#include <iostream>
#include <vector>
#include <string>
#include <set>
#include <limits>
#include <QString>
#include <QStringList>
#include <QRegExp>
#include <QHash>
#include <QList>
#include <QPair>
#include <QFile>
#include "copasi_api.h"
#include "copasi/copasi.h"
#include "copasi/report/CCopasiRootContainer.h"
#include "copasi/CopasiDataModel/CCopasiDataModel.h"
#include "copasi/model/CModel.h"
#include "copasi/model/CCompartment.h"
#include "copasi/model/CMetab.h"
#include "copasi/model/CReaction.h"
#include "copasi/model/CChemEq.h"
#include "copasi/model/CModelValue.h"
#include "copasi/function/CFunctionDB.h"
#include "copasi/function/CFunction.h"
#include "copasi/function/CEvaluationTree.h"
#include "copasi/report/CReport.h"
#include "copasi/report/CReportDefinition.h"
#include "copasi/report/CReportDefinitionVector.h"
#include "copasi/trajectory/CTrajectoryTask.h"
#include "copasi/trajectory/CTrajectoryMethod.h"
#include "copasi/trajectory/CTrajectoryProblem.h"
#include "copasi/scan/CScanTask.h"
#include "copasi/scan/CScanMethod.h"
#include "copasi/scan/CScanProblem.h"
#include "copasi/trajectory/CTimeSeries.h"
#include "copasi/steadystate/CSteadyStateTask.h"
#include "copasi/steadystate/CMCATask.h"
#include "copasi/steadystate/CMCAMethod.h"
#include "copasi/elementaryFluxModes/CFluxMode.h"
#include "copasi/elementaryFluxModes/CEFMTask.h"
#include "copasi/elementaryFluxModes/CEFMProblem.h"
#include "copasi/commandline/COptions.h"
#include "copasi/report/CCopasiContainer.h"
#include "copasi/parameterFitting/CFitTask.h"
#include "copasi/parameterFitting/CFitMethod.h"
#include "copasi/parameterFitting/CFitProblem.h"
#include "copasi/parameterFitting/CFitItem.h"
#include "copasi/parameterFitting/CExperimentSet.h"
#include "copasi/parameterFitting/CExperiment.h"
#include "copasi/parameterFitting/CExperimentObjectMap.h"
#include "copasi/report/CKeyFactory.h"
#include "GASStateGA.h"
#include "GA1DArrayGenome.h"
#include "libstructural.h"
#include "matrix.h"
#include "muParserDef.h"
#include "muParser.h"
#include "muParserInt.h"
#include "mtrand.h"
#include "src/antimony_api.h"

Classes
struct	CopasiPtr
struct	GAData
Defines
#define	COPASI_MAIN 1
#define	LIB_EXPORTS 1
Typedefs
typedef QHash< QString, CopasiPtr >	CQHash
typedef GA1DArrayGenome< float >	RealGenome
Functions
void	copasi_init ()
void	copasi_end ()
	initialize copasi -- MUST BE CALLED before calling any other functions
int	cSetAssignmentRuleHelper (copasi_model, CMetab , const char )
int	copasi_cleanup_assignments (copasi_model model, bool doWhile=false)
void	cRemoveModel (copasi_model model)
	remove a model
void	clearCopasiModel (copasi_model model)
copasi_model	cCreateModel (const char *name)
	create a model
void	cCreateSpecies (copasi_compartment compartment, const char *name, double iv)
	add a species to the model
copasi_compartment	cCreateCompartment (copasi_model model, const char *name, double volume)
	create compartment
int	cSetValue (copasi_model 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.
void	cSetVolume (copasi_model model, const char *name, double vol)
	set a volume of compartment
void	cSetConcentration (copasi_model model, const char *name, double conc)
	set a species as boundary or floating (will remove any assignment rules)
int	cSetGlobalParameter (copasi_model model, const char *name, double value)
	set the value of an existing global parameter or create a new global parameter
void	cSetBoundarySpecies (copasi_model model, const char *name, int isBoundary)
	set a species as boundary or floating (will remove any assignment rules)
int	cSetAssignmentRule (copasi_model model, const char name, const char formula)
	set the assignment rule for a species (automatically assumes boundary species)
int	cCreateVariable (copasi_model model, const char name, const char formula)
	create a new variable that is not a constant by a formula
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
copasi_reaction	cCreateReaction (copasi_model model, const char *name)
	add a species or set an existing species as fixed
void	cAddReactant (copasi_reaction reaction, const char *species, double stoichiometry)
	add a reactant to a reaction
void	cAddProduct (copasi_reaction reaction, const char *species, double stoichiometry)
	add a product to a reaction
int	cSetReactionRate (copasi_reaction reaction, const char *formula)
	set reaction rate equation
void	cCompileModel (copasi_model model, int subs)
	clear all contents of a model
tc_matrix	simulate (copasi_model model, double startTime, double endTime, int numSteps, CCopasiMethod::SubType method)
tc_matrix	cSimulateDeterministic (copasi_model model, double startTime, double endTime, int numSteps)
	simulate using LSODA numerical integrator
tc_matrix	cSimulateTauLeap (copasi_model model, double startTime, double endTime, int numSteps)
	simulate using Tau Leap stochastic algorithm
tc_matrix	cSimulateStochastic (copasi_model model, double startTime, double endTime, int numSteps)
	simulate using exact stochastic algorithm
tc_matrix	cSimulateHybrid (copasi_model model, double startTime, double endTime, int numSteps)
	simulate using Hybrid algorithm/deterministic algorithm
void	cWriteSBMLFile (copasi_model model, const char *filename)
	save a model as an SBML file
copasi_model	cReadAntimonyFile (const char *filename)
	create a model from an Antimony or SBML file
copasi_model	cReadSBMLFile (const char *filename)
	create a model from an SBML file
copasi_model	cReadSBMLString (const char *sbml)
	create a model from an SBML string
tc_matrix	cGetJacobian (copasi_model model)
	get the Jacobian at the current state
tc_matrix	cGetSteadyState2 (copasi_model model, int maxiter)
	bring the system to steady state using normal simulation
tc_matrix	cGetSteadyState (copasi_model model)
	bring the system to steady state
tc_matrix	cGetEigenvalues (copasi_model model)
	get the eigenvalues of the Jacobian at the current state
tc_matrix	cGetUnscaledElasticities (copasi_model model)
	unscaled elasticities
tc_matrix	cGetUnscaledConcentrationControlCoeffs (copasi_model model)
	unscaled elasticities
tc_matrix	cGetUnscaledFluxControlCoeffs (copasi_model model)
	unscaled flux control coefficients
tc_matrix	cGetScaledElasticities (copasi_model model)
	scaled elasticities
tc_matrix	cGetScaledConcentrationConcentrationCoeffs (copasi_model model)
	scaled concentration control coefficients
tc_matrix	cGetScaledFluxControlCoeffs (copasi_model model)
	scaled flux control coefficients
tc_matrix	cGetReducedStoichiometryMatrix (copasi_model model)
	reduced stoichiometry matrix
tc_matrix	cGetFullStoichiometryMatrix (copasi_model model)
	full stoichiometry matrix
tc_matrix	cGetElementaryFluxModes (copasi_model model)
	elementary flux modes
void	InitializeGenome (GAGenome &x)
tc_matrix	cOptimize (copasi_model model, const char *objective, tc_matrix params)
	fit the model parameters to time-series data
void	cSetOptimizerSize (int n)
void	cSetOptimizerIterations (int n)
void	cSetOptimizerMutationRate (double q)
void	cSetOptimizerCrossoverRate (double q)
tc_matrix	convertFromDoubleMatrix (DoubleMatrix &matrix, std::vector< std::string > &rowNames, std::vector< std::string > &colNames)
void	convertToDoubleMatrix (tc_matrix m, DoubleMatrix &matrix, std::vector< std::string > &rowNames, std::vector< std::string > &colNames)
tc_matrix	cGetGammaMatrix (copasi_model model)
	get Gamma matrix (i.e. conservation laws)
tc_matrix	cGetKMatrix (copasi_model model)
	get K matrix (right nullspace)
tc_matrix	cGetLinkMatrix (copasi_model model)
	get L matrix (left nullspace)
tc_matrix	cGetK0Matrix (copasi_model model)
	get K0 matrix
tc_matrix	cGetL0Matrix (copasi_model model)
	get L0 matrix

Define Documentation

#define COPASI_MAIN 1

#define LIB_EXPORTS 1

Typedef Documentation

typedef QHash< QString, CopasiPtr > CQHash

typedef GA1DArrayGenome<float> RealGenome

Function Documentation

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

add a product to a reaction

Parameters:

copasi_reaction	reaction
char	* product
double	stoichiometry

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

add a reactant to a reaction

Parameters:

copasi_reaction	reaction
char	* reactant
double	stoichiometry

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

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

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

copasi_model cCreateModel ( const char * name )

create a model

Parameters:

char* model name

Returns:: copasi_model a new copasi model

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

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)

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

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

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)

tc_matrix cGetFullStoichiometryMatrix ( copasi_model model )

full stoichiometry matrix

Parameters:

copasi_model model

Returns:: tc_matrix

tc_matrix cGetGammaMatrix ( copasi_model model )

get Gamma matrix (i.e. conservation laws)

Parameters:

copasi_model model

Returns:: tc_matrix

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

tc_matrix cGetK0Matrix ( copasi_model model )

get K0 matrix

Parameters:

copasi_model model

Returns:: tc_matrix

tc_matrix cGetKMatrix ( copasi_model model )

get K matrix (right nullspace)

Parameters:

copasi_model model

Returns:: tc_matrix

tc_matrix cGetL0Matrix ( copasi_model model )

get L0 matrix

Parameters:

copasi_model model

Returns:: tc_matrix

tc_matrix cGetLinkMatrix ( copasi_model model )

get L matrix (left nullspace)

Parameters:

copasi_model model

Returns:: tc_matrix

tc_matrix cGetReducedStoichiometryMatrix ( copasi_model model )

reduced stoichiometry matrix

Parameters:

copasi_model model

Returns:: tc_matrix

tc_matrix cGetScaledConcentrationConcentrationCoeffs ( copasi_model model )

scaled concentration control coefficients

Parameters:

copasi_model model

Returns:: tc_matrix

tc_matrix cGetScaledElasticities ( copasi_model model )

scaled elasticities

Parameters:

copasi_model model

Returns:: tc_matrix

TCAPIEXPORT tc_matrix cGetScaledFluxControlCoeffs ( copasi_model model )

scaled flux control coefficients

add a compartment to the model

Parameters:

copasi_model model

Returns:: tc_matrix

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

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

tc_matrix cGetUnscaledConcentrationControlCoeffs ( copasi_model model )

unscaled elasticities

unscaled concentration control coefficients

Parameters:

copasi_model model

Returns:: tc_matrix

tc_matrix cGetUnscaledElasticities ( copasi_model model )

unscaled elasticities

Parameters:

copasi_model model

Returns:: tc_matrix

tc_matrix cGetUnscaledFluxControlCoeffs ( copasi_model model )

unscaled flux control coefficients

Parameters:

copasi_model model

Returns:: tc_matrix

void clearCopasiModel ( copasi_model model )

tc_matrix convertFromDoubleMatrix	(	DoubleMatrix &	matrix,
		std::vector< std::string > &	rowNames,
		std::vector< std::string > &	colNames
	)

void convertToDoubleMatrix	(	tc_matrix	m,
		DoubleMatrix &	matrix,
		std::vector< std::string > &	rowNames,
		std::vector< std::string > &	colNames
	)

int copasi_cleanup_assignments	(	copasi_model	model,
		bool	doWhile = `false`
	)

void copasi_end ( )

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

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

void copasi_init ( )

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)

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

copasi_model cReadSBMLFile ( const char * filename )

create a model from an SBML file

Parameters:

char* file name

Returns:: copasi_model a new copasi model

copasi_model cReadSBMLString ( const char * sbml )

create a model from an SBML string

Parameters:

char* SBML string

Returns:: copasi_model a new copasi model

void cRemoveModel ( copasi_model model )

remove a model

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

int cSetAssignmentRuleHelper	(	copasi_model	model,
		CMetab *	pSpecies,
		const char *	formula
	)

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)

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

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

void cSetOptimizerCrossoverRate ( double q )

void cSetOptimizerIterations ( int n )

void cSetOptimizerMutationRate ( double q )

void cSetOptimizerSize ( int n )

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

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

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

set a volume of compartment

Parameters:

copasi_model	model
char	* compartment name
double	volume

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

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

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

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

void cWriteSBMLFile	(	copasi_model	model,
		const char *	filename
	)

save a model as an SBML file

Parameters:

copasi_model	copasi model
char*	file name

void InitializeGenome ( GAGenome & x )

tc_matrix simulate	(	copasi_model	model,
		double	startTime,
		double	endTime,
		int	numSteps,
		CCopasiMethod::SubType	method
	)

Classes

Defines

Typedefs

Functions

Define Documentation

Typedef Documentation

Function Documentation