roadrunner  2.6.0
Fast simulator for SBML models
rrModelData.h
1 #ifndef rrModelDataH
2 #define rrModelDataH
3 
9 #if defined(WIN32)
10 #define RR_CDECL __cdecl
11 #else
12 #define RR_CDECL
13 #endif
14 
15 #if defined __cplusplus
16 namespace rr
17 {
18 #endif
19 typedef struct SModelData *ModelDataP;
20 typedef double (RR_CDECL *EventDelayHandler)(ModelDataP);
21 typedef double* (RR_CDECL *ComputeEventAssignmentHandler)(ModelDataP);
22 typedef void (RR_CDECL *PerformEventAssignmentHandler)(ModelDataP, double*);
23 typedef void (RR_CDECL *EventAssignmentHandler)();
24 
48 typedef struct SModelData
49 {
53  double time; // 2
54 
58  unsigned numIndependentSpecies; // 3
59 
66  unsigned numDependentSpecies; // 4
67  double* dependentSpeciesConservedSums; // 5
68 
72  unsigned numGlobalParameters; // 6
73  double* globalParameters; // 7
74 
80  unsigned numReactions; // 8
81  double* reactionRates; // 9
82 
83  unsigned numRateRules; // 10
84 
93  double* rateRuleValues; // 11
94 
105  double* rateRuleRates; // 12
106 
119  unsigned* localParametersOffsets; // 12
120 
126  unsigned* localParametersNum; // 14
127 
132  double* localParameters; // 15
133 
144  unsigned numFloatingSpecies; // 16
145 
150 
155 
160 
164  double* floatingSpeciesAmounts; // 20
165 
172 
180  unsigned numBoundarySpecies; // 22
181  double* boundarySpeciesConcentrations; // 23
182  double* boundarySpeciesAmounts; // 24
183 
190 
195  unsigned numCompartments; // 26
196  double* compartmentVolumes; // 27
197 
198 
199  //Event stuff
200  unsigned numEvents; // 29
201  unsigned eventTypeSize; // 30
202  bool* eventType; // 31
203 
204  unsigned eventPersistentTypeSize; // 32
205  bool* eventPersistentType; // 33
206 
207  unsigned eventTestsSize; // 34
208  double* eventTests; // 35
209 
210  unsigned eventPrioritiesSize; // 36
211  double* eventPriorities; // 37
212 
213  unsigned eventStatusArraySize; // 38
214  bool* eventStatusArray; // 39
215 
216  unsigned previousEventStatusArraySize; // 40
217  bool* previousEventStatusArray; // 41
218 
219 
220  EventDelayHandler* eventDelays; // 47
221  EventAssignmentHandler* eventAssignments; // 48
222 
223  ComputeEventAssignmentHandler* computeEventAssignments; // 49
224  PerformEventAssignmentHandler* performEventAssignments; // 50
225 
229  char* modelName; // 51
230 
235  unsigned srSize; // 52
236  double* sr; // 53
237 } ModelData;
238 //#pragma pack(pop)
239 
240 #if defined __cplusplus
241 }
242 #endif
243 
244 
245 
246 #endif
A data structure that is that allows data to be exchanged with running SBML models.
Definition: rrModelData.h:49
double time
current time.
Definition: rrModelData.h:53
unsigned numGlobalParameters
number of global parameters
Definition: rrModelData.h:72
unsigned numCompartments
number of compartments, and compartment volumes.
Definition: rrModelData.h:195
double * floatingSpeciesAmountRates
amount rates of change for floating species.
Definition: rrModelData.h:159
unsigned * localParametersOffsets
LLVM specific C version does not support local parameters This is the offset, or starting index of th...
Definition: rrModelData.h:119
unsigned * boundarySpeciesCompartments
compartment index for each boundary species, e.g.
Definition: rrModelData.h:189
unsigned numDependentSpecies
number of linerly dependent rows in the stoichiometry matrix.
Definition: rrModelData.h:66
double * floatingSpeciesAmounts
The total amount of a species in a compartment.
Definition: rrModelData.h:164
unsigned numReactions
number of reactions, same as ratesSize.
Definition: rrModelData.h:80
char * modelName
model name
Definition: rrModelData.h:229
unsigned numBoundarySpecies
number of boundary species and boundary species concentrations.
Definition: rrModelData.h:180
double * rateRuleRates
the rate of change of all elements who's dynamics are determined by rate rules.
Definition: rrModelData.h:105
unsigned * localParametersNum
the number of local parameters for each reaction, so legnth is numReactions.
Definition: rrModelData.h:126
double * rateRuleValues
All of the elelments which have a rate rule are stored here.
Definition: rrModelData.h:93
unsigned numFloatingSpecies
The total ammounts of the floating species, i.e.
Definition: rrModelData.h:144
double * floatingSpeciesInitConcentrations
initial concentration values for floating species.
Definition: rrModelData.h:154
unsigned srSize
C species references, not working correctly...
Definition: rrModelData.h:235
double * floatingSpeciesConcentrations
number of floating species and floating species concentrations.
Definition: rrModelData.h:149
unsigned * floatingSpeciesCompartments
compartment index for each floating species, e.g.
Definition: rrModelData.h:171
unsigned numIndependentSpecies
number of linearly independent rows in the stochiometry matrix.
Definition: rrModelData.h:58
double * localParameters
All local parameters are stored in this array.
Definition: rrModelData.h:132