| addToObservables() | NFcore::Molecule | |
| bind(Molecule *m1, int cIndex1, Molecule *m2, int cIndex2) | NFcore::Molecule | [static] |
| bind(Molecule *m1, string compName1, Molecule *m2, string compName2) | NFcore::Molecule | [static] |
| bond | NFcore::Molecule | [protected] |
| breadthFirstSearch(list< Molecule * > &members, Molecule *m, int depth) | NFcore::Molecule | [static] |
| component | NFcore::Molecule | [protected] |
| depthFirstSearch(list< Molecule * > &members) | NFcore::Molecule | |
| getBondedMolecule(int bSiteIndex) const | NFcore::Molecule | |
| getBondedMoleculeBindingSiteIndex(int cIndex) const | NFcore::Molecule | |
| getComplex() const | NFcore::Molecule | [inline] |
| getComplexID() const | NFcore::Molecule | [inline] |
| getComponentIndexOfBond(int cIndex) const | NFcore::Molecule | [inline] |
| getComponentState(int cIndex) const | NFcore::Molecule | [inline] |
| getDegree() | NFcore::Molecule | |
| getLocalFunction(int localFunctionIndex) | NFcore::Molecule | |
| getLocalFunctionValue(int localFunctionIndex) | NFcore::Molecule | |
| getMoleculeType() const | NFcore::Molecule | [inline] |
| getMoleculeTypeName() const | NFcore::Molecule | [inline] |
| getMolListId() const | NFcore::Molecule | [inline] |
| getRxnListMappingId(int rxnIndex) const | NFcore::Molecule | [inline] |
| getUniqueID() const | NFcore::Molecule | [inline] |
| getUniqueIdCount() | NFcore::Molecule | [inline, static] |
| hasEvaluatedMolecule | NFcore::Molecule | |
| hasVisitedBond | NFcore::Molecule | |
| hasVisitedMolecule | NFcore::Molecule | |
| ID_complex | NFcore::Molecule | [protected] |
| ID_type | NFcore::Molecule | [protected] |
| ID_unique | NFcore::Molecule | [protected] |
| indexOfBond | NFcore::Molecule | [protected] |
| isAlive() const | NFcore::Molecule | [inline] |
| isAliveInSim | NFcore::Molecule | [protected] |
| isBindingSiteBonded(int bIndex) const | NFcore::Molecule | |
| isBindingSiteOpen(int bIndex) const | NFcore::Molecule | |
| isMatchedTo | NFcore::Molecule | |
| isObs(int oIndex) const | NFcore::Molecule | [inline] |
| isObservable | NFcore::Molecule | [protected] |
| isPrepared | NFcore::Molecule | [protected] |
| listId | NFcore::Molecule | [protected] |
| localFunctionValues | NFcore::Molecule | [protected] |
| Molecule(MoleculeType *parentMoleculeType, int listId) | NFcore::Molecule | |
| moveToNewComplex(int newComplexID) | NFcore::Molecule | [inline] |
| NOBOND | NFcore::Molecule | [static] |
| NOINDEX | NFcore::Molecule | [static] |
| NOSTATE | NFcore::Molecule | [static] |
| NOT_IN_RXN | NFcore::Molecule | [static] |
| nReactions | NFcore::Molecule | [protected] |
| numOfComponents | NFcore::Molecule | [protected] |
| parentMoleculeType | NFcore::Molecule | [protected] |
| prepareForSimulation() | NFcore::Molecule | |
| printDetails() | NFcore::Molecule | |
| printDetails(ostream &o) | NFcore::Molecule | |
| printMoleculeList(list< Molecule * > &members) | NFcore::Molecule | [static] |
| removeFromObservables() | NFcore::Molecule | |
| rxnListMappingId | NFcore::Molecule | [protected] |
| setAlive(bool isAlive) | NFcore::Molecule | [inline] |
| setBondTo(Molecule *m2, int bindingSiteIndex) | NFcore::Molecule | |
| setComplexID(int currentComplex) | NFcore::Molecule | [inline] |
| setComponentState(int cIndex, int newValue) | NFcore::Molecule | |
| setComponentState(string cName, int newValue) | NFcore::Molecule | |
| setIsObs(int oIndex, int isObs) | NFcore::Molecule | [inline] |
| setLocalFunctionValue(double newValue, int localFunctionIndex) | NFcore::Molecule | |
| setRxnListMappingId(int rxnIndex, int rxnListMappingId) | NFcore::Molecule | [inline] |
| setUpLocalFunctionList() | NFcore::Molecule | |
| traverseBondedNeighborhood(list< Molecule * > &members, int traversalLimit) | NFcore::Molecule | |
| unbind(Molecule *m1, int bSiteIndex) | NFcore::Molecule | [static] |
| unbind(Molecule *m1, char *bSiteName) | NFcore::Molecule | [static] |
| uniqueIdCount | NFcore::Molecule | [protected, static] |
| updateDORRxnValues() | NFcore::Molecule | |
| updateRxnMembership() | NFcore::Molecule | |
| updateTypeIIFunctions() | NFcore::Molecule | |
| useComplex | NFcore::Molecule | [protected] |
| ~Molecule() | NFcore::Molecule | |
