roadrunner  2.6.0
Fast simulator for SBML models
rr::CompiledModelGenerator Member List

This is the complete list of members for rr::CompiledModelGenerator, including all inherited members.

cleanEquation(ASTNode *ast)rr::CompiledModelGeneratorprotectedstatic
cleanEquation(const std::string &equation) (defined in rr::CompiledModelGenerator)rr::CompiledModelGeneratorprotectedstatic
CompiledModelGenerator() (defined in rr::CompiledModelGenerator)rr::CompiledModelGeneratorprotected
convertCompartmentToC(const std::string &compartmentName)=0 (defined in rr::CompiledModelGenerator)rr::CompiledModelGeneratorprotectedpure virtual
convertSpeciesToBc(const std::string &speciesName)=0 (defined in rr::CompiledModelGenerator)rr::CompiledModelGeneratorprotectedpure virtual
convertSpeciesToY(const std::string &speciesName)=0 (defined in rr::CompiledModelGenerator)rr::CompiledModelGeneratorprotectedpure virtual
convertSymbolToC(const std::string &compartmentName)=0 (defined in rr::CompiledModelGenerator)rr::CompiledModelGeneratorprotectedpure virtual
convertSymbolToGP(const std::string &parameterName)=0 (defined in rr::CompiledModelGenerator)rr::CompiledModelGeneratorprotectedpure virtual
convertUserFunctionExpression(const std::string &equation)=0 (defined in rr::CompiledModelGenerator)rr::CompiledModelGeneratorprotectedpure virtual
expressionContainsSymbol(ASTNode *ast, const std::string &symbol) (defined in rr::CompiledModelGenerator)rr::CompiledModelGeneratorprotected
expressionContainsSymbol(const std::string &expression, const std::string &symbol) (defined in rr::CompiledModelGenerator)rr::CompiledModelGeneratorprotected
findSymbol(const std::string &varName)=0 (defined in rr::CompiledModelGenerator)rr::CompiledModelGeneratorprotectedpure virtual
getInfo()rr::CompiledModelGeneratorprotectedvirtual
getSpecies(const std::string &id) (defined in rr::CompiledModelGenerator)rr::CompiledModelGeneratorprotected
initializeL0(int &nrRows, int &nrCols) (defined in rr::CompiledModelGenerator)rr::CompiledModelGeneratorprotected
mComputeAndAssignConsevationLaws (defined in rr::CompiledModelGenerator)rr::CompiledModelGeneratorprotected
mFixAmountCompartments (defined in rr::CompiledModelGenerator)rr::CompiledModelGeneratorprotected
mLibStructrr::CompiledModelGeneratorprotected
mNOMrr::CompiledModelGeneratorprotected
msrr::CompiledModelGeneratorprotected
mWarnings (defined in rr::CompiledModelGenerator)rr::CompiledModelGeneratorprotected
numAdditionalRates() (defined in rr::CompiledModelGenerator)rr::CompiledModelGeneratorprotected
readCompartments() (defined in rr::CompiledModelGenerator)rr::CompiledModelGeneratorprotected
readGlobalParameters() (defined in rr::CompiledModelGenerator)rr::CompiledModelGeneratorprotected
readLocalParameters(const int &numReactions, std::vector< int > &localParameterDimensions, int &totalLocalParmeters) (defined in rr::CompiledModelGenerator)rr::CompiledModelGeneratorprotected
reset() (defined in rr::CompiledModelGenerator)rr::CompiledModelGeneratorprotected
substituteEquation(const std::string &reactionName, Scanner &s, CodeBuilder &sb)=0 (defined in rr::CompiledModelGenerator)rr::CompiledModelGeneratorprotectedpure virtual
substituteTerms(const std::string &reactionName, const std::string &inputEquation, bool bFixAmounts) (defined in rr::CompiledModelGenerator)rr::CompiledModelGeneratorprotected
substituteTerms(const int &numReactions, const std::string &reactionName, const std::string &equation) (defined in rr::CompiledModelGenerator)rr::CompiledModelGeneratorprotected
substituteToken(const std::string &reactionName, bool bFixAmounts, Scanner &s, CodeBuilder &sb)=0 (defined in rr::CompiledModelGenerator)rr::CompiledModelGeneratorprotectedpure virtual
substituteWords(const std::string &reactionName, bool bFixAmounts, Scanner &s, CodeBuilder &sb)=0 (defined in rr::CompiledModelGenerator)rr::CompiledModelGeneratorprotectedpure virtual
writeAccessors(CodeBuilder &sb)=0 (defined in rr::CompiledModelGenerator)rr::CompiledModelGeneratorprotectedpure virtual
writeClassHeader(CodeBuilder &sb)=0 (defined in rr::CompiledModelGenerator)rr::CompiledModelGeneratorprotectedpure virtual
writeComputeAllRatesOfChange(CodeBuilder &sb, const int &numIndependentSpecies, const int &numDependentSpecies, ls::DoubleMatrix &L0)=0 (defined in rr::CompiledModelGenerator)rr::CompiledModelGeneratorprotectedpure virtual
writeComputeConservedTotals(CodeBuilder &sb, const int &numFloatingSpecies, const int &numDependentSpecies)=0 (defined in rr::CompiledModelGenerator)rr::CompiledModelGeneratorprotectedpure virtual
writeComputeReactionRates(CodeBuilder &sb, const int &numReactions)=0 (defined in rr::CompiledModelGenerator)rr::CompiledModelGeneratorprotectedpure virtual
writeComputeRules(CodeBuilder &sb, const int &numReactions)=0 (defined in rr::CompiledModelGenerator)rr::CompiledModelGeneratorprotectedpure virtual
writeConvertToAmounts(CodeBuilder &sb)=0 (defined in rr::CompiledModelGenerator)rr::CompiledModelGeneratorprotectedpure virtual
writeConvertToConcentrations(CodeBuilder &sb)=0 (defined in rr::CompiledModelGenerator)rr::CompiledModelGeneratorprotectedpure virtual
writeDouble(const double &value, const std::string &format="%G") (defined in rr::CompiledModelGenerator)rr::CompiledModelGeneratorprotected
writeEvalEvents(CodeBuilder &sb, const int &numEvents, const int &numFloatingSpecies)=0 (defined in rr::CompiledModelGenerator)rr::CompiledModelGeneratorprotectedpure virtual
writeEvalInitialAssignments(CodeBuilder &sb, const int &numReactions)=0 (defined in rr::CompiledModelGenerator)rr::CompiledModelGeneratorprotectedpure virtual
writeEvalModel(CodeBuilder &sb, const int &numReactions, const int &numIndependentSpecies, const int &numFloatingSpecies, const int &numOfRules)=0 (defined in rr::CompiledModelGenerator)rr::CompiledModelGeneratorprotectedpure virtual
writeEventAssignments(CodeBuilder &sb, const int &numReactions, const int &numEvents)=0 (defined in rr::CompiledModelGenerator)rr::CompiledModelGeneratorprotectedpure virtual
writeGetConcentration(CodeBuilder &sb)=0 (defined in rr::CompiledModelGenerator)rr::CompiledModelGeneratorprotectedpure virtual
writeOutVariables(CodeBuilder &sb)=0 (defined in rr::CompiledModelGenerator)rr::CompiledModelGeneratorprotectedpure virtual
writeProperties(CodeBuilder &sb)=0 (defined in rr::CompiledModelGenerator)rr::CompiledModelGeneratorprotectedpure virtual
writeResetEvents(CodeBuilder &sb, const int &numEvents)=0 (defined in rr::CompiledModelGenerator)rr::CompiledModelGeneratorprotectedpure virtual
writeSetBoundaryConditions(CodeBuilder &sb)=0 (defined in rr::CompiledModelGenerator)rr::CompiledModelGeneratorprotectedpure virtual
writeSetCompartmentVolumes(CodeBuilder &sb)=0 (defined in rr::CompiledModelGenerator)rr::CompiledModelGeneratorprotectedpure virtual
writeSetConcentration(CodeBuilder &sb)=0 (defined in rr::CompiledModelGenerator)rr::CompiledModelGeneratorprotectedpure virtual
writeSetInitialConditions(CodeBuilder &sb, const int &numFloatingSpecies)=0 (defined in rr::CompiledModelGenerator)rr::CompiledModelGeneratorprotectedpure virtual
writeSetParameterValues(CodeBuilder &sb, const int &numReactions)=0 (defined in rr::CompiledModelGenerator)rr::CompiledModelGeneratorprotectedpure virtual
writeTestConstraints(CodeBuilder &sb)=0 (defined in rr::CompiledModelGenerator)rr::CompiledModelGeneratorprotectedpure virtual
writeUpdateDependentSpecies(CodeBuilder &sb, const int &numIndependentSpecies, const int &numDependentSpecies, ls::DoubleMatrix &L0)=0 (defined in rr::CompiledModelGenerator)rr::CompiledModelGeneratorprotectedpure virtual
writeUserDefinedFunctions(CodeBuilder &sb)=0 (defined in rr::CompiledModelGenerator)rr::CompiledModelGeneratorprotectedpure virtual
~CompiledModelGenerator() (defined in rr::CompiledModelGenerator)rr::CompiledModelGeneratorprotectedvirtual