| addAllToObservables() | NFcore::MoleculeType | |
| addEquivalentComponents(vector< vector< string > > &identicalComponents) | NFcore::MoleculeType | |
| addLocalFunc_TypeI(LocalFunction *lf) | NFcore::MoleculeType | |
| addLocalFunc_TypeII(LocalFunction *lf) | NFcore::MoleculeType | |
| addMoleculeToRunningSystem(Molecule *&mol) | NFcore::MoleculeType | |
| addMolObs(MoleculesObservable *mo) | NFcore::MoleculeType | [inline] |
| addReactionClass(ReactionClass *r, int rPosition) | NFcore::MoleculeType | |
| addTemplateMolecule(TemplateMolecule *t) | NFcore::MoleculeType | |
| addToObservables(Molecule *m) | NFcore::MoleculeType | |
| allTemplates | NFcore::MoleculeType | [protected] |
| compName | NFcore::MoleculeType | [protected] |
| createComplex(Molecule *m) | NFcore::MoleculeType | [inline] |
| defaultCompState | NFcore::MoleculeType | [protected] |
| eqCompIndex | NFcore::MoleculeType | [protected] |
| eqCompName | NFcore::MoleculeType | [protected] |
| eqCompOriginalName | NFcore::MoleculeType | [protected] |
| eqCompSizes | NFcore::MoleculeType | [protected] |
| genDefaultMolecule() | NFcore::MoleculeType | |
| getCompIndexFromName(string cName) const | NFcore::MoleculeType | |
| getComponentName(int cIndex) const | NFcore::MoleculeType | |
| getComponentStateName(int cIndex, int cValue) | NFcore::MoleculeType | |
| getDefaultComponentState(int cIndex) const | NFcore::MoleculeType | [inline] |
| getDORrxn(int dorRxnIndex) const | NFcore::MoleculeType | [inline] |
| getDORrxnIndex(int dorRxnIndex) const | NFcore::MoleculeType | [inline] |
| getDORrxnPosition(int dorRxnIndex) const | NFcore::MoleculeType | [inline] |
| getEquivalencyClass(int *&components, int &n_components, string cName) const | NFcore::MoleculeType | |
| getEquivalencyClassCompNames() const | NFcore::MoleculeType | [inline] |
| getEquivalencyClassNumber(string cName) const | NFcore::MoleculeType | |
| getMolecule(int ID_molecule) const | NFcore::MoleculeType | |
| getMoleculeCount() const | NFcore::MoleculeType | |
| getMolObs(int obsIndex) const | NFcore::MoleculeType | [inline] |
| getMolObsCount(int obsIndex) const | NFcore::MoleculeType | |
| getMolObsName(int obsIndex) const | NFcore::MoleculeType | |
| getName() const | NFcore::MoleculeType | [inline] |
| getNumOfComponents() const | NFcore::MoleculeType | [inline] |
| getNumOfDORrxns() const | NFcore::MoleculeType | [inline] |
| getNumOfEquivalencyClasses() const | NFcore::MoleculeType | [inline] |
| getNumOfMolObs() const | NFcore::MoleculeType | [inline] |
| getNumOfTypeIFunctions() const | NFcore::MoleculeType | [inline] |
| getNumOfTypeIIFunctions() const | NFcore::MoleculeType | [inline] |
| getPossibleComponentStates(int cIndex, list< string > &nameList) | NFcore::MoleculeType | |
| getReactionCount() const | NFcore::MoleculeType | [inline] |
| getRxnIndex(ReactionClass *rxn, int rxnPosition) | NFcore::MoleculeType | |
| getStateValueFromName(int cIndex, string stateName) const | NFcore::MoleculeType | |
| getSystem() const | NFcore::MoleculeType | [inline] |
| getTypeID() const | NFcore::MoleculeType | [inline] |
| getTypeIILocalFunction(int index) | NFcore::MoleculeType | [inline] |
| getTypeILocalFunction(int index) | NFcore::MoleculeType | [inline] |
| indexOfDORrxns | NFcore::MoleculeType | [protected] |
| init(string name, vector< string > &compName, vector< string > &defaultCompState, vector< vector< string > > &possibleCompStates, vector< bool > isIntegerComponent, System *system) | NFcore::MoleculeType | [protected] |
| isEquivalentComponent(string cName) const | NFcore::MoleculeType | |
| isEquivalentComponent(int cIndex) const | NFcore::MoleculeType | |
| isIntegerComponent(string cName) const | NFcore::MoleculeType | |
| isIntegerComponent(int cIndex) const | NFcore::MoleculeType | |
| isIntegerCompState | NFcore::MoleculeType | [protected] |
| locFuncs_typeI | NFcore::MoleculeType | |
| locFuncs_typeII | NFcore::MoleculeType | |
| mList | NFcore::MoleculeType | [protected] |
| MoleculeType(string name, vector< string > &compName, System *s) | NFcore::MoleculeType | |
| MoleculeType(string name, vector< string > &compName, vector< string > &defaultCompState, System *s) | NFcore::MoleculeType | |
| MoleculeType(string name, vector< string > &compName, vector< string > &defaultCompState, vector< vector< string > > &possibleCompStates, System *system) | NFcore::MoleculeType | |
| MoleculeType(string name, vector< string > &compName, vector< string > &defaultCompState, vector< vector< string > > &possibleCompStates, vector< bool > isIntegerComponent, System *system) | NFcore::MoleculeType | |
| molObs | NFcore::MoleculeType | [protected] |
| n_eqComp | NFcore::MoleculeType | [protected] |
| name | NFcore::MoleculeType | [protected] |
| numOfComponents | NFcore::MoleculeType | [protected] |
| outputMolObsCounts(NFstream &fout) | NFcore::MoleculeType | |
| outputMolObsNames(NFstream &fout) | NFcore::MoleculeType | |
| populateWithDefaultMolecules(int moleculeCount) | NFcore::MoleculeType | |
| possibleCompStates | NFcore::MoleculeType | [protected] |
| prepareForSimulation() | NFcore::MoleculeType | |
| printAllMolecules() | NFcore::MoleculeType | |
| printDetails() const | NFcore::MoleculeType | |
| printMolObsCounts() | NFcore::MoleculeType | |
| printMolObsNames() | NFcore::MoleculeType | |
| reactionPositions | NFcore::MoleculeType | [protected] |
| reactions | NFcore::MoleculeType | [protected] |
| removeFromObservables(Molecule *m) | NFcore::MoleculeType | |
| removeFromRxns(Molecule *m) | NFcore::MoleculeType | |
| removeMoleculeFromRunningSystem(Molecule *&m) | NFcore::MoleculeType | |
| rxn | NFcore::MoleculeType | [protected] |
| setUpLocalFunctionListForMolecules() | NFcore::MoleculeType | |
| system | NFcore::MoleculeType | [protected] |
| type_id | NFcore::MoleculeType | [protected] |
| updateRxnMembership(Molecule *m) | NFcore::MoleculeType | |
| ~MoleculeType() | NFcore::MoleculeType | |
