| addAddMolecule(SpeciesCreator *sc) | NFcore::TransformationSet | |
| addBindingSeparateComplexTransform(TemplateMolecule *t1, string bSiteName1, TemplateMolecule *t2, string bSiteName2) | NFcore::TransformationSet | |
| addBindingTransform(TemplateMolecule *t1, string bSiteName1, TemplateMolecule *t2, string bSiteName2) | NFcore::TransformationSet | |
| addDecrementStateTransform(TemplateMolecule *t, string cName) | NFcore::TransformationSet | |
| addDeleteMolecule(TemplateMolecule *t, int deletionType) | NFcore::TransformationSet | |
| addIncrementStateTransform(TemplateMolecule *t, string cName) | NFcore::TransformationSet | |
| addLocalFunctionReference(TemplateMolecule *t, string PointerName, int scope) | NFcore::TransformationSet | |
| addMoleculeTransformations | NFcore::TransformationSet | [protected] |
| addStateChangeTransform(TemplateMolecule *t, string cName, int finalStateValue) | NFcore::TransformationSet | |
| addStateChangeTransform(TemplateMolecule *t, string cName, string finalStateValue) | NFcore::TransformationSet | |
| addUnbindingTransform(TemplateMolecule *t, string bSiteName, TemplateMolecule *t2, string bSiteName2) | NFcore::TransformationSet | |
| deleteList | NFcore::TransformationSet | [protected, static] |
| finalize() | NFcore::TransformationSet | |
| finalized | NFcore::TransformationSet | [protected] |
| find(TemplateMolecule *t) | NFcore::TransformationSet | [protected] |
| generateBlankMappingSet(unsigned int reactantIndex, unsigned int mappingSetId) | NFcore::TransformationSet | |
| getListOfProducts(MappingSet **mappingSets, list< Molecule * > &products, int traversalLimit) | NFcore::TransformationSet | |
| getNreactants() const | NFcore::TransformationSet | [inline] |
| getNumOfReactants() const | NFcore::TransformationSet | [inline] |
| getNumOfTransformations(int reactantIndex) const | NFcore::TransformationSet | [inline] |
| getTemplateMolecule(unsigned int reactantIndex) const | NFcore::TransformationSet | [inline] |
| getTransformation(int reactantIndex, int index) const | NFcore::TransformationSet | [inline] |
| hasSymBinding | NFcore::TransformationSet | [protected] |
| hasSymBindingTransform() const | NFcore::TransformationSet | [inline] |
| hasSymUnbinding | NFcore::TransformationSet | [protected] |
| hasSymUnbindingTransform() const | NFcore::TransformationSet | [inline] |
| isFinalized() const | NFcore::TransformationSet | [inline] |
| it | NFcore::TransformationSet | [protected, static] |
| n_reactants | NFcore::TransformationSet | [protected] |
| reactants | NFcore::TransformationSet | [protected] |
| transform(MappingSet **mappingSets) | NFcore::TransformationSet | |
| transformations | NFcore::TransformationSet | [protected] |
| TransformationSet(vector< TemplateMolecule * > reactantTemplates) | NFcore::TransformationSet | |
| updateAfterDeleteList | NFcore::TransformationSet | [protected, static] |
| ~TransformationSet() | NFcore::TransformationSet | |
