copasi/copasi_api.h File Reference

#include "TC_structs.h"

Go to the source code of this file.

Classes
struct	copasi_model
	this struct is used to contain a pointer to an instance of a COPASI class More...
struct	copasi_reaction
	this struct is used to contain a pointer to an instance of a COPASI class More...
struct	copasi_compartment
	this struct is used to contain a pointer to an instance of a COPASI class More...
Functions
BEGIN_C_DECLS TCAPIEXPORT void	copasi_end ()
	initialize copasi -- MUST BE CALLED before calling any other functions
TCAPIEXPORT copasi_model	cCreateModel (const char *name)
	create a model
TCAPIEXPORT void	cRemoveModel (copasi_model)
	remove a model
TCAPIEXPORT void	cCompileModel (copasi_model model, int substitute_nested_assignments)
	clear all contents of a model
TCAPIEXPORT copasi_model	cReadAntimonyFile (const char *filename)
	create a model from an Antimony or SBML file
TCAPIEXPORT copasi_model	cReadSBMLFile (const char *filename)
	create a model from an SBML file
TCAPIEXPORT copasi_model	cReadSBMLString (const char *sbml)
	create a model from an SBML string
TCAPIEXPORT void	cWriteSBMLFile (copasi_model model, const char *filename)
	save a model as an SBML file
TCAPIEXPORT tc_matrix	cGetScaledFluxControlCoeffs (copasi_model model)
	add a compartment to the model
TCAPIEXPORT copasi_compartment	cCreateCompartment (copasi_model model, const char *name, double volume)
	create compartment
TCAPIEXPORT void	cSetVolume (copasi_model, const char *compartment, double volume)
	set a volume of compartment
TCAPIEXPORT int	cSetValue (copasi_model, const char *name, double value)
	set the concentration of a species, volume of a compartment, or value of a parameter The function will figure out which using the name (fast lookup using hashtables). If the name does not exist in the model, a new global parameter will be created.
TCAPIEXPORT void	cCreateSpecies (copasi_compartment compartment, const char *name, double initialValue)
	add a species to the model
TCAPIEXPORT void	cSetBoundarySpecies (copasi_model model, const char *species, int isBoundary)
	set a species as boundary or floating (will remove any assignment rules)
TCAPIEXPORT void	cSetConcentration (copasi_model, const char *species, double value)
	set a species as boundary or floating (will remove any assignment rules)
TCAPIEXPORT int	cSetAssignmentRule (copasi_model model, const char *species, const char *formula)
	set the assignment rule for a species (automatically assumes boundary species)
TCAPIEXPORT int	cSetGlobalParameter (copasi_model model, const char *name, double value)
	set the value of an existing global parameter or create a new global parameter
TCAPIEXPORT int	cCreateVariable (copasi_model model, const char *name, const char *formula)
	create a new variable that is not a constant by a formula
TCAPIEXPORT int	cCreateEvent (copasi_model model, const char *name, const char *trigger, const char *variable, const char *formula)
	add a trigger and a response, where the response is defined by a target variable and an assignment formula
TCAPIEXPORT copasi_reaction	cCreateReaction (copasi_model model, const char *name)
	add a species or set an existing species as fixed
TCAPIEXPORT void	cAddReactant (copasi_reaction reaction, const char *species, double stoichiometry)
	add a reactant to a reaction
TCAPIEXPORT void	cAddProduct (copasi_reaction reaction, const char *species, double stoichiometry)
	add a product to a reaction
TCAPIEXPORT int	cSetReactionRate (copasi_reaction reaction, const char *formula)
	set reaction rate equation
TCAPIEXPORT tc_matrix	cSimulateDeterministic (copasi_model model, double startTime, double endTime, int numSteps)
	simulate using LSODA numerical integrator
TCAPIEXPORT tc_matrix	cSimulateStochastic (copasi_model model, double startTime, double endTime, int numSteps)
	simulate using exact stochastic algorithm
TCAPIEXPORT tc_matrix	cSimulateHybrid (copasi_model model, double startTime, double endTime, int numSteps)
	simulate using Hybrid algorithm/deterministic algorithm
TCAPIEXPORT tc_matrix	cSimulateTauLeap (copasi_model model, double startTime, double endTime, int numSteps)
	simulate using Tau Leap stochastic algorithm
TCAPIEXPORT tc_matrix	cGetSteadyState (copasi_model model)
	bring the system to steady state
TCAPIEXPORT tc_matrix	cGetSteadyState2 (copasi_model model, int iter)
	bring the system to steady state using normal simulation
TCAPIEXPORT tc_matrix	cGetJacobian (copasi_model model)
	get the Jacobian at the current state
TCAPIEXPORT tc_matrix	cGetEigenvalues (copasi_model model)
	get the eigenvalues of the Jacobian at the current state
TCAPIEXPORT tc_matrix	cGetUnscaledElasticities (copasi_model model)
	unscaled elasticities
TCAPIEXPORT tc_matrix	cGetUnscaledConcentrationControlCoeffs (copasi_model model)
	unscaled elasticities
TCAPIEXPORT tc_matrix	cGetUnscaledFluxControlCoeffs (copasi_model model)
	unscaled flux control coefficients
TCAPIEXPORT tc_matrix	cGetScaledElasticities (copasi_model model)
	scaled elasticities
TCAPIEXPORT tc_matrix	cGetScaledConcentrationConcentrationCoeffs (copasi_model model)
	scaled concentration control coefficients
TCAPIEXPORT tc_matrix	cGetFullStoichiometryMatrix (copasi_model model)
	full stoichiometry matrix
TCAPIEXPORT tc_matrix	cGetReducedStoichiometryMatrix (copasi_model model)
	reduced stoichiometry matrix
TCAPIEXPORT tc_matrix	cGetElementaryFluxModes (copasi_model model)
	elementary flux modes
TCAPIEXPORT tc_matrix	cGetGammaMatrix (copasi_model model)
	get Gamma matrix (i.e. conservation laws)
TCAPIEXPORT tc_matrix	cGetKMatrix (copasi_model model)
	get K matrix (right nullspace)
TCAPIEXPORT tc_matrix	cGetK0Matrix (copasi_model model)
	get K0 matrix
TCAPIEXPORT tc_matrix	cGetLinkMatrix (copasi_model model)
	get L matrix (left nullspace)
TCAPIEXPORT tc_matrix	cGetL0Matrix (copasi_model model)
	get L0 matrix
TCAPIEXPORT tc_matrix	cOptimize (copasi_model model, const char *objective, tc_matrix input)
	fit the model parameters to time-series data
TCAPIEXPORT void	cSetOptimizerIterations (int)
TCAPIEXPORT void	cSetOptimizerSize (int)
TCAPIEXPORT void	cSetOptimizerMutationRate (double)
TCAPIEXPORT void	cSetOptimizerCrossoverRate (double)

---

Function Documentation

TCAPIEXPORT void cAddProduct	(	copasi_reaction	reaction,
		const char *	species,
		double	stoichiometry
	)

add a product to a reaction

Parameters:

copasi_reaction	reaction
char	* product
double	stoichiometry

TCAPIEXPORT void cAddReactant	(	copasi_reaction	reaction,
		const char *	species,
		double	stoichiometry
	)

add a reactant to a reaction

Parameters:

copasi_reaction	reaction
char	* reactant
double	stoichiometry

TCAPIEXPORT void cCompileModel	(	copasi_model	model,
		int	substitute_nested_assignments
	)

clear all contents of a model

This function is only needed for calling COPASI methods not found in this library. This function compiles the COPASI model; it is called internally by the simulate and other anlysis functions.

Parameters:

copasi_model	model
int	substitute nested assignments

TCAPIEXPORT copasi_compartment cCreateCompartment	(	copasi_model	model,
		const char *	name,
		double	volume
	)

create compartment

Parameters:

char*	compartment name
double	volume

Returns:

copasi_compartment a new compartment

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

add a trigger and a response, where the response is defined by a target variable and an assignment formula

Parameters:

copasi_model	model
char	* event name
char	* trigger
char	* response: name of variable or species
char*	response: assignment formula

Returns:

int 0=failed 1=success

TCAPIEXPORT copasi_model cCreateModel

(

const char *

name

)

create a model

Parameters:

char*

model name

Returns:

copasi_model a new copasi model

TCAPIEXPORT copasi_reaction cCreateReaction	(	copasi_model	model,
		const char *	name
	)

add a species or set an existing species as fixed

Parameters:

copasi_model	model
char*	species name

Returns:

copasi_reaction a new reaction

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

add a species to the model

Parameters:

copasi_compartment	model
char*	species name
double	initial value (concentration or count, depending on the model)

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

create a new variable that is not a constant by a formula

Parameters:

copasi_model	model
char*	name of new variable
char*	formula

Returns:

int 0=failed 1=success

TCAPIEXPORT tc_matrix cGetEigenvalues

(

copasi_model

model

)

get the eigenvalues of the Jacobian at the current state

Parameters:

copasi_model

model

Returns:

tc_matrix matrix with 1 row and n columns, each containing an eigenvalue

TCAPIEXPORT tc_matrix cGetElementaryFluxModes

(

copasi_model

model

)

elementary flux modes

Parameters:

copasi_model

model

Returns:

tc_matrix matrix with reactions as rows (with rownames) and flux modes as columns (no column names)

TCAPIEXPORT tc_matrix cGetFullStoichiometryMatrix

(

copasi_model

model

)

full stoichiometry matrix

Parameters:

copasi_model

model

Returns:

tc_matrix

TCAPIEXPORT tc_matrix cGetGammaMatrix

(

copasi_model

model

)

get Gamma matrix (i.e. conservation laws)

Parameters:

copasi_model

model

Returns:

tc_matrix

TCAPIEXPORT tc_matrix cGetJacobian

(

copasi_model

model

)

get the Jacobian at the current state

Parameters:

copasi_model

model

Returns:

tc_matrix matrix with n rows and n columns, where n = number of species

TCAPIEXPORT tc_matrix cGetK0Matrix

(

copasi_model

model

)

get K0 matrix

Parameters:

copasi_model

model

Returns:

tc_matrix

TCAPIEXPORT tc_matrix cGetKMatrix

(

copasi_model

model

)

get K matrix (right nullspace)

Parameters:

copasi_model

model

Returns:

tc_matrix

TCAPIEXPORT tc_matrix cGetL0Matrix

(

copasi_model

model

)

get L0 matrix

Parameters:

copasi_model

model

Returns:

tc_matrix

TCAPIEXPORT tc_matrix cGetLinkMatrix

(

copasi_model

model

)

get L matrix (left nullspace)

Parameters:

copasi_model

model

Returns:

tc_matrix

TCAPIEXPORT tc_matrix cGetReducedStoichiometryMatrix

(

copasi_model

model

)

reduced stoichiometry matrix

Parameters:

copasi_model

model

Returns:

tc_matrix

TCAPIEXPORT tc_matrix cGetScaledConcentrationConcentrationCoeffs

(

copasi_model

model

)

scaled concentration control coefficients

Parameters:

copasi_model

model

Returns:

tc_matrix

TCAPIEXPORT tc_matrix cGetScaledElasticities

(

copasi_model

model

)

scaled elasticities

Parameters:

copasi_model

model

Returns:

tc_matrix

TCAPIEXPORT tc_matrix cGetScaledFluxControlCoeffs

(

copasi_model

model

)

add a compartment to the model

scaled flux control coefficients

Parameters:

copasi_model	model/*! scaled flux control coefficients
copasi_model	model

Returns:

tc_matrix

Parameters:

copasi_model

model

Returns:

tc_matrix

add a compartment to the model

Parameters:

copasi_model

model

Returns:

tc_matrix

TCAPIEXPORT tc_matrix cGetSteadyState

(

copasi_model

model

)

bring the system to steady state

Parameters:

copasi_model

model

Returns:

tc_matrix matrix with 1 row and n columns, where n = number of species

TCAPIEXPORT tc_matrix cGetSteadyState2	(	copasi_model	model,
		int	iter
	)

bring the system to steady state using normal simulation

Parameters:

copasi_model	model
int	max iterations (each iteration doubles the time duration)

Returns:

tc_matrix matrix with 1 row and n columns, where n = number of species

TCAPIEXPORT tc_matrix cGetUnscaledConcentrationControlCoeffs

(

copasi_model

model

)

unscaled elasticities

unscaled concentration control coefficients

Parameters:

copasi_model

model

Returns:

tc_matrix

TCAPIEXPORT tc_matrix cGetUnscaledElasticities

(

copasi_model

model

)

unscaled elasticities

Parameters:

copasi_model

model

Returns:

tc_matrix

TCAPIEXPORT tc_matrix cGetUnscaledFluxControlCoeffs

(

copasi_model

model

)

unscaled flux control coefficients

Parameters:

copasi_model

model

Returns:

tc_matrix

BEGIN_C_DECLS TCAPIEXPORT void copasi_end

(

)

initialize copasi -- MUST BE CALLED before calling any other functions

destroy copasi -- MUST BE CALLED at the end of program

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

fit the model parameters to time-series data

Parameters:

copasi_model	model
char	* filename (tab separated)
tc_matrix	parameters to optimize. rownames should contain parameter names, column 1 contains parameter min-values, and column 2 contains parameter max values
char	* pick method. Use of of the following: "GeneticAlgorithm", "LevenbergMarquardt", "SimulatedAnnealing", "NelderMead", "SRES", "ParticleSwarm", "SteepestDescent", "RandomSearch"

use genetic algorithms to generate a distribution of parameter values that satisfy an objective function or fit a data file

Parameters:

copasi_model	model
char	* objective function or filename
tc_matrix	parameter initial values and min and max values (3 columns)

TCAPIEXPORT copasi_model cReadAntimonyFile

(

const char *

filename

)

create a model from an Antimony or SBML file

Parameters:

char*

file name

Returns:

copasi_model a new copasi model

TCAPIEXPORT copasi_model cReadSBMLFile

(

const char *

filename

)

create a model from an SBML file

Parameters:

char*

file name

Returns:

copasi_model a new copasi model

TCAPIEXPORT copasi_model cReadSBMLString

(

const char *

sbml

)

create a model from an SBML string

Parameters:

char*

SBML string

Returns:

copasi_model a new copasi model

TCAPIEXPORT void cRemoveModel

(

copasi_model

)

remove a model

TCAPIEXPORT int cSetAssignmentRule	(	copasi_model	model,
		const char *	species,
		const char *	formula
	)

set the assignment rule for a species (automatically assumes boundary species)

Parameters:

copasi_model	model
char	* species name
char*	formula, use 0 to remove assignment rule

Returns:

int 0=failed 1=success

TCAPIEXPORT void cSetBoundarySpecies	(	copasi_model	model,
		const char *	species,
		int	isBoundary
	)

set a species as boundary or floating (will remove any assignment rules)

Parameters:

copasi_model	model
char	* name
int	boundary = 1, floating = 0 (default)

TCAPIEXPORT void cSetConcentration	(	copasi_model	,
		const char *	species,
		double	value
	)

set a species as boundary or floating (will remove any assignment rules)

Parameters:

copasi_model	model
char	* species name
double	concentration or count

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

set the value of an existing global parameter or create a new global parameter

Parameters:

copasi_model	model
char*	parameter name
double	value

Returns:

int 0=new value created 1=found existing value

TCAPIEXPORT void cSetOptimizerCrossoverRate

(

double

)

TCAPIEXPORT void cSetOptimizerIterations

(

int

)

TCAPIEXPORT void cSetOptimizerMutationRate

(

double

)

TCAPIEXPORT void cSetOptimizerSize

(

int

)

TCAPIEXPORT int cSetReactionRate	(	copasi_reaction	reaction,
		const char *	formula
	)

set reaction rate equation

Parameters:

copasi_reaction	reaction
char*	custom formula

Returns:

int success=1 failure=0

TCAPIEXPORT int cSetValue	(	copasi_model	,
		const char *	name,
		double	value
	)

set the concentration of a species, volume of a compartment, or value of a parameter The function will figure out which using the name (fast lookup using hashtables). If the name does not exist in the model, a new global parameter will be created.

Parameters:

copasi_model	model
char	* name
double	value

Returns:

0 if new variable was created. 1 if existing variable was found

TCAPIEXPORT void cSetVolume	(	copasi_model	,
		const char *	compartment,
		double	volume
	)

set a volume of compartment

Parameters:

copasi_model	model
char	* compartment name
double	volume

TCAPIEXPORT tc_matrix cSimulateDeterministic	(	copasi_model	model,
		double	startTime,
		double	endTime,
		int	numSteps
	)

simulate using LSODA numerical integrator

Parameters:

copasi_model	model
double	start time
double	end time
int	number of steps in the output

Returns:

tc_matrix matrix of concentration or particles

TCAPIEXPORT tc_matrix cSimulateHybrid	(	copasi_model	model,
		double	startTime,
		double	endTime,
		int	numSteps
	)

simulate using Hybrid algorithm/deterministic algorithm

Parameters:

copasi_model	model
double	start time
double	end time
int	number of steps in the output

Returns:

tc_matrix matrix of concentration or particles

TCAPIEXPORT tc_matrix cSimulateStochastic	(	copasi_model	model,
		double	startTime,
		double	endTime,
		int	numSteps
	)

simulate using exact stochastic algorithm

Parameters:

copasi_model	model
double	start time
double	end time
int	number of steps in the output

Returns:

tc_matrix matrix of concentration or particles

TCAPIEXPORT tc_matrix cSimulateTauLeap	(	copasi_model	model,
		double	startTime,
		double	endTime,
		int	numSteps
	)

simulate using Tau Leap stochastic algorithm

Parameters:

copasi_model	model
double	start time
double	end time
int	number of steps in the output

Returns:

tc_matrix matrix of concentration or particles

TCAPIEXPORT void cWriteSBMLFile	(	copasi_model	model,
		const char *	filename
	)

save a model as an SBML file

Parameters:

copasi_model	copasi model
char*	file name