odeModel.h File Reference

#include <sbml/SBMLTypes.h>
#include "sbmlsolver/odemodeldatatype.h"
#include "sbmlsolver/exportdefs.h"

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

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Typedef Documentation

typedef struct variableIndex variableIndex_t

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