roadrunner
2.6.0
Fast simulator for SBML models
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This is the complete list of members for rr::CompiledModelGenerator, including all inherited members.
cleanEquation(ASTNode *ast) | rr::CompiledModelGenerator | protectedstatic |
cleanEquation(const std::string &equation) (defined in rr::CompiledModelGenerator) | rr::CompiledModelGenerator | protectedstatic |
CompiledModelGenerator() (defined in rr::CompiledModelGenerator) | rr::CompiledModelGenerator | protected |
convertCompartmentToC(const std::string &compartmentName)=0 (defined in rr::CompiledModelGenerator) | rr::CompiledModelGenerator | protectedpure virtual |
convertSpeciesToBc(const std::string &speciesName)=0 (defined in rr::CompiledModelGenerator) | rr::CompiledModelGenerator | protectedpure virtual |
convertSpeciesToY(const std::string &speciesName)=0 (defined in rr::CompiledModelGenerator) | rr::CompiledModelGenerator | protectedpure virtual |
convertSymbolToC(const std::string &compartmentName)=0 (defined in rr::CompiledModelGenerator) | rr::CompiledModelGenerator | protectedpure virtual |
convertSymbolToGP(const std::string ¶meterName)=0 (defined in rr::CompiledModelGenerator) | rr::CompiledModelGenerator | protectedpure virtual |
convertUserFunctionExpression(const std::string &equation)=0 (defined in rr::CompiledModelGenerator) | rr::CompiledModelGenerator | protectedpure virtual |
expressionContainsSymbol(ASTNode *ast, const std::string &symbol) (defined in rr::CompiledModelGenerator) | rr::CompiledModelGenerator | protected |
expressionContainsSymbol(const std::string &expression, const std::string &symbol) (defined in rr::CompiledModelGenerator) | rr::CompiledModelGenerator | protected |
findSymbol(const std::string &varName)=0 (defined in rr::CompiledModelGenerator) | rr::CompiledModelGenerator | protectedpure virtual |
getInfo() | rr::CompiledModelGenerator | protectedvirtual |
getSpecies(const std::string &id) (defined in rr::CompiledModelGenerator) | rr::CompiledModelGenerator | protected |
initializeL0(int &nrRows, int &nrCols) (defined in rr::CompiledModelGenerator) | rr::CompiledModelGenerator | protected |
mComputeAndAssignConsevationLaws (defined in rr::CompiledModelGenerator) | rr::CompiledModelGenerator | protected |
mFixAmountCompartments (defined in rr::CompiledModelGenerator) | rr::CompiledModelGenerator | protected |
mLibStruct | rr::CompiledModelGenerator | protected |
mNOM | rr::CompiledModelGenerator | protected |
ms | rr::CompiledModelGenerator | protected |
mWarnings (defined in rr::CompiledModelGenerator) | rr::CompiledModelGenerator | protected |
numAdditionalRates() (defined in rr::CompiledModelGenerator) | rr::CompiledModelGenerator | protected |
readCompartments() (defined in rr::CompiledModelGenerator) | rr::CompiledModelGenerator | protected |
readGlobalParameters() (defined in rr::CompiledModelGenerator) | rr::CompiledModelGenerator | protected |
readLocalParameters(const int &numReactions, std::vector< int > &localParameterDimensions, int &totalLocalParmeters) (defined in rr::CompiledModelGenerator) | rr::CompiledModelGenerator | protected |
reset() (defined in rr::CompiledModelGenerator) | rr::CompiledModelGenerator | protected |
substituteEquation(const std::string &reactionName, Scanner &s, CodeBuilder &sb)=0 (defined in rr::CompiledModelGenerator) | rr::CompiledModelGenerator | protectedpure virtual |
substituteTerms(const std::string &reactionName, const std::string &inputEquation, bool bFixAmounts) (defined in rr::CompiledModelGenerator) | rr::CompiledModelGenerator | protected |
substituteTerms(const int &numReactions, const std::string &reactionName, const std::string &equation) (defined in rr::CompiledModelGenerator) | rr::CompiledModelGenerator | protected |
substituteToken(const std::string &reactionName, bool bFixAmounts, Scanner &s, CodeBuilder &sb)=0 (defined in rr::CompiledModelGenerator) | rr::CompiledModelGenerator | protectedpure virtual |
substituteWords(const std::string &reactionName, bool bFixAmounts, Scanner &s, CodeBuilder &sb)=0 (defined in rr::CompiledModelGenerator) | rr::CompiledModelGenerator | protectedpure virtual |
writeAccessors(CodeBuilder &sb)=0 (defined in rr::CompiledModelGenerator) | rr::CompiledModelGenerator | protectedpure virtual |
writeClassHeader(CodeBuilder &sb)=0 (defined in rr::CompiledModelGenerator) | rr::CompiledModelGenerator | protectedpure virtual |
writeComputeAllRatesOfChange(CodeBuilder &sb, const int &numIndependentSpecies, const int &numDependentSpecies, ls::DoubleMatrix &L0)=0 (defined in rr::CompiledModelGenerator) | rr::CompiledModelGenerator | protectedpure virtual |
writeComputeConservedTotals(CodeBuilder &sb, const int &numFloatingSpecies, const int &numDependentSpecies)=0 (defined in rr::CompiledModelGenerator) | rr::CompiledModelGenerator | protectedpure virtual |
writeComputeReactionRates(CodeBuilder &sb, const int &numReactions)=0 (defined in rr::CompiledModelGenerator) | rr::CompiledModelGenerator | protectedpure virtual |
writeComputeRules(CodeBuilder &sb, const int &numReactions)=0 (defined in rr::CompiledModelGenerator) | rr::CompiledModelGenerator | protectedpure virtual |
writeConvertToAmounts(CodeBuilder &sb)=0 (defined in rr::CompiledModelGenerator) | rr::CompiledModelGenerator | protectedpure virtual |
writeConvertToConcentrations(CodeBuilder &sb)=0 (defined in rr::CompiledModelGenerator) | rr::CompiledModelGenerator | protectedpure virtual |
writeDouble(const double &value, const std::string &format="%G") (defined in rr::CompiledModelGenerator) | rr::CompiledModelGenerator | protected |
writeEvalEvents(CodeBuilder &sb, const int &numEvents, const int &numFloatingSpecies)=0 (defined in rr::CompiledModelGenerator) | rr::CompiledModelGenerator | protectedpure virtual |
writeEvalInitialAssignments(CodeBuilder &sb, const int &numReactions)=0 (defined in rr::CompiledModelGenerator) | rr::CompiledModelGenerator | protectedpure virtual |
writeEvalModel(CodeBuilder &sb, const int &numReactions, const int &numIndependentSpecies, const int &numFloatingSpecies, const int &numOfRules)=0 (defined in rr::CompiledModelGenerator) | rr::CompiledModelGenerator | protectedpure virtual |
writeEventAssignments(CodeBuilder &sb, const int &numReactions, const int &numEvents)=0 (defined in rr::CompiledModelGenerator) | rr::CompiledModelGenerator | protectedpure virtual |
writeGetConcentration(CodeBuilder &sb)=0 (defined in rr::CompiledModelGenerator) | rr::CompiledModelGenerator | protectedpure virtual |
writeOutVariables(CodeBuilder &sb)=0 (defined in rr::CompiledModelGenerator) | rr::CompiledModelGenerator | protectedpure virtual |
writeProperties(CodeBuilder &sb)=0 (defined in rr::CompiledModelGenerator) | rr::CompiledModelGenerator | protectedpure virtual |
writeResetEvents(CodeBuilder &sb, const int &numEvents)=0 (defined in rr::CompiledModelGenerator) | rr::CompiledModelGenerator | protectedpure virtual |
writeSetBoundaryConditions(CodeBuilder &sb)=0 (defined in rr::CompiledModelGenerator) | rr::CompiledModelGenerator | protectedpure virtual |
writeSetCompartmentVolumes(CodeBuilder &sb)=0 (defined in rr::CompiledModelGenerator) | rr::CompiledModelGenerator | protectedpure virtual |
writeSetConcentration(CodeBuilder &sb)=0 (defined in rr::CompiledModelGenerator) | rr::CompiledModelGenerator | protectedpure virtual |
writeSetInitialConditions(CodeBuilder &sb, const int &numFloatingSpecies)=0 (defined in rr::CompiledModelGenerator) | rr::CompiledModelGenerator | protectedpure virtual |
writeSetParameterValues(CodeBuilder &sb, const int &numReactions)=0 (defined in rr::CompiledModelGenerator) | rr::CompiledModelGenerator | protectedpure virtual |
writeTestConstraints(CodeBuilder &sb)=0 (defined in rr::CompiledModelGenerator) | rr::CompiledModelGenerator | protectedpure virtual |
writeUpdateDependentSpecies(CodeBuilder &sb, const int &numIndependentSpecies, const int &numDependentSpecies, ls::DoubleMatrix &L0)=0 (defined in rr::CompiledModelGenerator) | rr::CompiledModelGenerator | protectedpure virtual |
writeUserDefinedFunctions(CodeBuilder &sb)=0 (defined in rr::CompiledModelGenerator) | rr::CompiledModelGenerator | protectedpure virtual |
~CompiledModelGenerator() (defined in rr::CompiledModelGenerator) | rr::CompiledModelGenerator | protectedvirtual |