libRoadRunner C API  1.0.0
 All Data Structures Files Functions Variables Typedefs Enumerations Enumerator Macros Modules Pages
_rrc_api.h
1 
41 #ifndef rrc_apiH
42 #define rrc_apiH
43 #include "rrc_exporter.h"
44 #include "rrc_types.h"
45 #include "rrc_utilities.h"
46 #include "rrc_logging_api.h"
47 #include "rrc_nom_api.h"
48 #include "rrc_libstruct_api.h"
49 
50 #if defined(__cplusplus)
51 namespace rrc { extern "C" {
52 #endif
53 
59 C_DECL_SPEC RRHandle rrcCallConv createRRInstance(void);
60 
71 C_DECL_SPEC RRHandle rrcCallConv createRRInstanceEx(const char* tempFolder, const char* compiler);
72 
78 C_DECL_SPEC bool rrcCallConv freeRRInstance(RRHandle handle);
79 
85 C_DECL_SPEC char* rrcCallConv getInstallFolder(void);
86 
93 C_DECL_SPEC bool rrcCallConv setInstallFolder(const char* folder);
94 
100 C_DECL_SPEC char* rrcCallConv getAPIVersion(void);
101 
108 C_DECL_SPEC char* rrcCallConv getCPPAPIVersion(RRHandle handle);
109 
120 C_DECL_SPEC int rrcCallConv getVersion();
121 
125 C_DECL_SPEC char* rrcCallConv getVersionStr();
126 
127 
131 C_DECL_SPEC char* rrcCallConv getVersionEx();
132 
138 C_DECL_SPEC char* rrcCallConv getExtendedAPIInfo();
139 
145 C_DECL_SPEC char* rrcCallConv getBuildDate(void);
146 
152 C_DECL_SPEC char* rrcCallConv getBuildTime(void);
153 
159 C_DECL_SPEC char* rrcCallConv getBuildDateTime(void);
160 
166 C_DECL_SPEC char* rrcCallConv getCopyright(void);
167 
174 C_DECL_SPEC char* rrcCallConv getInfo(RRHandle handle);
175 
182 C_DECL_SPEC char* rrcCallConv getlibSBMLVersion(RRHandle handle);
183 
195 C_DECL_SPEC bool rrcCallConv setTempFolder(RRHandle handle, const char* folder);
196 
207 C_DECL_SPEC char* rrcCallConv getTempFolder(RRHandle handle);
208 
215 C_DECL_SPEC char* rrcCallConv getWorkingDirectory(void);
216 
223 C_DECL_SPEC char* rrcCallConv getRRCAPILocation(void);
224 
225 
233 C_DECL_SPEC bool rrcCallConv setCompiler(RRHandle handle, const char* fNameWithPath);
234 
239 C_DECL_SPEC char* rrcCallConv getCompiler(RRHandle handle);
240 
249 C_DECL_SPEC bool rrcCallConv setCompilerLocation(RRHandle handle, const char* folder);
250 
259 C_DECL_SPEC char* rrcCallConv getCompilerLocation(RRHandle handle);
260 
268 C_DECL_SPEC bool rrcCallConv setSupportCodeFolder(RRHandle handle, const char* folder);
269 
278 C_DECL_SPEC char* rrcCallConv getSupportCodeFolder(RRHandle handle);
279 
293 C_DECL_SPEC bool rrcCallConv setCodeGenerationMode(RRHandle handle, int mode);
294 
295 
304 C_DECL_SPEC bool rrcCallConv hasError(void);
305 
314 C_DECL_SPEC char* rrcCallConv getLastError(void);
315 
316 // Flags/Options
324 C_DECL_SPEC bool rrcCallConv setComputeAndAssignConservationLaws(RRHandle handle, const bool On_Or_Off);
325 
326 // -----------------------------------------------------------------------
327 // Read and Write models
328 // -----------------------------------------------------------------------
329 
337 C_DECL_SPEC bool rrcCallConv loadSBML(RRHandle handle, const char* sbml);
338 
347 C_DECL_SPEC bool rrcCallConv loadSBMLEx(RRHandle handle, const char* sbml, bool forceRecompile);
348 
356 //C_DECL_SPEC bool rrcCallConv loadSBMLFromFile(const char* fileName);
357 C_DECL_SPEC bool rrcCallConv loadSBMLFromFile(RRHandle handle, const char* fileName);
358 
367 C_DECL_SPEC bool rrcCallConv loadSBMLFromFileE(RRHandle handle, const char* fileName, bool forceRecompile);
368 
375 C_DECL_SPEC bool rrcCallConv clearModel(RRHandle handle);
376 
383 C_DECL_SPEC bool rrcCallConv isModelLoaded(RRHandle handle);
384 
393 C_DECL_SPEC bool rrcCallConv loadSimulationSettings(RRHandle handle, const char* fileName);
394 
401 C_DECL_SPEC char* rrcCallConv getCurrentSBML(RRHandle handle);
402 
409 C_DECL_SPEC char* rrcCallConv getSBML(RRHandle handle);
410 
411 // -------------------------------------------------------------------------
412 // SBML utility methods
413 // -----------------------------------------------------------------------
426 C_DECL_SPEC char* rrcCallConv getParamPromotedSBML(RRHandle handle, const char* sArg);
427 
435 C_DECL_SPEC bool rrcCallConv setConfigurationXML (RRHandle handle, const char* caps);
436 
469 C_DECL_SPEC char* rrcCallConv getConfigurationXML(RRHandle handle);
470 
471 
479 C_DECL_SPEC bool rrcCallConv setTimeStart(RRHandle handle, double timeStart);
480 
488 C_DECL_SPEC bool rrcCallConv setTimeEnd(RRHandle handle, double timeEnd);
489 
497 C_DECL_SPEC bool rrcCallConv setNumPoints(RRHandle handle, int numberOfPoints);
498 
499 
516 C_DECL_SPEC bool rrcCallConv setTimeCourseSelectionList(RRHandle handle, const char* list);
517 //C_DECL_SPEC bool rrcCallConv setTimeCourseSelectionList(const char* list);
518 
526 C_DECL_SPEC RRStringArrayPtr rrcCallConv getTimeCourseSelectionList(RRHandle handle);
527 
538 C_DECL_SPEC RRCDataPtr rrcCallConv simulate(RRHandle handle);
539 
548 C_DECL_SPEC RRCDataPtr rrcCallConv getSimulationResult(RRHandle handle);
549 
550 
575 C_DECL_SPEC RRCDataPtr rrcCallConv simulateEx(RRHandle handle, const double timeStart, const double timeEnd, const int numberOfPoints);
576 
590 C_DECL_SPEC bool rrcCallConv oneStep(RRHandle handle, const double currentTime, const double stepSize, double *value);
591 
602 C_DECL_SPEC bool rrcCallConv getTimeStart(RRHandle handle, double* timeStart);
603 
614 C_DECL_SPEC bool rrcCallConv getTimeEnd(RRHandle handle, double* timeEnd);
615 
626 C_DECL_SPEC bool rrcCallConv getNumPoints (RRHandle handle, int* numPoints);
627 
640 C_DECL_SPEC bool rrcCallConv steadyState(RRHandle handle, double* value);
641 
652 C_DECL_SPEC RRVectorPtr rrcCallConv computeSteadyStateValues(RRHandle handle);
653 
675 C_DECL_SPEC bool rrcCallConv setSteadyStateSelectionList(RRHandle handle, const char* list);
676 
684 C_DECL_SPEC RRStringArrayPtr rrcCallConv getSteadyStateSelectionList(RRHandle handle);
685 
686 
687 // --------------------------------------------------------------------------------
688 // Get and Set Routines
689 // --------------------------------------------------------------------------------
690 
702 C_DECL_SPEC bool rrcCallConv getValue(RRHandle handle, const char* symbolId, double* value);
703 
704 
716 C_DECL_SPEC bool rrcCallConv setValue(RRHandle handle, const char* symbolId, const double value);
717 
718 
728 C_DECL_SPEC RRVectorPtr rrcCallConv getFloatingSpeciesConcentrations(RRHandle handle);
729 
730 
740 C_DECL_SPEC RRVectorPtr rrcCallConv getBoundarySpeciesConcentrations(RRHandle handle);
741 
742 // --------------------------------------------------------------------------------
743 // Parameter Group
744 // --------------------------------------------------------------------------------
745 
755 C_DECL_SPEC RRVectorPtr rrcCallConv getGlobalParameterValues(RRHandle handle);
756 
766 C_DECL_SPEC bool rrcCallConv setBoundarySpeciesByIndex(RRHandle handle, const int index, const double value);
767 
777 C_DECL_SPEC bool rrcCallConv setFloatingSpeciesInitialConcentrationByIndex(RRHandle handle, int index, double value);
778 
788 C_DECL_SPEC bool rrcCallConv getFloatingSpeciesInitialConcentrationByIndex(RRHandle handle, int index, double* value);
789 
799 C_DECL_SPEC bool rrcCallConv setFloatingSpeciesByIndex(RRHandle handle, const int index, const double value);
800 
810 C_DECL_SPEC bool rrcCallConv setGlobalParameterByIndex(RRHandle handle, const int index, const double value);
811 
820 C_DECL_SPEC bool rrcCallConv getBoundarySpeciesByIndex(RRHandle handle, const int index, double* value);
821 
831 C_DECL_SPEC bool rrcCallConv getFloatingSpeciesByIndex(RRHandle handle, const int index, double* value);
832 
841 C_DECL_SPEC bool rrcCallConv getGlobalParameterByIndex(RRHandle handle, const int index, double* value);
842 
852 C_DECL_SPEC bool rrcCallConv getCompartmentByIndex (RRHandle handle, const int index, double* value);
853 
854 
864 C_DECL_SPEC bool rrcCallConv setCompartmentByIndex (RRHandle handle, const int index, const double value);
865 
866 
885 C_DECL_SPEC bool rrcCallConv setFloatingSpeciesConcentrations(RRHandle handle, const RRVectorPtr vec);
886 
905 C_DECL_SPEC bool rrcCallConv setBoundarySpeciesConcentrations(RRHandle handle, const RRVectorPtr vec);
906 
907 
915 C_DECL_SPEC RRDoubleMatrixPtr rrcCallConv getFullJacobian(RRHandle handle);
916 
926 C_DECL_SPEC RRDoubleMatrixPtr rrcCallConv getReducedJacobian(RRHandle handle);
927 
935 C_DECL_SPEC RRDoubleMatrixPtr rrcCallConv getEigenvalues(RRHandle handle);
936 
937 
938 // --------------------------------------------------------------------------------
939 // Stoichiometry methods
940 // --------------------------------------------------------------------------------
941 
949 C_DECL_SPEC RRDoubleMatrixPtr rrcCallConv getStoichiometryMatrix(RRHandle handle);
950 
958 C_DECL_SPEC RRDoubleMatrixPtr rrcCallConv getLinkMatrix(RRHandle handle);
959 
967 C_DECL_SPEC RRDoubleMatrixPtr rrcCallConv getNrMatrix(RRHandle handle);
968 
978 C_DECL_SPEC RRDoubleMatrixPtr rrcCallConv getConservationMatrix(RRHandle handle);
979 
980 // --------------------------------------------------------------------------------
981 // Initial condition Methods
982 // --------------------------------------------------------------------------------
983 
994 C_DECL_SPEC bool rrcCallConv setFloatingSpeciesInitialConcentrations (RRHandle handle, const RRVectorPtr vec);
995 
1005 C_DECL_SPEC RRVectorPtr rrcCallConv getFloatingSpeciesInitialConcentrations (RRHandle handle);
1006 
1016 C_DECL_SPEC RRStringArrayPtr rrcCallConv getFloatingSpeciesInitialConditionIds(RRHandle handle);
1017 
1018 // --------------------------------------------------------------------------------
1019 // Reaction rates
1020 // --------------------------------------------------------------------------------
1021 
1031 C_DECL_SPEC int rrcCallConv getNumberOfReactions(RRHandle handle);
1032 
1033 
1043 C_DECL_SPEC bool rrcCallConv getReactionRate(RRHandle handle, const int index, double* rate);
1044 
1045 
1053 C_DECL_SPEC RRVectorPtr rrcCallConv getReactionRates(RRHandle handle);
1054 
1055 
1064 C_DECL_SPEC RRVectorPtr rrcCallConv getReactionRatesEx (RRHandle handle, const RRVectorPtr vec);
1065 
1066 
1076 C_DECL_SPEC RRVectorPtr rrcCallConv getRatesOfChange(RRHandle handle);
1077 
1087 C_DECL_SPEC RRStringArrayPtr rrcCallConv getRatesOfChangeIds(RRHandle handle);
1088 
1089 
1100 C_DECL_SPEC bool rrcCallConv getRateOfChange(RRHandle handle, const int, double* value);
1101 
1102 
1113 C_DECL_SPEC RRVectorPtr rrcCallConv getRatesOfChangeEx (RRHandle handle, const RRVectorPtr vec);
1114 
1122 C_DECL_SPEC bool rrcCallConv evalModel(RRHandle handle);
1123 
1124 // Get number family
1131 C_DECL_SPEC int rrcCallConv getNumberOfCompartments (RRHandle handle);
1132 
1133 
1139 C_DECL_SPEC int rrcCallConv getNumberOfBoundarySpecies(RRHandle handle);
1140 
1141 
1147 C_DECL_SPEC int rrcCallConv getNumberOfFloatingSpecies(RRHandle handle);
1148 
1149 
1155 C_DECL_SPEC int rrcCallConv getNumberOfGlobalParameters(RRHandle handle);
1156 
1157 // --------------------------------------------------------------------------------
1158 // Get number family
1159 // --------------------------------------------------------------------------------
1160 
1166 C_DECL_SPEC int rrcCallConv getNumberOfDependentSpecies(RRHandle handle);
1167 
1168 
1175 C_DECL_SPEC int rrcCallConv getNumberOfIndependentSpecies(RRHandle handle);
1176 
1177 // --------------------------------------------------------------------------------
1178 // Get Ids family
1179 // --------------------------------------------------------------------------------
1180 
1188 C_DECL_SPEC RRStringArrayPtr rrcCallConv getReactionIds(RRHandle handle);
1189 
1197 C_DECL_SPEC RRStringArrayPtr rrcCallConv getBoundarySpeciesIds(RRHandle handle);
1198 
1206 C_DECL_SPEC RRStringArrayPtr rrcCallConv getFloatingSpeciesIds(RRHandle handle);
1207 
1215 C_DECL_SPEC RRStringArrayPtr rrcCallConv getGlobalParameterIds(RRHandle handle);
1216 
1226 C_DECL_SPEC RRStringArrayPtr rrcCallConv getCompartmentIds(RRHandle handle);
1227 
1235 C_DECL_SPEC RRStringArrayPtr rrcCallConv getEigenvalueIds(RRHandle handle);
1236 
1244 C_DECL_SPEC RRListPtr rrcCallConv getAvailableTimeCourseSymbols(RRHandle handle);
1245 
1253 C_DECL_SPEC RRListPtr rrcCallConv getAvailableSteadyStateSymbols(RRHandle handle);
1254 
1255 // --------------------------------------------------------------------------------
1256 // MCA methods
1257 // --------------------------------------------------------------------------------
1258 
1266 C_DECL_SPEC RRListPtr rrcCallConv getElasticityCoefficientIds(RRHandle handle);
1267 
1275 C_DECL_SPEC RRListPtr rrcCallConv getUnscaledFluxControlCoefficientIds(RRHandle handle);
1276 
1284 C_DECL_SPEC RRListPtr rrcCallConv getFluxControlCoefficientIds(RRHandle handle);
1285 
1293 C_DECL_SPEC RRListPtr rrcCallConv getUnscaledConcentrationControlCoefficientIds(RRHandle handle);
1294 
1302 C_DECL_SPEC RRListPtr rrcCallConv getConcentrationControlCoefficientIds(RRHandle handle);
1303 
1311 C_DECL_SPEC RRDoubleMatrixPtr rrcCallConv getUnscaledElasticityMatrix(RRHandle handle);
1312 
1320 C_DECL_SPEC RRDoubleMatrixPtr rrcCallConv getScaledElasticityMatrix(RRHandle handle);
1321 
1322 
1333 C_DECL_SPEC bool rrcCallConv getScaledFloatingSpeciesElasticity(RRHandle handle, const char* reactionId, const char* speciesId, double* value);
1334 
1344 
1345 
1354 
1363 
1371 C_DECL_SPEC RRDoubleMatrixPtr rrcCallConv getScaledFluxControlCoefficientMatrix(RRHandle handle);
1372 
1383 C_DECL_SPEC bool rrcCallConv getuCC (RRHandle handle, const char* variable, const char* parameter, double* value);
1384 
1395 C_DECL_SPEC bool rrcCallConv getCC (RRHandle handle, const char* variable, const char* parameter, double* value);
1396 
1407 C_DECL_SPEC bool rrcCallConv getEE(RRHandle handle, const char* name, const char* species, double* value);
1408 
1419 C_DECL_SPEC bool rrcCallConv getuEE(RRHandle handle, const char* name, const char* species, double* value);
1420 
1421 // --------------------------------------------------------------------------------
1422 // Stochastic methods
1423 // --------------------------------------------------------------------------------
1424 
1433 C_DECL_SPEC bool rrcCallConv getSeed(RRHandle handle, long* seed);
1434 
1443 C_DECL_SPEC bool rrcCallConv setSeed(RRHandle handle, long seed);
1444 
1456 C_DECL_SPEC RRCDataPtr rrcCallConv gillespie(RRHandle handle);
1457 
1480 C_DECL_SPEC RRCDataPtr rrcCallConv gillespieEx(RRHandle handle, double timeStart, double timeEnd);
1481 
1493 C_DECL_SPEC RRCDataPtr rrcCallConv gillespieOnGrid(RRHandle handle);
1494 
1520 C_DECL_SPEC RRCDataPtr rrcCallConv gillespieOnGridEx(RRHandle handle, double timeStart, double timeEnd, int numberOfPoints);
1521 
1535 C_DECL_SPEC RRCDataPtr rrcCallConv gillespieMeanOnGrid(RRHandle handle, int numberOfSimulations);
1536 
1564 C_DECL_SPEC RRCDataPtr rrcCallConv gillespieMeanOnGridEx(RRHandle handle, double timeStart, double timeEnd, int numberOfPoints, int numberOfSimulations);
1565 
1580 C_DECL_SPEC RRCDataPtr rrcCallConv gillespieMeanSDOnGrid(RRHandle handle, int numberOfSimulations);
1581 
1582 
1612 C_DECL_SPEC RRCDataPtr rrcCallConv gillespieMeanSDOnGridEx(RRHandle handle, double timeStart, double timeEnd, int numberOfSteps, int numberOfSimulations);
1613 
1614 // --------------------------------------------------------------------------------
1615 // Reset methods
1616 // --------------------------------------------------------------------------------
1617 
1626 C_DECL_SPEC bool rrcCallConv reset(RRHandle handle);
1627 
1636 C_DECL_SPEC bool rrcCallConv resetAll(RRHandle handle);
1637 
1646 C_DECL_SPEC bool rrcCallConv resetToOrigin(RRHandle handle);
1647 
1648 #if defined( __cplusplus)
1649 }
1650 }//namespace
1651 
1652 #endif
1653 
1654 #endif
1655 
roadRunner C API 2012
Structure for a simple vector of strings.
Definition: rrc_types.h:65
char * getExtendedAPIInfo()
Retrieve extended API info.
Definition: _rrc_api.cpp:268
RRStringArrayPtr getSteadyStateSelectionList(RRHandle handle)
Get the selection list for the steady state analysis.
Definition: _rrc_api.cpp:1174
char * getRRCAPILocation(void)
Retrieve the directory path of the shared rrCApi library.
Definition: _rrc_api.cpp:230
bool getScaledFloatingSpeciesElasticity(RRHandle handle, const char *reactionId, const char *speciesId, double *value)
Retrieve the scaled elasticity matrix for the current model.
Definition: _rrc_api.cpp:1249
RRListPtr getConcentrationControlCoefficientIds(RRHandle handle)
Obtain the list of concentration coefficient Ids.
Definition: _rrc_api.cpp:1424
RRVectorPtr getFloatingSpeciesConcentrations(RRHandle handle)
Retrieve in a vector the concentrations for all the floating species.
Definition: _rrc_api.cpp:907
bool setBoundarySpeciesConcentrations(RRHandle handle, const RRVectorPtr vec)
Set the boundary species concentration to the vector vec.
Definition: _rrc_api.cpp:998
RRStringArrayPtr getGlobalParameterIds(RRHandle handle)
Obtain the list of global parameter Ids.
Definition: _rrc_api.cpp:878
bool setSupportCodeFolder(RRHandle handle, const char *folder)
Set the path to a folder containing support code for model generation.
Definition: _rrc_api.cpp:368
RRCDataPtr 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 p...
Definition: _rrc_api.cpp:607
bool getTimeEnd(RRHandle handle, double *timeEnd)
Get the value of the current time end.
Definition: _rrc_api.cpp:545
char * getSupportCodeFolder(RRHandle handle)
Get the path to a folder containing support code.
Definition: _rrc_api.cpp:383
RRCDataPtr gillespieMeanSDOnGrid(RRHandle handle, int numberOfSimulations)
Carry out a series of time-course simulations using the Gillespie algorithm with fixed step size...
Definition: _rrc_api.cpp:1949
RRListPtr getFluxControlCoefficientIds(RRHandle handle)
Obtain the list of flux control coefficient Ids.
Definition: _rrc_api.cpp:1332
bool setTimeCourseSelectionList(RRHandle handle, const char *list)
Set the selection list for output from simulate(void) or simulateEx(void)
Definition: _rrc_api.cpp:563
Definition: _rrc_api.cpp:84
bool resetAll(RRHandle handle)
Resets all variables of the model to their current initial values, and resets all parameters to their...
Definition: _rrc_api.cpp:2031
roadRunner C API 2012
RRVectorPtr computeSteadyStateValues(RRHandle handle)
A convenient method for returning a vector of the steady state species concentrations.
Definition: _rrc_api.cpp:1154
RRStringArrayPtr getRatesOfChangeIds(RRHandle handle)
Retrieve the string list of rates of change Ids.
Definition: _rrc_api.cpp:657
RRDoubleMatrixPtr getStoichiometryMatrix(RRHandle handle)
Retrieve the stoichiometry matrix for the current model.
Definition: _rrc_api.cpp:710
char * getLastError(void)
Retrieve the current error string.
Definition: _rrc_api.cpp:788
bool getuEE(RRHandle handle, const char *name, const char *species, double *value)
Retrieve a single unscaled elasticity coefficient.
Definition: _rrc_api.cpp:1092
int getNumberOfIndependentSpecies(RRHandle handle)
Returns the number of independent species in the model.
Definition: _rrc_api.cpp:1118
int getNumberOfDependentSpecies(RRHandle handle)
Returns the number of dependent species in the model.
Definition: _rrc_api.cpp:1110
RRHandle createRRInstance(void)
Initialize a new roadRunner instance and return a handle to it.
Definition: _rrc_api.cpp:145
char * getBuildDateTime(void)
Retrieve the current build date + time of the library.
Definition: _rrc_api.cpp:1494
RRStringArrayPtr getFloatingSpeciesInitialConditionIds(RRHandle handle)
Get the initial floating species Ids.
Definition: _rrc_api.cpp:1258
bool setFloatingSpeciesInitialConcentrationByIndex(RRHandle handle, int index, double value)
Set the initial concentration for a particular floating species.
Definition: _rrc_api.cpp:964
RRCDataPtr simulate(RRHandle handle)
Carry out a time-course simulation. setTimeStart, setTimeEnd, setNumPoints, etc are used to set the s...
Definition: _rrc_api.cpp:598
RRVectorPtr getRatesOfChangeEx(RRHandle handle, const RRVectorPtr vec)
Retrieve the vector of rates of change given a vector of floating species concentrations.
Definition: _rrc_api.cpp:1267
int getVersion()
Definition: _rrc_api.cpp:210
RRDoubleMatrixPtr getScaledElasticityMatrix(RRHandle handle)
Retrieve the scaled elasticity matrix for the current model.
Definition: _rrc_api.cpp:682
bool setFloatingSpeciesByIndex(RRHandle handle, const int index, const double value)
Set the concentration for a particular floating species.
Definition: _rrc_api.cpp:937
bool getFloatingSpeciesInitialConcentrationByIndex(RRHandle handle, int index, double *value)
Get the initial concentration for a particular floating species.
Definition: _rrc_api.cpp:893
RRDoubleMatrixPtr getReducedJacobian(RRHandle handle)
Retrieve the reduced Jacobian for the current model.
Definition: _rrc_api.cpp:1200
RRCDataPtr gillespieMeanSDOnGridEx(RRHandle handle, double timeStart, double timeEnd, int numberOfSteps, int numberOfSimulations)
Carry out a series of time-course simulations using the Gillespie algorithm with fixed step size...
Definition: _rrc_api.cpp:2013
char * getTempFolder(RRHandle handle)
Retrieve the current temporary folder path.
Definition: _rrc_api.cpp:313
char * getSBML(RRHandle handle)
Retrieve the SBML model that was last loaded into roadRunner.
Definition: _rrc_api.cpp:483
RRCDataPtr gillespie(RRHandle handle)
Carry out a time-course simulation using the Gillespie algorithm with variable step size...
Definition: _rrc_api.cpp:1844
RRDoubleMatrixPtr getNrMatrix(RRHandle handle)
Retrieve the reduced stoichiometry matrix for the current model.
Definition: _rrc_api.cpp:774
RRStringArrayPtr getEigenvalueIds(RRHandle handle)
Obtain the list of eigenvalue Ids.
Definition: _rrc_api.cpp:1323
RRDoubleMatrixPtr getUnscaledConcentrationControlCoefficientMatrix(RRHandle handle)
Retrieve the matrix of unscaled concentration control coefficients for the current model...
Definition: _rrc_api.cpp:1340
RRVectorPtr getRatesOfChange(RRHandle handle)
Retrieve the vector of rates of change as determined by the current state of the model.
Definition: _rrc_api.cpp:642
bool getSeed(RRHandle handle, long *seed)
Determine the current seed used by the random generator.
Definition: _rrc_api.cpp:1826
bool reset(RRHandle handle)
Resets all variables of the model to their current initial values. Does not change the parameters...
Definition: _rrc_api.cpp:2022
bool getEE(RRHandle handle, const char *name, const char *species, double *value)
Retrieve a single elasticity coefficient.
Definition: _rrc_api.cpp:1101
RRStringArrayPtr getFloatingSpeciesIds(RRHandle handle)
Obtain the list of floating species Id.
Definition: _rrc_api.cpp:855
Structure for a simple vector of doubles.
Definition: rrc_types.h:57
int getNumberOfReactions(RRHandle handle)
Obtain the number of reactions in the loaded model.
Definition: _rrc_api.cpp:797
bool hasError(void)
Check if there is an error string to retrieve.
Definition: _rrc_api.cpp:783
int getNumberOfBoundarySpecies(RRHandle handle)
Returns the number of boundary species in the model.
Definition: _rrc_api.cpp:824
RRListPtr getUnscaledConcentrationControlCoefficientIds(RRHandle handle)
Obtain the list of unscaled concentration control coefficient Ids.
Definition: _rrc_api.cpp:1433
RRListPtr getUnscaledFluxControlCoefficientIds(RRHandle handle)
Obtain the list of unscaled flux control coefficient Ids.
Definition: _rrc_api.cpp:1415
char * getInstallFolder(void)
Returns the folder in which the RoadRunner API is installed.
Definition: _rrc_api.cpp:180
Structure for a simple double Matrix type.
Definition: rrc_types.h:73
bool setSteadyStateSelectionList(RRHandle handle, const char *list)
Set the selection list of the steady state analysis.
Definition: _rrc_api.cpp:1164
bool setNumPoints(RRHandle handle, int numberOfPoints)
Set the number of points to generate in a time course simulation.
Definition: _rrc_api.cpp:526
char * getCompiler(RRHandle handle)
Get the name of the compiler currently being used by roadrunner.
Definition: _rrc_api.cpp:336
char * getBuildTime(void)
Retrieve the current build time (HH:MM:SS) of the library.
Definition: _rrc_api.cpp:1489
bool getReactionRate(RRHandle handle, const int index, double *rate)
Retrieve a give reaction rate as indicated by the index parameter.
Definition: _rrc_api.cpp:805
RRCDataPtr gillespieMeanOnGridEx(RRHandle handle, double timeStart, double timeEnd, int numberOfPoints, int numberOfSimulations)
Carry out a series of time-course simulations using the Gillespie algorithm with fixed step size...
Definition: _rrc_api.cpp:1940
RRDoubleMatrixPtr getLinkMatrix(RRHandle handle)
Retrieve the Link matrix for the current model.
Definition: _rrc_api.cpp:765
RRListPtr getAvailableTimeCourseSymbols(RRHandle handle)
Obtain the list of all available symbols.
Definition: _rrc_api.cpp:1028
roadRunner C API 2012
void * RRHandle
Void pointer to a RoadRunner instance.
Definition: rrc_types.h:50
RRDoubleMatrixPtr getScaledFluxControlCoefficientMatrix(RRHandle handle)
Retrieve the matrix of scaled flux control coefficients for the current model.
Definition: _rrc_api.cpp:1367
RRVectorPtr getReactionRatesEx(RRHandle handle, const RRVectorPtr vec)
Retrieve a vector of reaction rates given a vector of species concentrations.
Definition: _rrc_api.cpp:1279
bool setSeed(RRHandle handle, long seed)
Set the current seed used by the random generator.
Definition: _rrc_api.cpp:1835
bool setCodeGenerationMode(RRHandle handle, int mode)
Set the runtime generation option [Not yet implemented].
Definition: _rrc_api.cpp:1244
bool setFloatingSpeciesInitialConcentrations(RRHandle handle, const RRVectorPtr vec)
Set the initial floating species concentrations.
Definition: _rrc_api.cpp:973
bool setBoundarySpeciesByIndex(RRHandle handle, const int index, const double value)
Set the concentration for a particular boundary species.
Definition: _rrc_api.cpp:946
bool loadSBML(RRHandle handle, const char *sbml)
Load a model from an SBML string.
Definition: _rrc_api.cpp:440
RRVectorPtr getGlobalParameterValues(RRHandle handle)
Retrieve the values for all the global parameter values in a vector.
Definition: _rrc_api.cpp:1018
bool oneStep(RRHandle handle, const double currentTime, const double stepSize, double *value)
Carry out a one step integration of the model.
Definition: _rrc_api.cpp:1009
bool loadSimulationSettings(RRHandle handle, const char *fileName)
Load simulation settings from a file.
Definition: _rrc_api.cpp:465
bool getCompartmentByIndex(RRHandle handle, const int index, double *value)
Retrieve the compartment volume for a particular compartment.
Definition: _rrc_api.cpp:1449
char * getCopyright(void)
Retrieve the current copyright notice for the library.
Definition: _rrc_api.cpp:250
bool isModelLoaded(RRHandle handle)
check if a model is loaded
Definition: _rrc_api.cpp:491
int getNumberOfFloatingSpecies(RRHandle handle)
Returns the number of floating species in the model.
Definition: _rrc_api.cpp:847
RRDoubleMatrixPtr getFullJacobian(RRHandle handle)
Retrieve the full Jacobian for the current model.
Definition: _rrc_api.cpp:1191
RRCDataPtr getSimulationResult(RRHandle handle)
Retrieve the result of the last simulation.
Definition: _rrc_api.cpp:617
bool setInstallFolder(const char *folder)
Set the internal string containing the folder in where the RoadRunner C API is installed.
Definition: _rrc_api.cpp:189
RRCDataPtr gillespieOnGrid(RRHandle handle)
Carry out a time-course simulation using the Gillespie algorithm with fixed step size. setTimeStart, setTimeEnd, setNumPoints, etc are used to set the simulation characteristics.
Definition: _rrc_api.cpp:1863
RRHandle createRRInstanceEx(const char *tempFolder, const char *compiler)
Initialize a new roadRunner instance and return a handle to it.
Definition: _rrc_api.cpp:153
char * getCompilerLocation(RRHandle handle)
Get the path to a folder containing the compiler being used.
Definition: _rrc_api.cpp:360
RRCDataPtr gillespieMeanOnGrid(RRHandle handle, int numberOfSimulations)
Carry out a series of time-course simulations using the Gillespie algorithm with fixed step size...
Definition: _rrc_api.cpp:1883
char * getParamPromotedSBML(RRHandle handle, const char *sArg)
Promote any local parameters to global status.
Definition: _rrc_api.cpp:1144
char * getConfigurationXML(RRHandle handle)
Get the simulator's capabilities.
Definition: _rrc_api.cpp:1317
bool clearModel(RRHandle handle)
Unload current model.
Definition: _rrc_api.cpp:499
Structure for the result type from the simulate calls. The client is responsible for freeing the RRCD...
Definition: rrc_types.h:110
char * getCurrentSBML(RRHandle handle)
Retrieve the current state of the model in the form of an SBML string.
Definition: _rrc_api.cpp:286
A list type, stores int, double, strings and lists.
Definition: rrc_types.h:147
bool getGlobalParameterByIndex(RRHandle handle, const int index, double *value)
Retrieve the global parameter value.
Definition: _rrc_api.cpp:1064
RRDoubleMatrixPtr getUnscaledFluxControlCoefficientMatrix(RRHandle handle)
Retrieve the matrix of unscaled flux control coefficients for the current model.
Definition: _rrc_api.cpp:1358
bool setTimeStart(RRHandle handle, double timeStart)
Set the time start for a time course simulation.
Definition: _rrc_api.cpp:507
RRStringArrayPtr getTimeCourseSelectionList(RRHandle handle)
Get the current selection list for simulate(void) or simulateEx(void)
Definition: _rrc_api.cpp:573
char * getWorkingDirectory(void)
Retrieve the current working directory path.
Definition: _rrc_api.cpp:391
bool setCompiler(RRHandle handle, const char *fNameWithPath)
Set the path and filename to the compiler to be used by roadrunner.
Definition: _rrc_api.cpp:321
bool getNumPoints(RRHandle handle, int *numPoints)
Get the value of the current number of points.
Definition: _rrc_api.cpp:554
RRDoubleMatrixPtr getUnscaledElasticityMatrix(RRHandle handle)
Retrieve the unscaled elasticity matrix for the current model.
Definition: _rrc_api.cpp:672
char * getAPIVersion(void)
Retrieve the current version number of the C API library.
Definition: _rrc_api.cpp:196
roadRunner C API 2012
char * getBuildDate(void)
Retrieve the current build date of the library.
Definition: _rrc_api.cpp:1484
bool getBoundarySpeciesByIndex(RRHandle handle, const int index, double *value)
Retrieve the concentration for a particular floating species.
Definition: _rrc_api.cpp:1046
RRDoubleMatrixPtr getEigenvalues(RRHandle handle)
Retrieve the eigenvalue matrix for the current model.
Definition: _rrc_api.cpp:1209
int getNumberOfCompartments(RRHandle handle)
Returns the number of compartments in the model.
Definition: _rrc_api.cpp:1441
bool steadyState(RRHandle handle, double *value)
Compute the steady state of the current model.
Definition: _rrc_api.cpp:1126
RRListPtr getAvailableSteadyStateSymbols(RRHandle handle)
Obtain the list of all available steady state symbols.
Definition: _rrc_api.cpp:1037
RRListPtr getElasticityCoefficientIds(RRHandle handle)
Obtain the list of elasticity coefficient Ids.
Definition: _rrc_api.cpp:1302
char * getVersionEx()
Definition: _rrc_api.cpp:225
RRDoubleMatrixPtr getScaledConcentrationControlCoefficientMatrix(RRHandle handle)
Retrieve the matrix of scaled concentration control coefficients for the current model.
Definition: _rrc_api.cpp:1349
roadRunner C API 2012
char * getCPPAPIVersion(RRHandle handle)
Retrieve the current version number of the C++ API (Core RoadRunner API) library. ...
Definition: _rrc_api.cpp:203
bool setConfigurationXML(RRHandle handle, const char *caps)
Set the simulator's capabilities.
Definition: _rrc_api.cpp:1312
RRStringArrayPtr getBoundarySpeciesIds(RRHandle handle)
Obtain the list of boundary species Ids.
Definition: _rrc_api.cpp:832
bool loadSBMLFromFile(RRHandle handle, const char *fileName)
Load a model from a SBML file.
Definition: _rrc_api.cpp:398
RRVectorPtr getFloatingSpeciesInitialConcentrations(RRHandle handle)
Get the initial floating species concentrations.
Definition: _rrc_api.cpp:927
bool setTimeEnd(RRHandle handle, double timeEnd)
Set the time end for a time course simulation.
Definition: _rrc_api.cpp:516
char * getInfo(RRHandle handle)
Retrieve info about current state of roadrunner, e.g. loaded model, conservationAnalysis etc...
Definition: _rrc_api.cpp:260
bool getRateOfChange(RRHandle handle, const int, double *value)
Retrieve the rate of change for a given floating species.
Definition: _rrc_api.cpp:1475
bool freeRRInstance(RRHandle handle)
Free the roadRunner instance.
Definition: _rrc_api.cpp:1499
bool getTimeStart(RRHandle handle, double *timeStart)
Get the value of the current time start.
Definition: _rrc_api.cpp:536
roadRunner C API 2012
RRCDataPtr gillespieOnGridEx(RRHandle handle, double timeStart, double timeEnd, int numberOfPoints)
Carry out a time-course simulation using the Gillespie algorithm with fixed step size based on the gi...
Definition: _rrc_api.cpp:1874
RRVectorPtr getReactionRates(RRHandle handle)
Retrieve a vector of reaction rates as determined by the current state of the model.
Definition: _rrc_api.cpp:814
bool setGlobalParameterByIndex(RRHandle handle, const int index, const double value)
Set the value for a particular global parameter.
Definition: _rrc_api.cpp:955
RRStringArrayPtr getCompartmentIds(RRHandle handle)
Obtain the list of compartment Ids.
Definition: _rrc_api.cpp:1467
bool getuCC(RRHandle handle, const char *variable, const char *parameter, double *value)
Retrieve a single unscaled control coefficient.
Definition: _rrc_api.cpp:1073
bool loadSBMLFromFileE(RRHandle handle, const char *fileName, bool forceRecompile)
Load a model from a SBML file, force recompilation.
Definition: _rrc_api.cpp:416
RRDoubleMatrixPtr getConservationMatrix(RRHandle handle)
Retrieve the conservation matrix for the current model.
Definition: _rrc_api.cpp:742
RRVectorPtr getBoundarySpeciesConcentrations(RRHandle handle)
Retrieve the concentrations for all the boundary species in a vector.
Definition: _rrc_api.cpp:917
bool getFloatingSpeciesByIndex(RRHandle handle, const int index, double *value)
Retrieve the concentration for a particular floating species.
Definition: _rrc_api.cpp:1055
bool setValue(RRHandle handle, const char *symbolId, const double value)
Set the value for a given symbol, use getAvailableTimeCourseSymbols(void) for a list of symbols...
Definition: _rrc_api.cpp:701
bool getCC(RRHandle handle, const char *variable, const char *parameter, double *value)
Retrieve a single control coefficient.
Definition: _rrc_api.cpp:1083
bool evalModel(RRHandle handle)
Evaluate the current model, that it update all assignments and rates of change. Do not carry out an i...
Definition: _rrc_api.cpp:1135
bool setCompartmentByIndex(RRHandle handle, const int index, const double value)
Set the volume for a particular compartment.
Definition: _rrc_api.cpp:1458
bool resetToOrigin(RRHandle handle)
Resets the model to the state in which it was first loaded, including initial conditions, variables, and parameters.
Definition: _rrc_api.cpp:2040
bool setCompilerLocation(RRHandle handle, const char *folder)
Set the path to a folder containing the compiler to be used.
Definition: _rrc_api.cpp:345
int getNumberOfGlobalParameters(RRHandle handle)
Returns the number of global parameters in the model.
Definition: _rrc_api.cpp:870
char * getVersionStr()
Definition: _rrc_api.cpp:219
bool loadSBMLEx(RRHandle handle, const char *sbml, bool forceRecompile)
Load a model from an SBML string.
Definition: _rrc_api.cpp:449
RRStringArrayPtr getReactionIds(RRHandle handle)
Obtain the list of reaction Ids.
Definition: _rrc_api.cpp:628
bool setTempFolder(RRHandle handle, const char *folder)
Set the path to the temporary folder where the C code will be stored.
Definition: _rrc_api.cpp:304
RRCDataPtr gillespieEx(RRHandle handle, double timeStart, double timeEnd)
Carry out a time-course simulation using the Gillespie algorithm based on the given arguments...
Definition: _rrc_api.cpp:1855
bool setComputeAndAssignConservationLaws(RRHandle handle, const bool On_Or_Off)
Enable or disable conservation analysis.
Definition: _rrc_api.cpp:295
bool getValue(RRHandle handle, const char *symbolId, double *value)
Get the value for a given symbol, use getAvailableTimeCourseSymbols(void) for a list of symbols...
Definition: _rrc_api.cpp:692
bool setFloatingSpeciesConcentrations(RRHandle handle, const RRVectorPtr vec)
Set the floating species concentration to the vector vec.
Definition: _rrc_api.cpp:984
char * getlibSBMLVersion(RRHandle handle)
Retrieve the current version number of the libSBML library.
Definition: _rrc_api.cpp:279