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 |