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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 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 /* Registered Integrators *****************************************************/
472 
478 C_DECL_SPEC int rrcCallConv getNumRegisteredIntegrators ();
479 
486 C_DECL_SPEC char* rrcCallConv getRegisteredIntegratorName (int n);
487 
494 C_DECL_SPEC char* rrcCallConv getRegisteredIntegratorHint (int n);
495 
502 C_DECL_SPEC char* rrcCallConv getRegisteredIntegratorDescription (int n);
503 
504 /* Instantiated Integrators ***************************************************/
505 
513 C_DECL_SPEC int rrcCallConv getNumInstantiatedIntegrators (RRHandle handle);
514 
524 C_DECL_SPEC int rrcCallConv setCurrentIntegrator (RRHandle handle, char *nameOfIntegrator);
525 
532 C_DECL_SPEC char* rrcCallConv getCurrentIntegratorName (RRHandle handle);
533 
540 C_DECL_SPEC char* rrcCallConv getCurrentIntegratorDescription (RRHandle handle);
541 
548 C_DECL_SPEC char* rrcCallConv getCurrentIntegratorHint (RRHandle handle);
549 
556 C_DECL_SPEC int rrcCallConv getNumberOfCurrentIntegratorParameters (RRHandle handle);
557 
564 C_DECL_SPEC char* rrcCallConv getCurrentIntegratorNthParameterName (RRHandle handle, int n);
565 
572 C_DECL_SPEC char* rrcCallConv getCurrentIntegratorNthParameterDescription (RRHandle handle, int n);
573 
580 C_DECL_SPEC char* rrcCallConv getCurrentIntegratorNthParameterDisplayName (RRHandle handle, int n);
581 
588 C_DECL_SPEC char* rrcCallConv getCurrentIntegratorNthParameterHint (RRHandle handle, int n);
589 
596 C_DECL_SPEC int rrcCallConv getCurrentIntegratorNthParameterType (RRHandle handle, int n);
597 
604 C_DECL_SPEC int rrcCallConv resetCurrentIntegratorParameters (RRHandle handle);
605 
613 
621 C_DECL_SPEC char* rrcCallConv getCurrentIntegratorParameterDescription (RRHandle handle, char *parameterName);
622 
630 C_DECL_SPEC char* rrcCallConv getCurrentIntegratorParameterHint (RRHandle handle, char *parameterName);
631 
639 C_DECL_SPEC int rrcCallConv getCurrentIntegratorParameterType (RRHandle handle, char *parameterName);
640 
648 C_DECL_SPEC int rrcCallConv getCurrentIntegratorParameterInt (RRHandle handle, char *parameterName);
649 
658 C_DECL_SPEC int rrcCallConv setCurrentIntegratorParameterInt (RRHandle handle, char *parameterName, int value);
659 
667 C_DECL_SPEC unsigned int rrcCallConv getCurrentIntegratorParameterUInt (RRHandle handle, char *parameterName);
668 
677 C_DECL_SPEC int rrcCallConv setCurrentIntegratorParameterUInt (RRHandle handle, char *parameterName, unsigned int value);
678 
686 C_DECL_SPEC double rrcCallConv getCurrentIntegratorParameterDouble (RRHandle handle, char *parameterName);
687 
696 C_DECL_SPEC int rrcCallConv setCurrentIntegratorParameterDouble (RRHandle handle, char *parameterName, double value);
697 
705 C_DECL_SPEC char* rrcCallConv getCurrentIntegratorParameterString (RRHandle handle, char *parameterName);
706 
715 C_DECL_SPEC int rrcCallConv setCurrentIntegratorParameterString (RRHandle handle, char *parameterName, char* value);
716 
724 C_DECL_SPEC int rrcCallConv getCurrentIntegratorParameterBoolean (RRHandle handle, char *parameterName);
725 
734 C_DECL_SPEC int rrcCallConv setCurrentIntegratorParameterBoolean (RRHandle handle, char *parameterName, int value);
735 
736 
737 /* Steady State Solvers *******************************************************/
738 
744 C_DECL_SPEC int rrcCallConv getNumRegisteredSteadyStateSolvers ();
745 
752 C_DECL_SPEC char* rrcCallConv getRegisteredSteadyStateSolverName (int n);
753 
760 C_DECL_SPEC char* rrcCallConv getRegisteredSteadyStateSolverHint (int n);
761 
768 C_DECL_SPEC char* rrcCallConv getRegisteredSteadyStateSolverDescription (int n);
769 
770 
780 C_DECL_SPEC int rrcCallConv setCurrentSteadyStateSolver (RRHandle handle, char *nameOfSteadyStateSolver);
781 
788 C_DECL_SPEC char* rrcCallConv getCurrentSteadyStateSolverName (RRHandle handle);
789 
796 C_DECL_SPEC char* rrcCallConv getCurrentSteadyStateSolverDescription (RRHandle handle);
797 
804 C_DECL_SPEC char* rrcCallConv getCurrentSteadyStateSolverHint (RRHandle handle);
805 
812 C_DECL_SPEC int rrcCallConv getNumberOfCurrentSteadyStateSolverParameters (RRHandle handle);
813 
820 C_DECL_SPEC char* rrcCallConv getCurrentSteadyStateSolverNthParameterName (RRHandle handle, int n);
821 
828 C_DECL_SPEC char* rrcCallConv getCurrentSteadyStateSolverNthParameterDisplayName (RRHandle handle, int n);
829 
836 C_DECL_SPEC char* rrcCallConv getCurrentSteadyStateSolverNthParameterDescription (RRHandle handle, int n);
837 
844 C_DECL_SPEC char* rrcCallConv getCurrentSteadyStateSolverNthParameterHint (RRHandle handle, int n);
845 
852 C_DECL_SPEC int rrcCallConv getCurrentSteadyStateSolverNthParameterType (RRHandle handle, int n);
853 
860 C_DECL_SPEC int rrcCallConv resetCurrentSteadyStateSolverParameters (RRHandle handle);
861 
869 C_DECL_SPEC const char* rrcCallConv solverTypeToString (int code);
870 
878 
886 C_DECL_SPEC char* rrcCallConv getCurrentSteadyStateSolverParameterDescription (RRHandle handle, char *parameterName);
887 
895 C_DECL_SPEC char* rrcCallConv getCurrentSteadyStateSolverParameterHint (RRHandle handle, char *parameterName);
896 
904 C_DECL_SPEC int rrcCallConv getCurrentSteadyStateSolverParameterType (RRHandle handle, char *parameterName);
905 
913 C_DECL_SPEC int rrcCallConv getCurrentSteadyStateSolverParameterInt (RRHandle handle, char *parameterName);
914 
923 C_DECL_SPEC int rrcCallConv setCurrentSteadyStateSolverParameterInt (RRHandle handle, char *parameterName, int value);
924 
932 C_DECL_SPEC unsigned int rrcCallConv getCurrentSteadyStateSolverParameterUInt (RRHandle handle, char *parameterName);
933 
942 C_DECL_SPEC int rrcCallConv setCurrentSteadyStateSolverParameterUInt (RRHandle handle, char *parameterName, unsigned int value);
943 
951 C_DECL_SPEC double rrcCallConv getCurrentSteadyStateSolverParameterDouble (RRHandle handle, char *parameterName);
952 
961 C_DECL_SPEC int rrcCallConv setCurrentSteadyStateSolverParameterDouble (RRHandle handle, char *parameterName, double value);
962 
970 C_DECL_SPEC char* rrcCallConv getCurrentSteadyStateSolverParameterString (RRHandle handle, char *parameterName);
971 
980 C_DECL_SPEC int rrcCallConv setCurrentSteadyStateSolverParameterString (RRHandle handle, char *parameterName, char* value);
981 
989 C_DECL_SPEC int rrcCallConv getCurrentSteadyStateSolverParameterBoolean (RRHandle handle, char *parameterName);
990 
999 C_DECL_SPEC int rrcCallConv setCurrentSteadyStateSolverParameterBoolean (RRHandle handle, char *parameterName, int value);
1000 
1001 
1009 C_DECL_SPEC bool rrcCallConv setTimeStart(RRHandle handle, double timeStart);
1010 
1018 C_DECL_SPEC bool rrcCallConv setTimeEnd(RRHandle handle, double timeEnd);
1019 
1027 C_DECL_SPEC bool rrcCallConv setNumPoints(RRHandle handle, int numberOfPoints);
1028 
1029 
1046 C_DECL_SPEC bool rrcCallConv setTimeCourseSelectionList(RRHandle handle, const char* list);
1047 //C_DECL_SPEC bool rrcCallConv setTimeCourseSelectionList(const char* list);
1048 
1056 C_DECL_SPEC RRStringArrayPtr rrcCallConv getTimeCourseSelectionList(RRHandle handle);
1057 
1068 C_DECL_SPEC RRCDataPtr rrcCallConv simulate(RRHandle handle);
1069 
1078 C_DECL_SPEC RRCDataPtr rrcCallConv getSimulationResult(RRHandle handle);
1079 
1080 
1105 C_DECL_SPEC RRCDataPtr rrcCallConv simulateEx(RRHandle handle, const double timeStart, const double timeEnd, const int numberOfPoints);
1106 
1120 C_DECL_SPEC bool rrcCallConv oneStep(RRHandle handle, const double currentTime, const double stepSize, double *value);
1121 
1132 C_DECL_SPEC bool rrcCallConv getTimeStart(RRHandle handle, double* timeStart);
1133 
1144 C_DECL_SPEC bool rrcCallConv getTimeEnd(RRHandle handle, double* timeEnd);
1145 
1156 C_DECL_SPEC bool rrcCallConv getNumPoints (RRHandle handle, int* numPoints);
1157 
1170 C_DECL_SPEC bool rrcCallConv steadyState(RRHandle handle, double* value);
1171 
1182 C_DECL_SPEC RRVectorPtr rrcCallConv computeSteadyStateValues(RRHandle handle);
1183 
1205 C_DECL_SPEC bool rrcCallConv setSteadyStateSelectionList(RRHandle handle, const char* list);
1206 
1214 C_DECL_SPEC RRStringArrayPtr rrcCallConv getSteadyStateSelectionList(RRHandle handle);
1215 
1216 
1217 // --------------------------------------------------------------------------------
1218 // Get and Set Routines
1219 // --------------------------------------------------------------------------------
1220 
1232 C_DECL_SPEC bool rrcCallConv getValue(RRHandle handle, const char* symbolId, double* value);
1233 
1234 
1246 C_DECL_SPEC bool rrcCallConv setValue(RRHandle handle, const char* symbolId, const double value);
1247 
1248 
1258 C_DECL_SPEC RRVectorPtr rrcCallConv getFloatingSpeciesConcentrations(RRHandle handle);
1259 
1260 
1270 C_DECL_SPEC RRVectorPtr rrcCallConv getBoundarySpeciesConcentrations(RRHandle handle);
1271 
1272 // --------------------------------------------------------------------------------
1273 // Parameter Group
1274 // --------------------------------------------------------------------------------
1275 
1285 C_DECL_SPEC RRVectorPtr rrcCallConv getGlobalParameterValues(RRHandle handle);
1286 
1296 C_DECL_SPEC bool rrcCallConv setBoundarySpeciesByIndex(RRHandle handle, const int index, const double value);
1297 
1307 C_DECL_SPEC bool rrcCallConv setFloatingSpeciesInitialConcentrationByIndex(RRHandle handle, int index, double value);
1308 
1318 C_DECL_SPEC bool rrcCallConv getFloatingSpeciesInitialConcentrationByIndex(RRHandle handle, int index, double* value);
1319 
1329 C_DECL_SPEC bool rrcCallConv setFloatingSpeciesByIndex(RRHandle handle, const int index, const double value);
1330 
1340 C_DECL_SPEC bool rrcCallConv setGlobalParameterByIndex(RRHandle handle, const int index, const double value);
1341 
1350 C_DECL_SPEC bool rrcCallConv getBoundarySpeciesByIndex(RRHandle handle, const int index, double* value);
1351 
1361 C_DECL_SPEC bool rrcCallConv getFloatingSpeciesByIndex(RRHandle handle, const int index, double* value);
1362 
1371 C_DECL_SPEC bool rrcCallConv getGlobalParameterByIndex(RRHandle handle, const int index, double* value);
1372 
1382 C_DECL_SPEC bool rrcCallConv getCompartmentByIndex (RRHandle handle, const int index, double* value);
1383 
1384 
1394 C_DECL_SPEC bool rrcCallConv setCompartmentByIndex (RRHandle handle, const int index, const double value);
1395 
1396 
1415 C_DECL_SPEC bool rrcCallConv setFloatingSpeciesConcentrations(RRHandle handle, const RRVectorPtr vec);
1416 
1435 C_DECL_SPEC bool rrcCallConv setBoundarySpeciesConcentrations(RRHandle handle, const RRVectorPtr vec);
1436 
1437 
1445 C_DECL_SPEC RRDoubleMatrixPtr rrcCallConv getFullJacobian(RRHandle handle);
1446 
1456 C_DECL_SPEC RRDoubleMatrixPtr rrcCallConv getReducedJacobian(RRHandle handle);
1457 
1465 C_DECL_SPEC RRDoubleMatrixPtr rrcCallConv getEigenvalues(RRHandle handle);
1466 
1467 
1468 // --------------------------------------------------------------------------------
1469 // Stoichiometry methods
1470 // --------------------------------------------------------------------------------
1471 
1479 C_DECL_SPEC RRDoubleMatrixPtr rrcCallConv getStoichiometryMatrix(RRHandle handle);
1480 
1488 C_DECL_SPEC RRDoubleMatrixPtr rrcCallConv getLinkMatrix(RRHandle handle);
1489 
1497 C_DECL_SPEC RRDoubleMatrixPtr rrcCallConv getNrMatrix(RRHandle handle);
1498 
1508 C_DECL_SPEC RRDoubleMatrixPtr rrcCallConv getConservationMatrix(RRHandle handle);
1509 
1510 // --------------------------------------------------------------------------------
1511 // Initial condition Methods
1512 // --------------------------------------------------------------------------------
1513 
1524 C_DECL_SPEC bool rrcCallConv setFloatingSpeciesInitialConcentrations (RRHandle handle, const RRVectorPtr vec);
1525 
1535 C_DECL_SPEC RRVectorPtr rrcCallConv getFloatingSpeciesInitialConcentrations (RRHandle handle);
1536 
1546 C_DECL_SPEC RRStringArrayPtr rrcCallConv getFloatingSpeciesInitialConditionIds(RRHandle handle);
1547 
1548 // --------------------------------------------------------------------------------
1549 // Reaction rates
1550 // --------------------------------------------------------------------------------
1551 
1561 C_DECL_SPEC int rrcCallConv getNumberOfReactions(RRHandle handle);
1562 
1563 
1573 C_DECL_SPEC bool rrcCallConv getReactionRate(RRHandle handle, const int index, double* rate);
1574 
1575 
1583 C_DECL_SPEC RRVectorPtr rrcCallConv getReactionRates(RRHandle handle);
1584 
1585 
1594 C_DECL_SPEC RRVectorPtr rrcCallConv getReactionRatesEx (RRHandle handle, const RRVectorPtr vec);
1595 
1596 
1606 C_DECL_SPEC RRVectorPtr rrcCallConv getRatesOfChange(RRHandle handle);
1607 
1617 C_DECL_SPEC RRStringArrayPtr rrcCallConv getRatesOfChangeIds(RRHandle handle);
1618 
1619 
1630 C_DECL_SPEC bool rrcCallConv getRateOfChange(RRHandle handle, const int, double* value);
1631 
1632 
1643 C_DECL_SPEC RRVectorPtr rrcCallConv getRatesOfChangeEx (RRHandle handle, const RRVectorPtr vec);
1644 
1652 C_DECL_SPEC bool rrcCallConv evalModel(RRHandle handle);
1653 
1654 // Get number family
1661 C_DECL_SPEC int rrcCallConv getNumberOfCompartments (RRHandle handle);
1662 
1663 
1669 C_DECL_SPEC int rrcCallConv getNumberOfBoundarySpecies(RRHandle handle);
1670 
1671 
1677 C_DECL_SPEC int rrcCallConv getNumberOfFloatingSpecies(RRHandle handle);
1678 
1679 
1685 C_DECL_SPEC int rrcCallConv getNumberOfGlobalParameters(RRHandle handle);
1686 
1687 // --------------------------------------------------------------------------------
1688 // Get number family
1689 // --------------------------------------------------------------------------------
1690 
1696 C_DECL_SPEC int rrcCallConv getNumberOfDependentSpecies(RRHandle handle);
1697 
1698 
1705 C_DECL_SPEC int rrcCallConv getNumberOfIndependentSpecies(RRHandle handle);
1706 
1707 // --------------------------------------------------------------------------------
1708 // Get Ids family
1709 // --------------------------------------------------------------------------------
1710 
1718 C_DECL_SPEC RRStringArrayPtr rrcCallConv getReactionIds(RRHandle handle);
1719 
1727 C_DECL_SPEC RRStringArrayPtr rrcCallConv getBoundarySpeciesIds(RRHandle handle);
1728 
1736 C_DECL_SPEC RRStringArrayPtr rrcCallConv getFloatingSpeciesIds(RRHandle handle);
1737 
1745 C_DECL_SPEC RRStringArrayPtr rrcCallConv getGlobalParameterIds(RRHandle handle);
1746 
1756 C_DECL_SPEC RRStringArrayPtr rrcCallConv getCompartmentIds(RRHandle handle);
1757 
1765 C_DECL_SPEC RRStringArrayPtr rrcCallConv getEigenvalueIds(RRHandle handle);
1766 
1774 C_DECL_SPEC RRListPtr rrcCallConv getAvailableTimeCourseSymbols(RRHandle handle);
1775 
1783 C_DECL_SPEC RRListPtr rrcCallConv getAvailableSteadyStateSymbols(RRHandle handle);
1784 
1785 // --------------------------------------------------------------------------------
1786 // MCA methods
1787 // --------------------------------------------------------------------------------
1788 
1796 C_DECL_SPEC RRListPtr rrcCallConv getElasticityCoefficientIds(RRHandle handle);
1797 
1805 C_DECL_SPEC RRListPtr rrcCallConv getUnscaledFluxControlCoefficientIds(RRHandle handle);
1806 
1814 C_DECL_SPEC RRListPtr rrcCallConv getFluxControlCoefficientIds(RRHandle handle);
1815 
1823 C_DECL_SPEC RRListPtr rrcCallConv getUnscaledConcentrationControlCoefficientIds(RRHandle handle);
1824 
1832 C_DECL_SPEC RRListPtr rrcCallConv getConcentrationControlCoefficientIds(RRHandle handle);
1833 
1841 C_DECL_SPEC RRDoubleMatrixPtr rrcCallConv getUnscaledElasticityMatrix(RRHandle handle);
1842 
1850 C_DECL_SPEC RRDoubleMatrixPtr rrcCallConv getScaledElasticityMatrix(RRHandle handle);
1851 
1852 
1863 C_DECL_SPEC bool rrcCallConv getScaledFloatingSpeciesElasticity(RRHandle handle, const char* reactionId, const char* speciesId, double* value);
1864 
1874 
1875 
1884 
1893 
1901 C_DECL_SPEC RRDoubleMatrixPtr rrcCallConv getScaledFluxControlCoefficientMatrix(RRHandle handle);
1902 
1913 C_DECL_SPEC bool rrcCallConv getuCC (RRHandle handle, const char* variable, const char* parameter, double* value);
1914 
1925 C_DECL_SPEC bool rrcCallConv getCC (RRHandle handle, const char* variable, const char* parameter, double* value);
1926 
1937 C_DECL_SPEC bool rrcCallConv getEE(RRHandle handle, const char* name, const char* species, double* value);
1938 
1949 C_DECL_SPEC bool rrcCallConv getuEE(RRHandle handle, const char* name, const char* species, double* value);
1950 
1951 // --------------------------------------------------------------------------------
1952 // Stochastic methods
1953 // --------------------------------------------------------------------------------
1954 
1963 C_DECL_SPEC bool rrcCallConv getSeed(RRHandle handle, long* seed);
1964 
1973 C_DECL_SPEC bool rrcCallConv setSeed(RRHandle handle, long seed);
1974 
1986 C_DECL_SPEC RRCDataPtr rrcCallConv gillespie(RRHandle handle);
1987 
2010 C_DECL_SPEC RRCDataPtr rrcCallConv gillespieEx(RRHandle handle, double timeStart, double timeEnd);
2011 
2023 C_DECL_SPEC RRCDataPtr rrcCallConv gillespieOnGrid(RRHandle handle);
2024 
2050 C_DECL_SPEC RRCDataPtr rrcCallConv gillespieOnGridEx(RRHandle handle, double timeStart, double timeEnd, int numberOfPoints);
2051 
2065 C_DECL_SPEC RRCDataPtr rrcCallConv gillespieMeanOnGrid(RRHandle handle, int numberOfSimulations);
2066 
2094 C_DECL_SPEC RRCDataPtr rrcCallConv gillespieMeanOnGridEx(RRHandle handle, double timeStart, double timeEnd, int numberOfPoints, int numberOfSimulations);
2095 
2110 C_DECL_SPEC RRCDataPtr rrcCallConv gillespieMeanSDOnGrid(RRHandle handle, int numberOfSimulations);
2111 
2112 
2142 C_DECL_SPEC RRCDataPtr rrcCallConv gillespieMeanSDOnGridEx(RRHandle handle, double timeStart, double timeEnd, int numberOfSteps, int numberOfSimulations);
2143 
2144 // --------------------------------------------------------------------------------
2145 // Reset methods
2146 // --------------------------------------------------------------------------------
2147 
2156 C_DECL_SPEC bool rrcCallConv reset(RRHandle handle);
2157 
2166 C_DECL_SPEC bool rrcCallConv resetAll(RRHandle handle);
2167 
2176 C_DECL_SPEC bool rrcCallConv resetToOrigin(RRHandle handle);
2177 
2186 C_DECL_SPEC int rrcCallConv setConfigBool(const char* key, int value);
2187 
2195 C_DECL_SPEC int rrcCallConv getConfigBool(const char* key);
2196 
2205 C_DECL_SPEC int rrcCallConv setConfigInt(const char* key, int value);
2206 
2214 C_DECL_SPEC int rrcCallConv getConfigInt(const char* key);
2215 
2224 C_DECL_SPEC int rrcCallConv setConfigDouble(const char* key, double value);
2225 
2233 C_DECL_SPEC double rrcCallConv getConfigDouble(const char* key);
2234 
2240 C_DECL_SPEC RRStringArrayPtr rrcCallConv getListOfConfigKeys();
2241 
2242 #if defined( __cplusplus)
2243 }
2244 }//namespace
2245 
2246 #endif
2247 
2248 #endif
2249 
int getNumInstantiatedIntegrators(RRHandle handle)
Get the number of instantiated integrators. To instantiate an integrator, use setCurrentIntegrator.
Definition: rrc_api.cpp:1366
roadRunner C API 2012
char * getCurrentSteadyStateSolverName(RRHandle handle)
Obtain a description of the current steady state solver.
Definition: rrc_api.cpp:1711
int getCurrentIntegratorParameterBoolean(RRHandle handle, char *parameterName)
Get the boolean value for a specific integrator setting.
Definition: rrc_api.cpp:1625
RRStringArrayPtr getListOfCurrentSteadyStateSolverParameterNames(RRHandle handle)
Get the names of adjustable settings for the current steady state solver.
Definition: rrc_api.cpp:1843
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 * getCurrentSteadyStateSolverParameterHint(RRHandle handle, char *parameterName)
Get the hint for a specific steady state solver setting.
Definition: rrc_api.cpp:1863
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
int getNumRegisteredIntegrators()
Get the number of registered integrators.
Definition: rrc_api.cpp:1326
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
char * getCurrentIntegratorNthParameterDisplayName(RRHandle handle, int n)
Get the display name of a parameter of the current integrator.
Definition: rrc_api.cpp:1444
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
double getCurrentIntegratorParameterDouble(RRHandle handle, char *parameterName)
Get the double value for a specific integrator setting.
Definition: rrc_api.cpp:1579
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
int getCurrentIntegratorParameterInt(RRHandle handle, char *parameterName)
Get the integer value for a specific integrator setting.
Definition: rrc_api.cpp:1537
char * getCurrentIntegratorNthParameterHint(RRHandle handle, int n)
Get the hint of a parameter of the current integrator.
Definition: rrc_api.cpp:1454
double getCurrentSteadyStateSolverParameterDouble(RRHandle handle, char *parameterName)
Get the double value for a specific steady state solver setting.
Definition: rrc_api.cpp:1930
bool setTimeCourseSelectionList(RRHandle handle, const char *list)
Set the selection list for output from simulate(void) or simulateEx(void)
Definition: _rrc_api.cpp:563
int getCurrentSteadyStateSolverParameterType(RRHandle handle, char *parameterName)
Get the return type for a specific steady state solver setting.
Definition: rrc_api.cpp:1874
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
char * getRegisteredIntegratorHint(int n)
Get the hint of a registered integrator (e.g. cvode etc.)
Definition: rrc_api.cpp:1344
RRVectorPtr computeSteadyStateValues(RRHandle handle)
A convenient method for returning a vector of the steady state species concentrations.
Definition: _rrc_api.cpp:1154
int getNumRegisteredSteadyStateSolvers()
Get the number of registered steady state solvers.
Definition: rrc_api.cpp:1654
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
int setConfigBool(const char *key, int value)
Set a boolean configuration value.
Definition: rrc_api.cpp:2753
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
char * getCurrentSteadyStateSolverParameterDescription(RRHandle handle, char *parameterName)
Get the description for a specific steady state solver setting.
Definition: rrc_api.cpp:1852
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
int setConfigInt(const char *key, int value)
Set an integer configuration value.
Definition: rrc_api.cpp:2766
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
int setConfigDouble(const char *key, double value)
Set a double configuration value.
Definition: rrc_api.cpp:2779
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
int getCurrentSteadyStateSolverNthParameterType(RRHandle handle, int n)
Get the type of a parameter of the current steady state solver.
Definition: rrc_api.cpp:1774
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
int resetCurrentIntegratorParameters(RRHandle handle)
Reset the integrator parameters to their default values.
Definition: rrc_api.cpp:1483
char * getTempFolder(RRHandle handle)
Retrieve the current temporary folder path.
Definition: _rrc_api.cpp:313
int setCurrentIntegratorParameterInt(RRHandle handle, char *parameterName, int value)
Set the integer value for a specific integrator setting.
Definition: rrc_api.cpp:1547
char * getSBML(RRHandle handle)
Retrieve the SBML model that was last loaded into roadRunner.
Definition: _rrc_api.cpp:483
int resetCurrentSteadyStateSolverParameters(RRHandle handle)
Reset the steady state solver parameters to their default values.
Definition: rrc_api.cpp:1803
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
int setCurrentIntegratorParameterUInt(RRHandle handle, char *parameterName, unsigned int value)
Set the unsigned integer value for a specific integrator setting.
Definition: rrc_api.cpp:1568
RRDoubleMatrixPtr getUnscaledConcentrationControlCoefficientMatrix(RRHandle handle)
Retrieve the matrix of unscaled concentration control coefficients for the current model...
Definition: _rrc_api.cpp:1340
int getNumberOfCurrentIntegratorParameters(RRHandle handle)
Get the number of adjustable settings for the current integrator.
Definition: rrc_api.cpp:1424
char * getCurrentSteadyStateSolverHint(RRHandle handle)
Obtain a short hint for the current steady state solver.
Definition: rrc_api.cpp:1734
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
int getCurrentIntegratorParameterType(RRHandle handle, char *parameterName)
Get the return type for a specific integrator setting.
Definition: rrc_api.cpp:1523
char * getCurrentSteadyStateSolverNthParameterName(RRHandle handle, int n)
Get the name of a parameter of the current steady state solver.
Definition: rrc_api.cpp:1754
bool getEE(RRHandle handle, const char *name, const char *species, double *value)
Retrieve a single elasticity coefficient.
Definition: _rrc_api.cpp:1101
int getConfigBool(const char *key)
Get a boolean configuration value.
Definition: rrc_api.cpp:2760
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
char * getCurrentSteadyStateSolverNthParameterHint(RRHandle handle, int n)
Get the hint of a parameter of the current steady state solver.
Definition: rrc_api.cpp:1764
bool setSteadyStateSelectionList(RRHandle handle, const char *list)
Set the selection list of the steady state analysis.
Definition: _rrc_api.cpp:1164
unsigned int getCurrentSteadyStateSolverParameterUInt(RRHandle handle, char *parameterName)
Get the unsigned integer value for a specific steady state solver setting.
Definition: rrc_api.cpp:1909
bool setNumPoints(RRHandle handle, int numberOfPoints)
Set the number of points to generate in a time course simulation.
Definition: _rrc_api.cpp:526
double getConfigDouble(const char *key)
Get a double configuration value.
Definition: rrc_api.cpp:2786
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
char * getCurrentSteadyStateSolverNthParameterDisplayName(RRHandle handle, int n)
Get the display name of a parameter of the current steady state solver.
Definition: rrc_api.cpp:1783
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
int getConfigInt(const char *key)
Get an integer configuration value.
Definition: rrc_api.cpp:2773
RRListPtr getAvailableTimeCourseSymbols(RRHandle handle)
Obtain the list of all available symbols.
Definition: _rrc_api.cpp:1028
int setCurrentSteadyStateSolverParameterString(RRHandle handle, char *parameterName, char *value)
Set the string value for a specific steady state solver setting.
Definition: rrc_api.cpp:1964
roadRunner C API 2012
int setCurrentSteadyStateSolverParameterUInt(RRHandle handle, char *parameterName, unsigned int value)
Set the unsigned integer value for a specific steady state solver setting.
Definition: rrc_api.cpp:1919
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
char * getCurrentSteadyStateSolverDescription(RRHandle handle)
Obtain a description of the current steady state solver.
Definition: rrc_api.cpp:1724
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
char * getRegisteredIntegratorDescription(int n)
Get the description of a registered integrator (e.g. cvode etc.)
Definition: rrc_api.cpp:1355
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 * getRegisteredSteadyStateSolverName(int n)
Get the name of a registered steady state solver (e.g. cvode etc.)
Definition: rrc_api.cpp:1661
char * getCopyright(void)
Retrieve the current copyright notice for the library.
Definition: _rrc_api.cpp:250
int setCurrentSteadyStateSolverParameterDouble(RRHandle handle, char *parameterName, double value)
Set the double value for a specific steady state solver setting.
Definition: rrc_api.cpp:1940
bool isModelLoaded(RRHandle handle)
check if a model is loaded
Definition: _rrc_api.cpp:491
char * getRegisteredSteadyStateSolverHint(int n)
Get the hint of a registered steady state solver (e.g. cvode etc.)
Definition: rrc_api.cpp:1672
int getCurrentIntegratorNthParameterType(RRHandle handle, int n)
Get the type of a parameter of the current integrator.
Definition: rrc_api.cpp:1464
int setCurrentIntegratorParameterString(RRHandle handle, char *parameterName, char *value)
Set the string value for a specific integrator setting.
Definition: rrc_api.cpp:1613
int getCurrentSteadyStateSolverParameterInt(RRHandle handle, char *parameterName)
Get the integer value for a specific steady state solver setting.
Definition: rrc_api.cpp:1888
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
char * getRegisteredSteadyStateSolverDescription(int n)
Get the description of a registered steady state solver (e.g. cvode etc.)
Definition: rrc_api.cpp:1683
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 * getCurrentSteadyStateSolverParameterString(RRHandle handle, char *parameterName)
Get the string value for a specific steady state solver setting.
Definition: rrc_api.cpp:1952
char * getRegisteredIntegratorName(int n)
Get the name of a registered integrator (e.g. cvode etc.)
Definition: rrc_api.cpp:1333
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
RRStringArrayPtr getListOfCurrentIntegratorParameterNames(RRHandle handle)
Get the names of adjustable settings for the current integrator.
Definition: rrc_api.cpp:1492
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
const char * solverTypeToString(int code)
Get a string description of the type [STATIC MEMORY - DO NOT FREE] Can call on return value of e...
Definition: rrc_api.cpp:1813
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
int getNumberOfCurrentSteadyStateSolverParameters(RRHandle handle)
Get the number of adjustable settings for the current steady state solver.
Definition: rrc_api.cpp:1744
char * getAPIVersion(void)
Retrieve the current version number of the C API library.
Definition: _rrc_api.cpp:196
roadRunner C API 2012
int getCurrentSteadyStateSolverParameterBoolean(RRHandle handle, char *parameterName)
Get the boolean value for a specific steady state solver setting.
Definition: rrc_api.cpp:1976
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
char * getCurrentIntegratorParameterDescription(RRHandle handle, char *parameterName)
Get the description for a specific integrator setting.
Definition: rrc_api.cpp:1501
char * getCurrentIntegratorNthParameterName(RRHandle handle, int n)
Get the name of a parameter of the current integrator.
Definition: rrc_api.cpp:1434
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
int setCurrentIntegrator(RRHandle handle, char *nameOfIntegrator)
Specify the current integrator to be used for simulation. This method instantiates a new integrator ...
Definition: rrc_api.cpp:1374
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
RRStringArrayPtr getListOfConfigKeys()
Get a list of all possible config keys.
Definition: rrc_api.cpp:2792
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
char * getCurrentSteadyStateSolverNthParameterDescription(RRHandle handle, int n)
Get the description of a parameter of the current steady state solver.
Definition: rrc_api.cpp:1793
int setCurrentSteadyStateSolverParameterInt(RRHandle handle, char *parameterName, int value)
Set the integer value for a specific steady state solver setting.
Definition: rrc_api.cpp:1898
int setCurrentSteadyStateSolverParameterBoolean(RRHandle handle, char *parameterName, int value)
Set the boolean value for a specific steady state solver setting.
Definition: rrc_api.cpp:1987
RRVectorPtr getReactionRates(RRHandle handle)
Retrieve a vector of reaction rates as determined by the current state of the model.
Definition: _rrc_api.cpp:814
unsigned int getCurrentIntegratorParameterUInt(RRHandle handle, char *parameterName)
Get the unsigned integer value for a specific integrator setting.
Definition: rrc_api.cpp:1558
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
char * getCurrentIntegratorNthParameterDescription(RRHandle handle, int n)
Get the description of a parameter of the current integrator.
Definition: rrc_api.cpp:1473
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
int setCurrentIntegratorParameterBoolean(RRHandle handle, char *parameterName, int value)
Set the boolean value for a specific integrator setting.
Definition: rrc_api.cpp:1636
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
char * getCurrentIntegratorDescription(RRHandle handle)
Obtain a description of the current integrator.
Definition: rrc_api.cpp:1404
int setCurrentIntegratorParameterDouble(RRHandle handle, char *parameterName, double value)
Set the double value for a specific integrator setting.
Definition: rrc_api.cpp:1589
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
char * getCurrentIntegratorName(RRHandle handle)
Obtain a description of the current integrator.
Definition: rrc_api.cpp:1391
char * getCurrentIntegratorParameterHint(RRHandle handle, char *parameterName)
Get the hint for a specific integrator setting.
Definition: rrc_api.cpp:1512
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
char * getCurrentIntegratorHint(RRHandle handle)
Obtain a short hint for the current integrator.
Definition: rrc_api.cpp:1414
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
char * getCurrentIntegratorParameterString(RRHandle handle, char *parameterName)
Get the string value for a specific integrator setting.
Definition: rrc_api.cpp:1601
RRStringArrayPtr getReactionIds(RRHandle handle)
Obtain the list of reaction Ids.
Definition: _rrc_api.cpp:628
int setCurrentSteadyStateSolver(RRHandle handle, char *nameOfSteadyStateSolver)
Specify the current steady state solver to be used for simulation. This method instantiates a new st...
Definition: rrc_api.cpp:1694
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