copasi/copasi_api.h

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#ifndef COPASI_SIMPLE_C_API
#define COPASI_SIMPLE_C_API

/*
This is a C API for the COPASI C++ library. Rate equations in COPASI require the "complete name",   
e.g. instead of X, the rate must specify <model.compartment.X>. In this C API, those complete names
are stored in a hash table. The API replaces the simple strings, i.e. "C", with the complete names by
using the hash-table. This is mainly for speed; otherwise, every cSetReactionRate would be searching
through the entire model for each of its variables. The hash-table idea is used for functions such
as cSetValue, which can set the value of a parameter or that of a molecular species. Again, it uses the
hash table to identify what a variable is. 

The C API hides the C++ classes by casting some of the main classes into void pointers inside
C structs. 

QtCore is used for providing the hash-table feature and regular expression (QHash and QRegExp). This
should be replaced with the boost library at some point. 
*/

#include "TC_structs.h"

typedef struct  
{ 
        void * CopasiModelPtr;
        void * CopasiDataModelPtr;
        void * qHash;
        char * errorMessage; 
} copasi_model;

typedef struct  
{
        void * CopasiReactionPtr;
        void * CopasiModelPtr;
        void * qHash; 
} copasi_reaction;

typedef struct  
{
        void * CopasiCompartmentPtr;
        void * CopasiModelPtr; 
        void * qHash; 
} copasi_compartment;

BEGIN_C_DECLS

//TCAPIEXPORT void copasi_init();
TCAPIEXPORT void copasi_end();
TCAPIEXPORT copasi_model cCreateModel(const char * name);
TCAPIEXPORT void cRemoveModel(copasi_model);
//TCAPIEXPORT void clearCopasiModel(copasi_model);
TCAPIEXPORT void cCompileModel(copasi_model model, int substitute_nested_assignments);
TCAPIEXPORT copasi_model cReadAntimonyFile(const char * filename);
TCAPIEXPORT copasi_model cReadSBMLFile(const char * filename);
TCAPIEXPORT copasi_model cReadSBMLString(const char * sbml);
TCAPIEXPORT void cWriteSBMLFile(copasi_model model, const char * filename);
TCAPIEXPORT tc_matrix cGetScaledFluxControlCoeffs(copasi_model model);
TCAPIEXPORT copasi_compartment cCreateCompartment(copasi_model model, const char* name, double volume);
TCAPIEXPORT void cSetVolume(copasi_model, const char * compartment, double volume);
TCAPIEXPORT int cSetValue(copasi_model, const char * name, double value);

TCAPIEXPORT void cCreateSpecies(copasi_compartment compartment, const char* name, double initialValue);

TCAPIEXPORT void cSetBoundarySpecies(copasi_model model, const char * species, int isBoundary);
TCAPIEXPORT void cSetConcentration(copasi_model, const char * species, double value);
TCAPIEXPORT int cSetAssignmentRule(copasi_model model, const char * species, const char * formula);

TCAPIEXPORT int cSetGlobalParameter(copasi_model model, const char * name, double value);

TCAPIEXPORT int cCreateVariable(copasi_model model, const char * name, const char * formula);

TCAPIEXPORT int cCreateEvent(copasi_model model, const char * name, const char * trigger, const char * variable, const char * formula);

TCAPIEXPORT copasi_reaction cCreateReaction(copasi_model model, const char* name);
TCAPIEXPORT void cAddReactant(copasi_reaction reaction, const char * species, double stoichiometry);
TCAPIEXPORT void cAddProduct(copasi_reaction reaction, const char * species, double stoichiometry);
TCAPIEXPORT int cSetReactionRate(copasi_reaction reaction, const char * formula);

TCAPIEXPORT tc_matrix cSimulateDeterministic(copasi_model model, double startTime, double endTime, int numSteps);
TCAPIEXPORT tc_matrix cSimulateStochastic(copasi_model model, double startTime, double endTime, int numSteps);
TCAPIEXPORT tc_matrix cSimulateHybrid(copasi_model model, double startTime, double endTime, int numSteps);
TCAPIEXPORT tc_matrix cSimulateTauLeap(copasi_model model, double startTime, double endTime, int numSteps);

TCAPIEXPORT tc_matrix cGetSteadyState(copasi_model model);
TCAPIEXPORT tc_matrix cGetSteadyState2(copasi_model model, int iter);

TCAPIEXPORT tc_matrix cGetJacobian(copasi_model model);
TCAPIEXPORT tc_matrix cGetEigenvalues(copasi_model model);

TCAPIEXPORT tc_matrix cGetUnscaledElasticities(copasi_model model);

TCAPIEXPORT tc_matrix cGetUnscaledConcentrationControlCoeffs(copasi_model model);

TCAPIEXPORT tc_matrix cGetUnscaledFluxControlCoeffs(copasi_model model);

TCAPIEXPORT tc_matrix cGetScaledElasticities(copasi_model model);

TCAPIEXPORT tc_matrix cGetScaledConcentrationConcentrationCoeffs(copasi_model model);

TCAPIEXPORT tc_matrix cGetScaledFluxControlCoeffs(copasi_model model);

TCAPIEXPORT tc_matrix cGetFullStoichiometryMatrix(copasi_model model);

TCAPIEXPORT tc_matrix cGetReducedStoichiometryMatrix(copasi_model model);

TCAPIEXPORT tc_matrix cGetElementaryFluxModes(copasi_model model);

TCAPIEXPORT tc_matrix cGetGammaMatrix(copasi_model model);

TCAPIEXPORT tc_matrix cGetKMatrix(copasi_model model);

TCAPIEXPORT tc_matrix cGetK0Matrix(copasi_model model);

TCAPIEXPORT tc_matrix cGetLinkMatrix(copasi_model model);

TCAPIEXPORT tc_matrix cGetL0Matrix(copasi_model model);


//TCAPIEXPORT void cFitModelToData(copasi_model model, const char * filename, tc_matrix params, const char * method);

TCAPIEXPORT tc_matrix cOptimize(copasi_model model, const char * objective, tc_matrix input);

TCAPIEXPORT void cSetOptimizerIterations(int);

TCAPIEXPORT void cSetOptimizerSize(int);

TCAPIEXPORT void cSetOptimizerMutationRate(double);

TCAPIEXPORT void cSetOptimizerCrossoverRate(double);

END_C_DECLS
#endif