Deterministic, stochastic, and hybrid simulation algorithms. More...

Functions
bool	setConfigurationXML (RRHandle handle, const char *caps)
	Set the simulator's capabilities. More...

char *	getConfigurationXML (RRHandle handle)
	Get the simulator's capabilities. More...

bool	setTimeStart (RRHandle handle, double timeStart)
	Set the time start for a time course simulation. More...

bool	setTimeEnd (RRHandle handle, double timeEnd)
	Set the time end for a time course simulation. More...

bool	setNumPoints (RRHandle handle, int numberOfPoints)
	Set the number of points to generate in a time course simulation. More...

bool	setTimeCourseSelectionList (RRHandle handle, const char *list)
	Set the selection list for output from simulate(void) or simulateEx(void) More...

RRStringArrayPtr	getTimeCourseSelectionList (RRHandle handle)
	Get the current selection list for simulate(void) or simulateEx(void) More...

RRDataHandle	simulate (RRHandle handle)
	Carry out a time-course simulation, use setTimeStart, setTimeEnd and setNumPoints etc to set the simulation characteristics. More...

RRCDataPtr	getSimulationResult (RRHandle handle)
	Retrieve the result of the last simulation. More...

RRDataHandle	getRoadRunnerData (RRHandle handle)
	Retrieve a handle to RoadRunners internal data. More...

RRDataHandle	simulateEx (RRHandle handle, const double timeStart, const double timeEnd, const int numberOfPoints)
	Carry out a time-course simulation based on the given arguments, time start, time end and number of points. More...

bool	oneStep (RRHandle handle, const double currentTime, const double stepSize, double *value)
	Carry out a one step integration of the model. More...

bool	getTimeStart (RRHandle handle, double *timeStart)
	Get the value of the current time start. More...

bool	getTimeEnd (RRHandle handle, double *timeEnd)
	Get the value of the current time end. More...

bool	getNumPoints (RRHandle handle, int *numPoints)
	Get the value of the current number of points. More...

bool	reset (RRHandle handle)
	Reset all floating species concentrations to their intial conditions. More...

Detailed Description

Deterministic, stochastic, and hybrid simulation algorithms.

Function Documentation

char* getConfigurationXML ( RRHandle handle )

Get the simulator's capabilities.

Example:

 <caps name="RoadRunner" description="Settings For RoadRunner">
  <section name="integration" method="CVODE" description="CVODE Integrator">
    <cap name="BDFOrder" value="5" hint="Maximum order for BDF Method" type="integer" />
    <cap name="AdamsOrder" value="12" hint="Maximum order for Adams Method" type="integer" />
    <cap name="rtol" value="1E-06" hint="Relative Tolerance" type="double" />
    <cap name="atol" value="1E-12" hint="Absolute Tolerance" type="double" />
    <cap name="maxsteps" value="10000" hint="Maximum number of internal stepsc" type="integer" />
    <cap name="initstep" value="0" hint="the initial step size" type="double" />
    <cap name="minstep" value="0" hint="specifies a lower bound on the magnitude of the step size." type="double" />
    <cap name="maxstep" value="0" hint="specifies an upper bound on the magnitude of the step size." type="double" />
    <cap name="conservation" value="1" hint="enables (=1) or disables (=0) the conservation analysis of models for timecourse simulations." type="int" />
    <cap name="allowRandom" value="1" hint="if enabled (=1), reinterprets certain function definitions as distributions and draws random numbers for it." type="int" />
    <cap name="usekinsol" value="0" hint="Is KinSol used as steady state integrator" type="int" />
  </section>
  <section name="SteadyState" method="NLEQ2" description="NLEQ2 Steady State Solver">
    <cap name="MaxIterations" value="100" hint="Maximum number of newton iterations" type="integer" />
    <cap name="relativeTolerance" value="0.0001" hint="Relative precision of solution components" type="double" />
  </section>
</caps>

Parameters

[in] handle Handle to a RoadRunner instance

Returns: Returns null if it fails, otherwise it returns the simulator's capabilities in the form of an XML string

bool getNumPoints	(	RRHandle	handle,
		int *	numPoints
	)

Get the value of the current number of points.

Example:

status = getNumPoints (rrHandle, &numberOfPoints);

Parameters

[in]	handle	Handle to a RoadRunner instance
	numPoints	The current value for the number of points

Returns: Returns true if successful

RRDataHandle getRoadRunnerData ( RRHandle handle )

Retrieve a handle to RoadRunners internal data.

Parameters

[in] handle Handle to a RoadRunner instance

Returns: Returns an handle to roadrunners internal data object

RRCDataPtr getSimulationResult ( RRHandle handle )

Retrieve the result of the last simulation.

Parameters

[in] handle Handle to a RoadRunner instance

Returns: Returns an handle to roadrunners internal data object; Returns an array (RRCDataPtr) of columns containing the results of the simulation including string labels for the individual columms.

RRStringArrayPtr getTimeCourseSelectionList ( RRHandle handle )

Get the current selection list for simulate(void) or simulateEx(void)

Parameters

[in] handle Handle to a RoadRunner instance

Returns: A list of symbol Ids indicating the current selection list

bool getTimeEnd	(	RRHandle	handle,
		double *	timeEnd
	)

Get the value of the current time end.

Example:

status = getTimeEnd (rrHandle, &timeEnd);

Parameters

[in]	handle	Handle to a RoadRunner instance
	timeEnd	The current value for the time end

Returns: Returns true if successful

bool getTimeStart	(	RRHandle	handle,
		double *	timeStart
	)

Get the value of the current time start.

Example:

status = getTimeStart (rrHandle, &timeStart);

Parameters

[in]	handle	Handle to a RoadRunner instance
[out]	timeStart	The current value for the time start

Returns: Returns true if successful

bool oneStep	(	RRHandle	handle,
		const double	currentTime,
		const double	stepSize,
		double *	value
	)

Carry out a one step integration of the model.

Example:

status = OneStep (rrHandle, currentTime, timeStep, newTimeStep);

Parameters

[in]	handle	Handle to a RoadRunner instance
[in]	currentTime	The current time in the simulation
[in]	stepSize	The step size to use in the integration
[in]	value	The new time (currentTime + stepSize)

Returns: Returns true if successful

bool reset ( RRHandle handle )

Reset all floating species concentrations to their intial conditions.

Example:

status = reset (RRHandle handle);

Parameters

[in] handle Handle to a RoadRunner instance

Returns: Returns true if successful

bool setConfigurationXML	(	RRHandle	handle,
		const char *	caps
	)

Set the simulator's capabilities.

Parameters

[in]	handle	Handle to a RoadRunner instance
[out]	caps	An XML string that specifies the simulators capabilities

Returns: Returns true if sucessful

bool setNumPoints	(	RRHandle	handle,
		int	numberOfPoints
	)

Set the number of points to generate in a time course simulation.

Parameters

[in]	handle	Handle to a RoadRunner instance
[in]	numberOfPoints	Number of points to generate in the time course simulation

Returns: Returns true if sucessful

bool setTimeCourseSelectionList	(	RRHandle	handle,
		const char *	list
	)

Set the selection list for output from simulate(void) or simulateEx(void)

Use getAvailableTimeCourseSymbols(void) to retrieve the list of all possible symbols.

Example:

setTimeCourseSelectionList ("Time, S1, J1, J2");

or

setTimeCourseSelectionList ("Time S1 J1 J2")

Parameters

[in]	handle	Handle to a RoadRunner instance
[in]	list	A string of Ids separated by spaces or comma characters

Returns: Returns true if sucessful

bool setTimeEnd	(	RRHandle	handle,
		double	timeEnd
	)

Set the time end for a time course simulation.

Parameters

[in]	handle	Handle to a RoadRunner instance
[in]	timeEnd

Returns: Returns true if sucessful

bool setTimeStart	(	RRHandle	handle,
		double	timeStart
	)

Set the time start for a time course simulation.

Parameters

[in]	handle	Handle to a RoadRunner instance
[in]	timeStart

Returns: Returns True if sucessful

RRDataHandle simulate ( RRHandle handle )

Carry out a time-course simulation, use setTimeStart, setTimeEnd and setNumPoints etc to set the simulation characteristics.

Parameters

[in] handle Handle to a RoadRunner instance

Returns: Returns a handle to roadrunners internal data object.

RRDataHandle simulateEx	(	RRHandle	handle,
		const double	timeStart,
		const double	timeEnd,
		const int	numberOfPoints
	)

Carry out a time-course simulation based on the given arguments, time start, time end and number of points.

Example:

RRCDataPtr m;
double timeStart = 0.0;
double timeEnd = 25;
int numberOfPoints = 200;
m = simulateEx (rrHandle, timeStart, timeEnd, numberOfPoints);

Parameters

[in]	handle	Handle to a RoadRunner instance
[in]	timeStart	Time start
[in]	timeEnd	Time end
[in]	numberOfPoints	Number of points to generate

Returns: Returns a handle to roadrunners internal data object.

Functions

Detailed Description

Function Documentation