT_KIND_KILOGRAM);
pU->setExponent(unit.getExponent());
pUdef->addUnit(pU);
delete pU;
pU = new Unit(UnitConversionFactory::SBML_LEVEL, UnitConversionFactory::SBML_VERSION);
pU->setKind(UNIT_KIND_METER);
pU->setExponent(2*unit.getExponent());
pUdef->addUnit(pU);
delete pU;
pU = new Unit(UnitConversionFactory::SBML_LEVEL, UnitConversionFactory::SBML_VERSION);
pU->setKind(UNIT_KIND_SECOND);
pU->setExponent(-3*unit.getExponent());
pUdef->addUnit(pU);
delete pU;
return pUdef;
}
/*
* Converts a frequency Unit into the corresponding UnitDefinition
* consisting only of SI units. This could be e.g. a Hertz or Bequerel unit.
* If the given unit does not have the correct kind, a NULL pointer is
* returned.
* It is up to the receiver to free the memory of the returned
* UnitDefinition.
* @param const Unit& unit
* @return UnitDefinition* result
*/
LIBSBML_EXTERN
UnitDefinition* UnitConversionFactory::convertFrequencyToSI(const Unit& unit)
{
UnitKind_t uKind = unit.getKind();
if (uKind != UNIT_KIND_HERTZ && uKind != UNIT_KIND_BECQUEREL) return NULL;
UnitDefinition* pUdef = new UnitDefinition(UnitConversionFactory::SBML_LEVEL, UnitConversionFactory::SBML_VERSION);
Unit* pU = new Unit(unit);
pU->setKind(UNIT_KIND_SECOND);
pU->setOffset(0.0);
pU->setExponent(-1*pU->getExponent());
return pUdef;
}
END_TEST
START_TEST (test_WriteL3SBML_Unit)
{
const char* expected = "<unit kind=\"kilogram\" exponent=\"0.2\""
" scale=\"-3\" multiplier=\"3.2\"/>";
Unit* u = D->createModel()->createUnitDefinition()->createUnit();
u->setKind(UNIT_KIND_KILOGRAM);
double exp = 0.2;
u->setExponent(exp);
u->setScale(-3);
u->setMultiplier(3.2);
char* sbml = u->toSBML();
fail_unless( equals(expected, sbml) );
safe_free(sbml);
}
/*
* Converts a Coulomb Unit into the corresponding UnitDefinition
* consisting only of SI units.
* If the given unit does not have the correct kind, a NULL pointer is
* returned.
* It is up to the receiver to free the memory of the returned
* UnitDefinition.
* @param const Unit& unit
* @return UnitDefinition* result
*/
LIBSBML_EXTERN
UnitDefinition* UnitConversionFactory::convertCoulombToSI(const Unit& unit)
{
UnitKind_t uKind = unit.getKind();
if (uKind != UNIT_KIND_COULOMB) return NULL;
UnitDefinition* pUdef = new UnitDefinition(UnitConversionFactory::SBML_LEVEL, UnitConversionFactory::SBML_VERSION);
Unit* pU = new Unit(unit);
pU->setKind(UNIT_KIND_AMPERE);
pU->setOffset(0.0);
pUdef->addUnit(pU);
delete pU;
pU = new Unit(UnitConversionFactory::SBML_LEVEL, UnitConversionFactory::SBML_VERSION);
pU->setKind(UNIT_KIND_SECOND);
pU->setExponent(unit.getExponent());
pUdef->addUnit(pU);
delete pU;
return pUdef;
}
/**
*
* Creates an SBML model represented in "7.2 Example involving units"
* in the SBML Level 2 Version 4 Specification.
*
*/
SBMLDocument* createExampleInvolvingUnits()
{
const unsigned int level = Level;
const unsigned int version = Version;
//---------------------------------------------------------------------------
//
// Creates an SBMLDocument object
//
//---------------------------------------------------------------------------
SBMLDocument* sbmlDoc = new SBMLDocument(level,version);
// Adds the namespace for XHTML to the SBMLDocument object. We need this
// because we will add notes to the model. (By default, the SBML document
// created by SBMLDocument only declares the SBML XML namespace.)
sbmlDoc->getNamespaces()->add("http://www.w3.org/1999/xhtml", "xhtml");
//---------------------------------------------------------------------------
//
// Creates a Model object inside the SBMLDocument object.
//
//---------------------------------------------------------------------------
Model* model = sbmlDoc->createModel();
model->setId("unitsExample");
//---------------------------------------------------------------------------
//
// Creates UnitDefinition objects inside the Model object.
//
//---------------------------------------------------------------------------
// Temporary pointers (reused more than once below).
UnitDefinition* unitdef;
Unit *unit;
//---------------------------------------------------------------------------
// (UnitDefinition1) Creates an UnitDefinition object ("substance").
//
// This has the effect of redefining the default unit of subtance for the
// whole model.
//---------------------------------------------------------------------------
unitdef = model->createUnitDefinition();
unitdef->setId("substance");
// Creates an Unit inside the UnitDefinition object
unit = unitdef->createUnit();
unit->setKind(UNIT_KIND_MOLE);
unit->setScale(-3);
//--------------------------------------------------------------------------------
// (UnitDefinition2) Creates an UnitDefinition object ("mmls")
//--------------------------------------------------------------------------------
// Note that we can reuse the pointers 'unitdef' and 'unit' because the
// actual UnitDefinition object (along with the Unit objects within it)
// is already attached to the Model object.
unitdef = model->createUnitDefinition();
unitdef->setId("mmls");
// Creates an Unit inside the UnitDefinition object ("mmls")
unit = unitdef->createUnit();
unit->setKind(UNIT_KIND_MOLE);
unit->setScale(-3);
// Creates an Unit inside the UnitDefinition object ("mmls")
unit = unitdef->createUnit();
unit->setKind(UNIT_KIND_LITRE);
unit->setExponent(-1);
// Creates an Unit inside the UnitDefinition object ("mmls")
unit = unitdef->createUnit();
unit->setKind(UNIT_KIND_SECOND);
unit->setExponent(-1);
//--------------------------------------------------------------------------------
// (UnitDefinition3) Creates an UnitDefinition object ("mml")
//--------------------------------------------------------------------------------
unitdef = model->createUnitDefinition();
unitdef->setId("mml");
// Creates an Unit inside the UnitDefinition object ("mml")
unit = unitdef->createUnit();
unit->setKind(UNIT_KIND_MOLE);
unit->setScale(-3);
// Creates an Unit inside the UnitDefinition object ("mml")
unit = unitdef->createUnit();
unit->setKind(UNIT_KIND_LITRE);
unit->setExponent(-1);
//---------------------------------------------------------------------------
//
// Creates a Compartment object inside the Model object.
//
//---------------------------------------------------------------------------
Compartment* comp;
const string compName = "cell";
// Creates a Compartment object ("cell")
comp = model->createCompartment();
comp->setId(compName);
// Sets the "size" attribute of the Compartment object.
//
// The units of this Compartment object is the default SBML
// units of volume (litre), and thus we don't have to explicitly invoke
// setUnits("litre") function to set the default units.
//
comp->setSize(1);
//---------------------------------------------------------------------------
//
// Creates Species objects inside the Model object.
//
//---------------------------------------------------------------------------
// Temporary pointer (reused more than once below).
Species *sp;
//---------------------------------------------------------------------------
// (Species1) Creates a Species object ("x0")
//---------------------------------------------------------------------------
sp = model->createSpecies();
sp->setId("x0");
// Sets the "compartment" attribute of the Species object to identify the
// compartnet in which the Species object located.
sp->setCompartment(compName);
// Sets the "initialConcentration" attribute of the Species object.
//
// The units of this Species object is determined by two attributes of this
// Species object ("substanceUnits" and "hasOnlySubstanceUnits") and the
// "spatialDimensions" attribute of the Compartment object ("cytosol") in which
// this species object is located.
// Since the default values are used for "substanceUnits" (substance (mole))
// and "hasOnlySubstanceUnits" (false) and the value of "spatialDimension" (3)
// is greater than 0, the units of this Species object is moles/liters .
//
sp->setInitialConcentration(1);
//---------------------------------------------------------------------------
// (Species2) Creates a Species object ("x1")
//---------------------------------------------------------------------------
sp = model->createSpecies();
sp->setId("x1");
sp->setCompartment(compName);
sp->setInitialConcentration(1);
//---------------------------------------------------------------------------
// (Species3) Creates a Species object ("s1")
//---------------------------------------------------------------------------
sp = model->createSpecies();
sp->setCompartment(compName);
sp->setId("s1");
sp->setInitialConcentration(1);
//---------------------------------------------------------------------------
// (Species4) Creates a Species object ("s2")
//---------------------------------------------------------------------------
sp = model->createSpecies();
sp->setCompartment(compName);
sp->setId("s2");
sp->setInitialConcentration(1);
//---------------------------------------------------------------------------
//
// Creates global Parameter objects inside the Model object.
//
//---------------------------------------------------------------------------
Parameter* para;
// Creates a Parameter ("vm")
para = model->createParameter();
para->setId("vm");
para->setValue(2);
para->setUnits("mmls");
// Creates a Parameter ("km")
para = model->createParameter();
para->setId("km");
para->setValue(2);
para->setUnits("mml");
//---------------------------------------------------------------------------
//
// Creates Reaction objects inside the Model object.
//
//---------------------------------------------------------------------------
// Temporary pointers.
Reaction* reaction;
SpeciesReference* spr;
KineticLaw* kl;
//---------------------------------------------------------------------------
// (Reaction1) Creates a Reaction object ("v1").
//---------------------------------------------------------------------------
reaction = model->createReaction();
reaction->setId("v1");
//---------------------------------------------------------------------------
// Creates Reactant objects inside the Reaction object ("v1").
//---------------------------------------------------------------------------
// (Reactant1) Creates a Reactant object that references Species "x0"
// in the model.
spr = reaction->createReactant();
spr->setSpecies("x0");
//---------------------------------------------------------------------------
// Creates a Product object inside the Reaction object ("v1").
//---------------------------------------------------------------------------
// Creates a Product object that references Species "s1" in the model.
spr = reaction->createProduct();
spr->setSpecies("s1");
//---------------------------------------------------------------------------
// Creates a KineticLaw object inside the Reaction object ("v1").
//---------------------------------------------------------------------------
kl = reaction->createKineticLaw();
// Creates a <notes> element in the KineticLaw object.
// Here we illustrate how to do it using a literal string. This requires
// known the required syntax of XHTML and the requirements for SBML <notes>
// elements. Later below, we show how to create notes using objects instead
// of strings.
string notesString = "<xhtml:p> ((vm * s1)/(km + s1)) * cell </xhtml:p>";
kl->setNotes(notesString);
//---------------------------------------------------------------------------
// Creates an ASTNode object which represents the following KineticLaw object.
//
// <math xmlns=\"http://www.w3.org/1998/Math/MathML\">
// <apply>
// <times/>
// <apply>
// <divide/>
// <apply>
// <times/>
// <ci> vm </ci>
// <ci> s1 </ci>
// </apply>
// <apply>
// <plus/>
// <ci> km </ci>
// <ci> s1 </ci>
// </apply>
// </apply>
// <ci> cell </ci>
// </apply>
// </math>
//---------------------------------------------------------------------------
//
// In the following code, ASTNode objects, which construct an ASTNode tree
// of the above math, are created and added in the order of preorder traversal
// of the tree (i.e. the order corresponds to the nested structure of the above
// MathML elements), and thus the following code maybe a bit more efficient but
// maybe a bit difficult to read.
//
ASTNode* astMath = new ASTNode(AST_TIMES);
astMath->addChild(new ASTNode(AST_DIVIDE));
ASTNode* astDivide = astMath->getLeftChild();
astDivide->addChild(new ASTNode(AST_TIMES));
ASTNode* astTimes = astDivide->getLeftChild();
astTimes->addChild(new ASTNode(AST_NAME));
astTimes->getLeftChild()->setName("vm");
astTimes->addChild(new ASTNode(AST_NAME));
astTimes->getRightChild()->setName("s1");
astDivide->addChild(new ASTNode(AST_PLUS));
ASTNode* astPlus = astDivide->getRightChild();
astPlus->addChild(new ASTNode(AST_NAME));
astPlus->getLeftChild()->setName("km");
astPlus->addChild(new ASTNode(AST_NAME));
astPlus->getRightChild()->setName("s1");
astMath->addChild(new ASTNode(AST_NAME));
astMath->getRightChild()->setName("cell");
//---------------------------------------------
//
// set the Math element
//
//------------------------------------------------
kl->setMath(astMath);
delete astMath;
//---------------------------------------------------------------------------
// (Reaction2) Creates a Reaction object ("v2").
//---------------------------------------------------------------------------
reaction = model->createReaction();
reaction->setId("v2");
//---------------------------------------------------------------------------
// Creates Reactant objects inside the Reaction object ("v2").
//---------------------------------------------------------------------------
// (Reactant2) Creates a Reactant object that references Species "s1"
// in the model.
spr = reaction->createReactant();
spr->setSpecies("s1");
//---------------------------------------------------------------------------
// Creates a Product object inside the Reaction object ("v2").
//---------------------------------------------------------------------------
// Creates a Product object that references Species "s2" in the model.
spr = reaction->createProduct();
spr->setSpecies("s2");
//---------------------------------------------------------------------------
// Creates a KineticLaw object inside the Reaction object ("v2").
//---------------------------------------------------------------------------
kl = reaction->createKineticLaw();
// Sets a notes (by XMLNode) to the KineticLaw object.
//
// The following code is an alternative to using setNotes(const string&).
// The equivalent code would be like this:
//
// notesString = "<xhtml:p>((vm * s2)/(km + s2))*cell</xhtml:p>";
// kl->setNotes(notesString);
// Creates an XMLNode of start element (<xhtml:p>) without attributes.
XMLNode notesXMLNode(XMLTriple("p", "", "xhtml"), XMLAttributes());
// Adds a text element to the start element.
notesXMLNode.addChild(XMLNode(" ((vm * s2)/(km + s2)) * cell "));
// Adds it to the kineticLaw object.
kl->setNotes(¬esXMLNode);
//---------------------------------------------------------------------------
// Sets a math (ASTNode object) to the KineticLaw object.
//---------------------------------------------------------------------------
// To create mathematical expressions, one would typically construct
// an ASTNode tree as the above example code which creates a math of another
// KineticLaw object. Here, to save some space and illustrate another approach
// of doing it, we will write out the formula in MathML form and then use a
// libSBML convenience function to create the ASTNode tree for us.
// (This is a bit dangerous; it's very easy to make mistakes when writing MathML
// by hand, so in a real program, we would not really want to do it this way.)
string mathXMLString = "<math xmlns=\"http://www.w3.org/1998/Math/MathML\">"
" <apply>"
" <times/>"
" <apply>"
" <divide/>"
" <apply>"
" <times/>"
" <ci> vm </ci>"
" <ci> s2 </ci>"
" </apply>"
" <apply>"
" <plus/>"
" <ci> km </ci>"
" <ci> s2 </ci>"
" </apply>"
" </apply>"
" <ci> cell </ci>"
" </apply>"
"</math>";
astMath = readMathMLFromString(mathXMLString.c_str());
kl->setMath(astMath);
delete astMath;
//---------------------------------------------------------------------------
// (Reaction3) Creates a Reaction object ("v3").
//---------------------------------------------------------------------------
reaction = model->createReaction();
reaction->setId("v3");
//---------------------------------------------------------------------------
// Creates Reactant objects inside the Reaction object ("v3").
//---------------------------------------------------------------------------
// (Reactant2) Creates a Reactant object that references Species "s2"
// in the model.
spr = reaction->createReactant();
spr->setSpecies("s2");
//---------------------------------------------------------------------------
// Creates a Product object inside the Reaction object ("v3").
//---------------------------------------------------------------------------
// Creates a Product object that references Species "x1" in the model.
spr = reaction->createProduct();
spr->setSpecies("x1");
//---------------------------------------------------------------------------
// Creates a KineticLaw object inside the Reaction object ("v3").
//---------------------------------------------------------------------------
kl = reaction->createKineticLaw();
// Sets a notes (by string) to the KineticLaw object.
notesString = "<xhtml:p> ((vm * x1)/(km + x1)) * cell </xhtml:p>";
kl->setNotes(notesString);
//---------------------------------------------------------------------------
// Sets a math (ASTNode object) to the KineticLaw object.
//---------------------------------------------------------------------------
mathXMLString = "<math xmlns=\"http://www.w3.org/1998/Math/MathML\">"
" <apply>"
" <times/>"
" <apply>"
" <divide/>"
" <apply>"
" <times/>"
" <ci> vm </ci>"
" <ci> x1 </ci>"
" </apply>"
" <apply>"
" <plus/>"
" <ci> km </ci>"
" <ci> x1 </ci>"
" </apply>"
" </apply>"
" <ci> cell </ci>"
" </apply>"
"</math>";
astMath = readMathMLFromString(mathXMLString.c_str());
kl->setMath(astMath);
delete astMath;
// Returns the created SBMLDocument object.
// The returned object must be explicitly deleted by the caller,
// otherwise memory leak will happen.
return sbmlDoc;
}
/**
*
* Creates an SBML model represented in "7.1 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;
}
/* in L1 and L2 there were built in values for key units
* such as 'volume', 'length', 'area', 'substance' and 'time'
* In L3 these have been removed - thus if a model uses one of these
* it needs a unitDefinition to define it
*/
void
Model::addDefinitionsForDefaultUnits()
{
/* create a list of unit values */
IdList unitsUsed;
unsigned int n;
bool implicitVolume = false;
bool implicitArea = false;
bool implicitLength = false;
bool implicitSubstance = false;
for (n = 0; n < getNumCompartments(); n++)
{
if (getCompartment(n)->isSetUnits())
{
unitsUsed.append(getCompartment(n)->getUnits());
}
else
{
if (getCompartment(n)->getSpatialDimensions() == 3)
{
implicitVolume = true;
getCompartment(n)->setUnits("volume");
}
else if (getCompartment(n)->getSpatialDimensions() == 2)
{
implicitArea = true;
getCompartment(n)->setUnits("area");
}
else if (getCompartment(n)->getSpatialDimensions() == 1)
{
implicitLength = true;
getCompartment(n)->setUnits("length");
}
}
}
for (n = 0; n < getNumSpecies(); n++)
{
if (getSpecies(n)->isSetSubstanceUnits())
{
unitsUsed.append(getSpecies(n)->getSubstanceUnits());
}
else
{
implicitSubstance = true;
getSpecies(n)->setSubstanceUnits("substance");
}
if (getSpecies(n)->isSetSpatialSizeUnits())
unitsUsed.append(getSpecies(n)->getSpatialSizeUnits());
}
for (n = 0; n < getNumParameters(); n++)
{
if (getParameter(n)->isSetUnits())
unitsUsed.append(getParameter(n)->getUnits());
}
if (getUnitDefinition("volume") == NULL)
{
if (unitsUsed.contains("volume") || implicitVolume)
{
UnitDefinition * ud = createUnitDefinition();
ud->setId("volume");
Unit * u = ud->createUnit();
u->setKind(UnitKind_forName("litre"));
u->setScale(0);
u->setExponent(1.0);
u->setMultiplier(1.0);
setVolumeUnits("volume");
}
else
{
setVolumeUnits("litre");
}
}
else
{
setVolumeUnits("volume");
}
if (getUnitDefinition("substance") == NULL)
{
if (unitsUsed.contains("substance") || implicitSubstance)
{
UnitDefinition * ud = createUnitDefinition();
ud->setId("substance");
Unit * u = ud->createUnit();
u->setKind(UnitKind_forName("mole"));
u->setScale(0);
u->setExponent(1.0);
u->setMultiplier(1.0);
setSubstanceUnits("substance");
setExtentUnits("substance");
}
else
{
setSubstanceUnits("mole");
setExtentUnits("mole");
}
}
else
{
setSubstanceUnits("substance");
setExtentUnits("substance");
}
if (getUnitDefinition("area") == NULL)
{
UnitDefinition * ud = createUnitDefinition();
ud->setId("area");
Unit * u = ud->createUnit();
u->setKind(UnitKind_forName("metre"));
u->setScale(0);
u->setExponent(2.0);
u->setMultiplier(1.0);
setAreaUnits("area");
}
else
{
setAreaUnits("area");
}
if (getUnitDefinition("length") == NULL)
{
if (unitsUsed.contains("length") || implicitLength)
{
UnitDefinition * ud = createUnitDefinition();
ud->setId("length");
Unit * u = ud->createUnit();
u->setKind(UnitKind_forName("metre"));
u->setScale(0);
u->setExponent(1.0);
u->setMultiplier(1.0);
setLengthUnits("length");
}
else
{
setLengthUnits("metre");
}
}
else
{
setLengthUnits("length");
}
if (getUnitDefinition("time") == NULL)
{
setTimeUnits("second");
}
else
{
setTimeUnits("time");
}
}
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);
}
}
}
}
/*
* Converts a Unit into the corresponding UnitDefinition that consists
* only of SI units.
* Possible offsets are ignored.
* Freeing the memory for the returned UnitDefinition is up to the
* receiver.
* On failure a NULL pointer is returned.
* @param const Unit& unit
* @return UnitDefinition* result
*/
LIBSBML_EXTERN
UnitDefinition* UnitConversionFactory::convertToSI(const Unit& unit)
{
UnitDefinition* pUdef = NULL;
Unit* pU = NULL;
if (!unit.isSetKind()) return pUdef;
UnitKind_t uKind = unit.getKind();
switch (uKind)
{
case UNIT_KIND_AMPERE:
pUdef = convertAmpereToSI(unit);
break;
case UNIT_KIND_BECQUEREL:
case UNIT_KIND_HERTZ:
pUdef = convertFrequencyToSI(unit);
break;
case UNIT_KIND_CANDELA:
pUdef = convertCandelaToSI(unit);
break;
case UNIT_KIND_CELSIUS:
pUdef = convertCelsiusToSI(unit);
break;
case UNIT_KIND_COULOMB:
pUdef = convertCoulombToSI(unit);
break;
case UNIT_KIND_DIMENSIONLESS:
case UNIT_KIND_ITEM:
case UNIT_KIND_RADIAN:
case UNIT_KIND_STERADIAN:
pUdef = convertDimensionlessToSI(unit);
break;
case UNIT_KIND_FARAD:
pUdef = convertFaradToSI(unit);
break;
case UNIT_KIND_GRAM:
pU = new Unit(unit);
pU->setScale(pU->getScale() - 3);
pU->setKind(UNIT_KIND_KILOGRAM);
pUdef = convertKilogramToSI(*pU);
delete pU;
break;
case UNIT_KIND_GRAY:
case UNIT_KIND_SIEVERT:
pUdef = convertDoseToSI(unit);
break;
case UNIT_KIND_HENRY:
pUdef = convertHenryToSI(unit);
break;
case UNIT_KIND_JOULE:
pUdef = convertJouleToSI(unit);
break;
case UNIT_KIND_KATAL:
pUdef = convertKatalToSI(unit);
break;
case UNIT_KIND_KELVIN:
pUdef = convertKelvinToSI(unit);
break;
case UNIT_KIND_KILOGRAM:
pUdef = convertKilogramToSI(unit);
break;
case UNIT_KIND_LITER:
case UNIT_KIND_LITRE:
pU = new Unit(unit);
pU->setKind(UNIT_KIND_METER);
pU->setExponent(pU->getExponent()*3);
pU->setScale(pU->getScale() - 3);
pUdef = convertMeterToSI(*pU);
delete pU;
break;
case UNIT_KIND_LUMEN:
pUdef = convertLumenToSI(unit);
break;
case UNIT_KIND_LUX:
pUdef = convertLuxToSI(unit);
break;
case UNIT_KIND_METER:
case UNIT_KIND_METRE:
pUdef = convertMeterToSI(unit);
break;
case UNIT_KIND_MOLE:
#if LIBSBML_VERSION >= 40100
// this may be not totally correct, but this is the way we currently intend to
// handle it in COPASI
case UNIT_KIND_AVOGADRO:
#endif // LIBSBML_VERSION
pUdef = convertMoleToSI(unit);
break;
case UNIT_KIND_NEWTON:
pUdef = convertNewtonToSI(unit);
break;
case UNIT_KIND_OHM:
pUdef = convertOhmToSI(unit);
break;
case UNIT_KIND_PASCAL:
pUdef = convertPascalToSI(unit);
break;
case UNIT_KIND_SECOND:
pUdef = convertSecondToSI(unit);
break;
case UNIT_KIND_SIEMENS:
pUdef = convertSiemensToSI(unit);
break;
case UNIT_KIND_TESLA:
pUdef = convertTeslaToSI(unit);
break;
case UNIT_KIND_VOLT:
pUdef = convertVoltToSI(unit);
break;
case UNIT_KIND_WATT:
pUdef = convertWattToSI(unit);
break;
case UNIT_KIND_WEBER:
pUdef = convertWeberToSI(unit);
break;
case UNIT_KIND_INVALID:
delete pUdef;
pUdef = NULL;
break;
}
if (pUdef != NULL)
{
unsigned int num = 1;
std::stringstream ss;
ss << "UnitDefinition_" << num;
while (!UnitConversionFactory::isIdUnused(ss.str()))
{
++num;
ss.str("");
ss << "UnitDefinition_" << num;
}
std::string id = ss.str();
usedIds.push_back(id);
pUdef->setId(id);
UnitKind_t uKind = unit.getKind();
pUdef->setName(UnitKind_toString(uKind));
}
return pUdef;
}
/*
* Combines two UnitDefinitions by combining the equivalent units from
* both UnitDefinitions.
* A new UnitDefinition containing the combination is returned.
* If two eqivalent units have a different offset, the function returns a
* NULL pointer.
* It is up to the receiver to free the memory of the returned UnitDefinition.
* @param const UnitDefinition& uDef1
* @param const UnitDefinition& uDef2
* @return UnitDefinition* result
*/
LIBSBML_EXTERN
UnitDefinition* UnitConversionFactory::combine(const UnitDefinition& uDef1, const UnitDefinition& uDef2)
{
// take all Units from the first UnitDefinition make copies and put them into the new UnitDefinition
// go through all Units in the second UnitDefinition, if the same unit already exists in the new
// UnitDefinition combine them, else add a copy of the Unit to the new UnitDefinition
UnitDefinition* pResult = new UnitDefinition(UnitConversionFactory::SBML_LEVEL, UnitConversionFactory::SBML_VERSION);
unsigned int maxUnits = uDef1.getNumUnits();
unsigned int i;
for (i = 0; i < maxUnits; ++i)
{
const Unit* pSrcUnit = uDef1.getUnit(i);
unsigned int maxUnits2 = pResult->getNumUnits();
unsigned int j;
bool exists = false;
for (j = 0; j < maxUnits2; ++j)
{
Unit* pResultUnit = pResult->getUnit(j);
if (pResultUnit->getKind() == pSrcUnit->getKind())
{
exists = true;
// if the offsets are different, we can not combine the units
if (pResultUnit->getOffset() != pSrcUnit->getOffset())
{
delete pResult;
return NULL;
}
pResultUnit->setMultiplier(pResultUnit->getMultiplier()*pSrcUnit->getMultiplier()*pow(10.0, pResultUnit->getScale() - pSrcUnit->getScale()));
pResultUnit->setExponent(pResultUnit->getExponent() + pSrcUnit->getExponent());
// if the resulting scale is 0, the units have canceled each other out
// and we set the kind to dimensionless so that it can be eliminated
// later on
if (pResultUnit->getExponent() == 0)
{
pResultUnit->setKind(UNIT_KIND_DIMENSIONLESS);
}
}
}
if (!exists)
{
Unit* tmpUnit = new Unit(*pSrcUnit);
pResult->addUnit(tmpUnit);
delete tmpUnit;
}
}
maxUnits = uDef2.getNumUnits();
for (i = 0; i < maxUnits; ++i)
{
const Unit* pSrcUnit = uDef2.getUnit(i);
unsigned int maxUnits2 = pResult->getNumUnits();
unsigned int j;
bool exists = false;
for (j = 0; j < maxUnits2; ++j)
{
Unit* pResultUnit = pResult->getUnit(j);
if (pResultUnit->getKind() == pSrcUnit->getKind())
{
exists = true;
// if the offsets are different, we can not combine the units
if (pResultUnit->getOffset() != pSrcUnit->getOffset())
{
delete pResult;
return NULL;
}
pResultUnit->setMultiplier(pResultUnit->getMultiplier()*pSrcUnit->getMultiplier()*pow(10.0, pResultUnit->getScale() - pSrcUnit->getScale()));
pResultUnit->setExponent(pResultUnit->getExponent() + pSrcUnit->getExponent());
// if the resulting scale is 0, the units have canceled each other out
// and we set the kind to dimensionless so that it can be eliminated
// later on
if (pResultUnit->getExponent() == 0)
{
pResultUnit->setKind(UNIT_KIND_DIMENSIONLESS);
}
}
}
if (!exists)
{
Unit* tmpUnit = new Unit(*pSrcUnit);
pResult->addUnit(tmpUnit);
delete tmpUnit;
}
}
UnitDefinition* pTmp = UnitConversionFactory::eliminateDimensionless(pResult);
if (pTmp)
{
delete pResult;
pResult = pTmp;
}
return pResult;
}
