NFcore::DORRxnClass Class Reference

#include <reaction.hh>

Inheritance diagram for NFcore::DORRxnClass:


List of all members.

Public Member Functions

 DORRxnClass (string name, double baseRate, string baseRateName, TransformationSet *transformationSet, CompositeFunction *function, vector< string > &lfArgumentPointerNameList, System *s)
virtual ~DORRxnClass ()
virtual void init ()
virtual void prepareForSimulation ()
virtual bool tryToAdd (Molecule *m, unsigned int reactantPos)
virtual void remove (Molecule *m, unsigned int reactantPos)
virtual double update_a ()
virtual int getDORreactantPosition () const
virtual void notifyRateFactorChange (Molecule *m, int reactantIndex, int rxnListIndex)
virtual unsigned int getReactantCount (unsigned int reactantIndex) const
virtual void printDetails () const
virtual void printFullDetails () const
void directAddForDebugging (Molecule *m)
void printTreeForDebugging ()

Static Public Member Functions

static void test1 (System *s)

Protected Member Functions

virtual double evaluateLocalFunctions (MappingSet *ms)
virtual void pickMappingSets (double randNumber) const

Protected Attributes

ReactantList ** reactantLists
int DORreactantIndex
int n_argMolecules
int * argIndexIntoMappingSet
Molecule ** argMappedMolecule
int * argScope

Constructor & Destructor Documentation

DORRxnClass::DORRxnClass ( string  name,
double  baseRate,
string  baseRateName,
TransformationSet transformationSet,
CompositeFunction function,
vector< string > &  lfArgumentPointerNameList,
System s 

Step 3: Wheh! now we can finally get on the business of creating the reactant lists and the reactant tree and setting the usual reactionClass parameters

DORRxnClass::~DORRxnClass (  )  [virtual]

Member Function Documentation

void DORRxnClass::init (  )  [virtual]

Implements NFcore::ReactionClass.

virtual void NFcore::DORRxnClass::prepareForSimulation (  )  [inline, virtual]

Implements NFcore::ReactionClass.

bool DORRxnClass::tryToAdd ( Molecule m,
unsigned int  reactantPos 
) [virtual]

Implements NFcore::ReactionClass.

void DORRxnClass::remove ( Molecule m,
unsigned int  reactantPos 
) [virtual]

Implements NFcore::ReactionClass.

double DORRxnClass::update_a (  )  [virtual]

Implements NFcore::ReactionClass.

virtual int NFcore::DORRxnClass::getDORreactantPosition (  )  const [inline, virtual]

Reimplemented from NFcore::ReactionClass.

void DORRxnClass::notifyRateFactorChange ( Molecule m,
int  reactantIndex,
int  rxnListIndex 
) [virtual]

Implements NFcore::ReactionClass.

unsigned int DORRxnClass::getReactantCount ( unsigned int  reactantIndex  )  const [virtual]

Implements NFcore::ReactionClass.

void DORRxnClass::printDetails (  )  const [virtual]

Reimplemented from NFcore::ReactionClass.

virtual void NFcore::DORRxnClass::printFullDetails (  )  const [inline, virtual]

Implements NFcore::ReactionClass.

void NFcore::DORRxnClass::directAddForDebugging ( Molecule m  ) 

void NFcore::DORRxnClass::printTreeForDebugging (  ) 

static void NFcore::DORRxnClass::test1 ( System s  )  [static]

double DORRxnClass::evaluateLocalFunctions ( MappingSet ms  )  [protected, virtual]

void DORRxnClass::pickMappingSets ( double  randNumber  )  const [protected, virtual]

Implements NFcore::ReactionClass.

Member Data Documentation

ReactantList** NFcore::DORRxnClass::reactantLists [protected]

ReactantTree* NFcore::DORRxnClass::reactantTree [protected]

MappingSet* NFcore::DORRxnClass::ms [protected]

CompositeFunction* NFcore::DORRxnClass::cf [protected]

int NFcore::DORRxnClass::DORreactantIndex [protected]

int NFcore::DORRxnClass::n_argMolecules [protected]

int* NFcore::DORRxnClass::argIndexIntoMappingSet [protected]

Molecule** NFcore::DORRxnClass::argMappedMolecule [protected]

int* NFcore::DORRxnClass::argScope [protected]

The documentation for this class was generated from the following files:
Generated on Thu Dec 9 11:02:48 2010 for NFsim by  doxygen 1.5.4