NFcore::TransformationFactory Class Reference

#include <transformation.hh>

List of all members.

Detailed Description

Static object that generates transformations with the given sites.
Michael Sneddon

Static Public Member Functions

static TransformationgenStateChangeTransform (unsigned int cIndex, int newValue)
static TransformationgenBindingTransform1 (unsigned int bSiteIndex, unsigned int otherReactantIndex, unsigned int otherMappingIndex)
static TransformationgenBindingSeparateComplexTransform1 (unsigned int bSiteIndex, unsigned int otherReactantIndex, unsigned int otherMappingIndex)
static TransformationgenBindingTransform2 (unsigned int bSiteIndex)
static TransformationgenUnbindingTransform (unsigned int bSiteIndex)
static TransformationgenAddMoleculeTransform (SpeciesCreator *sc)
static TransformationgenRemoveMoleculeTransform (int removalType)
static TransformationgenEmptyTransform ()
static TransformationgenIncrementStateTransform (unsigned int cIndex)
static TransformationgenDecrementStateTransform (unsigned int cIndex)
static TransformationgenLocalFunctionReference (string PointerName, int type, TemplateMolecule *tm)

Static Public Attributes

static const int COMPLETE_SPECIES_REMOVAL = 0
static const int DELETE_MOLECULES = 1
static const int DELETE_MOLECULES_NO_KEYWORD = 2
static const unsigned int STATE_CHANGE = 0
static const unsigned int BINDING = 1
static const unsigned int UNBINDING = 2
static const unsigned int REMOVE = 3
static const unsigned int ADD = 4
static const unsigned int EMPTY = 5
static const unsigned int INCREMENT_STATE = 6
static const unsigned int DECREMENT_STATE = 7
static const unsigned int LOCAL_FUNCTION_REFERENCE = 8

Member Function Documentation

NFcore::Transformation * TransformationFactory::genStateChangeTransform ( unsigned int  cIndex,
int  newValue 
) [static]

Generates a state change Transformation for transforming the given state at the given index into the new state value.

Michael Sneddon

NFcore::Transformation * TransformationFactory::genBindingTransform1 ( unsigned int  bSiteIndex,
unsigned int  otherReactantIndex,
unsigned int  otherMappingIndex 
) [static]

Generates a binding transformation for one of the two binding sites in the binding Transform. You will have to tell it where the other Transformation object lives (TransformationSet has this information).

Michael Sneddon

NFcore::Transformation * TransformationFactory::genBindingSeparateComplexTransform1 ( unsigned int  bSiteIndex,
unsigned int  otherReactantIndex,
unsigned int  otherMappingIndex 
) [static]

NFcore::Transformation * TransformationFactory::genBindingTransform2 ( unsigned int  bSiteIndex  )  [static]

Generates the second half of a binding transform. The other site already knows about this site, so all you need here is the index of the binding site that must be bonded.

Michael Sneddon

NFcore::Transformation * TransformationFactory::genUnbindingTransform ( unsigned int  bSiteIndex  )  [static]

Generates an unbinding transformation for a particular binding site. Only one of the binding sites must be specified as a Transformation - the other is automatically taken care of.

Michael Sneddon

NFcore::Transformation * TransformationFactory::genAddMoleculeTransform ( SpeciesCreator sc  )  [static]

Generates an Add Molecule transformation.

Michael Sneddon

NFcore::Transformation * TransformationFactory::genRemoveMoleculeTransform ( int  removalType  )  [static]

Generates a removal of a molecule from the system. The removalType specifies how the molecule should be removed (either everything that is connected, or just the molecules, or just the molecules conditional on how it is connected)

Michael Sneddon

NFcore::Transformation * TransformationFactory::genEmptyTransform (  )  [static]

Generates an empty transformation. This is used in cases where there is a reactant that is not transformed in a reaction, but that still needs to be counted and marked so that the rate of the reaction is correct.

Michael Sneddon

NFcore::Transformation * TransformationFactory::genIncrementStateTransform ( unsigned int  cIndex  )  [static]

Generates an IncrementState transformation.

Michael Sneddon

NFcore::Transformation * TransformationFactory::genDecrementStateTransform ( unsigned int  cIndex  )  [static]

Generates an DecrementState transformation.

Michael Sneddon

Transformation * TransformationFactory::genLocalFunctionReference ( string  PointerName,
int  type,
TemplateMolecule tm 
) [static]

Return a pointer to the transformation that is needed by a local function

Member Data Documentation

const int NFcore::TransformationFactory::COMPLETE_SPECIES_REMOVAL = 0 [static]

Indicates that a delete transform deletes the entire connected species

const int NFcore::TransformationFactory::DELETE_MOLECULES = 1 [static]

Indicates that a delete transform deletes only the pointed-to molecule

const int NFcore::TransformationFactory::DELETE_MOLECULES_NO_KEYWORD = 2 [static]

Delete only pointed-to molecules, only if deleting it creates only one remaining species

const unsigned int NFcore::TransformationFactory::STATE_CHANGE = 0 [static]

Indicates a state change transformation or mapping onto a state

const unsigned int NFcore::TransformationFactory::BINDING = 1 [static]

Indicates a binding transformation or mapping onto a binding site

const unsigned int NFcore::TransformationFactory::UNBINDING = 2 [static]

Indicates an unbinding transformation or mapping onto a binding site

const unsigned int NFcore::TransformationFactory::REMOVE = 3 [static]

Indicates a removal transform or mapping onto an entire Molecule

const unsigned int NFcore::TransformationFactory::ADD = 4 [static]

Indicates an addition transform

const unsigned int NFcore::TransformationFactory::EMPTY = 5 [static]

Indicates no transformation is needed (or is the second partner in a binding transform and so should be skipped when applying transforms

const unsigned int NFcore::TransformationFactory::INCREMENT_STATE = 6 [static]

Indicates an increment transformation

const unsigned int NFcore::TransformationFactory::DECREMENT_STATE = 7 [static]

Indicates a decrement transformation

const unsigned int NFcore::TransformationFactory::LOCAL_FUNCTION_REFERENCE = 8 [static]

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