#include <transformation.hh>
Static Public Member Functions | |
| static Transformation * | genStateChangeTransform (unsigned int cIndex, int newValue) |
| static Transformation * | genBindingTransform1 (unsigned int bSiteIndex, unsigned int otherReactantIndex, unsigned int otherMappingIndex) |
| static Transformation * | genBindingSeparateComplexTransform1 (unsigned int bSiteIndex, unsigned int otherReactantIndex, unsigned int otherMappingIndex) |
| static Transformation * | genBindingTransform2 (unsigned int bSiteIndex) |
| static Transformation * | genUnbindingTransform (unsigned int bSiteIndex) |
| static Transformation * | genAddMoleculeTransform (SpeciesCreator *sc) |
| static Transformation * | genRemoveMoleculeTransform (int removalType) |
| static Transformation * | genEmptyTransform () |
| static Transformation * | genIncrementStateTransform (unsigned int cIndex) |
| static Transformation * | genDecrementStateTransform (unsigned int cIndex) |
| static Transformation * | genLocalFunctionReference (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 |
| 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.
| 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).
| 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.
| 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.
| NFcore::Transformation * TransformationFactory::genAddMoleculeTransform | ( | SpeciesCreator * | sc | ) | [static] |
Generates an Add Molecule transformation.
| 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)
| 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.
| NFcore::Transformation * TransformationFactory::genIncrementStateTransform | ( | unsigned int | cIndex | ) | [static] |
Generates an IncrementState transformation.
| NFcore::Transformation * TransformationFactory::genDecrementStateTransform | ( | unsigned int | cIndex | ) | [static] |
Generates an DecrementState transformation.
| Transformation * TransformationFactory::genLocalFunctionReference | ( | string | PointerName, | |
| int | type, | |||
| TemplateMolecule * | tm | |||
| ) | [static] |
Return a pointer to the transformation that is needed by a local function
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] |
1.5.4