| a_tot | NFcore::System | [protected] |
| addCompositeFunction(CompositeFunction *cf) | NFcore::System | |
| addGlobalFunction(GlobalFunction *gf) | NFcore::System | |
| addLocalFunction(LocalFunction *lf) | NFcore::System | |
| addMoleculeType(MoleculeType *moleculeType) | NFcore::System | |
| addNecessaryUpdateReaction(ReactionClass *reaction) | NFcore::System | |
| addObservableForOutput(Observable *o) | NFcore::System | |
| addOutputter(Outputter *op) | NFcore::System | |
| addParameter(string name, double value) | NFcore::System | |
| addReaction(ReactionClass *reaction) | NFcore::System | |
| allComplexes | NFcore::System | [protected] |
| allMoleculeTypes | NFcore::System | [protected] |
| allOutputters | NFcore::System | [protected] |
| allReactions | NFcore::System | [protected] |
| compositeFunctions | NFcore::System | [protected] |
| csvFormat | NFcore::System | [protected] |
| current_time | NFcore::System | [protected] |
| ds | NFcore::System | [protected] |
| dumpOutputters() | NFcore::System | |
| equilibrate(double duration) | NFcore::System | |
| equilibrate(double duration, int statusReports) | NFcore::System | |
| evaluateAllLocalFunctions() | NFcore::System | |
| finalizeCompositeFunctions() | NFcore::System | |
| get_A_tot() const | NFcore::System | [inline, protected] |
| getAllComplexes() | NFcore::System | [inline] |
| getAverageGroupValue(string groupName, int valIndex) | NFcore::System | |
| getCompositeFunctionByName(string fName) | NFcore::System | |
| getCurrentTime() const | NFcore::System | [inline] |
| getGlobalFunctionByName(string fName) | NFcore::System | |
| getGlobalMoleculeLimit() const | NFcore::System | [inline] |
| getLocalFunction(string funcName) const | NFcore::System | [inline] |
| getLocalFunctionByName(string fName) | NFcore::System | |
| getMoleculeByUid(int uid) | NFcore::System | |
| getMoleculeType(int mtIndex) | NFcore::System | [inline] |
| getMoleculeTypeByName(string name) | NFcore::System | |
| getMolObsCount(int moleculeTypeIndex, int observableIndex) const | NFcore::System | |
| getName() const | NFcore::System | [inline] |
| getNextRxn() | NFcore::System | [protected] |
| getNumOfMolecules() | NFcore::System | |
| getNumOfMoleculeTypes() | NFcore::System | [inline] |
| getNumOfSpeciesObs() const | NFcore::System | |
| getObservableByName(string obsName) | NFcore::System | |
| getOutputFileStream() | NFcore::System | |
| getParameter(string name) | NFcore::System | |
| getReaction(int rIndex) | NFcore::System | [inline] |
| getRxnIndex(int rxnId, int rxnPos) const | NFcore::System | [inline] |
| getSpeciesObs(int index) const | NFcore::System | |
| globalEventCounter | NFcore::System | [protected] |
| globalFunctions | NFcore::System | [protected] |
| globalMoleculeLimit | NFcore::System | [protected] |
| isOutputtingBinary() | NFcore::System | [inline] |
| isUsingComplex() | NFcore::System | [inline] |
| localFunctions | NFcore::System | [protected] |
| name | NFcore::System | [protected] |
| necessaryUpdateRxns | NFcore::System | [protected] |
| Netgen class | NFcore::System | [friend] |
| nextReaction | NFcore::System | [protected] |
| NULL_EVENT_COUNTER | NFcore::System | [static] |
| obsToOutput | NFcore::System | [protected] |
| onTheFlyObservables | NFcore::System | [protected] |
| outputAllObservableCounts() | NFcore::System | |
| outputAllObservableCounts(double cSampleTime) | NFcore::System | |
| outputAllObservableCounts(double cSampleTime, int eventCounter) | NFcore::System | |
| outputAllObservableNames() | NFcore::System | |
| outputAllPropensities(double time, int rxnFired) | NFcore::System | [protected] |
| outputEventCounter | NFcore::System | [protected] |
| outputFileStream | NFcore::System | [protected] |
| outputGlobalFunctionValues | NFcore::System | [protected] |
| outputGroupDataHeader() | NFcore::System | [protected] |
| paramMap | NFcore::System | [protected] |
| prepareForSimulation() | NFcore::System | |
| printAllFunctions() | NFcore::System | |
| printAllMoleculeTypes() | NFcore::System | |
| printAllObservableCounts() | NFcore::System | |
| printAllObservableCounts(double cSampleTime) | NFcore::System | |
| printAllObservableCounts(double cSampleTime, int eventCounter) | NFcore::System | |
| printAllParameters() | NFcore::System | |
| printAllReactions() | NFcore::System | |
| printIndexAndNames() | NFcore::System | |
| propensityDumpStream | NFcore::System | [protected] |
| recompute_A_tot() | NFcore::System | [protected] |
| registerOutputFileLocation(string filename) | NFcore::System | |
| registerRxnIndex(int rxnId, int rxnPos, int rxnIndex) | NFcore::System | [inline] |
| rxnIndexMap | NFcore::System | [protected] |
| selector | NFcore::System | [protected] |
| setDumpOutputter(DumpSystem *ds) | NFcore::System | |
| setOutputToBinary() | NFcore::System | |
| setParameter(string name, double value) | NFcore::System | |
| setUniversalTraversalLimit(int utl) | NFcore::System | |
| sim(double time, long int sampleTimes) | NFcore::System | |
| sim(double time, long int sampleTimes, bool verbose) | NFcore::System | |
| singleStep() | NFcore::System | |
| speciesObservables | NFcore::System | [protected] |
| stepTo(double stoppingTime) | NFcore::System | |
| System(string name) | NFcore::System | |
| System(string name, bool useComplex) | NFcore::System | |
| System(string name, bool useComplex, int globalMoleculeLimit) | NFcore::System | |
| tagReaction(int rID) | NFcore::System | |
| tryToDump() | NFcore::System | |
| turnOff_OnTheFlyObs() | NFcore::System | |
| turnOffGlobalFuncOut() | NFcore::System | [inline] |
| turnOnCSVformat() | NFcore::System | [inline] |
| turnOnGlobalFuncOut() | NFcore::System | [inline] |
| turnOnOutputEventCounter() | NFcore::System | [inline] |
| universalTraversalLimit | NFcore::System | [protected] |
| update_A_tot(ReactionClass *r, double old_a, double new_a) | NFcore::System | |
| updateSystemWithNewParameters() | NFcore::System | |
| useBinaryOutput | NFcore::System | [protected] |
| useComplex | NFcore::System | [protected] |
| ~System() | NFcore::System | |
