| Crrllvm::ASTNodeCodeGen | All of the LLVM IR generation is handled here |
| Crrllvm::ASTNodeCodeGenScalarTicket | Used in LoadSymbolResolverBase::loadReactionRate when resolving a kinetic law |
| Crrllvm::ASTNodeFactory | Manages a set of ASTNodes |
| Crrllvm::CodeGen | Base class for code generation |
| ►Crrllvm::CodeGenBase< FunctionPtrType > | Convenience class to pull the vars out of a context, and store them as ivars |
| ►Crrllvm::GetEventValueCodeGenBase< GetEventTriggerCodeGen, GetEventTriggerCodeGen_FunctionPtr > | |
| Crrllvm::GetEventTriggerCodeGen | Get the trigger of an SBML Event |
| ►Crrllvm::CodeGenBase< EvalConversionFactorCodeGen_FunctionPtr > | |
| Crrllvm::EvalConversionFactorCodeGen | Evaluate conversion factors, which change the units of species objects in SBML |
| ►Crrllvm::CodeGenBase< EvalInitialConditions_FunctionPtr > | |
| Crrllvm::EvalInitialConditionsCodeGen | Generates a function called 'modeldata_initialvalues_set', which evaluates all of the initial conditions specified in the sbml model (initial values, initial assigments, etc...) and stores these values in the appropriate fields in the LLVMModelData structure |
| ►Crrllvm::CodeGenBase< EvalRateRuleRates_FunctionPtr > | |
| Crrllvm::EvalRateRuleRatesCodeGen | Evaluate the current model state and store the results in ModelData.reactionRates |
| ►Crrllvm::CodeGenBase< EvalReactionRates_FunctionPtr > | |
| Crrllvm::EvalReactionRatesCodeGen | Evaluate the current model state and store the results in ModelData.reactionRates |
| ►Crrllvm::CodeGenBase< EvalVolatileStoichCodeGen_FunctionPtr > | |
| Crrllvm::EvalVolatileStoichCodeGen | Evaluate 'volatile stoichiometries', or, stoichiometries that can change over the course of a simulation |
| ►Crrllvm::CodeGenBase< EventCodeGenBase_FunctionPtr > | |
| ►Crrllvm::EventCodeGenBase< EventTriggerCodeGen > | |
| Crrllvm::EventTriggerCodeGen | The trigger of an SBML Event |
| ►Crrllvm::EventCodeGenBase< EventAssignCodeGen > | |
| Crrllvm::EventAssignCodeGen | Evaluate SBML Event Assignments (which execute after the event is triggered) |
| Crrllvm::EventCodeGenBase< Derived > | Base class for evaluating various types of SBML events |
| ►Crrllvm::CodeGenBase< GetEventValueCodeGenBase_FunctionPtr > | |
| ►Crrllvm::GetEventValueCodeGenBase< GetEventDelayCodeGen > | |
| Crrllvm::GetEventDelayCodeGen | Get the delay of an SBML Event |
| ►Crrllvm::GetEventValueCodeGenBase< GetEventPriorityCodeGen > | |
| Crrllvm::GetEventPriorityCodeGen | Get the priority of an SBML Event |
| Crrllvm::GetEventValueCodeGenBase< Derived, FunctionPtrType > | Base class for getting event values |
| ►Crrllvm::CodeGenBase< GetInitialValueCodeGenBase_FunctionPtr > | |
| ►Crrllvm::GetInitialValueCodeGenBase< GetFloatingSpeciesInitAmountCodeGen, true > | |
| Crrllvm::GetFloatingSpeciesInitAmountCodeGen | Get the initial amount of a floating species |
| ►Crrllvm::GetInitialValueCodeGenBase< GetBoundarySpeciesInitAmountCodeGen, true > | |
| Crrllvm::GetBoundarySpeciesInitAmountCodeGen | Get the initial amount of a boundary species |
| ►Crrllvm::GetInitialValueCodeGenBase< GetBoundarySpeciesInitConcentrationCodeGen, false > | |
| Crrllvm::GetBoundarySpeciesInitConcentrationCodeGen | Get the initial concentration of a boundary species |
| ►Crrllvm::GetInitialValueCodeGenBase< GetFloatingSpeciesInitConcentrationCodeGen, false > | |
| Crrllvm::GetFloatingSpeciesInitConcentrationCodeGen | Get the initial concentration of a floating species |
| ►Crrllvm::GetInitialValueCodeGenBase< GetCompartmentInitVolumeCodeGen, false > | |
| Crrllvm::GetCompartmentInitVolumeCodeGen | Get the initial volume of a compartment |
| ►Crrllvm::GetInitialValueCodeGenBase< GetGlobalParameterInitValueCodeGen, false > | |
| Crrllvm::GetGlobalParameterInitValueCodeGen | Get the initial value of a parameter |
| Crrllvm::GetInitialValueCodeGenBase< Derived, substanceUnits > | Base class for getting the initial value of an element |
| ►Crrllvm::CodeGenBase< GetPiecewiseTriggerCodeGen_FunctionPtr > | |
| Crrllvm::GetPiecewiseTriggerCodeGen | Class for getting piecewise trigger values |
| ►Crrllvm::CodeGenBase< GetValueCodeGenBase_FunctionPtr > | |
| ►Crrllvm::GetValueCodeGenBase< GetFloatingSpeciesConcentrationCodeGen, false > | |
| Crrllvm::GetFloatingSpeciesConcentrationCodeGen | Get the current concentration of a floating species |
| ►Crrllvm::GetValueCodeGenBase< GetBoundarySpeciesAmountCodeGen, true > | |
| Crrllvm::GetBoundarySpeciesAmountCodeGen | Get the current amount of a boundary species |
| ►Crrllvm::GetValueCodeGenBase< GetFloatingSpeciesAmountCodeGen, true > | |
| Crrllvm::GetFloatingSpeciesAmountCodeGen | Get the current amount of a floating species |
| ►Crrllvm::GetValueCodeGenBase< GetCompartmentVolumeCodeGen, false > | |
| Crrllvm::GetCompartmentVolumeCodeGen | Get the current volume of a compartment |
| ►Crrllvm::GetValueCodeGenBase< GetBoundarySpeciesConcentrationCodeGen, false > | |
| Crrllvm::GetBoundarySpeciesConcentrationCodeGen | Get the current concentration of a boundary species |
| ►Crrllvm::GetValueCodeGenBase< GetGlobalParameterCodeGen, false > | |
| Crrllvm::GetGlobalParameterCodeGen | Get the current value of a parameter |
| Crrllvm::GetValueCodeGenBase< Derived, substanceUnits > | Base class for getting the current value of an element |
| ►Crrllvm::CodeGenBase< SetValueCodeGenBase_FunctionPtr > | |
| Crrllvm::SetValueCodeGenBase< Derived, substanceUnits > | Base class for setting values |
| ►Crr::CompiledModelGenerator | Both compiled model generators (C and CSharp) share a lot of functionality, so implement that here |
| Crr::CModelGenerator | Generate executable SBML models by generating and compiling C source code into shared libraries with an external C compiler |
| Crr::CompiledModelState | Saves the 'state' of a Model |
| ►Crr::Compiler | Interface to manipulate 'compiler' settings |
| Crr::CCompiler | Compiler class for the C based model system |
| Crrllvm::LLVMCompiler | Class LLVMCompiler |
| Crr::Config | Read or store default values |
| Crrllvm::SymbolForest::ConstIterator | Syntatically the same as a std::map<std::string, const libsbml::ASTNode*>::const_iterator |
| ►Crr::Dictionary | This class is frozen, no new features A dictionary interface that objects can implement |
| ►Crr::BasicDictionary | This class is frozen, no new features Basic implementation of the Dictionary interface which uses a std unordered std::map to store the values |
| Crr::LoadSBMLOptions | Options for loading SBML into RoadRunner |
| ►Cstd::disjunction | |
| Crr::isValidVariantType< T, std::variant< ALL_T... > > | |
| Crr::Event | |
| Crrllvm::Event | The Event class, which mirrors an SBML Event |
| Crr::EventListener | Notifies the user of SBML events |
| Crrllvm::EventPredicate | Struct to check the event ID number of an event ID |
| Crrllvm::EventQueue | When events are queued to execute, but have not yet executed |
| ►Cstd::exception | |
| Crr::EventListenerException | |
| ►Crr::Exception | The RoadRunner exception class |
| Crr::CVODEException | Exception class for scanners |
| Crr::CoreException | Generic exception class |
| Crr::DidNotConvergeException | Exception class for scanners |
| Crr::InvalidKeyException | Exception class for scanners |
| Crr::KinsolException | Exception class for scanners |
| Crr::NLEQException | Exception class for scanners |
| Crr::NOMException | Exception class for scanners |
| Crr::NotImplementedException | Exception class for scanners |
| Crr::NullPointerException | Exception class for scanners |
| Crr::ScannerException | Exception class for scanners |
| Crr::UninitializedValueException | Thrown whenever an uninitialized value is encountered, see https://github.com/sys-bio/roadrunner/issues/180 |
| ►Crr::ExecutableModel | Base class for all code generation systems; allows compiling and evaluating the model |
| Crr::CompiledExecutableModel | Both the CModelGenerator and the CSharpModelGenerator use the same paradigm of producing source code, calling a external compiler and loadig the resulting shared library |
| Crrllvm::LLVMExecutableModel | LLVM executable model |
| Crr::ExecutableModelFactory | A factory class to create ExecutableModel objects |
| Crr::IntegratorListener | IntegratorListener listens for integrator events |
| Crr::isValidVariantType< T, ALL_T > | Generic type checking mechanism for membership of type T in variant ALL_T |
| ►Crrllvm::Jit | Superclass of all Jit types |
| Crrllvm::LLJit | Thin layer around the llvm::orc::LLJit |
| Crrllvm::JitFactory | Use the options in LoadSBMLOptions.ModelGeneratorOpt or fall back on the global Config settings to create a Jit |
| Crrllvm::LLVMModelData | A data structure that is that allows data to be exchanged with running SBML models |
| Crrllvm::LLVMModelDataIRBuilderTesting | Testing class |
| Crrllvm::LLVMModelDataSymbols | Stores the names of all the symbols in the sbml model and thier indexes in the ModelData arrays |
| Crrllvm::LLVMModelGenerator | General concepts: |
| ►Crrllvm::LoadSymbolResolver | LLVM load instruction class |
| Crrllvm::FunctionResolver | Not thread safe – but perfectly fine if stack allocated |
| Crrllvm::KineticLawParameterResolver | Sorts out local parameters in a kinetic law |
| ►Crrllvm::LoadSymbolResolverBase | Provide common sbml model functionality to three kinds of resolvers |
| Crrllvm::SBMLInitialValueSymbolResolver | Pulls values from the original sbml document |
| Crr::Logger | The roadrunner logger |
| Crr::LoggingBuffer | Poco LogStream dumps to the log when a newline i.e |
| ►Cstd::map | |
| Crr::IntStringHashTable | |
| Crr::StringSymbolHashTable | |
| ►Cls::Matrix | |
| Crr::Matrix< T > | A basic local matrix class, based on the libstruct version |
| Crr::Matrix3D< IndexType, DataType > | A basic local 3D version of the Matrix class, based on initializer_list |
| Crrllvm::ModelDataIRBuilder | The model data IR builder |
| Crrllvm::ModelGeneratorContext | All LLVM code generating objects basically need at a minimum three things to operate: |
| Crrllvm::ModelResourceProvider | |
| Crr::ModelSharedLibrary | Access an actual compiled shared library (.so, .dll or .dylib) that was compiled by a ModelGenerator and provides access to the exported C functions |
| Crr::ModelSymbols | |
| ►CMTRand_int32 | |
| CMTRand | |
| CMTRand53 | |
| CMTRand_closed | |
| CMTRand_open | |
| Crr::NOMSupport | Methods to query various information from an SBML document |
| ►Cllvm::ObjectCache | |
| Crrllvm::SBMLModelObjectCache | Stores SBML model as object files for later use |
| Crr::PendingAssignment | Holds a handle to a block of memory allocated by the model, the model is also responsible for freeing this block |
| Crr::Random | |
| Crrllvm::Random | Define and collect ways to generate random values and values from random distributions |
| Crrllvm::LLVMModelSymbols::ReactionSymbols | Hold the symbols that belong to a reactions |
| ►Crr::Registrable | Handles constructing a solver and contains meta information about it |
| ►Crr::Solver | Base class for all integrators and steady state solvers |
| ►Crr::Integrator | Integrator is an abstract base class that provides an interface to specific integrator class implementations |
| Crr::CVODEIntegrator | A RoadRunner integrator based on CVODE; serves as RoadRunner's main integrator for ODEs |
| Crr::EulerIntegrator | An example class intended to show how to create an Integrator |
| Crr::GillespieIntegrator | RoadRunner's implementation of the Gillespie SSA |
| Crr::RK45Integrator | A Runge-Kutta Fehlberg method for roadrunner |
| Crr::RK4Integrator | A super basic 4'th order fixed step integrator |
| ►Crr::SensitivitySolver | Generic interface for all SensitivitySolvers |
| Crr::SteadyStateSensitivitySolver | Genetic interface for sensitivity solvers that solve for steady state before computing model sensitivities |
| ►Crr::TimeSeriesSensitivitySolver | Generic interface for sensitivity solvers that integrate the model and compute sensitivities at each time point |
| Crr::ForwardSensitivitySolver | Time based sensivitity solver |
| ►Crr::SteadyStateSolver | SteadyStateSolver is an abstract base class that provides an interface to specific steady-state solver class implementations |
| ►Crr::KinsolSteadyStateSolver | Base class to steady state solvers from the Sundials package |
| Crr::FixedPointIteration | Implementation of the fixed point iteration form of the kinsol steady state solver |
| ►Crr::NewtonIteration | Implementation of the newton iteration form of the kinsol steady state solver |
| Crr::BasicNewtonIteration | Solve for steady state using Kinsol's implementation of Newton Iteration |
| Crr::LinesearchNewtonIteration | Solve for steady state using Kinsol's implementation of Newton Iteration with linesearch globalization |
| Crr::NLEQSolver | Base class for NLEQ type steady state solvers |
| ►Crr::SteadyStateSolverDecorator | The base class Decorator follows the same interface as other SteadyStateSolvers |
| Crr::PresimulationDecorator | Wrapper class to change the solve() method of SteadyStateSolver types |
| Crr::PresimulationProgramDecorator | Wrapper class to change the solve() method of SteadyStateSolver types |
| ►Crr::RegistrationFactory | Constructs new integrators |
| Crr::IntegratorFactory | Constructs new integrators |
| Crr::SensitivitySolverFactory | Constructs new integrators |
| Crr::SteadyStateSolverFactory | Constructs new integrators |
| Crr::RoadRunner | The main RoadRunner class |
| Crr::RoadRunnerData | Used for simulation output, and provides a wrapper around 2D matrix data |
| Crr::RoadRunnerImpl | Implemention class, hide all details here |
| Crr::RoadRunnerMap | Hash table designed for storing RoadRunner models |
| Crr::RoadRunnerOptions | A set of options that determine how the top level RoadRunner class should behave |
| CRRCData | Structure for the result type from the simulate calls. The client is responsible for freeing the RRCDataPtr |
| CRRComplex | Structure for a complex number |
| CRRComplexMatrix | Structure for a simple complex Matrix type |
| CRRComplexVector | Structure for a simple complex Vector type |
| CRRDoubleMatrix | Structure for a simple double Matrix type |
| CRRList | A list type, stores int, double, strings and lists |
| CRRListItem | A single list element type |
| Crr::RRRule | |
| CRRStringArray | Structure for a simple vector of strings |
| CRRVector | Structure for a simple vector of doubles |
| ►Cstd::runtime_error | |
| Crr::IntegratorException | The exception class thrown by the Integrator |
| Crr::SBMLReader | Read an sbml document from either disk, a remote url, or as a std::string |
| Crr::SBMLSymbol | |
| Crr::SBMLSymbolDependencies | |
| ►Clibsbml::SBMLVisitor | |
| Crrllvm::AssignmentRuleEvaluator | Attaches to an existing symbol forest and applies any asigment rule found in the model to the forest |
| Crrllvm::LLVMModelSymbols | Hold all the un-evaluated symbolic inforamtion in the model |
| Crr::Scanner | |
| Crr::SelectionRecord | Way to find sbml model elements using the RoadRunner syntax |
| Crr::Setting | Store a roadrunner option (or setting) as a Variant type |
| Crr::SimulateOptions | This class is frozen, no new features RoadRunner simulation options |
| CSModelData | A data structure that is that allows data to be exchanged with running SBML models |
| Crr::sort_pred | |
| Crr::SortByPriority | |
| Crrllvm::LLVMModelDataSymbols::SpeciesReferenceInfo | Info about an entry in the stoich matrix |
| Crrllvm::StoreSymbolResolver | LLVM store symbol class |
| ►Crr::StringBuilder | |
| Crr::CodeBuilder | |
| Crr::StringList | |
| Crr::StringListContainer | |
| Crr::SVD | The routine computes the singular value decomposition (SVD) of a real m-by-n matrix |
| Crr::Symbol | An SBML species definition |
| Crrllvm::SymbolForest | Similar to a symbol table, except instead of a name / value, we have a name / tree, where the tree is the root of an ASTNode tree |
| Crr::Token | |
| Crr::Variant | A basic type to hold a variety of data types |
| Crr::VariantImpl | |
| ►Cstd::vector | |
| Crr::SymbolList | |
