roadrunner  2.6.0
Fast simulator for SBML models
rrc_api.h
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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 char* 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 
333 C_DECL_SPEC int rrcCallConv getComputeAndAssignConservationLaws(RRHandle handle, int* value);
334 
335 // -----------------------------------------------------------------------
336 // Read and Write models
337 // -----------------------------------------------------------------------
338 
346 C_DECL_SPEC bool rrcCallConv loadSBML(RRHandle handle, const char* sbml);
347 
356 C_DECL_SPEC bool rrcCallConv loadSBMLEx(RRHandle handle, const char* sbml, bool forceRecompile);
357 
365 C_DECL_SPEC bool rrcCallConv saveState(RRHandle handle, const char* filename);
366 
367 
375 C_DECL_SPEC bool rrcCallConv loadState(RRHandle handle, const char* filename);
376 
384 //C_DECL_SPEC bool rrcCallConv loadSBMLFromFile(const char* fileName);
385 C_DECL_SPEC bool rrcCallConv loadSBMLFromFile(RRHandle handle, const char* fileName);
386 
395 C_DECL_SPEC bool rrcCallConv loadSBMLFromFileE(RRHandle handle, const char* fileName, bool forceRecompile);
396 
403 C_DECL_SPEC bool rrcCallConv clearModel(RRHandle handle);
404 
411 C_DECL_SPEC bool rrcCallConv isModelLoaded(RRHandle handle);
412 
421 C_DECL_SPEC bool rrcCallConv loadSimulationSettings(RRHandle handle, const char* fileName);
422 
429 C_DECL_SPEC char* rrcCallConv getCurrentSBML(RRHandle handle);
430 
437 C_DECL_SPEC char* rrcCallConv getSBML(RRHandle handle);
438 
439 
440 // -------------------------------------------------------------------------------------
441 // Model editing methods
442 // -------------------------------------------------------------------------------------
443 
444 
456 C_DECL_SPEC bool rrcCallConv addSpeciesAmount (RRHandle handle, const char* sid, const char* compartment, double initialAmount, bool hasOnlySubstanceUnits, bool boundaryCondition);
457 
469 C_DECL_SPEC bool rrcCallConv addSpeciesConcentration (RRHandle handle, const char* sid, const char* compartment, double initialConcentration, bool hasOnlySubstanceUnits, bool boundaryCondition);
470 
483 C_DECL_SPEC bool rrcCallConv addSpeciesConcentrationNoRegen(RRHandle handle, const char* sid, const char* compartment, double initialConcentration, bool hasOnlySubstanceUnits, bool boundaryCondition);
484 
485 
498 C_DECL_SPEC bool rrcCallConv addSpeciesAmountNoRegen(RRHandle handle, const char* sid, const char* compartment, double initialAmount, bool hasOnlySubstanceUnits, bool boundaryCondition);
499 
500 
508 C_DECL_SPEC bool rrcCallConv removeSpecies(RRHandle handle, const char* sid);
509 
518 C_DECL_SPEC bool rrcCallConv removeSpeciesNoRegen(RRHandle handle, const char* sid);
519 
528 C_DECL_SPEC bool rrcCallConv setBoundary(RRHandle handle, const char* sid, bool boundaryCondition);
529 
539 C_DECL_SPEC bool rrcCallConv setBoundaryNoRegen(RRHandle handle, const char* sid, bool boundaryCondition);
540 
541 
550 C_DECL_SPEC bool rrcCallConv setHasOnlySubstanceUnits(RRHandle handle, const char* sid, bool hasOnlySubstanceUnits);
551 
561 C_DECL_SPEC bool rrcCallConv setHasOnlySubstanceUnitsNoRegen(RRHandle handle, const char* sid, bool hasOnlySubstanceUnits);
562 
563 
564 
573 C_DECL_SPEC bool rrcCallConv setInitAmount(RRHandle handle, const char* sid, double initAmount);
574 
584 C_DECL_SPEC bool rrcCallConv setInitAmountNoRegen(RRHandle handle, const char* sid, double initAmount);
585 
594 C_DECL_SPEC bool rrcCallConv setInitConcentration(RRHandle handle, const char* sid, double initConcentration);
595 
605 C_DECL_SPEC bool rrcCallConv setInitConcentrationNoRegen(RRHandle handle, const char* sid, double initConcentration);
606 
607 
616 C_DECL_SPEC bool rrcCallConv setConstant(RRHandle handle, const char* sid, bool constant);
617 
627 C_DECL_SPEC bool rrcCallConv setConstantNoRegen(RRHandle handle, const char* sid, bool constant);
628 
629 
637 C_DECL_SPEC bool rrcCallConv addReactionFromSBML(RRHandle handle, const char* sbmlRep);
638 
647 C_DECL_SPEC bool rrcCallConv addReactionFromSBMLNoRegen(RRHandle handle, const char* sbmlRep);
648 
661 C_DECL_SPEC bool rrcCallConv addReaction(RRHandle handle, const char* rid, const char** reactants, int numReactants,
662  const char** products, int numProducts, const char* kineticLaw);
663 
677 C_DECL_SPEC bool rrcCallConv addReactionNoRegen(RRHandle handle, const char* rid, const char** reactants, int numReactants,
678  const char** products, int numProducts, const char* kineticLaw);
679 
687 C_DECL_SPEC bool rrcCallConv removeReaction(RRHandle handle, const char* rid);
688 
689 
698 C_DECL_SPEC bool rrcCallConv removeReactionNoRegen(RRHandle handle, const char* rid);
699 
708 C_DECL_SPEC bool rrcCallConv setReversible(RRHandle handle, const char* rid, bool reversible);
709 
719 C_DECL_SPEC bool rrcCallConv setReversibleNoRegen(RRHandle handle, const char* rid, bool reversible);
720 
721 
730 C_DECL_SPEC bool rrcCallConv setKineticLaw(RRHandle handle, const char* rid, const char* kineticLaw);
731 
741 C_DECL_SPEC bool rrcCallConv setKineticLawNoRegen(RRHandle handle, const char* rid, const char* kineticLaw);
742 
743 
751 C_DECL_SPEC char* rrcCallConv getKineticLaw(RRHandle handle, const char* rid);
752 
761 C_DECL_SPEC bool rrcCallConv addParameter(RRHandle handle, const char* pid, double value);
771 C_DECL_SPEC bool rrcCallConv addParameterNoRegen(RRHandle handle, const char* pid, double value);
772 
780 C_DECL_SPEC bool rrcCallConv removeParameter(RRHandle handle, const char* pid);
781 
782 
791 C_DECL_SPEC bool rrcCallConv removeParameterNoRegen(RRHandle handle, const char* pid);
792 
793 
802 C_DECL_SPEC bool rrcCallConv addCompartment(RRHandle handle, const char* cid, double initVolume);
812 C_DECL_SPEC bool rrcCallConv addCompartmentNoRegen(RRHandle handle, const char* cid, double initVolume);
813 
814 
822 C_DECL_SPEC bool rrcCallConv removeCompartment(RRHandle handle, const char* cid);
823 
824 
833 C_DECL_SPEC bool rrcCallConv removeCompartmentNoRegen(RRHandle handle, const char* cid);
834 
845 C_DECL_SPEC bool rrcCallConv addInitialAssignment (RRHandle handle, const char* vid, const char* formula, bool forceRegenerate);
846 
847 
856 C_DECL_SPEC bool rrcCallConv addAssignmentRule(RRHandle handle, const char* vid, const char* formula);
857 
867 C_DECL_SPEC bool rrcCallConv addAssignmentRuleNoRegen(RRHandle handle, const char* vid, const char* formula);
868 
877 C_DECL_SPEC bool rrcCallConv addRateRule(RRHandle handle, const char* vid, const char* formula);
878 
888 C_DECL_SPEC bool rrcCallConv addRateRuleNoRegen(RRHandle handle, const char* vid, const char* formula);
889 
897 C_DECL_SPEC bool rrcCallConv removeRules(RRHandle handle, const char* vid);
898 
899 
908 C_DECL_SPEC bool rrcCallConv removeRulesNoRegen(RRHandle handle, const char* vid);
909 
919 C_DECL_SPEC bool rrcCallConv addEvent(RRHandle handle, const char* eid, bool useValuesFromTriggerTime, const char* trigger);
920 
931 C_DECL_SPEC bool rrcCallConv addEventNoRegen(RRHandle handle, const char* eid, bool useValuesFromTriggerTime, const char* trigger);
932 
942 C_DECL_SPEC bool rrcCallConv addTrigger(RRHandle handle, const char* eid, const char* trigger);
943 
954 C_DECL_SPEC bool rrcCallConv addTriggerNoRegen(RRHandle handle, const char* eid, const char* trigger);
955 
964 C_DECL_SPEC bool rrcCallConv setPersistent(RRHandle handle, const char* eid, bool persistent);
965 
975 C_DECL_SPEC bool rrcCallConv setPersistentNoRegen(RRHandle handle, const char* eid, bool persistent);
976 
977 
986 C_DECL_SPEC bool rrcCallConv setTriggerInitialValue(RRHandle handle, const char* eid, bool initValue);
987 
997 C_DECL_SPEC bool rrcCallConv setTriggerInitialValueNoRegen(RRHandle handle, const char* eid, bool initValue);
998 
999 
1009 C_DECL_SPEC bool rrcCallConv addPriority(RRHandle handle, const char* eid, const char* priority);
1010 
1021 C_DECL_SPEC bool rrcCallConv addPriorityNoRegen(RRHandle handle, const char* eid, const char* priority);
1022 
1032 C_DECL_SPEC bool rrcCallConv addDelay(RRHandle handle, const char* eid, const char* delay);
1033 
1044 C_DECL_SPEC bool rrcCallConv addDelayNoRegen(RRHandle handle, const char* eid, const char* delay);
1045 
1055 C_DECL_SPEC bool rrcCallConv addEventAssignment(RRHandle handle, const char* eid, const char* vid, const char* formula);
1056 
1067 C_DECL_SPEC bool rrcCallConv addEventAssignmentNoRegen(RRHandle handle, const char* eid, const char* vid, const char* formula);
1068 
1077 C_DECL_SPEC bool rrcCallConv removeEventAssignments(RRHandle handle, const char* eid, const char* vid);
1078 
1088 C_DECL_SPEC bool rrcCallConv removeEventAssignmentsNoRegen(RRHandle handle, const char* eid, const char* vid);
1089 
1097 C_DECL_SPEC bool rrcCallConv removeEvent(RRHandle handle, const char* eid);
1098 
1107 C_DECL_SPEC bool rrcCallConv removeEventsNoRegen(RRHandle handle, const char* eid);
1108 
1109 
1117 C_DECL_SPEC bool rrcCallConv regenerate (RRHandle handle);
1118 
1125 C_DECL_SPEC bool rrcCallConv validateCurrentSBML(RRHandle handle);
1126 
1127 
1128 // -------------------------------------------------------------------------
1129 // SBML utility methods
1130 // -----------------------------------------------------------------------
1143 C_DECL_SPEC char* rrcCallConv getParamPromotedSBML(RRHandle handle, const char* sArg);
1144 
1152 C_DECL_SPEC bool rrcCallConv setConfigurationXML (RRHandle handle, const char* caps);
1153 
1186 C_DECL_SPEC char* rrcCallConv getConfigurationXML(RRHandle handle);
1187 
1188 /* Registered Integrators *****************************************************/
1189 
1195 C_DECL_SPEC int rrcCallConv getNumRegisteredIntegrators ();
1196 
1203 C_DECL_SPEC char* rrcCallConv getRegisteredIntegratorName (int n);
1204 
1211 C_DECL_SPEC char* rrcCallConv getRegisteredIntegratorHint (int n);
1212 
1219 C_DECL_SPEC char* rrcCallConv getRegisteredIntegratorDescription (int n);
1220 
1221 /* Instantiated Integrators ***************************************************/
1222 
1230 C_DECL_SPEC int rrcCallConv getNumInstantiatedIntegrators (RRHandle handle);
1231 
1241 C_DECL_SPEC int rrcCallConv setCurrentIntegrator (RRHandle handle, const char* nameOfIntegrator);
1242 
1249 C_DECL_SPEC char* rrcCallConv getCurrentIntegratorName (RRHandle handle);
1250 
1257 C_DECL_SPEC char* rrcCallConv getCurrentIntegratorDescription (RRHandle handle);
1258 
1265 C_DECL_SPEC char* rrcCallConv getCurrentIntegratorHint (RRHandle handle);
1266 
1273 C_DECL_SPEC int rrcCallConv getNumberOfCurrentIntegratorParameters (RRHandle handle);
1274 
1281 C_DECL_SPEC char* rrcCallConv getCurrentIntegratorNthParameterName (RRHandle handle, int n);
1282 
1289 C_DECL_SPEC char* rrcCallConv getCurrentIntegratorNthParameterDescription (RRHandle handle, int n);
1290 
1297 C_DECL_SPEC char* rrcCallConv getCurrentIntegratorNthParameterDisplayName (RRHandle handle, int n);
1298 
1305 C_DECL_SPEC char* rrcCallConv getCurrentIntegratorNthParameterHint (RRHandle handle, int n);
1306 
1313 C_DECL_SPEC int rrcCallConv getCurrentIntegratorNthParameterType (RRHandle handle, int n);
1314 
1321 C_DECL_SPEC int rrcCallConv resetCurrentIntegratorParameters (RRHandle handle);
1322 
1330 
1338 C_DECL_SPEC char* rrcCallConv getCurrentIntegratorParameterDescription (RRHandle handle, const char *parameterName);
1339 
1347 C_DECL_SPEC char* rrcCallConv getCurrentIntegratorParameterHint (RRHandle handle, const char *parameterName);
1348 
1356 C_DECL_SPEC int rrcCallConv getCurrentIntegratorParameterType (RRHandle handle, const char *parameterName);
1357 
1365 C_DECL_SPEC int rrcCallConv getCurrentIntegratorParameterInt (RRHandle handle, const char *parameterName);
1366 
1375 C_DECL_SPEC int rrcCallConv setCurrentIntegratorParameterInt (RRHandle handle, const char *parameterName, int value);
1376 
1384 C_DECL_SPEC unsigned int rrcCallConv getCurrentIntegratorParameterUInt (RRHandle handle, const char *parameterName);
1385 
1394 C_DECL_SPEC int rrcCallConv setCurrentIntegratorParameterUInt (RRHandle handle, const char *parameterName, unsigned int value);
1395 
1403 C_DECL_SPEC double rrcCallConv getCurrentIntegratorParameterDouble (RRHandle handle, const char *parameterName);
1404 
1413 C_DECL_SPEC int rrcCallConv setCurrentIntegratorParameterDouble (RRHandle handle, const char *parameterName, double value);
1414 
1422 C_DECL_SPEC char* rrcCallConv getCurrentIntegratorParameterString (RRHandle handle, const char *parameterName);
1423 
1432 C_DECL_SPEC int rrcCallConv setCurrentIntegratorParameterString (RRHandle handle, const char *parameterName, const char* value);
1433 
1441 C_DECL_SPEC int rrcCallConv getCurrentIntegratorParameterBoolean (RRHandle handle, const char *parameterName);
1442 
1451 C_DECL_SPEC int rrcCallConv setCurrentIntegratorParameterBoolean (RRHandle handle, const char *parameterName, int value);
1452 
1453 
1463 C_DECL_SPEC int rrcCallConv getCurrentIntegratorParameterDoubleArray (RRHandle handle, const char *parameterName, double** value, int* len);
1464 
1474 C_DECL_SPEC int rrcCallConv setCurrentIntegratorParameterDoubleArray(RRHandle handle, const char *parameterName, double* value, int len);
1475 
1476 
1485 C_DECL_SPEC int rrcCallConv setCurrentIntegratorIndividualTolerance(RRHandle handle, const char* sid, double value);
1486 
1487 
1488 /* Steady State Solvers *******************************************************/
1489 
1495 C_DECL_SPEC int rrcCallConv getNumRegisteredSteadyStateSolvers ();
1496 
1503 C_DECL_SPEC char* rrcCallConv getRegisteredSteadyStateSolverName (int n);
1504 
1511 C_DECL_SPEC char* rrcCallConv getRegisteredSteadyStateSolverHint (int n);
1512 
1519 C_DECL_SPEC char* rrcCallConv getRegisteredSteadyStateSolverDescription (int n);
1520 
1521 
1531 C_DECL_SPEC int rrcCallConv setCurrentSteadyStateSolver (RRHandle handle, const char *nameOfSteadyStateSolver);
1532 
1539 C_DECL_SPEC char* rrcCallConv getCurrentSteadyStateSolverName (RRHandle handle);
1540 
1547 C_DECL_SPEC char* rrcCallConv getCurrentSteadyStateSolverDescription (RRHandle handle);
1548 
1555 C_DECL_SPEC char* rrcCallConv getCurrentSteadyStateSolverHint (RRHandle handle);
1556 
1563 C_DECL_SPEC int rrcCallConv getNumberOfCurrentSteadyStateSolverParameters (RRHandle handle);
1564 
1571 C_DECL_SPEC char* rrcCallConv getCurrentSteadyStateSolverNthParameterName (RRHandle handle, int n);
1572 
1579 C_DECL_SPEC char* rrcCallConv getCurrentSteadyStateSolverNthParameterDisplayName (RRHandle handle, int n);
1580 
1587 C_DECL_SPEC char* rrcCallConv getCurrentSteadyStateSolverNthParameterDescription (RRHandle handle, int n);
1588 
1595 C_DECL_SPEC char* rrcCallConv getCurrentSteadyStateSolverNthParameterHint (RRHandle handle, int n);
1596 
1603 C_DECL_SPEC int rrcCallConv getCurrentSteadyStateSolverNthParameterType (RRHandle handle, int n);
1604 
1611 C_DECL_SPEC int rrcCallConv resetCurrentSteadyStateSolverParameters (RRHandle handle);
1612 
1620 C_DECL_SPEC const char* rrcCallConv solverTypeToString (int code);
1621 
1629 
1637 C_DECL_SPEC char* rrcCallConv getCurrentSteadyStateSolverParameterDescription (RRHandle handle, const char *parameterName);
1638 
1646 C_DECL_SPEC char* rrcCallConv getCurrentSteadyStateSolverParameterHint (RRHandle handle, const char *parameterName);
1647 
1655 C_DECL_SPEC int rrcCallConv getCurrentSteadyStateSolverParameterType (RRHandle handle, const char *parameterName);
1656 
1664 C_DECL_SPEC int rrcCallConv getCurrentSteadyStateSolverParameterInt (RRHandle handle, const char *parameterName);
1665 
1674 C_DECL_SPEC int rrcCallConv setCurrentSteadyStateSolverParameterInt (RRHandle handle, const char *parameterName, int value);
1675 
1683 C_DECL_SPEC unsigned int rrcCallConv getCurrentSteadyStateSolverParameterUInt (RRHandle handle, const char *parameterName);
1684 
1693 C_DECL_SPEC int rrcCallConv setCurrentSteadyStateSolverParameterUInt (RRHandle handle, const char *parameterName, unsigned int value);
1694 
1702 C_DECL_SPEC double rrcCallConv getCurrentSteadyStateSolverParameterDouble (RRHandle handle, const char *parameterName);
1703 
1712 C_DECL_SPEC int rrcCallConv setCurrentSteadyStateSolverParameterDouble (RRHandle handle, const char *parameterName, double value);
1713 
1721 C_DECL_SPEC char* rrcCallConv getCurrentSteadyStateSolverParameterString (RRHandle handle, const char *parameterName);
1722 
1731 C_DECL_SPEC int rrcCallConv setCurrentSteadyStateSolverParameterString (RRHandle handle, const char *parameterName, const char* value);
1732 
1740 C_DECL_SPEC int rrcCallConv getCurrentSteadyStateSolverParameterBoolean (RRHandle handle, const char *parameterName);
1741 
1750 C_DECL_SPEC int rrcCallConv setCurrentSteadyStateSolverParameterBoolean (RRHandle handle, const char *parameterName, int value);
1751 
1752 
1760 C_DECL_SPEC bool rrcCallConv setTimeStart(RRHandle handle, double timeStart);
1761 
1769 C_DECL_SPEC bool rrcCallConv setTimeEnd(RRHandle handle, double timeEnd);
1770 
1778 C_DECL_SPEC bool rrcCallConv setNumPoints(RRHandle handle, int numberOfPoints);
1779 
1780 
1789 C_DECL_SPEC bool rrcCallConv setTimes(RRHandle handle, double* times, int size);
1790 
1791 
1808 C_DECL_SPEC bool rrcCallConv setTimeCourseSelectionList(RRHandle handle, const char* list);
1809 //C_DECL_SPEC bool rrcCallConv setTimeCourseSelectionList(const char* list);
1810 
1818 C_DECL_SPEC RRStringArrayPtr rrcCallConv getTimeCourseSelectionList(RRHandle handle);
1819 
1830 C_DECL_SPEC RRCDataPtr rrcCallConv simulate(RRHandle handle);
1831 
1842 C_DECL_SPEC bool rrcCallConv simulateNoReturn(RRHandle handle);
1843 
1852 C_DECL_SPEC RRCDataPtr rrcCallConv getSimulationResult(RRHandle handle);
1853 
1854 
1862 C_DECL_SPEC RRHandle rrcCallConv getSimulationResultAsDoubleMatrix(RRHandle handle);
1863 
1864 
1889 C_DECL_SPEC RRCDataPtr rrcCallConv simulateEx(RRHandle handle, const double timeStart, const double timeEnd, const int numberOfPoints);
1890 
1915 C_DECL_SPEC bool rrcCallConv simulateExNoReturn(RRHandle handle, const double timeStart, const double timeEnd, const int numberOfPoints);
1916 
1938 C_DECL_SPEC RRCDataPtr rrcCallConv simulateTimes(RRHandle handle, const double* times, int size);
1939 
1953 C_DECL_SPEC bool rrcCallConv oneStep(RRHandle handle, const double currentTime, const double stepSize, double *value);
1954 
1965 C_DECL_SPEC bool rrcCallConv getTimeStart(RRHandle handle, double* timeStart);
1966 
1977 C_DECL_SPEC bool rrcCallConv getTimeEnd(RRHandle handle, double* timeEnd);
1978 
1989 C_DECL_SPEC bool rrcCallConv getNumPoints (RRHandle handle, int* numPoints);
1990 
2003 C_DECL_SPEC bool rrcCallConv steadyState(RRHandle handle, double* value);
2004 
2015 C_DECL_SPEC RRVectorPtr rrcCallConv computeSteadyStateValues(RRHandle handle);
2016 
2038 C_DECL_SPEC bool rrcCallConv setSteadyStateSelectionList(RRHandle handle, const char* list);
2039 
2048 
2049 
2050 // --------------------------------------------------------------------------------
2051 // Get and Set Routines
2052 // --------------------------------------------------------------------------------
2053 
2065 C_DECL_SPEC bool rrcCallConv getValue(RRHandle handle, const char* symbolId, double* value);
2066 
2067 
2079 C_DECL_SPEC bool rrcCallConv setValue(RRHandle handle, const char* symbolId, const double value);
2080 
2081 
2092 
2102 C_DECL_SPEC RRVectorPtr rrcCallConv getFloatingSpeciesAmounts(RRHandle handle);
2103 
2112 
2121 
2130 
2139 
2140 
2151 
2161 C_DECL_SPEC RRVectorPtr rrcCallConv getBoundarySpeciesAmounts(RRHandle handle);
2162 
2163 // --------------------------------------------------------------------------------
2164 // Parameter Group
2165 // --------------------------------------------------------------------------------
2166 
2176 C_DECL_SPEC RRVectorPtr rrcCallConv getGlobalParameterValues(RRHandle handle);
2177 
2187 C_DECL_SPEC bool rrcCallConv setBoundarySpeciesByIndex(RRHandle handle, const unsigned int index, const double value);
2188 
2198 C_DECL_SPEC bool rrcCallConv setFloatingSpeciesInitialConcentrationByIndex(RRHandle handle, int index, double value);
2199 
2209 C_DECL_SPEC bool rrcCallConv getFloatingSpeciesInitialConcentrationByIndex(RRHandle handle, int index, double* value);
2210 
2220 C_DECL_SPEC bool rrcCallConv setFloatingSpeciesByIndex(RRHandle handle, const int index, const double value);
2221 
2231 C_DECL_SPEC bool rrcCallConv setGlobalParameterByIndex(RRHandle handle, const int index, const double value);
2232 
2241 C_DECL_SPEC bool rrcCallConv getBoundarySpeciesByIndex(RRHandle handle, const int index, double* value);
2242 
2252 C_DECL_SPEC bool rrcCallConv getFloatingSpeciesByIndex(RRHandle handle, const int index, double* value);
2253 
2262 C_DECL_SPEC bool rrcCallConv getGlobalParameterByIndex(RRHandle handle, const int index, double* value);
2263 
2273 C_DECL_SPEC bool rrcCallConv getCompartmentByIndex (RRHandle handle, const int index, double* value);
2274 
2275 
2285 C_DECL_SPEC bool rrcCallConv setCompartmentByIndex (RRHandle handle, const int index, const double value);
2286 
2287 
2306 C_DECL_SPEC bool rrcCallConv setFloatingSpeciesConcentrations(RRHandle handle, const RRVectorPtr vec);
2307 
2326 C_DECL_SPEC bool rrcCallConv setBoundarySpeciesConcentrations(RRHandle handle, const RRVectorPtr vec);
2327 
2328 
2336 C_DECL_SPEC RRDoubleMatrixPtr rrcCallConv getFullJacobian(RRHandle handle);
2337 
2347 C_DECL_SPEC RRDoubleMatrixPtr rrcCallConv getReducedJacobian(RRHandle handle);
2348 
2356 C_DECL_SPEC RRDoubleMatrixPtr rrcCallConv getEigenvalues(RRHandle handle);
2357 
2358 
2359 // --------------------------------------------------------------------------------
2360 // Stoichiometry methods
2361 // --------------------------------------------------------------------------------
2362 
2370 C_DECL_SPEC RRDoubleMatrixPtr rrcCallConv getStoichiometryMatrix(RRHandle handle);
2371 
2379 C_DECL_SPEC RRDoubleMatrixPtr rrcCallConv getLinkMatrix(RRHandle handle);
2380 
2388 C_DECL_SPEC RRDoubleMatrixPtr rrcCallConv getNrMatrix(RRHandle handle);
2389 
2399 C_DECL_SPEC RRDoubleMatrixPtr rrcCallConv getConservationMatrix(RRHandle handle);
2400 
2401 // --------------------------------------------------------------------------------
2402 // Initial condition Methods
2403 // --------------------------------------------------------------------------------
2404 
2415 C_DECL_SPEC bool rrcCallConv setFloatingSpeciesInitialConcentrations (RRHandle handle, const RRVectorPtr vec);
2416 
2427 
2439 
2450 
2451 
2452 // --------------------------------------------------------------------------------
2453 // Reaction rates
2454 // --------------------------------------------------------------------------------
2455 
2465 C_DECL_SPEC int rrcCallConv getNumberOfReactions(RRHandle handle);
2466 
2467 
2477 C_DECL_SPEC bool rrcCallConv getReactionRate(RRHandle handle, const int index, double* rate);
2478 
2479 
2487 C_DECL_SPEC RRVectorPtr rrcCallConv getReactionRates(RRHandle handle);
2488 
2489 
2498 C_DECL_SPEC RRVectorPtr rrcCallConv getReactionRatesEx (RRHandle handle, const RRVectorPtr vec);
2499 
2500 
2510 C_DECL_SPEC RRVectorPtr rrcCallConv getRatesOfChange(RRHandle handle);
2511 
2521 C_DECL_SPEC RRStringArrayPtr rrcCallConv getRatesOfChangeIds(RRHandle handle);
2522 
2523 
2534 C_DECL_SPEC bool rrcCallConv getRateOfChange(RRHandle handle, const int, double* value);
2535 
2536 
2547 C_DECL_SPEC RRVectorPtr rrcCallConv getRatesOfChangeEx (RRHandle handle, const RRVectorPtr vec);
2548 
2556 C_DECL_SPEC bool rrcCallConv evalModel(RRHandle handle);
2557 
2558 // Get number family
2565 C_DECL_SPEC int rrcCallConv getNumberOfCompartments (RRHandle handle);
2566 
2567 
2573 C_DECL_SPEC int rrcCallConv getNumberOfBoundarySpecies(RRHandle handle);
2574 
2575 
2581 C_DECL_SPEC int rrcCallConv getNumberOfFloatingSpecies(RRHandle handle);
2582 
2583 
2589 C_DECL_SPEC int rrcCallConv getNumberOfGlobalParameters(RRHandle handle);
2590 
2591 // --------------------------------------------------------------------------------
2592 // Get number family
2593 // --------------------------------------------------------------------------------
2594 
2600 C_DECL_SPEC int rrcCallConv getNumberOfDependentSpecies(RRHandle handle);
2601 
2602 
2609 C_DECL_SPEC int rrcCallConv getNumberOfIndependentSpecies(RRHandle handle);
2610 
2611 // --------------------------------------------------------------------------------
2612 // Get Ids family
2613 // --------------------------------------------------------------------------------
2614 
2622 C_DECL_SPEC RRStringArrayPtr rrcCallConv getReactionIds(RRHandle handle);
2623 
2631 C_DECL_SPEC RRStringArrayPtr rrcCallConv getBoundarySpeciesIds(RRHandle handle);
2632 
2633 
2642 
2650 C_DECL_SPEC RRStringArrayPtr rrcCallConv getFloatingSpeciesIds(RRHandle handle);
2651 
2659 
2668 
2669 
2678 
2679 
2687 C_DECL_SPEC RRStringArrayPtr rrcCallConv getGlobalParameterIds(RRHandle handle);
2688 
2698 C_DECL_SPEC RRStringArrayPtr rrcCallConv getCompartmentIds(RRHandle handle);
2699 
2707 C_DECL_SPEC RRStringArrayPtr rrcCallConv getEigenvalueIds(RRHandle handle);
2708 
2716 C_DECL_SPEC RRListPtr rrcCallConv getAvailableTimeCourseSymbols(RRHandle handle);
2717 
2725 C_DECL_SPEC RRListPtr rrcCallConv getAvailableSteadyStateSymbols(RRHandle handle);
2726 
2727 // --------------------------------------------------------------------------------
2728 // MCA methods
2729 // --------------------------------------------------------------------------------
2730 
2738 C_DECL_SPEC RRListPtr rrcCallConv getElasticityCoefficientIds(RRHandle handle);
2739 
2748 
2757 
2765 C_DECL_SPEC RRListPtr rrcCallConv getFluxControlCoefficientIds(RRHandle handle);
2766 
2775 
2784 
2793 
2801 C_DECL_SPEC RRDoubleMatrixPtr rrcCallConv getScaledElasticityMatrix(RRHandle handle);
2802 
2803 
2814 C_DECL_SPEC bool rrcCallConv getScaledFloatingSpeciesElasticity(RRHandle handle, const char* reactionId, const char* speciesId, double* value);
2815 
2825 
2826 
2835 
2844 
2853 
2864 C_DECL_SPEC bool rrcCallConv getuCC (RRHandle handle, const char* variable, const char* parameter, double* value);
2865 
2876 C_DECL_SPEC bool rrcCallConv getCC (RRHandle handle, const char* variable, const char* parameter, double* value);
2877 
2886 C_DECL_SPEC bool rrcCallConv getDiffStepSize(RRHandle handle, double* value);
2887 
2896 C_DECL_SPEC bool rrcCallConv setDiffStepSize(RRHandle handle, const double value);
2897 
2908 C_DECL_SPEC bool rrcCallConv getEE(RRHandle handle, const char* name, const char* species, double* value);
2909 
2920 C_DECL_SPEC bool rrcCallConv getuEE(RRHandle handle, const char* name, const char* species, double* value);
2921 
2922 // --------------------------------------------------------------------------------
2923 // Stochastic methods
2924 // --------------------------------------------------------------------------------
2925 
2937 C_DECL_SPEC RRCDataPtr rrcCallConv gillespie(RRHandle handle);
2938 
2961 C_DECL_SPEC RRCDataPtr rrcCallConv gillespieEx(RRHandle handle, double timeStart, double timeEnd);
2962 
2974 C_DECL_SPEC RRCDataPtr rrcCallConv gillespieOnGrid(RRHandle handle);
2975 
3001 C_DECL_SPEC RRCDataPtr rrcCallConv gillespieOnGridEx(RRHandle handle, double timeStart, double timeEnd, int numberOfPoints);
3002 
3016 C_DECL_SPEC RRCDataPtr rrcCallConv gillespieMeanOnGrid(RRHandle handle, int numberOfSimulations);
3017 
3045 C_DECL_SPEC RRCDataPtr rrcCallConv gillespieMeanOnGridEx(RRHandle handle, double timeStart, double timeEnd, int numberOfPoints, int numberOfSimulations);
3046 
3061 C_DECL_SPEC RRCDataPtr rrcCallConv gillespieMeanSDOnGrid(RRHandle handle, int numberOfSimulations);
3062 
3063 
3093 C_DECL_SPEC RRCDataPtr rrcCallConv gillespieMeanSDOnGridEx(RRHandle handle, double timeStart, double timeEnd, int numberOfSteps, int numberOfSimulations);
3094 
3095 // --------------------------------------------------------------------------------
3096 // Reset methods
3097 // --------------------------------------------------------------------------------
3098 
3107 C_DECL_SPEC bool rrcCallConv reset(RRHandle handle);
3108 
3117 C_DECL_SPEC bool rrcCallConv resetAll(RRHandle handle);
3118 
3127 C_DECL_SPEC bool rrcCallConv resetToOrigin(RRHandle handle);
3128 
3136 C_DECL_SPEC bool rrcCallConv resetParameter(RRHandle handle);
3137 
3146 C_DECL_SPEC int rrcCallConv setConfigBool(const char* key, int value);
3147 
3155 C_DECL_SPEC int rrcCallConv getConfigBool(const char* key);
3156 
3165 C_DECL_SPEC int rrcCallConv setConfigInt(const char* key, int value);
3166 
3174 C_DECL_SPEC int rrcCallConv getConfigInt(const char* key);
3175 
3184 C_DECL_SPEC int rrcCallConv setConfigDouble(const char* key, double value);
3185 
3186 
3187 //RRPlugins
3192 C_DECL_SPEC int rrcCallConv _getNumIndFloatingSpecies(RRHandle handle);
3193 
3197 C_DECL_SPEC int rrcCallConv _getNumRateRules(RRHandle handle);
3198 
3202 C_DECL_SPEC double rrcCallConv _getTime(RRHandle handle);
3203 
3207 C_DECL_SPEC int rrcCallConv _getStateVector(RRHandle handle);
3208 
3212 C_DECL_SPEC void rrcCallConv _getStateVectorRate(RRHandle handle,double time, double *value);
3213 
3214 
3222 C_DECL_SPEC double rrcCallConv getConfigDouble(const char* key);
3223 
3229 C_DECL_SPEC RRStringArrayPtr rrcCallConv getListOfConfigKeys();
3230 
3242 C_DECL_SPEC bool rrcCallConv setTimeCourseSelectionListEx(RRHandle handle, int length, const char** list);
3243 
3259 C_DECL_SPEC bool rrcCallConv setSteadyStateSelectionListEx(RRHandle handle, int length, const char** list);
3260 
3261 
3262 
3263 #if defined( __cplusplus)
3264 }
3265 }//namespace
3266 
3267 #endif
3268 
3269 #endif
C_DECL_SPEC RRDoubleMatrixPtr rrcCallConv getReducedJacobian(RRHandle handle)
Retrieve the reduced Jacobian for the current model.
C_DECL_SPEC RRDoubleMatrixPtr rrcCallConv getStoichiometryMatrix(RRHandle handle)
Retrieve the stoichiometry matrix for the current model.
C_DECL_SPEC RRDoubleMatrixPtr rrcCallConv getEigenvalues(RRHandle handle)
Retrieve the eigenvalue matrix for the current model.
C_DECL_SPEC RRDoubleMatrixPtr rrcCallConv getFullJacobian(RRHandle handle)
Retrieve the full Jacobian for the current model.
C_DECL_SPEC RRDoubleMatrixPtr rrcCallConv getNrMatrix(RRHandle handle)
Retrieve the reduced stoichiometry matrix for the current model.
C_DECL_SPEC RRDoubleMatrixPtr rrcCallConv getConservationMatrix(RRHandle handle)
Retrieve the conservation matrix for the current model.
C_DECL_SPEC RRDoubleMatrixPtr rrcCallConv getLinkMatrix(RRHandle handle)
Retrieve the Link matrix for the current model.
C_DECL_SPEC bool rrcCallConv setBoundarySpeciesByIndex(RRHandle handle, const unsigned int index, const double value)
Set the concentration for a particular boundary species.
C_DECL_SPEC RRStringArrayPtr rrcCallConv getBoundarySpeciesConcentrationIds(RRHandle handle)
Obtain the list of boundary species concentration Ids.
C_DECL_SPEC RRStringArrayPtr rrcCallConv getBoundarySpeciesIds(RRHandle handle)
Obtain the list of boundary species Ids.
C_DECL_SPEC RRVectorPtr rrcCallConv getBoundarySpeciesAmounts(RRHandle handle)
Retrieve the amounts for all the boundary species in a vector.
C_DECL_SPEC bool rrcCallConv getBoundarySpeciesByIndex(RRHandle handle, const int index, double *value)
Retrieve the concentration for a particular floating species.
C_DECL_SPEC int rrcCallConv getNumberOfBoundarySpecies(RRHandle handle)
Returns the number of boundary species in the model.
C_DECL_SPEC RRVectorPtr rrcCallConv getBoundarySpeciesConcentrations(RRHandle handle)
Retrieve the concentrations for all the boundary species in a vector.
C_DECL_SPEC bool rrcCallConv setBoundarySpeciesConcentrations(RRHandle handle, const RRVectorPtr vec)
Set the boundary species concentration to the vector vec.
C_DECL_SPEC RRStringArrayPtr rrcCallConv getCompartmentIds(RRHandle handle)
Obtain the list of compartment Ids.
C_DECL_SPEC bool rrcCallConv getCompartmentByIndex(RRHandle handle, const int index, double *value)
Retrieve the compartment volume for a particular compartment.
C_DECL_SPEC bool rrcCallConv setCompartmentByIndex(RRHandle handle, const int index, const double value)
Set the volume for a particular compartment.
C_DECL_SPEC int rrcCallConv getNumberOfCompartments(RRHandle handle)
Returns the number of compartments in the model.
C_DECL_SPEC int rrcCallConv getConfigBool(const char *key)
Get a boolean configuration value.
C_DECL_SPEC int rrcCallConv setConfigBool(const char *key, int value)
Set a boolean configuration value.
C_DECL_SPEC double rrcCallConv getConfigDouble(const char *key)
Get a double configuration value.
C_DECL_SPEC int rrcCallConv setConfigInt(const char *key, int value)
Set an integer configuration value.
C_DECL_SPEC int rrcCallConv setConfigDouble(const char *key, double value)
Set a double configuration value.
C_DECL_SPEC int rrcCallConv getConfigInt(const char *key)
Get an integer configuration value.
C_DECL_SPEC RRStringArrayPtr rrcCallConv getListOfConfigKeys()
Get a list of all possible config keys.
C_DECL_SPEC bool rrcCallConv removeEventAssignments(RRHandle handle, const char *eid, const char *vid)
Remove event assignments for given variable from an existing event.
C_DECL_SPEC bool rrcCallConv removeParameterNoRegen(RRHandle handle, const char *pid)
Remove a parameter from the current model, without regenerating it The last modification must regener...
C_DECL_SPEC bool rrcCallConv setKineticLawNoRegen(RRHandle handle, const char *rid, const char *kineticLaw)
Set the kinetic law for a existing reaction in the current model, without regenerating it The last mo...
C_DECL_SPEC bool rrcCallConv addAssignmentRuleNoRegen(RRHandle handle, const char *vid, const char *formula)
Add an assignment rule to the current model, without regenerating it The last modification must regen...
C_DECL_SPEC bool rrcCallConv removeReaction(RRHandle handle, const char *rid)
Remove a reaction from the current model.
C_DECL_SPEC bool rrcCallConv removeEventAssignmentsNoRegen(RRHandle handle, const char *eid, const char *vid)
Remove event assignments for given variable from an existing event, without regenerating it The last ...
C_DECL_SPEC bool rrcCallConv addReactionNoRegen(RRHandle handle, const char *rid, const char **reactants, int numReactants, const char **products, int numProducts, const char *kineticLaw)
Add a reaction to the current model, without regenerating it The last modification must regenerate fo...
C_DECL_SPEC bool rrcCallConv addSpeciesConcentration(RRHandle handle, const char *sid, const char *compartment, double initialConcentration, bool hasOnlySubstanceUnits, bool boundaryCondition)
Add a species to the current model.
C_DECL_SPEC bool rrcCallConv setHasOnlySubstanceUnits(RRHandle handle, const char *sid, bool hasOnlySubstanceUnits)
Set the hasOnlySubstanceUnits attribute for an existing species.
C_DECL_SPEC bool rrcCallConv addReactionFromSBML(RRHandle handle, const char *sbmlRep)
Add a reaction to the current model.
C_DECL_SPEC bool rrcCallConv setReversible(RRHandle handle, const char *rid, bool reversible)
Set the reversible attribut for an existing reaction in the current model.
C_DECL_SPEC bool rrcCallConv removeEventsNoRegen(RRHandle handle, const char *eid)
Remove an event from the current model, without regenerating it The last modification must regenerate...
C_DECL_SPEC bool rrcCallConv setReversibleNoRegen(RRHandle handle, const char *rid, bool reversible)
Set the reversible attribut for an existing reaction in the current model, without regenerating it Th...
C_DECL_SPEC bool rrcCallConv removeRulesNoRegen(RRHandle handle, const char *vid)
Remove rules related to given variable from the current model, without regenerating it The last modif...
C_DECL_SPEC bool rrcCallConv addDelayNoRegen(RRHandle handle, const char *eid, const char *delay)
Add delay to an existing event in the model, without regenerating it The last modification must regen...
C_DECL_SPEC bool rrcCallConv addEvent(RRHandle handle, const char *eid, bool useValuesFromTriggerTime, const char *trigger)
Add an event to the current model.
C_DECL_SPEC bool rrcCallConv addEventAssignmentNoRegen(RRHandle handle, const char *eid, const char *vid, const char *formula)
Add an event assignment to an existing event in the current model, without regenerating it The last m...
C_DECL_SPEC bool rrcCallConv addPriorityNoRegen(RRHandle handle, const char *eid, const char *priority)
Add priority to an existing event in the model, without regenerating it The last modification must re...
C_DECL_SPEC bool rrcCallConv removeReactionNoRegen(RRHandle handle, const char *rid)
Remove a reaction from the current model, without regenerating it The last modification must regenera...
C_DECL_SPEC bool rrcCallConv addSpeciesConcentrationNoRegen(RRHandle handle, const char *sid, const char *compartment, double initialConcentration, bool hasOnlySubstanceUnits, bool boundaryCondition)
Add a species to the current model, without regenerating it The last modification must regenerate for...
C_DECL_SPEC bool rrcCallConv addTriggerNoRegen(RRHandle handle, const char *eid, const char *trigger)
Add trigger to an existing event in the model, without regenerating it The last modification must reg...
C_DECL_SPEC bool rrcCallConv addParameterNoRegen(RRHandle handle, const char *pid, double value)
Add a parameter to the current model, without regenerating it The last modification must regenerate f...
C_DECL_SPEC bool rrcCallConv setInitConcentration(RRHandle handle, const char *sid, double initConcentration)
Set initial concentration for an existing species. Initial amount/concentration set before will be un...
C_DECL_SPEC bool rrcCallConv setPersistent(RRHandle handle, const char *eid, bool persistent)
Set the persistent attribute of the trigger of given event.
C_DECL_SPEC bool rrcCallConv validateCurrentSBML(RRHandle handle)
Validate the current SBML file.
C_DECL_SPEC bool rrcCallConv setKineticLaw(RRHandle handle, const char *rid, const char *kineticLaw)
Set the kinetic law for a existing reaction in the current model.
C_DECL_SPEC bool rrcCallConv setConstant(RRHandle handle, const char *sid, bool constant)
Set the constant attribute for an existing species/ parameter/ compartment.
C_DECL_SPEC bool rrcCallConv addRateRule(RRHandle handle, const char *vid, const char *formula)
Add a rate rule to the current model.
C_DECL_SPEC bool rrcCallConv addSpeciesAmountNoRegen(RRHandle handle, const char *sid, const char *compartment, double initialAmount, bool hasOnlySubstanceUnits, bool boundaryCondition)
Add a species to the current model, without regenerating it The last modification must regenerate for...
C_DECL_SPEC bool rrcCallConv setConstantNoRegen(RRHandle handle, const char *sid, bool constant)
Set the constant attribute for an existing species/ parameter/ compartment, without regenerating it T...
C_DECL_SPEC bool rrcCallConv addPriority(RRHandle handle, const char *eid, const char *priority)
Add priority to an existing event in the model If the given event already has a priority object,...
C_DECL_SPEC bool rrcCallConv addCompartment(RRHandle handle, const char *cid, double initVolume)
Add a compartment to the current model.
C_DECL_SPEC bool rrcCallConv setInitAmountNoRegen(RRHandle handle, const char *sid, double initAmount)
Set initial amount for an existing species, without regenerating it The last modification must regene...
C_DECL_SPEC bool rrcCallConv setTriggerInitialValueNoRegen(RRHandle handle, const char *eid, bool initValue)
Set the initial value attribute of the trigger of given event, without regenerating it The last modif...
C_DECL_SPEC bool rrcCallConv setBoundary(RRHandle handle, const char *sid, bool boundaryCondition)
Set the boundary condition of an existing species.
C_DECL_SPEC bool rrcCallConv addEventNoRegen(RRHandle handle, const char *eid, bool useValuesFromTriggerTime, const char *trigger)
Add an event to the current model, without regenerating it The last modification must regenerate for ...
C_DECL_SPEC bool rrcCallConv setInitAmount(RRHandle handle, const char *sid, double initAmount)
Set initial amount for an existing species. Initial amount/concentration set before will be unset.
C_DECL_SPEC bool rrcCallConv setHasOnlySubstanceUnitsNoRegen(RRHandle handle, const char *sid, bool hasOnlySubstanceUnits)
Set the hasOnlySubstanceUnits attribute for an existing species, without regenerating it The last mod...
C_DECL_SPEC bool rrcCallConv addEventAssignment(RRHandle handle, const char *eid, const char *vid, const char *formula)
Add an event assignment to an existing event in the current model.
C_DECL_SPEC bool rrcCallConv removeSpeciesNoRegen(RRHandle handle, const char *sid)
Remove a species from the current model, without regenerating it The last modification must regenerat...
C_DECL_SPEC bool rrcCallConv addReaction(RRHandle handle, const char *rid, const char **reactants, int numReactants, const char **products, int numProducts, const char *kineticLaw)
Add a reaction to the current model.
C_DECL_SPEC bool rrcCallConv addRateRuleNoRegen(RRHandle handle, const char *vid, const char *formula)
Add a rate rule to the current model, without regenerating it The last modification must regenerate f...
C_DECL_SPEC bool rrcCallConv addTrigger(RRHandle handle, const char *eid, const char *trigger)
Add trigger to an existing event in the model If the given event already has a trigger object,...
C_DECL_SPEC bool rrcCallConv setBoundaryNoRegen(RRHandle handle, const char *sid, bool boundaryCondition)
Set the boundary condition of an existing species, without regenerating it The last modification must...
C_DECL_SPEC bool rrcCallConv addCompartmentNoRegen(RRHandle handle, const char *cid, double initVolume)
Add a compartment to the current model, without regenerating it The last modification must regenerate...
C_DECL_SPEC bool rrcCallConv addAssignmentRule(RRHandle handle, const char *vid, const char *formula)
Add an assignment rule to the current model.
C_DECL_SPEC bool rrcCallConv removeParameter(RRHandle handle, const char *pid)
Remove a parameter from the current model.
C_DECL_SPEC bool rrcCallConv removeRules(RRHandle handle, const char *vid)
Remove rules related to given variable from the current model.
C_DECL_SPEC bool rrcCallConv setTriggerInitialValue(RRHandle handle, const char *eid, bool initValue)
Set the initial value attribute of the trigger of given event.
C_DECL_SPEC bool rrcCallConv addParameter(RRHandle handle, const char *pid, double value)
Add a parameter to the current model.
C_DECL_SPEC bool rrcCallConv addDelay(RRHandle handle, const char *eid, const char *delay)
Add delay to an existing event in the model If the given event already has a delay object,...
C_DECL_SPEC bool rrcCallConv addReactionFromSBMLNoRegen(RRHandle handle, const char *sbmlRep)
Add a reaction to the current model, without regenerating it The last modification must regenerate fo...
C_DECL_SPEC char *rrcCallConv getKineticLaw(RRHandle handle, const char *rid)
Get the kinetic law for a existing reaction in the current model.
C_DECL_SPEC bool rrcCallConv setInitConcentrationNoRegen(RRHandle handle, const char *sid, double initConcentration)
Set initial concentration for an existing species, without regenerating it The last modification must...
C_DECL_SPEC bool rrcCallConv setPersistentNoRegen(RRHandle handle, const char *eid, bool persistent)
Set the persistent attribute of the trigger of given event, without regenerating it The last modifica...
C_DECL_SPEC bool rrcCallConv regenerate(RRHandle handle)
After a model has been edited, it needs to be compiled. Call regenerate to recompile a model so that ...
C_DECL_SPEC bool rrcCallConv addSpeciesAmount(RRHandle handle, const char *sid, const char *compartment, double initialAmount, bool hasOnlySubstanceUnits, bool boundaryCondition)
Add a species to the current model.
C_DECL_SPEC bool rrcCallConv removeSpecies(RRHandle handle, const char *sid)
Remove a species from the current model.
C_DECL_SPEC bool rrcCallConv removeCompartment(RRHandle handle, const char *cid)
Remove a compartment from the current model.
C_DECL_SPEC bool rrcCallConv removeEvent(RRHandle handle, const char *eid)
Remove an event from the current model.
C_DECL_SPEC bool rrcCallConv removeCompartmentNoRegen(RRHandle handle, const char *cid)
Remove a compartment from the current model, without regenerating it The last modification must regen...
C_DECL_SPEC bool rrcCallConv hasError(void)
Check if there is an error string to retrieve.
C_DECL_SPEC char *rrcCallConv getLastError(void)
Retrieve the current error string.
C_DECL_SPEC RRVectorPtr rrcCallConv getFloatingSpeciesConcentrations(RRHandle handle)
Retrieve in a vector the concentrations for all the floating species.
C_DECL_SPEC bool rrcCallConv setFloatingSpeciesInitialConcentrationByIndex(RRHandle handle, int index, double value)
Set the initial concentration for a particular floating species.
C_DECL_SPEC RRVectorPtr rrcCallConv getIndependentFloatingSpeciesAmounts(RRHandle handle)
Retrieve in a vector the amounts of all the independent floating species.
C_DECL_SPEC int rrcCallConv getNumberOfDependentSpecies(RRHandle handle)
Returns the number of dependent species in the model.
C_DECL_SPEC RRVectorPtr rrcCallConv getFloatingSpeciesAmounts(RRHandle handle)
Retrieve in a vector the amounts for all the floating species.
C_DECL_SPEC RRStringArrayPtr rrcCallConv getDependentFloatingSpeciesIds(RRHandle handle)
Obtain the list of dependent floating species Id.
C_DECL_SPEC RRVectorPtr rrcCallConv getDependentFloatingSpeciesAmounts(RRHandle handle)
Retrieve in a vector the amounts of all the dependent floating species.
C_DECL_SPEC bool rrcCallConv getFloatingSpeciesInitialConcentrationByIndex(RRHandle handle, int index, double *value)
Get the initial concentration for a particular floating species.
C_DECL_SPEC bool rrcCallConv setFloatingSpeciesByIndex(RRHandle handle, const int index, const double value)
Set the concentration for a particular floating species.
C_DECL_SPEC RRVectorPtr rrcCallConv getDependentFloatingSpeciesConcentrations(RRHandle handle)
Retrieve in a vector the concentrations of all the dependent floating species.
C_DECL_SPEC bool rrcCallConv getFloatingSpeciesByIndex(RRHandle handle, const int index, double *value)
Retrieve the concentration for a particular floating species.
C_DECL_SPEC RRVectorPtr rrcCallConv getIndependentFloatingSpeciesConcentrations(RRHandle handle)
Retrieve in a vector the concentrations of all the independent floating species.
C_DECL_SPEC int rrcCallConv getNumberOfFloatingSpecies(RRHandle handle)
Returns the number of floating species in the model.
C_DECL_SPEC bool rrcCallConv setFloatingSpeciesConcentrations(RRHandle handle, const RRVectorPtr vec)
Set the floating species concentration to the vector vec.
C_DECL_SPEC RRStringArrayPtr rrcCallConv getFloatingSpeciesIds(RRHandle handle)
Obtain the list of floating species Id.
C_DECL_SPEC RRStringArrayPtr rrcCallConv getIndependentFloatingSpeciesIds(RRHandle handle)
Obtain the list of independent floating species Id.
C_DECL_SPEC RRStringArrayPtr rrcCallConv getFloatingSpeciesConcentrationIds(RRHandle handle)
Obtain the list of floating species concentrations Id.
C_DECL_SPEC int rrcCallConv getNumberOfIndependentSpecies(RRHandle handle)
Returns the number of independent species in the model.
C_DECL_SPEC RRStringArrayPtr rrcCallConv getFloatingSpeciesInitialConditionIds(RRHandle handle)
Get the initial floating species Ids.
C_DECL_SPEC RRStringArrayPtr rrcCallConv getFloatingSpeciesInitialConcentrationIds(RRHandle handle)
Get the initial floating species Ids.
C_DECL_SPEC bool rrcCallConv setFloatingSpeciesInitialConcentrations(RRHandle handle, const RRVectorPtr vec)
Set the initial floating species concentrations.
C_DECL_SPEC RRVectorPtr rrcCallConv getFloatingSpeciesInitialConcentrations(RRHandle handle)
Get the initial floating species concentrations.
C_DECL_SPEC RRHandle rrcCallConv createRRInstanceEx(const char *tempFolder, const char *compiler)
Initialize a new roadRunner instance and return a handle to it.
C_DECL_SPEC RRHandle rrcCallConv createRRInstance(void)
Initialize a new roadRunner instance and return a handle to it.
C_DECL_SPEC int rrcCallConv getComputeAndAssignConservationLaws(RRHandle handle, int *value)
Get the value of the moiety conservation setting.
C_DECL_SPEC bool rrcCallConv setInstallFolder(const char *folder)
Set the internal string containing the folder in where the RoadRunner C wrappers is installed.
C_DECL_SPEC bool rrcCallConv setComputeAndAssignConservationLaws(RRHandle handle, const bool On_Or_Off)
Enable or disable conservation analysis.
char * getInstallFolder(void)
Returns the folder in which the RoadRunner wrappers is installed.
C_DECL_SPEC bool rrcCallConv freeRRInstance(RRHandle handle)
Free the roadRunner instance.
C_DECL_SPEC bool rrcCallConv loadSBMLFromFile(RRHandle handle, const char *fileName)
Load a model from a SBML file.
C_DECL_SPEC bool rrcCallConv isModelLoaded(RRHandle handle)
check if a model is loaded
C_DECL_SPEC bool rrcCallConv loadSBMLEx(RRHandle handle, const char *sbml, bool forceRecompile)
Load a model from an SBML string.
C_DECL_SPEC bool rrcCallConv loadSimulationSettings(RRHandle handle, const char *fileName)
Load simulation settings from a file.
C_DECL_SPEC char *rrcCallConv getSBML(RRHandle handle)
Retrieve the SBML model that was last loaded into roadRunner.
C_DECL_SPEC bool rrcCallConv loadState(RRHandle handle, const char *filename)
Reload a road runner instance's state saved by saveState.
C_DECL_SPEC bool rrcCallConv loadSBMLFromFileE(RRHandle handle, const char *fileName, bool forceRecompile)
Load a model from a SBML file, force recompilation.
C_DECL_SPEC bool rrcCallConv clearModel(RRHandle handle)
Unload current model.
C_DECL_SPEC char *rrcCallConv getCurrentSBML(RRHandle handle)
Retrieve the current state of the model in the form of an SBML string.
C_DECL_SPEC bool rrcCallConv saveState(RRHandle handle, const char *filename)
Save a road runner instance's state to a platform-specific binary file.
C_DECL_SPEC bool rrcCallConv loadSBML(RRHandle handle, const char *sbml)
Load a model from an SBML string.
C_DECL_SPEC bool rrcCallConv getuEE(RRHandle handle, const char *name, const char *species, double *value)
Retrieve a single unscaled elasticity coefficient.
C_DECL_SPEC bool rrcCallConv setDiffStepSize(RRHandle handle, const double value)
Sets the differential step size used in routines such as getCC.
C_DECL_SPEC bool rrcCallConv getCC(RRHandle handle, const char *variable, const char *parameter, double *value)
Retrieve a single control coefficient.
C_DECL_SPEC bool rrcCallConv getEE(RRHandle handle, const char *name, const char *species, double *value)
Retrieve a single elasticity coefficient.
C_DECL_SPEC RRDoubleMatrixPtr rrcCallConv getUnscaledElasticityMatrix(RRHandle handle)
Retrieve the unscaled elasticity matrix for the current model.
C_DECL_SPEC RRListPtr rrcCallConv getFluxControlCoefficientIds(RRHandle handle)
Obtain the list of flux control coefficient Ids.
C_DECL_SPEC RRListPtr rrcCallConv getElasticityCoefficientIds(RRHandle handle)
Obtain the list of elasticity coefficient Ids.
C_DECL_SPEC bool rrcCallConv getDiffStepSize(RRHandle handle, double *value)
Retrieve the differential step size used in routines such as getCC.
C_DECL_SPEC RRDoubleMatrixPtr rrcCallConv getScaledElasticityMatrix(RRHandle handle)
Retrieve the scaled elasticity matrix for the current model.
C_DECL_SPEC RRDoubleMatrixPtr rrcCallConv getUnscaledFluxControlCoefficientMatrix(RRHandle handle)
Retrieve the matrix of unscaled flux control coefficients for the current model.
C_DECL_SPEC RRListPtr rrcCallConv getConcentrationControlCoefficientIds(RRHandle handle)
Obtain the list of concentration coefficient Ids.
C_DECL_SPEC RRDoubleMatrixPtr rrcCallConv getScaledFluxControlCoefficientMatrix(RRHandle handle)
Retrieve the matrix of scaled flux control coefficients for the current model.
C_DECL_SPEC RRListPtr rrcCallConv getUnscaledConcentrationControlCoefficientIds(RRHandle handle)
Obtain the list of unscaled concentration control coefficient Ids.
C_DECL_SPEC RRDoubleMatrixPtr rrcCallConv getUnscaledConcentrationControlCoefficientMatrix(RRHandle handle)
Retrieve the matrix of unscaled concentration control coefficients for the current model.
C_DECL_SPEC RRListPtr rrcCallConv getUnscaledFluxControlCoefficientIds(RRHandle handle)
Obtain the list of unscaled flux control coefficient Ids.
C_DECL_SPEC RRListPtr rrcCallConv getUnscaledElasticityCoefficientIds(RRHandle handle)
Obtain the list of unscaled elasticity coefficient Ids.
C_DECL_SPEC bool rrcCallConv getScaledFloatingSpeciesElasticity(RRHandle handle, const char *reactionId, const char *speciesId, double *value)
Retrieve the scaled elasticity matrix for the current model.
C_DECL_SPEC bool rrcCallConv getuCC(RRHandle handle, const char *variable, const char *parameter, double *value)
Retrieve a single unscaled control coefficient.
C_DECL_SPEC RRDoubleMatrixPtr rrcCallConv getScaledConcentrationControlCoefficientMatrix(RRHandle handle)
Retrieve the matrix of scaled concentration control coefficients for the current model.
C_DECL_SPEC RRStringArrayPtr rrcCallConv getGlobalParameterIds(RRHandle handle)
Obtain the list of global parameter Ids.
C_DECL_SPEC bool rrcCallConv setGlobalParameterByIndex(RRHandle handle, const int index, const double value)
Set the value for a particular global parameter.
C_DECL_SPEC int rrcCallConv getNumberOfGlobalParameters(RRHandle handle)
Returns the number of global parameters in the model.
C_DECL_SPEC RRVectorPtr rrcCallConv getGlobalParameterValues(RRHandle handle)
Retrieve the values for all the global parameter values in a vector.
C_DECL_SPEC bool rrcCallConv getGlobalParameterByIndex(RRHandle handle, const int index, double *value)
Retrieve the global parameter value.
C_DECL_SPEC RRVectorPtr rrcCallConv getRatesOfChangeEx(RRHandle handle, const RRVectorPtr vec)
Retrieve the vector of rates of change given a vector of floating species concentrations.
C_DECL_SPEC RRStringArrayPtr rrcCallConv getRatesOfChangeIds(RRHandle handle)
Retrieve the string list of rates of change Ids.
C_DECL_SPEC bool rrcCallConv getRateOfChange(RRHandle handle, const int, double *value)
Retrieve the rate of change for a given floating species.
C_DECL_SPEC RRVectorPtr rrcCallConv getRatesOfChange(RRHandle handle)
Retrieve the vector of rates of change as determined by the current state of the model.
C_DECL_SPEC RRVectorPtr rrcCallConv getReactionRatesEx(RRHandle handle, const RRVectorPtr vec)
Retrieve a vector of reaction rates given a vector of species concentrations.
C_DECL_SPEC bool rrcCallConv getReactionRate(RRHandle handle, const int index, double *rate)
Retrieve a give reaction rate as indicated by the index parameter.
C_DECL_SPEC RRStringArrayPtr rrcCallConv getReactionIds(RRHandle handle)
Obtain the list of reaction Ids.
C_DECL_SPEC int rrcCallConv getNumberOfReactions(RRHandle handle)
Obtain the number of reactions in the loaded model.
C_DECL_SPEC RRVectorPtr rrcCallConv getReactionRates(RRHandle handle)
Retrieve a vector of reaction rates as determined by the current state of the model.
C_DECL_SPEC bool rrcCallConv resetToOrigin(RRHandle handle)
Resets the model to the state in which it was first loaded, including initial conditions,...
C_DECL_SPEC bool rrcCallConv resetAll(RRHandle handle)
Resets all variables of all types in the model to their current initial values.
C_DECL_SPEC bool rrcCallConv reset(RRHandle handle)
Resets all variables of the model to their current initial values. Does not change the parameters.
C_DECL_SPEC bool rrcCallConv resetParameter(RRHandle handle)
Resets all parameters of the model to their current initial values.
C_DECL_SPEC int rrcCallConv setCurrentIntegratorParameterString(RRHandle handle, const char *parameterName, const char *value)
Set the string value for a specific integrator setting.
C_DECL_SPEC int rrcCallConv setCurrentIntegrator(RRHandle handle, const char *nameOfIntegrator)
Specify the current integrator to be used for simulation. This method instantiates a new integrator o...
C_DECL_SPEC char *rrcCallConv getCurrentIntegratorNthParameterHint(RRHandle handle, int n)
Get the hint of a parameter of the current integrator.
C_DECL_SPEC char *rrcCallConv getCurrentSteadyStateSolverNthParameterDescription(RRHandle handle, int n)
Get the description of a parameter of the current steady state solver.
C_DECL_SPEC int rrcCallConv setCurrentSteadyStateSolverParameterBoolean(RRHandle handle, const char *parameterName, int value)
Set the boolean value for a specific steady state solver setting.
C_DECL_SPEC int rrcCallConv getCurrentIntegratorParameterBoolean(RRHandle handle, const char *parameterName)
Get the boolean value for a specific integrator setting.
C_DECL_SPEC int rrcCallConv resetCurrentIntegratorParameters(RRHandle handle)
Reset the integrator parameters to their default values.
C_DECL_SPEC char *rrcCallConv getCurrentIntegratorParameterDescription(RRHandle handle, const char *parameterName)
Get the description for a specific integrator setting.
C_DECL_SPEC int rrcCallConv getCurrentIntegratorParameterInt(RRHandle handle, const char *parameterName)
Get the integer value for a specific integrator setting.
C_DECL_SPEC int rrcCallConv getNumberOfCurrentSteadyStateSolverParameters(RRHandle handle)
Get the number of adjustable settings for the current steady state solver.
C_DECL_SPEC char *rrcCallConv getCurrentIntegratorParameterHint(RRHandle handle, const char *parameterName)
Get the hint for a specific integrator setting.
C_DECL_SPEC int rrcCallConv getCurrentSteadyStateSolverParameterBoolean(RRHandle handle, const char *parameterName)
Get the boolean value for a specific steady state solver setting.
C_DECL_SPEC int rrcCallConv setCurrentIntegratorParameterDouble(RRHandle handle, const char *parameterName, double value)
Set the double value for a specific integrator setting.
C_DECL_SPEC char *rrcCallConv getRegisteredSteadyStateSolverDescription(int n)
Get the description of a registered steady state solver (e.g. cvode etc.)
C_DECL_SPEC int rrcCallConv resetCurrentSteadyStateSolverParameters(RRHandle handle)
Reset the steady state solver parameters to their default values.
C_DECL_SPEC int rrcCallConv getCurrentIntegratorNthParameterType(RRHandle handle, int n)
Get the type of a parameter of the current integrator.
C_DECL_SPEC RRStringArrayPtr rrcCallConv getListOfCurrentIntegratorParameterNames(RRHandle handle)
Get the names of adjustable settings for the current integrator.
C_DECL_SPEC char *rrcCallConv getCurrentSteadyStateSolverNthParameterHint(RRHandle handle, int n)
Get the hint of a parameter of the current steady state solver.
C_DECL_SPEC char *rrcCallConv getCurrentSteadyStateSolverHint(RRHandle handle)
Obtain a short hint for the current steady state solver.
C_DECL_SPEC char *rrcCallConv getRegisteredSteadyStateSolverHint(int n)
Get the hint of a registered steady state solver (e.g. cvode etc.)
C_DECL_SPEC char *rrcCallConv getCurrentIntegratorHint(RRHandle handle)
Obtain a short hint for the current integrator.
C_DECL_SPEC const char *rrcCallConv solverTypeToString(int code)
Get a string description of the type [STATIC MEMORY - DO NOT FREE] Can call on return value of e....
C_DECL_SPEC int rrcCallConv getCurrentSteadyStateSolverParameterInt(RRHandle handle, const char *parameterName)
Get the integer value for a specific steady state solver setting.
C_DECL_SPEC int rrcCallConv getCurrentSteadyStateSolverNthParameterType(RRHandle handle, int n)
Get the type of a parameter of the current steady state solver.
C_DECL_SPEC int rrcCallConv setCurrentIntegratorParameterUInt(RRHandle handle, const char *parameterName, unsigned int value)
Set the unsigned integer value for a specific integrator setting.
C_DECL_SPEC int rrcCallConv setCurrentIntegratorParameterInt(RRHandle handle, const char *parameterName, int value)
Set the integer value for a specific integrator setting.
C_DECL_SPEC char *rrcCallConv getRegisteredIntegratorDescription(int n)
Get the description of a registered integrator (e.g. cvode etc.)
C_DECL_SPEC int rrcCallConv getNumRegisteredSteadyStateSolvers()
Get the number of registered steady state solvers.
C_DECL_SPEC char *rrcCallConv getCurrentSteadyStateSolverName(RRHandle handle)
Obtain a description of the current steady state solver.
C_DECL_SPEC int rrcCallConv getNumberOfCurrentIntegratorParameters(RRHandle handle)
Get the number of adjustable settings for the current integrator.
C_DECL_SPEC char *rrcCallConv getCurrentIntegratorNthParameterName(RRHandle handle, int n)
Get the name of a parameter of the current integrator.
C_DECL_SPEC int rrcCallConv setCurrentIntegratorParameterDoubleArray(RRHandle handle, const char *parameterName, double *value, int len)
Set the double array value for a specific integrator setting. Should only used for absoluate tolerace...
C_DECL_SPEC char *rrcCallConv getCurrentIntegratorNthParameterDisplayName(RRHandle handle, int n)
Get the display name of a parameter of the current integrator.
C_DECL_SPEC int rrcCallConv setCurrentSteadyStateSolverParameterDouble(RRHandle handle, const char *parameterName, double value)
Set the double value for a specific steady state solver setting.
C_DECL_SPEC int rrcCallConv getCurrentIntegratorParameterDoubleArray(RRHandle handle, const char *parameterName, double **value, int *len)
Get the double array value for a specific integrator setting. Should only used for absoluate tolerace...
C_DECL_SPEC double rrcCallConv getCurrentSteadyStateSolverParameterDouble(RRHandle handle, const char *parameterName)
Get the double value for a specific steady state solver setting.
C_DECL_SPEC unsigned int rrcCallConv getCurrentIntegratorParameterUInt(RRHandle handle, const char *parameterName)
Get the unsigned integer value for a specific integrator setting.
C_DECL_SPEC char *rrcCallConv getCurrentSteadyStateSolverParameterHint(RRHandle handle, const char *parameterName)
Get the hint for a specific steady state solver setting.
C_DECL_SPEC int rrcCallConv getCurrentIntegratorParameterType(RRHandle handle, const char *parameterName)
Get the return type for a specific integrator setting.
C_DECL_SPEC int rrcCallConv setCurrentSteadyStateSolver(RRHandle handle, const char *nameOfSteadyStateSolver)
Specify the current steady state solver to be used for simulation. This method instantiates a new ste...
C_DECL_SPEC int rrcCallConv getNumInstantiatedIntegrators(RRHandle handle)
Get the number of instantiated integrators. To instantiate an integrator, use setCurrentIntegrator.
C_DECL_SPEC int rrcCallConv setCurrentIntegratorParameterBoolean(RRHandle handle, const char *parameterName, int value)
Set the boolean value for a specific integrator setting.
C_DECL_SPEC unsigned int rrcCallConv getCurrentSteadyStateSolverParameterUInt(RRHandle handle, const char *parameterName)
Get the unsigned integer value for a specific steady state solver setting.
C_DECL_SPEC int rrcCallConv getNumRegisteredIntegrators()
Get the number of registered integrators.
C_DECL_SPEC char *rrcCallConv getRegisteredIntegratorName(int n)
Get the name of a registered integrator (e.g. cvode etc.)
C_DECL_SPEC char *rrcCallConv getCurrentIntegratorDescription(RRHandle handle)
Obtain a description of the current integrator.
C_DECL_SPEC char *rrcCallConv getCurrentIntegratorName(RRHandle handle)
Obtain a description of the current integrator.
C_DECL_SPEC char *rrcCallConv getRegisteredIntegratorHint(int n)
Get the hint of a registered integrator (e.g. cvode etc.)
C_DECL_SPEC int rrcCallConv setCurrentSteadyStateSolverParameterString(RRHandle handle, const char *parameterName, const char *value)
Set the string value for a specific steady state solver setting.
C_DECL_SPEC int rrcCallConv setCurrentSteadyStateSolverParameterUInt(RRHandle handle, const char *parameterName, unsigned int value)
Set the unsigned integer value for a specific steady state solver setting.
C_DECL_SPEC char *rrcCallConv getCurrentSteadyStateSolverParameterString(RRHandle handle, const char *parameterName)
Get the string value for a specific steady state solver setting.
C_DECL_SPEC int rrcCallConv getCurrentSteadyStateSolverParameterType(RRHandle handle, const char *parameterName)
Get the return type for a specific steady state solver setting.
C_DECL_SPEC int rrcCallConv setCurrentIntegratorIndividualTolerance(RRHandle handle, const char *sid, double value)
Set the double array value for a specific integrator setting. Should only used for absoluate tolerace...
C_DECL_SPEC int rrcCallConv setCurrentSteadyStateSolverParameterInt(RRHandle handle, const char *parameterName, int value)
Set the integer value for a specific steady state solver setting.
C_DECL_SPEC char *rrcCallConv getRegisteredSteadyStateSolverName(int n)
Get the name of a registered steady state solver (e.g. cvode etc.)
C_DECL_SPEC char *rrcCallConv getCurrentIntegratorNthParameterDescription(RRHandle handle, int n)
Get the description of a parameter of the current integrator.
C_DECL_SPEC char *rrcCallConv getCurrentSteadyStateSolverNthParameterName(RRHandle handle, int n)
Get the name of a parameter of the current steady state solver.
C_DECL_SPEC char *rrcCallConv getCurrentSteadyStateSolverDescription(RRHandle handle)
Obtain a description of the current steady state solver.
C_DECL_SPEC char *rrcCallConv getCurrentIntegratorParameterString(RRHandle handle, const char *parameterName)
Get the string value for a specific integrator setting.
C_DECL_SPEC double rrcCallConv getCurrentIntegratorParameterDouble(RRHandle handle, const char *parameterName)
Get the double value for a specific integrator setting.
C_DECL_SPEC char *rrcCallConv getCurrentSteadyStateSolverParameterDescription(RRHandle handle, const char *parameterName)
Get the description for a specific steady state solver setting.
C_DECL_SPEC RRStringArrayPtr rrcCallConv getListOfCurrentSteadyStateSolverParameterNames(RRHandle handle)
Get the names of adjustable settings for the current steady state solver.
C_DECL_SPEC char *rrcCallConv getCurrentSteadyStateSolverNthParameterDisplayName(RRHandle handle, int n)
Get the display name of a parameter of the current steady state solver.
C_DECL_SPEC bool rrcCallConv getTimeStart(RRHandle handle, double *timeStart)
Get the value of the current time start.
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 p...
C_DECL_SPEC bool rrcCallConv setNumPoints(RRHandle handle, int numberOfPoints)
Set the number of points to generate in a time course simulation.
C_DECL_SPEC bool rrcCallConv simulateNoReturn(RRHandle handle)
Carry out a time-course simulation. setTimeStart, setTimeEnd, setNumPoints, etc are used to set the s...
C_DECL_SPEC bool rrcCallConv setTimeCourseSelectionList(RRHandle handle, const char *list)
Set the selection list for output from simulate(void) or simulateEx(void)
C_DECL_SPEC bool rrcCallConv setTimeStart(RRHandle handle, double timeStart)
Set the time start for a time course simulation.
C_DECL_SPEC bool rrcCallConv setConfigurationXML(RRHandle handle, const char *caps)
Set the simulator's capabilities.
C_DECL_SPEC bool rrcCallConv setTimes(RRHandle handle, double *times, int size)
Set the times vector to output in a time course simulation.
C_DECL_SPEC bool rrcCallConv getTimeEnd(RRHandle handle, double *timeEnd)
Get the value of the current time end.
C_DECL_SPEC char *rrcCallConv getConfigurationXML(RRHandle handle)
Get the simulator's capabilities.
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 setTimeCourseSelectionL...
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.
C_DECL_SPEC bool rrcCallConv setTimeEnd(RRHandle handle, double timeEnd)
Set the time end for a time course simulation.
C_DECL_SPEC RRCDataPtr rrcCallConv simulate(RRHandle handle)
Carry out a time-course simulation. setTimeStart, setTimeEnd, setNumPoints, etc are used to set the s...
C_DECL_SPEC RRCDataPtr rrcCallConv getSimulationResult(RRHandle handle)
Retrieve the result of the last simulation.
C_DECL_SPEC bool rrcCallConv getNumPoints(RRHandle handle, int *numPoints)
Get the value of the current number of points.
C_DECL_SPEC RRStringArrayPtr rrcCallConv getTimeCourseSelectionList(RRHandle handle)
Get the current selection list for simulate(void) or simulateEx(void)
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 p...
C_DECL_SPEC RRHandle rrcCallConv getSimulationResultAsDoubleMatrix(RRHandle handle)
Retrieve the result of the last simulation as a DoubleMatrix.
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 p...
C_DECL_SPEC bool rrcCallConv evalModel(RRHandle handle)
Evaluate the current model, that it update all assignments and rates of change. Do not carry out an i...
C_DECL_SPEC RRStringArrayPtr rrcCallConv getEigenvalueIds(RRHandle handle)
Obtain the list of eigenvalue Ids.
C_DECL_SPEC RRListPtr rrcCallConv getAvailableTimeCourseSymbols(RRHandle handle)
Obtain the list of all available symbols.
C_DECL_SPEC bool rrcCallConv getValue(RRHandle handle, const char *symbolId, double *value)
Get the value for a given symbol, use getAvailableTimeCourseSymbols(void) for a list of symbols.
C_DECL_SPEC bool rrcCallConv setValue(RRHandle handle, const char *symbolId, const double value)
Set the value for a given symbol, use getAvailableTimeCourseSymbols(void) for a list of symbols.
C_DECL_SPEC RRListPtr rrcCallConv getAvailableSteadyStateSymbols(RRHandle handle)
Obtain the list of all available steady state symbols.
C_DECL_SPEC RRVectorPtr rrcCallConv computeSteadyStateValues(RRHandle handle)
A convenient method for returning a vector of the steady state species concentrations.
C_DECL_SPEC RRStringArrayPtr rrcCallConv getSteadyStateSelectionList(RRHandle handle)
Get the selection list for the steady state analysis.
C_DECL_SPEC bool rrcCallConv steadyState(RRHandle handle, double *value)
Compute the steady state of the current model.
C_DECL_SPEC bool rrcCallConv setSteadyStateSelectionListEx(RRHandle handle, int length, const char **list)
Set the selection list for the steady-state analysis Use setSteadyStateSelectionListEx(handle,...
C_DECL_SPEC bool rrcCallConv setSteadyStateSelectionList(RRHandle handle, const char *list)
Set the selection list of the steady state analysis.
C_DECL_SPEC RRCDataPtr rrcCallConv 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,...
C_DECL_SPEC RRCDataPtr rrcCallConv gillespieOnGrid(RRHandle handle)
Carry out a time-course simulation using the Gillespie algorithm with fixed step size....
C_DECL_SPEC RRCDataPtr rrcCallConv gillespieMeanOnGrid(RRHandle handle, int numberOfSimulations)
Carry out a series of time-course simulations using the Gillespie algorithm with fixed step size,...
C_DECL_SPEC RRCDataPtr rrcCallConv gillespieMeanSDOnGrid(RRHandle handle, int numberOfSimulations)
Carry out a series of time-course simulations using the Gillespie algorithm with fixed step size,...
C_DECL_SPEC RRCDataPtr rrcCallConv gillespieEx(RRHandle handle, double timeStart, double timeEnd)
Carry out a time-course simulation using the Gillespie algorithm based on the given arguments,...
C_DECL_SPEC RRCDataPtr rrcCallConv 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,...
C_DECL_SPEC RRCDataPtr rrcCallConv 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...
C_DECL_SPEC RRCDataPtr rrcCallConv gillespie(RRHandle handle)
Carry out a time-course simulation using the Gillespie algorithm with variable step size....
C_DECL_SPEC char *rrcCallConv getCPPAPIVersion(RRHandle handle)
Retrieve the current version number of the C++ wrappers (Core RoadRunner wrappers) library.
C_DECL_SPEC bool rrcCallConv setSupportCodeFolder(RRHandle handle, const char *folder)
Set the path to a folder containing support code for model generation.
C_DECL_SPEC char *rrcCallConv getRRCAPILocation(void)
Retrieve the directory path of the shared rrCApi library.
C_DECL_SPEC char *rrcCallConv getlibSBMLVersion(RRHandle handle)
Retrieve the current version number of the libSBML library.
C_DECL_SPEC char *rrcCallConv getCompilerLocation(RRHandle handle)
Get the path to a folder containing the compiler being used.
C_DECL_SPEC char *rrcCallConv getBuildTime(void)
Retrieve the current build time (HH:MM:SS) of the library.
C_DECL_SPEC char *rrcCallConv getTempFolder(RRHandle handle)
Retrieve the current temporary folder path.
C_DECL_SPEC char *rrcCallConv getBuildDateTime(void)
Retrieve the current build date + time of the library.
C_DECL_SPEC bool rrcCallConv setTempFolder(RRHandle handle, const char *folder)
Set the path to the temporary folder where the C code will be stored.
C_DECL_SPEC bool rrcCallConv setCompiler(RRHandle handle, const char *fNameWithPath)
Set the path and filename to the compiler to be used by roadrunner.
C_DECL_SPEC char *rrcCallConv getExtendedAPIInfo()
Retrieve extended wrappers info.
C_DECL_SPEC char *rrcCallConv getCopyright(void)
Retrieve the current copyright notice for the library.
C_DECL_SPEC char *rrcCallConv getInfo(RRHandle handle)
Retrieve info about current state of roadrunner, e.g. loaded model, conservationAnalysis etc.
C_DECL_SPEC bool rrcCallConv setCodeGenerationMode(RRHandle handle, int mode)
Set the runtime generation option [Not yet implemented].
C_DECL_SPEC bool rrcCallConv setCompilerLocation(RRHandle handle, const char *folder)
Set the path to a folder containing the compiler to be used.
C_DECL_SPEC char *rrcCallConv getBuildDate(void)
Retrieve the current build date of the library.
C_DECL_SPEC char *rrcCallConv getSupportCodeFolder(RRHandle handle)
Get the path to a folder containing support code.
C_DECL_SPEC char *rrcCallConv getWorkingDirectory(void)
Retrieve the current working directory path.
C_DECL_SPEC char *rrcCallConv getCompiler(RRHandle handle)
Get the name of the compiler currently being used by roadrunner.
C_DECL_SPEC char *rrcCallConv getAPIVersion(void)
Retrieve the current version number of the C wrappers library.
C_DECL_SPEC double rrcCallConv _getTime(RRHandle handle)
C_DECL_SPEC char *rrcCallConv getParamPromotedSBML(RRHandle handle, const char *sArg)
Promote any local parameters to global status.
C_DECL_SPEC int rrcCallConv getVersion()
C_DECL_SPEC char *rrcCallConv getVersionStr()
C_DECL_SPEC void rrcCallConv _getStateVectorRate(RRHandle handle, double time, double *value)
C_DECL_SPEC int rrcCallConv _getStateVector(RRHandle handle)
C_DECL_SPEC int rrcCallConv _getNumIndFloatingSpecies(RRHandle handle)
C_DECL_SPEC char *rrcCallConv getVersionEx()
C_DECL_SPEC bool rrcCallConv addInitialAssignment(RRHandle handle, const char *vid, const char *formula, bool forceRegenerate)
Add an initial assignment to an exsiting symbol of the current model.
C_DECL_SPEC int rrcCallConv _getNumRateRules(RRHandle handle)
roadRunner C wrappers 2012
roadRunner C wrappers 2012
roadRunner C wrappers 2012
roadRunner C wrappers 2012
roadRunner C wrappers 2012
void * RRHandle
Void pointer to a RoadRunner instance.
Definition: rrc_types.h:50
roadRunner C wrappers 2012
Structure for the result type from the simulate calls. The client is responsible for freeing the RRCD...
Definition: rrc_types.h:111
Structure for a simple double Matrix type.
Definition: rrc_types.h:74
A list type, stores int, double, strings and lists.
Definition: rrc_types.h:148
Structure for a simple vector of strings.
Definition: rrc_types.h:66
Structure for a simple vector of doubles.
Definition: rrc_types.h:58