CVODEIntegrator
+CVODEIntegrator
-
class CVODEIntegrator : public rr::Integrator
- LLVM Docs @@ -118,9 +120,9 @@
- » -
- The LibRoadRunner C++ Library » -
- Dictionary +
- +
- The LibRoadRunner C++ Library +
- Dictionary
- View page source @@ -131,7 +133,7 @@
-
class Dictionary
- Utility Functions
- Accessing the SBML Model Variables
- Using RoadRunner from C++ -
- rrPlugins Documentation +
- rrPlugins
- Python RoadRunner API Reference
- The LibRoadRunner C++ Library
- LLVM Docs @@ -118,9 +120,9 @@
- » -
- The LibRoadRunner C++ Library » -
- EulerIntegrator +
- +
- The LibRoadRunner C++ Library +
- EulerIntegrator
- View page source @@ -131,7 +133,7 @@
-
class EulerIntegrator : public rr::Integrator
- Utility Functions
- Accessing the SBML Model Variables
- Using RoadRunner from C++ -
- rrPlugins Documentation +
- rrPlugins
- Python RoadRunner API Reference
- The LibRoadRunner C++ Library
- LLVM Docs @@ -118,9 +120,9 @@
- » -
- The LibRoadRunner C++ Library » -
- ExecutableModelFactory +
- +
- The LibRoadRunner C++ Library +
- ExecutableModelFactory
- View page source @@ -131,7 +133,7 @@
-
class ExecutableModelFactory
- Utility Functions
- Accessing the SBML Model Variables
- Using RoadRunner from C++ -
- rrPlugins Documentation +
- rrPlugins
- Python RoadRunner API Reference
- The LibRoadRunner C++ Library
- LLVM Docs @@ -118,9 +120,9 @@
- » -
- The LibRoadRunner C++ Library » -
- GillespieIntegrator +
- +
- The LibRoadRunner C++ Library +
- GillespieIntegrator
- View page source @@ -131,7 +133,7 @@
-
class GillespieIntegrator : public rr::Integrator
- Utility Functions
- Accessing the SBML Model Variables
- Using RoadRunner from C++ -
- rrPlugins Documentation +
- rrPlugins
- Python RoadRunner API Reference
- The LibRoadRunner C++ Library
- LLVM Docs @@ -118,9 +120,9 @@
- » -
- The LibRoadRunner C++ Library » -
- Integrator +
- +
- The LibRoadRunner C++ Library +
- Integrator
- View page source @@ -131,7 +133,7 @@
-
class Integrator : public rr::Solver
- Utility Functions
- Accessing the SBML Model Variables
- Using RoadRunner from C++ -
- rrPlugins Documentation +
- rrPlugins
- Python RoadRunner API Reference
- The LibRoadRunner C++ Library
- LLVM Docs @@ -118,9 +120,9 @@
- » -
- The LibRoadRunner C++ Library » -
- IntegratorRegistration +
- +
- The LibRoadRunner C++ Library +
- IntegratorRegistration
- View page source @@ -131,7 +133,7 @@
- Utility Functions
- Accessing the SBML Model Variables
- Using RoadRunner from C++ -
- rrPlugins Documentation +
- rrPlugins
- Python RoadRunner API Reference
- The LibRoadRunner C++ Library
- LLVM Docs @@ -118,9 +120,9 @@
- » -
- The LibRoadRunner C++ Library » -
- NLEQ1Solver +
- +
- The LibRoadRunner C++ Library +
- NLEQ1Solver
- View page source @@ -131,7 +133,7 @@
-
class NLEQ1Solver : public rr::NLEQSolver
- Utility Functions
- Accessing the SBML Model Variables
- Using RoadRunner from C++ -
- rrPlugins Documentation +
- rrPlugins
- Python RoadRunner API Reference
- The LibRoadRunner C++ Library
- LLVM Docs @@ -118,9 +120,9 @@
- » -
- The LibRoadRunner C++ Library » -
- NLEQ2Solver +
- +
- The LibRoadRunner C++ Library +
- NLEQ2Solver
- View page source @@ -131,7 +133,7 @@
-
class NLEQ2Solver : public rr::NLEQSolver
- Utility Functions
- Accessing the SBML Model Variables
- Using RoadRunner from C++ -
- rrPlugins Documentation +
- rrPlugins
- Python RoadRunner API Reference
- The LibRoadRunner C++ Library
- LLVM Docs @@ -118,9 +120,9 @@
- » -
- The LibRoadRunner C++ Library » -
- RK45Integrator +
- +
- The LibRoadRunner C++ Library +
- RK45Integrator
- View page source @@ -131,7 +133,7 @@
-
class RK45Integrator : public rr::Integrator
- Utility Functions
- Accessing the SBML Model Variables
- Using RoadRunner from C++ -
- rrPlugins Documentation +
- rrPlugins
- Python RoadRunner API Reference
- The LibRoadRunner C++ Library
- LLVM Docs @@ -118,9 +120,9 @@
- » -
- The LibRoadRunner C++ Library » -
- RK4Integrator +
- +
- The LibRoadRunner C++ Library +
- RK4Integrator
- View page source @@ -131,7 +133,7 @@
-
class RK4Integrator : public rr::Integrator
- Utility Functions
- Accessing the SBML Model Variables
- Using RoadRunner from C++ -
- rrPlugins Documentation +
- rrPlugins
- Python RoadRunner API Reference
- The LibRoadRunner C++ Library
- Developers Documentation @@ -73,8 +75,8 @@
- » -
- RoadRunnerMap +
- +
- RoadRunnerMap
- View page source @@ -85,7 +87,7 @@
-
class RoadRunnerMap
- Utility Functions
- Accessing the SBML Model Variables
- Using RoadRunner from C++ -
- rrPlugins Documentation +
- rrPlugins
- Python RoadRunner API Reference
- The LibRoadRunner C++ Library
- LLVM Docs @@ -118,9 +120,9 @@
- » -
- The LibRoadRunner C++ Library » -
- SBMLValidator +
- +
- The LibRoadRunner C++ Library +
- SBMLValidator
- View page source @@ -131,7 +133,7 @@
-
enum rr::ValidateSBML
- Utility Functions
- Accessing the SBML Model Variables
- Using RoadRunner from C++ -
- rrPlugins Documentation +
- rrPlugins
- Python RoadRunner API Reference
- The LibRoadRunner C++ Library
- LLVM Docs @@ -118,9 +120,9 @@
- » -
- The LibRoadRunner C++ Library » -
- Solver +
- +
- The LibRoadRunner C++ Library +
- Solver
- View page source @@ -131,7 +133,7 @@
-
class Solver : public rr::Registrable
- Utility Functions
- Accessing the SBML Model Variables
- Using RoadRunner from C++ -
- rrPlugins Documentation +
- rrPlugins
- Python RoadRunner API Reference
- The LibRoadRunner C++ Library
- LLVM Docs @@ -118,9 +120,9 @@
- » -
- The LibRoadRunner C++ Library » -
- SolverRegistration +
- +
- The LibRoadRunner C++ Library +
- SolverRegistration
- View page source @@ -131,7 +133,7 @@
- Utility Functions
- Accessing the SBML Model Variables
- Using RoadRunner from C++ -
- rrPlugins Documentation +
- rrPlugins
- Python RoadRunner API Reference
- The LibRoadRunner C++ Library
- LLVM Docs @@ -118,9 +120,9 @@
- » -
- The LibRoadRunner C++ Library » -
- SteadyStateSolver +
- +
- The LibRoadRunner C++ Library +
- SteadyStateSolver
- View page source @@ -131,7 +133,7 @@
-
class SteadyStateSolver : public rr::Solver
- Utility Functions
- Accessing the SBML Model Variables
- Using RoadRunner from C++ -
- rrPlugins Documentation +
- rrPlugins
- Python RoadRunner API Reference
- The LibRoadRunner C++ Library
- LLVM Docs @@ -118,9 +120,9 @@
- » -
- The LibRoadRunner C++ Library » -
- Variant +
- +
- The LibRoadRunner C++ Library +
- Variant
- View page source @@ -131,7 +133,7 @@
-
class Variant
- Utility Functions
- Accessing the SBML Model Variables
- Using RoadRunner from C++ -
- rrPlugins Documentation +
- rrPlugins
- Python RoadRunner API Reference
- The LibRoadRunner C++ Library
- LLVM Docs @@ -118,8 +120,8 @@
- » -
- The LibRoadRunner C++ Library +
- +
- The LibRoadRunner C++ Library
- View page source @@ -130,16 +132,16 @@
- Utility Functions
- Accessing the SBML Model Variables
- Using RoadRunner from C++ -
- rrPlugins Documentation +
- rrPlugins
- Python RoadRunner API Reference
- The LibRoadRunner C++ Library
- LLVM Docs
-
@@ -156,10 +158,10 @@
- » -
- The LibRoadRunner C++ Library » -
- LLVM Docs » -
- ASTNodeCodeGen +
- +
- The LibRoadRunner C++ Library +
- LLVM Docs +
- ASTNodeCodeGen
- View page source @@ -170,7 +172,7 @@
-
class ASTNodeCodeGen
- Utility Functions
- Accessing the SBML Model Variables
- Using RoadRunner from C++ -
- rrPlugins Documentation +
- rrPlugins
- Python RoadRunner API Reference
- The LibRoadRunner C++ Library
- LLVM Docs
-
@@ -156,10 +158,10 @@
- » -
- The LibRoadRunner C++ Library » -
- LLVM Docs » -
- ASTNodeFactory +
- +
- The LibRoadRunner C++ Library +
- LLVM Docs +
- ASTNodeFactory
- View page source @@ -170,7 +172,7 @@
-
class ASTNodeFactory
- Utility Functions
- Accessing the SBML Model Variables
- Using RoadRunner from C++ -
- rrPlugins Documentation +
- rrPlugins
- Python RoadRunner API Reference
- The LibRoadRunner C++ Library
- LLVM Docs
-
@@ -156,10 +158,10 @@
- » -
- The LibRoadRunner C++ Library » -
- LLVM Docs » -
- AssignmentRuleEvaluator +
- +
- The LibRoadRunner C++ Library +
- LLVM Docs +
- AssignmentRuleEvaluator
- View page source @@ -170,7 +172,7 @@
-
class AssignmentRuleEvaluator : public libsbml::SBMLVisitor
- Utility Functions
- Accessing the SBML Model Variables
- Using RoadRunner from C++ -
- rrPlugins Documentation +
- rrPlugins
- Python RoadRunner API Reference
- The LibRoadRunner C++ Library
- LLVM Docs
-
@@ -156,10 +158,10 @@
- » -
- The LibRoadRunner C++ Library » -
- LLVM Docs » -
- CodeGen +
- +
- The LibRoadRunner C++ Library +
- LLVM Docs +
- CodeGen
- View page source @@ -170,7 +172,7 @@
-
class CodeGen
- Utility Functions
- Accessing the SBML Model Variables
- Using RoadRunner from C++ -
- rrPlugins Documentation +
- rrPlugins
- Python RoadRunner API Reference
- The LibRoadRunner C++ Library
- LLVM Docs
-
@@ -156,10 +158,10 @@
- » -
- The LibRoadRunner C++ Library » -
- LLVM Docs » -
- CodeGenBase +
- +
- The LibRoadRunner C++ Library +
- LLVM Docs +
- CodeGenBase
- View page source @@ -170,7 +172,7 @@
-
template<typename FunctionPtrType>
class CodeGenBase
diff --git a/docs/docs-build/C++APIReference/llvm/EvalConversionFactorCodeGen.html b/docs/docs-build/C++APIReference/llvm/EvalConversionFactorCodeGen.html
index d803b8c356..6a68a2049f 100644
--- a/docs/docs-build/C++APIReference/llvm/EvalConversionFactorCodeGen.html
+++ b/docs/docs-build/C++APIReference/llvm/EvalConversionFactorCodeGen.html
@@ -15,7 +15,9 @@
+
+
@@ -56,7 +58,7 @@
- Utility Functions
- Accessing the SBML Model Variables
- Using RoadRunner from C++ -
- rrPlugins Documentation +
- rrPlugins
- Python RoadRunner API Reference
- The LibRoadRunner C++ Library
- LLVM Docs
-
@@ -156,10 +158,10 @@
- » -
- The LibRoadRunner C++ Library » -
- LLVM Docs » -
- EvalConversionFactorCodeGen +
- +
- The LibRoadRunner C++ Library +
- LLVM Docs +
- EvalConversionFactorCodeGen
- View page source @@ -170,7 +172,7 @@
-
class EvalConversionFactorCodeGen : public rrllvm::CodeGenBase<EvalConversionFactorCodeGen_FunctionPtr>
- Utility Functions
- Accessing the SBML Model Variables
- Using RoadRunner from C++ -
- rrPlugins Documentation +
- rrPlugins
- Python RoadRunner API Reference
- The LibRoadRunner C++ Library
- LLVM Docs
-
@@ -156,10 +158,10 @@
- » -
- The LibRoadRunner C++ Library » -
- LLVM Docs » -
- EvalInitialConditionsCodeGen +
- +
- The LibRoadRunner C++ Library +
- LLVM Docs +
- EvalInitialConditionsCodeGen
- View page source @@ -170,7 +172,7 @@
-
class EvalInitialConditionsCodeGen : public rrllvm::CodeGenBase<EvalInitialConditions_FunctionPtr>
- Utility Functions
- Accessing the SBML Model Variables
- Using RoadRunner from C++ -
- rrPlugins Documentation +
- rrPlugins
- Python RoadRunner API Reference
- The LibRoadRunner C++ Library
- LLVM Docs
-
@@ -156,10 +158,10 @@
- » -
- The LibRoadRunner C++ Library » -
- LLVM Docs » -
- EvalRateRuleRatesCodeGen +
- +
- The LibRoadRunner C++ Library +
- LLVM Docs +
- EvalRateRuleRatesCodeGen
- View page source @@ -170,7 +172,7 @@
-
class EvalRateRuleRatesCodeGen : public rrllvm::CodeGenBase<EvalRateRuleRates_FunctionPtr>
- Utility Functions
- Accessing the SBML Model Variables
- Using RoadRunner from C++ -
- rrPlugins Documentation +
- rrPlugins
- Python RoadRunner API Reference
- The LibRoadRunner C++ Library
- LLVM Docs
-
@@ -156,10 +158,10 @@
- » -
- The LibRoadRunner C++ Library » -
- LLVM Docs » -
- EvalReactionRatesCodeGen +
- +
- The LibRoadRunner C++ Library +
- LLVM Docs +
- EvalReactionRatesCodeGen
- View page source @@ -170,7 +172,7 @@
-
class EvalReactionRatesCodeGen : public rrllvm::CodeGenBase<EvalReactionRates_FunctionPtr>
- Utility Functions
- Accessing the SBML Model Variables
- Using RoadRunner from C++ -
- rrPlugins Documentation +
- rrPlugins
- Python RoadRunner API Reference
- The LibRoadRunner C++ Library
- LLVM Docs
-
@@ -156,10 +158,10 @@
- » -
- The LibRoadRunner C++ Library » -
- LLVM Docs » -
- EvalVolatileStoichCodeGen +
- +
- The LibRoadRunner C++ Library +
- LLVM Docs +
- EvalVolatileStoichCodeGen
- View page source @@ -170,7 +172,7 @@
-
class EvalVolatileStoichCodeGen : public rrllvm::CodeGenBase<EvalVolatileStoichCodeGen_FunctionPtr>
- Utility Functions
- Accessing the SBML Model Variables
- Using RoadRunner from C++ -
- rrPlugins Documentation +
- rrPlugins
- Python RoadRunner API Reference
- The LibRoadRunner C++ Library
- LLVM Docs
-
@@ -156,10 +158,10 @@
- » -
- The LibRoadRunner C++ Library » -
- LLVM Docs » -
- EventAssignCodeGen +
- +
- The LibRoadRunner C++ Library +
- LLVM Docs +
- EventAssignCodeGen
- View page source @@ -170,7 +172,7 @@
-
class EventAssignCodeGen : public rrllvm::EventCodeGenBase<EventAssignCodeGen>
- Utility Functions
- Accessing the SBML Model Variables
- Using RoadRunner from C++ -
- rrPlugins Documentation +
- rrPlugins
- Python RoadRunner API Reference
- The LibRoadRunner C++ Library
- LLVM Docs
-
@@ -156,10 +158,10 @@
- » -
- The LibRoadRunner C++ Library » -
- LLVM Docs » -
- EventCodeGenBase +
- +
- The LibRoadRunner C++ Library +
- LLVM Docs +
- EventCodeGenBase
- View page source @@ -170,7 +172,7 @@
-
template<typename Derived>
class EventCodeGenBase : public rrllvm::CodeGenBase<EventCodeGenBase_FunctionPtr>
diff --git a/docs/docs-build/C++APIReference/llvm/EventQueue.html b/docs/docs-build/C++APIReference/llvm/EventQueue.html
index 0fb6fbed3f..77bc6c457b 100644
--- a/docs/docs-build/C++APIReference/llvm/EventQueue.html
+++ b/docs/docs-build/C++APIReference/llvm/EventQueue.html
@@ -15,7 +15,9 @@
+
+
@@ -56,7 +58,7 @@
- Utility Functions
- Accessing the SBML Model Variables
- Using RoadRunner from C++ -
- rrPlugins Documentation +
- rrPlugins
- Python RoadRunner API Reference
- The LibRoadRunner C++ Library
- LLVM Docs
-
@@ -156,10 +158,10 @@
-
-
- LLVM Docs
-
-
- EventCodeGenBase
+EventCodeGenBase
- LLVM Docs
-
-
- EventAssignCodeGen
+EventAssignCodeGen
- LLVM Docs
-
-
- EvalVolatileStoichCodeGen
+EvalVolatileStoichCodeGen
- LLVM Docs
-
-
- EvalReactionRatesCodeGen
+EvalReactionRatesCodeGen
- LLVM Docs
-
-
- EvalRateRuleRatesCodeGen
+EvalRateRuleRatesCodeGen
- LLVM Docs
-
-
- EvalInitialConditionsCodeGen
+EvalInitialConditionsCodeGen
- LLVM Docs
-
-
- EvalConversionFactorCodeGen
+EvalConversionFactorCodeGen
- LLVM Docs
-
-
- CodeGenBase
+CodeGenBase
- LLVM Docs
-
-
- CodeGen
+CodeGen
- LLVM Docs
-
-
- AssignmentRuleEvaluator
+AssignmentRuleEvaluator
- LLVM Docs
-
-
- ASTNodeFactory
+ASTNodeFactory
- LLVM Docs
-
-
- ASTNodeCodeGen
+ASTNodeCodeGen
- LLVM Docs
-
-
- The LibRoadRunner C++ Library
+The LibRoadRunner C++ Library
- Introduction
+Introduction
This document describes the application programming interface (wrappers) of RoadRunner, an open source (BSD) library for computing structural characteristics of cellular networks.
- Creating a new Integrator
+Creating a new Integrator
One of the key design goals of the LibRoadRunner library is extensibility. This means that the library is designed with the idea that most internal components are loosely coupled and that it is simple to add new solvers such as new steady state solvers or integrators. This section @@ -153,16 +155,16 @@
Creating a new Integrator
BasicDictionary d; -d.setItem("integrator", "MyIntegratorName") -r.simulate(&d); +
BasicDictionary d; +d.setItem("integrator", "MyIntegratorName") +rr.simulate(&d);
To create a new integrator, one first needs to create an object that implments the Integrator interface, tell RoadRunner about it.
- Implementing the Integrator interface
+Implementing the Integrator interface
The IntegratorFactory is the ONLY object that creates integrators.
Integrators are created when the IntegratorFactory::New method is called, typically by the top level RoadRunner object. New Integrators are given a pointer to an @@ -245,7 +247,7 @@
Implementing the Integrator interface -
Telling RoadRunner about the new Integrator
+Telling RoadRunner about the new Integrator
In order for the RoadRunner::simulate method use the new integrator, it needs to know about it. The IntegratorFactory is the only object that knows about all the integrators, and a few lines of code need to be added in the implementation of this object so that it can construct one.
@@ -281,14 +283,14 @@Telling RoadRunner about the new Integrator -
A complete example of creating an integrator
+A complete example of creating an integrator
This section includes the complete Euler integrator implemented in EulerIntegrator.h as an example of creating a new integrator. This class has two demo paramters which may be set via the keyword arguments to RoadRunner.simulate in Python, or set via the Dictionary::setItem method on the dictionary that is given to the RoadRunner::simulate method in C++. In Python, this would be:
-r.simulate(integrator='euler', exampleParameter1=123456, exampleParameter2='some value'); -print(r.integrator) +
rr.simulate(integrator='euler', exampleParameter1=123456, exampleParameter2='some value'); +print(rr.integrator)
In Python, all the keyword arguments to the simulate method are packaged up and added to the diff --git a/docs/docs-build/C++APIReference/llvm/ASTNodeCodeGen.html b/docs/docs-build/C++APIReference/llvm/ASTNodeCodeGen.html index 1da3063157..2e6b5e60cc 100644 --- a/docs/docs-build/C++APIReference/llvm/ASTNodeCodeGen.html +++ b/docs/docs-build/C++APIReference/llvm/ASTNodeCodeGen.html @@ -15,7 +15,9 @@ + + @@ -56,7 +58,7 @@
-
-
- Variant
+Variant
-
-
- SteadyStateSolver
+SteadyStateSolver
-
-
- SolverRegistration
+SolverRegistration
Warning
doxygenclass: Cannot find class “rr::SolverRegistrationMgr” in doxygen xml output for project “roadrunner” from directory: /home/vsts/work/1/s/docs/doxygen-output/xml
diff --git a/docs/docs-build/C++APIReference/SteadyStateSolver.html b/docs/docs-build/C++APIReference/SteadyStateSolver.html index f531528c1b..81dd326184 100644 --- a/docs/docs-build/C++APIReference/SteadyStateSolver.html +++ b/docs/docs-build/C++APIReference/SteadyStateSolver.html @@ -15,7 +15,9 @@ + + @@ -56,7 +58,7 @@
-
-
- Solver
+Solver
-
-
- SBMLValidator
+SBMLValidator
-
-
- RK4Integrator
+RK4Integrator
-
-
- RoadRunnerMap
+RoadRunnerMap
-
-
- RK45Integrator
+RK45Integrator
-
-
- NLEQ2Solver
+NLEQ2Solver
-
-
- NLEQ1Solver
+NLEQ1Solver
-
-
- IntegratorRegistration
+IntegratorRegistration
Warning
doxygenclass: Cannot find class “rr::IntegratorRegistrationMgr” in doxygen xml output for project “roadrunner” from directory: /home/vsts/work/1/s/docs/doxygen-output/xml
diff --git a/docs/docs-build/C++APIReference/NLEQ1Solver.html b/docs/docs-build/C++APIReference/NLEQ1Solver.html index 4080e81ff3..789648ab86 100644 --- a/docs/docs-build/C++APIReference/NLEQ1Solver.html +++ b/docs/docs-build/C++APIReference/NLEQ1Solver.html @@ -15,7 +15,9 @@ + + @@ -56,7 +58,7 @@
-
-
- Integrator
+Integrator
-
-
- GillespieIntegrator
+GillespieIntegrator
-
-
- ExecutableModelFactory
+ExecutableModelFactory
-
-
- EulerIntegrator
+EulerIntegrator
-
-