rr::RoadRunner Class Reference

#include <rrRoadRunner.h>

Inheritance diagram for rr::RoadRunner:

Public Member Functions
	RoadRunner (const std::string &compiler="", const std::string &tempDir="", const std::string &supportCodeDir="")
virtual	~RoadRunner ()
int	getInstanceID ()
int	getInstanceCount ()
std::string	getInfo ()
class Compiler *	getCompiler ()
bool	setCompiler (const std::string &compiler)
Integrator *	getIntegrator ()
std::string	getModelName ()
double	oneStep (double currentTime, double stepSize, bool reset=true)
const RoadRunnerData *	simulate (const SimulateOptions *options=0)
RoadRunnerData *	getSimulationResult ()
SimulateOptions &	getSimulateOptions ()
std::string	getSBML ()
void	reset ()
ModelGenerator *	getModelGenerator ()
ExecutableModel *	getModel ()
bool	load (const std::string &uriOrSBML, const LoadSBMLOptions *options=0)
virtual _xmlNode *	createConfigNode ()
virtual void	loadConfig (const _xmlDoc *doc)
std::string	getConfigurationXML ()
void	setConfigurationXML (const std::string &xml)
rr::SelectionRecord	createSelection (const std::string &str)
std::vector < rr::SelectionRecord > &	getSelections ()
double	getValue (const std::string &sel)
std::vector< double >	getSelectedValues ()
void	getIds (int types, std::list< std::string > &ids)
int	getSupportedIdTypes ()
bool	setValue (const std::string &id, double value)
ls::DoubleMatrix	getFullJacobian ()
ls::DoubleMatrix	getReducedJacobian ()
ls::DoubleMatrix	getEigenvalues ()
std::vector< std::string >	getEigenvalueIds ()
double	getUnscaledParameterElasticity (const string &reactionName, const string &parameterName)
void	setConservedMoietyAnalysis (bool value)
bool	getConservedMoietyAnalysis ()
std::string	getCurrentSBML ()
void	evalModel ()
double	getuCC (const std::string &variableName, const std::string &parameterName)
double	getCC (const std::string &variableName, const std::string &parameterName)
double	getuEE (const std::string &reactionName, const std::string &parameterName)
double	getuEE (const std::string &reactionName, const std::string &parameterName, bool computeSteadystate)
double	getEE (const std::string &reactionName, const std::string &parameterName)
double	getEE (const std::string &reactionName, const std::string &parameterName, bool computeSteadyState)
ls::DoubleMatrix	getUnscaledElasticityMatrix ()
ls::DoubleMatrix	getScaledElasticityMatrix ()
double	getScaledFloatingSpeciesElasticity (const std::string &reactionName, const std::string &speciesName)
double	getUnscaledSpeciesElasticity (int reactionId, int speciesIndex)
double	steadyState ()
std::vector < rr::SelectionRecord > &	getSteadyStateSelections ()
void	setSteadyStateSelections (const std::vector< std::string > &steadyStateSelections)
void	setSteadyStateSelections (const std::vector< rr::SelectionRecord > &steadyStateSelections)
std::vector< double >	getSteadyStateValues ()

Static Public Member Functions
static std::string	getParamPromotedSBML (const std::string &sArg)
static std::string	getExtendedVersionInfo ()
Static Public Member Functions inherited from rr::Configurable
static void	loadXmlConfig (const std::string &xml, Configurable *configurable)
static std::string	xmlFromConfigNode (_xmlNode *config)
static _xmlNode *	createCapabilityNode (const std::string &name, const std::string &method, const std::string &desc)
static _xmlNode *	createCapabilitiesNode (const std::string &name, const std::string &desc)
static _xmlNode *	addChild (_xmlNode *parent, _xmlNode *cur)
static _xmlNode *	createParameterNode (const std::string &name, const std::string &hint, const std::string &value)
static _xmlNode *	createParameterNode (const std::string &name, const std::string &hint, int value)
static _xmlNode *	createParameterNode (const std::string &name, const std::string &hint, double value)
static std::string	getParameterStringValue (const _xmlDoc *doc, const std::string &capabilityName, const std::string &parameterName)
static int	getParameterIntValue (const _xmlDoc *doc, const std::string &capabilityName, const std::string &parameterName)
static double	getParameterDoubleValue (const _xmlDoc *doc, const std::string &capabilityName, const std::string &parameterName)

Detailed Description

The main RoadRunner class.

The RoadRunner class is responsible for loading and simulating SBML models.

MemoryManagment: Any pointer returned by a get... method is owned by the RoadRunner object and does NOT have to be deleted.

Constructor & Destructor Documentation

rr::RoadRunner::RoadRunner	(	const std::string &	compiler = "",
		const std::string &	tempDir = "",
		const std::string &	supportCodeDir = ""
	)

All three of the RoadRunner options default to the empty string, in this case, the default values are used.

Parameters

compiler,:	If LLVM build is enabled, the compiler defaults to LLVM.
tempDir,:	If the old external C compiler is used, this is the where the C files are written to.
supportCodeDir,:	If the old external C compiler is used, this is the location where roadrunner C include files are.

rr::RoadRunner::~RoadRunner ( )

virtual

free any memory this class allocated

Member Function Documentation

_xmlNode * rr::RoadRunner::createConfigNode ( )

virtual

creates a new xml element that represent the current state of this Configurable object and all if its child objects.

This node needs to be consumed by Configurable::xmlFromConfigNode

Implements rr::Configurable.

SelectionRecord rr::RoadRunner::createSelection

(

const std::string &

str

)

create a selection record. This record can be used to select values.

void rr::RoadRunner::evalModel

(

)

The C back end requires this to be called to update model variables if anyting is changes. Does nothing in LLVM back end as everything is automatically handled with lazy evaluation.

double rr::RoadRunner::getCC	(	const std::string &	variableName,
		const std::string &	parameterName
	)

Get scaled control coefficient with respect to a global parameter

The variableName must be either a reaction id, or a floating species id.

The parameterName must be either a global parameter, boundary species, or conserved sum.

Compiler * rr::RoadRunner::getCompiler

(

)

The Compiler that the ModelGenerator is using to compile / interpret sbml code.

std::string rr::RoadRunner::getConfigurationXML

(

)

recurse through all of the child configurable objects that this class ownes and build an assemble all of thier configuration parameters into a single xml document which is returned as a string.

The value of this result depends on what child objects are presently loaded.

bool rr::RoadRunner::getConservedMoietyAnalysis

(

)

is conservation analysis enabled. This is set

string rr::RoadRunner::getCurrentSBML

(

)

Returns the SBML with the current parameterset.

double rr::RoadRunner::getEE	(	const std::string &	reactionName,
		const std::string &	parameterName
	)

Get scaled elasticity coefficient with respect to a global parameter or species

double rr::RoadRunner::getEE	(	const std::string &	reactionName,
		const std::string &	parameterName,
		bool	computeSteadyState
	)

Get scaled elasticity coefficient with respect to a global parameter or species. Optionally the model is brought to steady state after the computation.

vector< string > rr::RoadRunner::getEigenvalueIds

(

)

returns the list of floating species, but with a "eigen(...)" string wrapped around them.

DoubleMatrix rr::RoadRunner::getEigenvalues

(

)

Returns eigenvalues, first column real part, second column imaginary part

string rr::RoadRunner::getExtendedVersionInfo ( )

static

getVersion plus info about dependent libs versions..

DoubleMatrix rr::RoadRunner::getFullJacobian

(

)

compute the full Jacobian at the current operating point

void rr::RoadRunner::getIds	(	int	types,
		std::list< std::string > &	ids
	)

populates a given list with all the ids that this class can accept.

string rr::RoadRunner::getInfo

(

)

information about the current state of this object.

int rr::RoadRunner::getInstanceCount

(

)

Number of currently running RoadRunner instances.

int rr::RoadRunner::getInstanceID

(

)

When there are multiple instances of RoadRunner, this is the instance id.

Integrator * rr::RoadRunner::getIntegrator

(

)

get a pointer to the integrator which is currently being used to time evolve the system.

ExecutableModel * rr::RoadRunner::getModel

(

)

get a pointer to the ExecutableModel owned by the RoadRunner object.

ModelGenerator * rr::RoadRunner::getModelGenerator

(

)

get the ModelGenerator that is used to create executable (runnable) models.

string rr::RoadRunner::getModelName

(

)

returns the model name if a model is loaded, empty string otherwise.

string rr::RoadRunner::getParamPromotedSBML ( const std::string &  sArg )

static

given an sbml document, this method moves all the local parameters to global parameters.

DoubleMatrix rr::RoadRunner::getReducedJacobian

(

)

Compute the reduced Jacobian at the current operating point.

string rr::RoadRunner::getSBML

(

)

get the currently loaded sbml document as a string.

DoubleMatrix rr::RoadRunner::getScaledElasticityMatrix

(

)

Compute the unscaled elasticity matrix at the current operating point

double rr::RoadRunner::getScaledFloatingSpeciesElasticity	(	const std::string &	reactionName,
		const std::string &	speciesName
	)

Compute the scaled elasticity for a given reaction and given species

vector< double > rr::RoadRunner::getSelectedValues

(

)

returns the values selected with SimulateOptions for the current model time / timestep")

std::vector< rr::SelectionRecord > & rr::RoadRunner::getSelections

(

)

Returns the currently selected columns that will be returned by calls to simulate() or simulateEx(,,).

SimulateOptions & rr::RoadRunner::getSimulateOptions

(

)

get a reference to the SimulateOptions that were set either by setSimulateOptions or simulate.

RoadRunnerData * rr::RoadRunner::getSimulationResult

(

)

obtain a pointer to the simulation result.

This is owned by the RoadRunner object.

vector< SelectionRecord > & rr::RoadRunner::getSteadyStateSelections

(

)

returns the current set of steady state selections.

vector< double > rr::RoadRunner::getSteadyStateValues

(

)

Performs a steady state calculation (evolves the system to a steady state), then calculates and returns the set of values specifed by the steady state selections.

int rr::RoadRunner::getSupportedIdTypes

(

)

returns a bit field of the ids that this class supports.

double rr::RoadRunner::getuCC	(	const std::string &	variableName,
		const std::string &	parameterName
	)

Get unscaled control coefficient with respect to a global parameter

variableName must be either a reaction or floating species.

parameterName must be eithe a global parameter, boundary species, or conserved sum.

double rr::RoadRunner::getuEE	(	const std::string &	reactionName,
		const std::string &	parameterName
	)

Get unscaled elasticity coefficient with respect to a global parameter or species

double rr::RoadRunner::getuEE	(	const std::string &	reactionName,
		const std::string &	parameterName,
		bool	computeSteadystate
	)

Get unscaled elasticity coefficient with respect to a global parameter or species. Optionally the model is brought to steady state after the computation.

DoubleMatrix rr::RoadRunner::getUnscaledElasticityMatrix

(

)

Compute the unscaled species elasticity matrix at the current operating point

double rr::RoadRunner::getUnscaledParameterElasticity	(	const string &	reactionName,
		const string &	parameterName
	)

Returns the unscaled elasticity for a named reaction with respect to a named parameter

double rr::RoadRunner::getUnscaledSpeciesElasticity	(	int	reactionId,
		int	speciesIndex
	)

Get a single species elasticity value IMPORTANT: Assumes that the reaction rates have been precomputed at the operating point !!

double rr::RoadRunner::getValue

(

const std::string &

sel

)

Creates a new selection based on the selection string, and returns the value it queries.

bool rr::RoadRunner::load	(	const std::string &	uriOrSBML,
		const LoadSBMLOptions *	options = 0
	)

load an sbml document from anywhere.

If options is not null, then the RoadRunner::computeAndAssignConservationLaws flag is set to whatever value is specified in the options struct.

Parameters

uriOrSBML,:	a URI, local path or sbml document contents.
options,:	an options struct, if null, default values are used.

void rr::RoadRunner::loadConfig ( const _xmlDoc *  doc )

virtual

Given an xml element, the Configurable object should pick its needed values that are stored in the element and use them to set its internal configuration state.

Implements rr::Configurable.

double rr::RoadRunner::oneStep	(	double	currentTime,
		double	stepSize,
		bool	reset = true
	)

Carry out a single integration step using a stepsize as indicated in the method call. Arguments: double CurrentTime, double StepSize, bool: reset integrator if true, Return Value: new CurrentTime.

void rr::RoadRunner::reset

(

)

Reset the simulator back to the initial conditions specified in the SBML model, provided an SBML model is loaded.

bool rr::RoadRunner::setCompiler

(

const std::string &

compiler

)

Set the name of the externa compiler to use. Some ModelGenerators may have no use for this value.

void rr::RoadRunner::setConfigurationXML

(

const std::string &

xml

)

given a xml document, which should have been returned from getConfigurationXML, this method recurses though all the child configurable elements and sets thier configuration to the values specified in the document.

void rr::RoadRunner::setConservedMoietyAnalysis

(

bool

value

)

This method turns on / off the computation and adherence to conservation laws.

void rr::RoadRunner::setSteadyStateSelections

(

const std::vector< std::string > &

steadyStateSelections

)

parses the given list of strings and generates selections records which will be used for the steady state selections.

void rr::RoadRunner::setSteadyStateSelections

(

const std::vector< rr::SelectionRecord > &

steadyStateSelections

)

makes a copy of an existing list of selection records. These will be saved and used for selection values in getSteadyStateValues().

bool rr::RoadRunner::setValue	(	const std::string &	id,
		double	value
	)

sets the value coresponding to the given selection string

const RoadRunnerData * rr::RoadRunner::simulate

(

const SimulateOptions *

options = 0

)

simulate the current SBML model.

If options is null, then the current simulation settings (start time, end time, n steps) are used. If options is not null, then the current simulation settings are set to the values specified by options and they are used.

Returns

a RoadRunnerData object which is owned by the the RoadRunner object if successfull, 0 on failure.

double rr::RoadRunner::steadyState

(

)

Compute the steady state of the model, returns the sum of squares of the solution

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The documentation for this class was generated from the following files:

• rrRoadRunner.h
• rrRoadRunner.cpp