roadrunner
2.6.0
Fast simulator for SBML models
|
Deterministic, stochastic, and hybrid simulation algorithms. More...
Functions | |
C_DECL_SPEC bool rrcCallConv | setConfigurationXML (RRHandle handle, const char *caps) |
Set the simulator's capabilities. More... | |
C_DECL_SPEC char *rrcCallConv | getConfigurationXML (RRHandle handle) |
Get the simulator's capabilities. More... | |
C_DECL_SPEC bool rrcCallConv | setTimeStart (RRHandle handle, double timeStart) |
Set the time start for a time course simulation. More... | |
C_DECL_SPEC bool rrcCallConv | setTimeEnd (RRHandle handle, double timeEnd) |
Set the time end for a time course simulation. More... | |
C_DECL_SPEC bool rrcCallConv | setNumPoints (RRHandle handle, int numberOfPoints) |
Set the number of points to generate in a time course simulation. More... | |
C_DECL_SPEC bool rrcCallConv | setTimes (RRHandle handle, double *times, int size) |
Set the times vector to output in a time course simulation. More... | |
C_DECL_SPEC bool rrcCallConv | setTimeCourseSelectionList (RRHandle handle, const char *list) |
Set the selection list for output from simulate(void) or simulateEx(void) More... | |
C_DECL_SPEC RRStringArrayPtr rrcCallConv | getTimeCourseSelectionList (RRHandle handle) |
Get the current selection list for simulate(void) or simulateEx(void) More... | |
C_DECL_SPEC RRCDataPtr rrcCallConv | simulate (RRHandle handle) |
Carry out a time-course simulation. setTimeStart, setTimeEnd, setNumPoints, etc are used to set the simulation characteristics. More... | |
C_DECL_SPEC bool rrcCallConv | simulateNoReturn (RRHandle handle) |
Carry out a time-course simulation. setTimeStart, setTimeEnd, setNumPoints, etc are used to set the simulation characteristics. More... | |
C_DECL_SPEC RRCDataPtr rrcCallConv | getSimulationResult (RRHandle handle) |
Retrieve the result of the last simulation. More... | |
C_DECL_SPEC RRHandle rrcCallConv | getSimulationResultAsDoubleMatrix (RRHandle handle) |
Retrieve the result of the last simulation as a DoubleMatrix. More... | |
C_DECL_SPEC RRCDataPtr rrcCallConv | 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... | |
C_DECL_SPEC bool rrcCallConv | simulateExNoReturn (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, but do not return results. More... | |
C_DECL_SPEC RRCDataPtr rrcCallConv | simulateTimes (RRHandle handle, const double *times, int size) |
Carry out a time-course simulation based on the given arguments, time start, time end and number of points. More... | |
C_DECL_SPEC bool rrcCallConv | oneStep (RRHandle handle, const double currentTime, const double stepSize, double *value) |
Carry out a one step integration of the model. More... | |
C_DECL_SPEC bool rrcCallConv | getTimeStart (RRHandle handle, double *timeStart) |
Get the value of the current time start. More... | |
C_DECL_SPEC bool rrcCallConv | getTimeEnd (RRHandle handle, double *timeEnd) |
Get the value of the current time end. More... | |
C_DECL_SPEC bool rrcCallConv | getNumPoints (RRHandle handle, int *numPoints) |
Get the value of the current number of points. More... | |
C_DECL_SPEC bool rrcCallConv | setTimeCourseSelectionListEx (RRHandle handle, int length, const char **list) |
Set the selection list for output from simulate(void) or simulateEx(void) Use setTimeCourseSelectionListEx(handle, length, list) to set the simulate selection list. Compared to setTimeCourseSelectionList, setTimeCourseSelectionListEx, expects a list of char* strings otherwise it has identical functionality. More... | |
Deterministic, stochastic, and hybrid simulation algorithms.
C_DECL_SPEC char* rrcCallConv getConfigurationXML | ( | RRHandle | handle | ) |
Get the simulator's capabilities.
Example:
[in] | handle | Handle to a RoadRunner instance |
C_DECL_SPEC bool rrcCallConv getNumPoints | ( | RRHandle | handle, |
int * | numPoints | ||
) |
Get the value of the current number of points.
Example:
[in] | handle | Handle to a RoadRunner instance |
numPoints | The current value for the number of points |
C_DECL_SPEC RRCDataPtr rrcCallConv getSimulationResult | ( | RRHandle | handle | ) |
Retrieve the result of the last simulation.
[in] | handle | Handle to a RoadRunner instance |
Retrieve the result of the last simulation as a DoubleMatrix.
[in] | handle | Handle to a RoadRunner instance |
C_DECL_SPEC RRStringArrayPtr rrcCallConv getTimeCourseSelectionList | ( | RRHandle | handle | ) |
Get the current selection list for simulate(void) or simulateEx(void)
[in] | handle | Handle to a RoadRunner instance |
C_DECL_SPEC bool rrcCallConv getTimeEnd | ( | RRHandle | handle, |
double * | timeEnd | ||
) |
Get the value of the current time end.
Example:
[in] | handle | Handle to a RoadRunner instance |
timeEnd | The current value for the time end |
C_DECL_SPEC bool rrcCallConv getTimeStart | ( | RRHandle | handle, |
double * | timeStart | ||
) |
Get the value of the current time start.
Example:
[in] | handle | Handle to a RoadRunner instance |
[out] | timeStart | The current value for the time start |
C_DECL_SPEC bool rrcCallConv oneStep | ( | RRHandle | handle, |
const double | currentTime, | ||
const double | stepSize, | ||
double * | value | ||
) |
Carry out a one step integration of the model.
Example:
[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) |
C_DECL_SPEC bool rrcCallConv setConfigurationXML | ( | RRHandle | handle, |
const char * | caps | ||
) |
Set the simulator's capabilities.
[in] | handle | Handle to a RoadRunner instance |
[out] | caps | An XML string that specifies the simulators capabilities |
C_DECL_SPEC bool rrcCallConv setNumPoints | ( | RRHandle | handle, |
int | numberOfPoints | ||
) |
Set the number of points to generate in a time course simulation.
[in] | handle | Handle to a RoadRunner instance |
[in] | numberOfPoints | Number of points to generate in the time course simulation |
C_DECL_SPEC bool rrcCallConv 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:
or
setTimeCourseSelectionList ("Time S1 J1 J2")
[in] | handle | Handle to a RoadRunner instance |
[in] | list | A string of Ids separated by spaces or comma characters |
C_DECL_SPEC bool rrcCallConv setTimeCourseSelectionListEx | ( | RRHandle | handle, |
int | length, | ||
const char ** | list | ||
) |
Set the selection list for output from simulate(void) or simulateEx(void) Use setTimeCourseSelectionListEx(handle, length, list) to set the simulate selection list. Compared to setTimeCourseSelectionList, setTimeCourseSelectionListEx, expects a list of char* strings otherwise it has identical functionality.
[in] | handle | Handle to a RoadRunner instance |
[in] | length | Number of elements in the list |
[in] | list | A list of char* strings of Ids |
C_DECL_SPEC bool rrcCallConv setTimeEnd | ( | RRHandle | handle, |
double | timeEnd | ||
) |
Set the time end for a time course simulation.
[in] | handle | Handle to a RoadRunner instance |
[in] | timeEnd |
C_DECL_SPEC bool rrcCallConv setTimes | ( | RRHandle | handle, |
double * | times, | ||
int | size | ||
) |
Set the times vector to output in a time course simulation.
[in] | handle | Handle to a RoadRunner instance |
[in] | times | vector of doubles to use as time output points. |
[in] | size | length of the times vector. |
C_DECL_SPEC bool rrcCallConv setTimeStart | ( | RRHandle | handle, |
double | timeStart | ||
) |
Set the time start for a time course simulation.
[in] | handle | Handle to a RoadRunner instance |
[in] | timeStart |
C_DECL_SPEC RRCDataPtr rrcCallConv simulate | ( | RRHandle | handle | ) |
Carry out a time-course simulation. setTimeStart, setTimeEnd, setNumPoints, etc are used to set the simulation characteristics.
[in] | handle | Handle to a RoadRunner instance |
C_DECL_SPEC RRCDataPtr rrcCallConv 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:
[in] | handle | Handle to a RoadRunner instance |
[in] | timeStart | Time start |
[in] | timeEnd | Time end |
[in] | numberOfPoints | Number of points to generate |
C_DECL_SPEC bool rrcCallConv simulateExNoReturn | ( | 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, but do not return results.
Example:
[in] | handle | Handle to a RoadRunner instance |
[in] | timeStart | Time start |
[in] | timeEnd | Time end |
[in] | numberOfPoints | Number of points to generate |
C_DECL_SPEC bool rrcCallConv simulateNoReturn | ( | RRHandle | handle | ) |
Carry out a time-course simulation. setTimeStart, setTimeEnd, setNumPoints, etc are used to set the simulation characteristics.
[in] | handle | Handle to a RoadRunner instance |
C_DECL_SPEC RRCDataPtr rrcCallConv simulateTimes | ( | RRHandle | handle, |
const double * | times, | ||
int | size | ||
) |
Carry out a time-course simulation based on the given arguments, time start, time end and number of points.
Example:
[in] | handle | Handle to a RoadRunner instance |
[in] | times | array of time points |
[in] | size | size of time point array |