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roadrunner
2.6.0
Fast simulator for SBML models
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| ►Nrr | |
| CVariantImpl | |
| CVariant | A basic type to hold a variety of data types |
| CBasicNewtonIteration | Solve for steady state using Kinsol's implementation of Newton Iteration |
| CCVODEIntegrator | A RoadRunner integrator based on CVODE; serves as RoadRunner's main integrator for ODEs |
| CDictionary | This class is frozen, no new features A dictionary interface that objects can implement |
| CBasicDictionary | This class is frozen, no new features Basic implementation of the Dictionary interface which uses a std unordered std::map to store the values |
| CEulerIntegrator | An example class intended to show how to create an Integrator |
| CExecutableModelFactory | A factory class to create ExecutableModel objects |
| CFixedPointIteration | Implementation of the fixed point iteration form of the kinsol steady state solver |
| CForwardSensitivitySolver | Time based sensivitity solver |
| CGillespieIntegrator | RoadRunner's implementation of the Gillespie SSA |
| CIntegratorListener | IntegratorListener listens for integrator events |
| CIntegrator | Integrator is an abstract base class that provides an interface to specific integrator class implementations |
| CIntegratorException | The exception class thrown by the Integrator |
| CIntegratorFactory | Constructs new integrators |
| CKinsolSteadyStateSolver | Base class to steady state solvers from the Sundials package |
| CLinesearchNewtonIteration | Solve for steady state using Kinsol's implementation of Newton Iteration with linesearch globalization |
| CMatrix | A basic local matrix class, based on the libstruct version |
| CMatrix3D | A basic local 3D version of the Matrix class, based on initializer_list |
| CNewtonIteration | Implementation of the newton iteration form of the kinsol steady state solver |
| CNLEQSolver | Base class for NLEQ type steady state solvers |
| CPresimulationDecorator | Wrapper class to change the solve() method of SteadyStateSolver types |
| CPresimulationProgramDecorator | Wrapper class to change the solve() method of SteadyStateSolver types |
| CRegistrable | Handles constructing a solver and contains meta information about it |
| CRegistrationFactory | Constructs new integrators |
| CRK45Integrator | A Runge-Kutta Fehlberg method for roadrunner |
| CRK4Integrator | A super basic 4'th order fixed step integrator |
| CCompiler | Interface to manipulate 'compiler' settings |
| CConfig | Read or store default values |
| CException | The RoadRunner exception class |
| CCoreException | Generic exception class |
| CScannerException | Exception class for scanners |
| CNLEQException | Exception class for scanners |
| CNOMException | Exception class for scanners |
| CCVODEException | Exception class for scanners |
| CKinsolException | Exception class for scanners |
| CDidNotConvergeException | Exception class for scanners |
| CNullPointerException | Exception class for scanners |
| CNotImplementedException | Exception class for scanners |
| CInvalidKeyException | Exception class for scanners |
| CUninitializedValueException | Thrown whenever an uninitialized value is encountered, see https://github.com/sys-bio/roadrunner/issues/180 |
| CEventListener | Notifies the user of SBML events |
| CEventListenerException | |
| CExecutableModel | Base class for all code generation systems; allows compiling and evaluating the model |
| CLoggingBuffer | Poco LogStream dumps to the log when a newline i.e |
| CLogger | The roadrunner logger |
| CRoadRunnerImpl | Implemention class, hide all details here |
| CRoadRunner | The main RoadRunner class |
| CRoadRunnerData | Used for simulation output, and provides a wrapper around 2D matrix data |
| CRoadRunnerMap | Hash table designed for storing RoadRunner models |
| CLoadSBMLOptions | Options for loading SBML into RoadRunner |
| CSimulateOptions | This class is frozen, no new features RoadRunner simulation options |
| CRoadRunnerOptions | A set of options that determine how the top level RoadRunner class should behave |
| CSBMLReader | Read an sbml document from either disk, a remote url, or as a std::string |
| CSelectionRecord | Way to find sbml model elements using the RoadRunner syntax |
| Csort_pred | |
| CSensitivitySolver | Generic interface for all SensitivitySolvers |
| CTimeSeriesSensitivitySolver | Generic interface for sensitivity solvers that integrate the model and compute sensitivities at each time point |
| CSteadyStateSensitivitySolver | Genetic interface for sensitivity solvers that solve for steady state before computing model sensitivities |
| CSensitivitySolverFactory | Constructs new integrators |
| CSetting | Store a roadrunner option (or setting) as a Variant type |
| CisValidVariantType | Generic type checking mechanism for membership of type T in variant ALL_T |
| CisValidVariantType< T, std::variant< ALL_T... > > | |
| CSolver | Base class for all integrators and steady state solvers |
| CSteadyStateSolver | SteadyStateSolver is an abstract base class that provides an interface to specific steady-state solver class implementations |
| CSteadyStateSolverDecorator | The base class Decorator follows the same interface as other SteadyStateSolvers |
| CSteadyStateSolverFactory | Constructs new integrators |
| CSVD | The routine computes the singular value decomposition (SVD) of a real m-by-n matrix |
| CCCompiler | Compiler class for the C based model system |
| CCModelGenerator | Generate executable SBML models by generating and compiling C source code into shared libraries with an external C compiler |
| CCodeBuilder | |
| CCompiledExecutableModel | Both the CModelGenerator and the CSharpModelGenerator use the same paradigm of producing source code, calling a external compiler and loadig the resulting shared library |
| CCompiledModelGenerator | Both compiled model generators (C and CSharp) share a lot of functionality, so implement that here |
| CCompiledModelState | Saves the 'state' of a Model |
| CEvent | |
| CSortByPriority | |
| CStringSymbolHashTable | |
| CIntStringHashTable | |
| CModelSharedLibrary | Access an actual compiled shared library (.so, .dll or .dylib) that was compiled by a ModelGenerator and provides access to the exported C functions |
| CModelSymbols | |
| CNOMSupport | Methods to query various information from an SBML document |
| CPendingAssignment | Holds a handle to a block of memory allocated by the model, the model is also responsible for freeing this block |
| CRandom | |
| CRRRule | |
| CSBMLSymbol | |
| CSBMLSymbolDependencies | |
| CScanner | |
| CStringBuilder | |
| CStringList | |
| CStringListContainer | |
| CSymbol | An SBML species definition |
| CSymbolList | |
| CToken | |
| ►Nrrllvm | |
| CAssignmentRuleEvaluator | Attaches to an existing symbol forest and applies any asigment rule found in the model to the forest |
| CASTNodeCodeGen | All of the LLVM IR generation is handled here |
| CASTNodeCodeGenScalarTicket | Used in LoadSymbolResolverBase::loadReactionRate when resolving a kinetic law |
| CASTNodeFactory | Manages a set of ASTNodes |
| CCodeGen | Base class for code generation |
| CLoadSymbolResolver | LLVM load instruction class |
| CStoreSymbolResolver | LLVM store symbol class |
| CCodeGenBase | Convenience class to pull the vars out of a context, and store them as ivars |
| CEvalConversionFactorCodeGen | Evaluate conversion factors, which change the units of species objects in SBML |
| CEvalInitialConditionsCodeGen | 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 |
| CEvalRateRuleRatesCodeGen | Evaluate the current model state and store the results in ModelData.reactionRates |
| CEvalReactionRatesCodeGen | Evaluate the current model state and store the results in ModelData.reactionRates |
| CEvalVolatileStoichCodeGen | Evaluate 'volatile stoichiometries', or, stoichiometries that can change over the course of a simulation |
| CEventAssignCodeGen | Evaluate SBML Event Assignments (which execute after the event is triggered) |
| CEventCodeGenBase | Base class for evaluating various types of SBML events |
| CEventPredicate | Struct to check the event ID number of an event ID |
| CEvent | The Event class, which mirrors an SBML Event |
| CEventQueue | When events are queued to execute, but have not yet executed |
| CEventTriggerCodeGen | The trigger of an SBML Event |
| CFunctionResolver | Not thread safe – but perfectly fine if stack allocated |
| CGetEventValueCodeGenBase | Base class for getting event values |
| CGetEventTriggerCodeGen | Get the trigger of an SBML Event |
| CGetEventPriorityCodeGen | Get the priority of an SBML Event |
| CGetEventDelayCodeGen | Get the delay of an SBML Event |
| CGetInitialValueCodeGenBase | Base class for getting the initial value of an element |
| CGetFloatingSpeciesInitConcentrationCodeGen | Get the initial concentration of a floating species |
| CGetBoundarySpeciesInitConcentrationCodeGen | Get the initial concentration of a boundary species |
| CGetFloatingSpeciesInitAmountCodeGen | Get the initial amount of a floating species |
| CGetBoundarySpeciesInitAmountCodeGen | Get the initial amount of a boundary species |
| CGetCompartmentInitVolumeCodeGen | Get the initial volume of a compartment |
| CGetGlobalParameterInitValueCodeGen | Get the initial value of a parameter |
| CGetPiecewiseTriggerCodeGen | Class for getting piecewise trigger values |
| CGetValueCodeGenBase | Base class for getting the current value of an element |
| CGetBoundarySpeciesAmountCodeGen | Get the current amount of a boundary species |
| CGetFloatingSpeciesAmountCodeGen | Get the current amount of a floating species |
| CGetBoundarySpeciesConcentrationCodeGen | Get the current concentration of a boundary species |
| CGetFloatingSpeciesConcentrationCodeGen | Get the current concentration of a floating species |
| CGetCompartmentVolumeCodeGen | Get the current volume of a compartment |
| CGetGlobalParameterCodeGen | Get the current value of a parameter |
| CJit | Superclass of all Jit types |
| CJitFactory | Use the options in LoadSBMLOptions.ModelGeneratorOpt or fall back on the global Config settings to create a Jit |
| CKineticLawParameterResolver | Sorts out local parameters in a kinetic law |
| CLLJit | Thin layer around the llvm::orc::LLJit |
| CLLVMCompiler | Class LLVMCompiler |
| CLLVMExecutableModel | LLVM executable model |
| CLLVMModelData | A data structure that is that allows data to be exchanged with running SBML models |
| ►CLLVMModelDataSymbols | Stores the names of all the symbols in the sbml model and thier indexes in the ModelData arrays |
| CSpeciesReferenceInfo | Info about an entry in the stoich matrix |
| CLLVMModelGenerator | General concepts: |
| ►CLLVMModelSymbols | Hold all the un-evaluated symbolic inforamtion in the model |
| CReactionSymbols | Hold the symbols that belong to a reactions |
| CLoadSymbolResolverBase | Provide common sbml model functionality to three kinds of resolvers |
| CModelDataIRBuilder | The model data IR builder |
| CLLVMModelDataIRBuilderTesting | Testing class |
| CModelGeneratorContext | All LLVM code generating objects basically need at a minimum three things to operate: |
| CModelResourceProvider | |
| CRandom | Define and collect ways to generate random values and values from random distributions |
| CSBMLInitialValueSymbolResolver | Pulls values from the original sbml document |
| CSBMLModelObjectCache | Stores SBML model as object files for later use |
| CSetValueCodeGenBase | Base class for setting values |
| ►CSymbolForest | 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 |
| CConstIterator | Syntatically the same as a std::map<std::string, const libsbml::ASTNode*>::const_iterator |
| CMTRand | |
| CMTRand53 | |
| CMTRand_closed | |
| CMTRand_int32 | |
| CMTRand_open | |
| 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 |
| CRRStringArray | Structure for a simple vector of strings |
| CRRVector | Structure for a simple vector of doubles |
| CSModelData | A data structure that is that allows data to be exchanged with running SBML models |
1.9.1