| allocateModel(const vector< Id > &elist) | Stoich | |
| allocateModelObject(Id id) | Stoich | |
| allowNegative_ | Stoich | private |
| bufPoolVec_ | Stoich | private |
| buildFuncLookup() | Stoich | |
| buildPoolLookup() | Stoich | |
| buildRateTermLookup() | Stoich | |
| compartment_ | Stoich | private |
| convertIdToFuncIndex(Id id) const | Stoich | |
| convertIdToPoolIndex(Id id) const | Stoich | |
| convertIdToReacIndex(Id id) const | Stoich | |
| convertRatesToStochasticForm() | Stoich | |
| dinterface_ | Stoich | private |
| dsolve_ | Stoich | private |
| enzVec_ | Stoich | private |
| funcLookup_ | Stoich | private |
| funcs(unsigned int i) const | Stoich | |
| funcs_ | Stoich | private |
| funcTarget_ | Stoich | private |
| getAllowNegative() const | Stoich | |
| getColIndex() const | Stoich | |
| getCompartment() const | Stoich | |
| getDsolve() const | Stoich | |
| getEnzK2(const Eref &e) const | Stoich | |
| getEnzK3(const Eref &e) const | Stoich | |
| getEnzNumK1(const Eref &e) const | Stoich | |
| getKsolve() const | Stoich | |
| getMatrixEntry() const | Stoich | |
| getMMenzKcat(const Eref &e) const | Stoich | |
| getMMenzNumKm(const Eref &e) const | Stoich | |
| getNumAllPools() const | Stoich | |
| getNumBufPools() const | Stoich | |
| getNumCoreRates() const | Stoich | |
| getNumFuncs() const | Stoich | |
| getNumProxyPools() const | Stoich | |
| getNumRates() const | Stoich | |
| getNumVarPools() const | Stoich | |
| getOffSolverCompts() const | Stoich | |
| getOffSolverPools() const | Stoich | |
| getOneWay() const | Stoich | |
| getPath(const Eref &e) const | Stoich | |
| getPoolByIndex(unsigned int index) const | Stoich | |
| getPoolIdMap() const | Stoich | |
| getProxyPools(Id i) const | Stoich | |
| getR1(const Eref &e) const | Stoich | |
| getR1offset1(const Eref &e) const | Stoich | |
| getR1offset2(const Eref &e) const | Stoich | |
| getR2(const Eref &e) const | Stoich | |
| getRateTerms() const | Stoich | |
| getRowStart() const | Stoich | |
| getSpecies(unsigned int poolIndex) const | Stoich | |
| getStatus() const | Stoich | |
| getStoichiometryMatrix() const | Stoich | |
| incrementFuncVec_ | Stoich | private |
| initCinfo() | Stoich | static |
| innerInstallReaction(Id reacId, const vector< Id > &subs, const vector< Id > &prds) | Stoich | |
| installAndUnschedFunc(Id func, Id pool, double volScale) | Stoich | |
| installAndUnschedFuncRate(Id func, Id pool) | Stoich | |
| installAndUnschedFuncReac(Id func, Id reac) | Stoich | |
| installDummyEnzyme(Id enzId, Id enzMolId) | Stoich | |
| installEnzyme(Id enzId, Id enzMolId, Id cplxId, const vector< Id > &subs, const vector< Id > &prds) | Stoich | |
| installEnzyme(ZeroOrder *r1, ZeroOrder *r2, ZeroOrder *r3, Id enzId, Id enzMolId, const vector< Id > &prds) | Stoich | |
| installMMenz(Id enzId, const vector< Id > &enzMolId, const vector< Id > &subs, const vector< Id > &prds) | Stoich | |
| installMMenz(MMEnzymeBase *meb, unsigned int rateIndex, const vector< Id > &subs, const vector< Id > &prds) | Stoich | |
| installReaction(Id reacId, const vector< Id > &subs, const vector< Id > &prds) | Stoich | |
| isFuncTarget(unsigned int poolIndex) const | Stoich | |
| kinterface_ | Stoich | private |
| ksolve_ | Stoich | private |
| locateOffSolverReacs(Id myCompt, vector< Id > &elist) | Stoich | |
| makeHalfReaction(double rate, const vector< Id > &reactants) | Stoich | |
| mmEnzVec_ | Stoich | private |
| N_ | Stoich | private |
| numVoxels_ | Stoich | private |
| offSolverEnzCompts_ | Stoich | private |
| offSolverEnzVec_ | Stoich | private |
| offSolverMMenzCompts_ | Stoich | private |
| offSolverMMenzVec_ | Stoich | private |
| offSolverPoolMap(Id compt) const | Stoich | |
| offSolverPoolMap_ | Stoich | private |
| offSolverPoolVec_ | Stoich | private |
| offSolverReacCompts_ | Stoich | private |
| offSolverReacVec_ | Stoich | private |
| path_ | Stoich | private |
| poolFuncVec_ | Stoich | private |
| PoolIsNotOnSolver | Stoich | static |
| poolLookup_ | Stoich | private |
| prdComptVec_ | Stoich | private |
| print() const | Stoich | |
| printRates() const | Stoich | |
| rates(unsigned int i) const | Stoich | |
| rates_ | Stoich | private |
| rateTermLookup_ | Stoich | private |
| reacFuncVec_ | Stoich | private |
| reacVec_ | Stoich | private |
| resizeArrays() | Stoich | |
| scaleBufsAndRates(unsigned int index, double volScale) | Stoich | |
| setAllowNegative(bool v) | Stoich | |
| setCompartment(Id v) | Stoich | |
| setDsolve(Id v) | Stoich | |
| setElist(const Eref &e, const vector< ObjId > &elist) | Stoich | |
| setEnzK1(const Eref &e, double v) const | Stoich | |
| setEnzK2(const Eref &e, double v) const | Stoich | |
| setEnzK3(const Eref &e, double v) const | Stoich | |
| setFunctionExpr(const Eref &e, string expr) | Stoich | |
| setKsolve(Id v) | Stoich | |
| setMMenzKcat(const Eref &e, double v) const | Stoich | |
| setMMenzKm(const Eref &e, double v) const | Stoich | |
| setOneWay(bool v) | Stoich | |
| setPath(const Eref &e, string path) | Stoich | |
| setReacKb(const Eref &e, double v) const | Stoich | |
| setReacKf(const Eref &e, double v) const | Stoich | |
| setSpecies(unsigned int poolIndex, unsigned int s) | Stoich | |
| species_ | Stoich | private |
| status_ | Stoich | private |
| Stoich() | Stoich | |
| subComptVec_ | Stoich | private |
| unZombifyModel() | Stoich | |
| unZombifyPools() | Stoich | |
| updateFuncs(double *s, double t) const | Stoich | |
| updateRatesAfterRemesh() | Stoich | |
| updateReacVelocities(const double *s, vector< double > &vel, unsigned int volIndex) const | Stoich | |
| useOneWay_ | Stoich | private |
| varPoolVec_ | Stoich | private |
| zombifyChemCompt(Id compt) | Stoich | |
| zombifyModel(const Eref &e, const vector< Id > &elist) | Stoich | |
| zombifyPoolFuncWithScaling(Id pool) | Stoich | |
| ~Stoich() | Stoich | |
1.8.6 
