public function __construct($tpl, $off, $text = "")
{
parent::__construct($tpl, $off);
$this->text = $text;
}
/**
* The magic sleep method will be called by PHP's runtime environment right
* before an instance of this class gets serialized. It should return an
* array with those property names that should be serialized for this class.
*
* @return array(string)
* @since 0.10.0
*/
public function __sleep()
{
return array_merge(array('default'), parent::__sleep());
}
/**
*
* Creates an SBML model represented in "7.1 A Simple example application of SBML"
* in the SBML Level 2 Version 4 Specification.
*
*/
function createExampleEnzymaticReaction()
{
global $Level, $Version;
//---------------------------------------------------------------------------
//
// Creates an SBMLDocument object
//
//---------------------------------------------------------------------------
$sbmlDoc = new SBMLDocument($Level, $Version);
//---------------------------------------------------------------------------
//
// Creates a Model object inside the SBMLDocument object.
//
//---------------------------------------------------------------------------
$model = $sbmlDoc->createModel();
$model->setId("EnzymaticReaction");
//---------------------------------------------------------------------------
//
// Creates UnitDefinition objects inside the Model object.
//
//---------------------------------------------------------------------------
//---------------------------------------------------------------------------
// (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.
//
//---------------------------------------------------------------------------
$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(1.0E-14);
//---------------------------------------------------------------------------
//
// Creates Species objects inside the Model object.
//
//---------------------------------------------------------------------------
//---------------------------------------------------------------------------
// (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(9.999999999999999E-21);
//---------------------------------------------------------------------------
// (Species4) Creates a Species object ("E")
//---------------------------------------------------------------------------
$sp = $model->createSpecies();
$sp->setCompartment($compName);
$sp->setId("E");
$sp->setName("E");
$sp->setInitialAmount(5.0E-21);
//---------------------------------------------------------------------------
//
// Creates Reaction objects inside the Model object.
//
//---------------------------------------------------------------------------
//---------------------------------------------------------------------------
// (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
//
//------------------------------------------
$astCytosol = new ASTNode(AST_NAME);
$astCytosol->setName("cytosol");
$astKon = new ASTNode(AST_NAME);
$astKon->setName("kon");
$astKoff = new ASTNode(AST_NAME);
$astKoff->setName("koff");
$astE = new ASTNode(AST_NAME);
$astE->setName("E");
$astS = new ASTNode(AST_NAME);
$astS->setName("S");
$astES = new ASTNode(AST_NAME);
$astES->setName("ES");
//--------------------------------------------
//
// create node representing
// <apply>
// <times/>
// <ci> koff </ci>
// <ci> ES </ci>
// </apply>
//
//--------------------------------------------
$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.
//
//--------------------------------------------
$astTimes2 = new ASTNode(AST_TIMES);
$astTimes2->addChild($astE);
$astTimes2->addChild($astS);
$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>
//
//--------------------------------------------
$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>
//
//--------------------------------------------
$astMath = new ASTNode(AST_TIMES);
$astMath->addChild($astCytosol);
$astMath->addChild($astMinus);
//---------------------------------------------
//
// set the Math element
//
//------------------------------------------------
$kl->setMath($astMath);
//---------------------------------------------------------------------------
// Creates local Parameter objects inside the KineticLaw object.
//---------------------------------------------------------------------------
// Creates a Parameter ("kon")
$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.)
$mathXMLString = '<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> cytosol </ci>
<ci> kcat </ci>
<ci> ES </ci>
</apply>
</math>';
$astMath = libsbml::readMathMLFromString($mathXMLString);
$kl->setMath($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 $sbmlDoc;
}
public function __construct($tpl, $off, $name = "")
{
parent::__construct($tpl, $off);
$this->name = $name;
}
/**
* This method adds a new child node to this node instance.
*
* @param \PDepend\Source\AST\ASTNode $node
* @return void
*/
public function addChild(ASTNode $node)
{
$this->nodes[] = $node;
$node->setParent($this);
}
