| a | NFcore::ReactionClass | [protected] |
| apply(vector< Molecule * > &product_molecules) | NFcore::ReactionClass | |
| argIndexIntoMappingSet | NFcore::DORRxnClass | [protected] |
| argMappedMolecule | NFcore::DORRxnClass | [protected] |
| argScope | NFcore::DORRxnClass | [protected] |
| baseRate | NFcore::ReactionClass | [protected] |
| baseRateParameterName | NFcore::ReactionClass | [protected] |
| BASIC_RXN | NFcore::ReactionClass | [static] |
| cf | NFcore::DORRxnClass | [protected] |
| directAddForDebugging(Molecule *m) | NFcore::DORRxnClass | |
| DOR_RXN | NFcore::ReactionClass | [static] |
| DORreactantIndex | NFcore::DORRxnClass | [protected] |
| DORRxnClass(string name, double baseRate, string baseRateName, TransformationSet *transformationSet, CompositeFunction *function, vector< string > &lfArgumentPointerNameList, System *s) | NFcore::DORRxnClass | |
| evaluateLocalFunctions(MappingSet *ms) | NFcore::DORRxnClass | [protected, virtual] |
| fire(double random_A_number) | NFcore::ReactionClass | |
| fireCounter | NFcore::ReactionClass | [protected] |
| get_a() const | NFcore::ReactionClass | [inline] |
| getBaseRate() const | NFcore::ReactionClass | [inline] |
| getDORreactantPosition() const | NFcore::DORRxnClass | [inline, virtual] |
| getName() const | NFcore::ReactionClass | [inline] |
| getNumOfReactants() const | NFcore::ReactionClass | [inline] |
| getReactantCount(unsigned int reactantIndex) const | NFcore::DORRxnClass | [virtual] |
| getRxnId() const | NFcore::ReactionClass | [inline] |
| getRxnType() const | NFcore::ReactionClass | [inline] |
| init() | NFcore::DORRxnClass | [virtual] |
| isDimerStyle | NFcore::ReactionClass | [protected] |
| mappingSet | NFcore::ReactionClass | [protected] |
| molIter | NFcore::ReactionClass | [protected] |
| ms | NFcore::DORRxnClass | [protected] |
| n_argMolecules | NFcore::DORRxnClass | [protected] |
| n_reactants | NFcore::ReactionClass | [protected] |
| name | NFcore::ReactionClass | [protected] |
| NO_LIMIT | NFcore::ReactionClass | [static] |
| notifyRateFactorChange(Molecule *m, int reactantIndex, int rxnListIndex) | NFcore::DORRxnClass | [virtual] |
| OBS_DEPENDENT_RXN | NFcore::ReactionClass | [static] |
| onTheFlyObservables | NFcore::ReactionClass | [protected] |
| pickMappingSets(double randNumber) const | NFcore::DORRxnClass | [protected, virtual] |
| prepareForSimulation() | NFcore::DORRxnClass | [inline, virtual] |
| printDetails() const | NFcore::DORRxnClass | [virtual] |
| printFullDetails() const | NFcore::DORRxnClass | [inline, virtual] |
| printTreeForDebugging() | NFcore::DORRxnClass | |
| products | NFcore::ReactionClass | [protected] |
| reactantLists | NFcore::DORRxnClass | [protected] |
| reactantTemplates | NFcore::ReactionClass | [protected] |
| reactantTree | NFcore::DORRxnClass | [protected] |
| ReactionClass(string name, double rate, string baseRateParameterName, TransformationSet *transformationSet, System *s) | NFcore::ReactionClass | |
| reactionType | NFcore::ReactionClass | [protected] |
| remove(Molecule *m, unsigned int reactantPos) | NFcore::DORRxnClass | [virtual] |
| resetBaseRateFromSystemParamter() | NFcore::ReactionClass | |
| rxnId | NFcore::ReactionClass | [protected] |
| set_match(vector< MappingSet * > &match_set) | NFcore::ReactionClass | |
| setBaseRate(double newBaseRate, string newBaseRateName) | NFcore::ReactionClass | [inline] |
| setRxnId(int rxnId) | NFcore::ReactionClass | [inline] |
| setTotalRateFlag(bool totalRate) | NFcore::ReactionClass | [inline] |
| setTraversalLimit(int limit) | NFcore::ReactionClass | [inline] |
| system | NFcore::ReactionClass | [protected] |
| tag() | NFcore::ReactionClass | [inline] |
| tagged | NFcore::ReactionClass | [protected] |
| test1(System *s) | NFcore::DORRxnClass | [static] |
| totalRateFlag | NFcore::ReactionClass | [protected] |
| transformationSet | NFcore::ReactionClass | [protected] |
| traversalLimit | NFcore::ReactionClass | [protected] |
| tryToAdd(Molecule *m, unsigned int reactantPos) | NFcore::DORRxnClass | [virtual] |
| turnOff_OnTheFlyObs() | NFcore::ReactionClass | [inline] |
| update_a() | NFcore::DORRxnClass | [virtual] |
| updatedComplexes | NFcore::ReactionClass | [protected] |
| ~DORRxnClass() | NFcore::DORRxnClass | [virtual] |
| ~ReactionClass() | NFcore::ReactionClass | [virtual] |
