#include "sbmlsolver/odeModel.h"#include <string.h>#include <malloc.h>#include <stdlib.h>#include "sbmlsolver/sbml.h"#include "sbmlsolver/odeConstruct.h"#include "sbmlsolver/processAST.h"#include "sbmlsolver/variableIndex.h"#include "sbmlsolver/solverError.h"#include "sbmlsolver/modelSimplify.h"Include dependency graph for odeModel.c:
Functions | |
| SBML_ODESOLVER_API odeModel_t * | ODEModel_create (Model_t *m) |
| Create internal model odeModel from a reaction network, represented as libSBML's Model_t structure. | |
| SBML_ODESOLVER_API odeModel_t * | ODEModel_createFromFile (char *sbmlFileName) |
| Create internal model odeModel from an SBML file, that contains level 1 or level 2 SBML. | |
| SBML_ODESOLVER_API odeModel_t * | ODEModel_createFromSBML2 (SBMLDocument_t *d) |
| Create internal model odeModel_t from SBMLDocument containing a level 2 SBML model. | |
| SBML_ODESOLVER_API void | ODEModel_free (odeModel_t *om) |
| Frees the odeModel structures. | |
| SBML_ODESOLVER_API int | ODEModel_hasVariable (odeModel_t *model, const char *symbol) |
| Returns 1 if a variable or parameter with the SBML id exists in the ODEModel. | |
| SBML_ODESOLVER_API int | ODEModel_getNumValues (odeModel_t *om) |
| Returns the total number of values in oodeModel, equivalent to ODEModel_getNeq + ODEModel_getNumAssignments + ODEModel_getNumConstants. | |
| SBML_ODESOLVER_API const char * | ODEModel_getVariableName (odeModel_t *om, variableIndex_t *vi) |
| Returns the name of the variable corresponding to passed variableIndex. | |
| SBML_ODESOLVER_API int | ODEModel_getNeq (odeModel_t *om) |
| SBML_ODESOLVER_API int | ODEModel_getNsens (odeModel_t *om) |
| Returns the number parameters for which sensitivity analysis might be requested. | |
| SBML_ODESOLVER_API const ASTNode_t * | ODEModel_getOde (odeModel_t *om, variableIndex_t *vi) |
| Returns the ODE from the odeModel for the variable with variableIndex vi. | |
| SBML_ODESOLVER_API int | ODEModel_getNumAssignments (odeModel_t *om) |
| Returns the number of variable assignments in the odeModel. | |
| SBML_ODESOLVER_API const ASTNode_t * | ODEModel_getAssignment (odeModel_t *om, variableIndex_t *vi) |
| Returns the assignment formula from the odeModel for the variable with variableIndex vi. | |
| SBML_ODESOLVER_API int | ODEModel_getNumConstants (odeModel_t *om) |
| Returns the number of constant parameters of the odeModel. | |
| SBML_ODESOLVER_API int | ODEModel_getNalg (odeModel_t *om) |
| Returns the number variables that are defined by an algebraic rule. | |
| SBML_ODESOLVER_API void | ODEModel_dumpNames (odeModel_t *om) |
| Prints the names (SBML IDs) of all model variables and parameters. | |
| SBML_ODESOLVER_API const Model_t * | ODEModel_getModel (odeModel_t *om) |
| Returns the SBML model that has been extracted from the input SBML model's reaction network and structures. | |
| SBML_ODESOLVER_API int | ODEModel_constructJacobian (odeModel_t *om) |
| Construct Jacobian Matrix for ODEModel. | |
| SBML_ODESOLVER_API const ASTNode_t * | ODEModel_getJacobianIJEntry (odeModel_t *om, int i, int j) |
| Returns the ith/jth entry of the jacobian matrix. | |
| SBML_ODESOLVER_API const ASTNode_t * | ODEModel_getJacobianEntry (odeModel_t *om, variableIndex_t *vi1, variableIndex_t *vi2) |
| Returns the entry (d(vi1)/dt)/d(vi2) of the jacobian matrix. | |
| SBML_ODESOLVER_API ASTNode_t * | ODEModel_constructDeterminant (odeModel_t *om) |
| Constructs and returns the determinant of the jacobian matrix. | |
| SBML_ODESOLVER_API int | ODEModel_constructSensitivity (odeModel_t *om) |
| Construct Sensitivity R.H.S. | |
| SBML_ODESOLVER_API void | ODEModel_freeSensitivity (odeModel_t *om) |
| Free Sensitivity R.H.S. | |
| SBML_ODESOLVER_API const ASTNode_t * | ODEModel_getSensIJEntry (odeModel_t *om, int i, int j) |
| Returns the ith/jth entry of the parametric matrix. | |
| SBML_ODESOLVER_API const ASTNode_t * | ODEModel_getSensEntry (odeModel_t *om, variableIndex_t *vi1, variableIndex_t *vi2) |
| Returns the entry (d(vi1)/dt)/d(vi2) of the parametric matrix. | |
| SBML_ODESOLVER_API variableIndex_t * | ODEModel_getSensParamIndexByNum (odeModel_t *om, int j) |
| Returns the variableIndex for the jth parameter for which sensitivity analysis was requested, where 0 < j < ODEModel_getNsens;. | |
| SBML_ODESOLVER_API variableIndex_t * | ODEModel_getVariableIndexByNum (odeModel_t *om, int i) |
| Creates and returns a variable index for ith variable. | |
| SBML_ODESOLVER_API variableIndex_t * | ODEModel_getVariableIndex (odeModel_t *om, const char *symbol) |
| Creates and returns the variableIndex for the string "symbol". | |
| SBML_ODESOLVER_API variableIndex_t * | ODEModel_getOdeVariableIndex (odeModel_t *om, int i) |
| Creates and returns a variable index for ith ODE variable. | |
| SBML_ODESOLVER_API variableIndex_t * | ODEModel_getAssignedVariableIndex (odeModel_t *om, int i) |
| Creates and returns a variable index for ith assigned variable. | |
| SBML_ODESOLVER_API variableIndex_t * | ODEModel_getConstantIndex (odeModel_t *om, int i) |
| Creates and returns a variable index for ith constant. | |
| SBML_ODESOLVER_API void | VariableIndex_free (variableIndex_t *vi) |
| Frees a variableIndex structure. | |
1.4.4