AgentCell Class Reference

#include <cell.hh>

List of all members.

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Detailed Description

The basic unit of the NG chemotaxis simulation. This is the core class needed to run simulations of swimming cells in a 3D environment. It is basically a wrapper for a NG network free simulator object (

See also:

ng.hh) that has additional functions that allow it to swim according to the correct E.Coli statistics. It allows interaction with the given environment, but does not yet have the capability to interact with other cells yet.

Public Member Functions
	AgentCell (System *s, Environment *e, double speed, double rotDiffusionConstant, double cheYpThreshold, double startTime, string outputDirectoryPath)
	~AgentCell ()
double	stepTo (double endTime, double dt)
void	equilibriate (double duration, double dt)
double	getXposition () const
double	getYposition () const
double	getZposition () const
double	getXdirection () const
double	getYdirection () const
double	getZdirection () const
void	swimToNewPosition (double elapsedTime)
void	outputCellValues ()
Static Public Attributes
static const int	X = 0
static const int	Y = 1
static const int	Z = 2
static const int	TUMBLE = 0
static const int	SWIM = 1
static const int	APART = 0
static const int	BUNDLED = 1
Protected Member Functions
void	changeDirRandom ()
void	changeDirDistribution ()
void	changeDirRotDiffusion (double elapsedTime)
void	moveToNewPosition (double elapsedTime)
void	outputCellHeader ()
Protected Attributes
double	speed
double	rotDiffusionConstant
double *	cheYhistory
int	cheYhisPos
int	cheYpThreshold
int	motorState
int	flagellaState
int	lastFlagellaState
double	apartDuration
bool	droppingTumble
double	boxcarTimeWidth
int	cheYhistorySize
double	meanCheYp
double	cheYhistorySum
int	cellId
double	pos [3]
double	dir [3]
double	up [3]
double	rotMat [3][3]
double	lastPos [3]
double	lastDir [3]
double	lastUp [3]
double	currentTime
int	currentMovement
int	lastMovement
double	currentLigConc
System *	system
Environment *	env
ofstream	motorFileStream
ofstream	outputFileStream
double	runTimeSpent
string	fileName
unsigned int	binaryFileOutputCounter
Static Protected Attributes
static const double	DefaultGammaAlpha = 4.
static const double	DefaultGammaBeta = 1./18.32045567939674
static const double	DefaultGammaOffset = -4.606176605609249
static const double	DefaultSpeed = 20
static const double	DefaultRotDifConst = 0.06205
static const int	CW = 1
static const int	CCW = 0

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Constructor & Destructor Documentation

AgentCell::AgentCell	(	System *	s,
		Environment *	e,
		double	speed,
		double	rotDiffusionConstant,
		double	cheYpThreshold,
		double	startTime,
		string	outputDirectoryPath
	)

AgentCell::~AgentCell

(

)

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Member Function Documentation

double AgentCell::stepTo	(	double	endTime,
		double	dt
	)

void AgentCell::equilibriate	(	double	duration,
		double	dt
	)

double AgentCell::getXposition

(

)

const [inline]

double AgentCell::getYposition

(

)

const [inline]

double AgentCell::getZposition

(

)

const [inline]

double AgentCell::getXdirection

(

)

const [inline]

double AgentCell::getYdirection

(

)

const [inline]

double AgentCell::getZdirection

(

)

const [inline]

void AgentCell::swimToNewPosition

(

double

elapsedTime

)

void AgentCell::outputCellValues

(

)

void AgentCell::changeDirRandom

(

)

[protected]

void AgentCell::changeDirDistribution

(

)

[protected]

void AgentCell::changeDirRotDiffusion

(

double

elapsedTime

)

[protected]

void AgentCell::moveToNewPosition

(

double

elapsedTime

)

[protected]

void AgentCell::outputCellHeader

(

)

[protected]

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Member Data Documentation

const int AgentCell::X = 0 [static]

const int AgentCell::Y = 1 [static]

const int AgentCell::Z = 2 [static]

const int AgentCell::TUMBLE = 0 [static]

const int AgentCell::SWIM = 1 [static]

const int AgentCell::APART = 0 [static]

const int AgentCell::BUNDLED = 1 [static]

double AgentCell::speed [protected]

double AgentCell::rotDiffusionConstant [protected]

double* AgentCell::cheYhistory [protected]

int AgentCell::cheYhisPos [protected]

int AgentCell::cheYpThreshold [protected]

int AgentCell::motorState [protected]

int AgentCell::flagellaState [protected]

int AgentCell::lastFlagellaState [protected]

double AgentCell::apartDuration [protected]

bool AgentCell::droppingTumble [protected]

double AgentCell::boxcarTimeWidth [protected]

int AgentCell::cheYhistorySize [protected]

double AgentCell::meanCheYp [protected]

double AgentCell::cheYhistorySum [protected]

int AgentCell::cellId [protected]

double AgentCell::pos[3] [protected]

double AgentCell::dir[3] [protected]

double AgentCell::up[3] [protected]

double AgentCell::rotMat[3][3] [protected]

double AgentCell::lastPos[3] [protected]

double AgentCell::lastDir[3] [protected]

double AgentCell::lastUp[3] [protected]

double AgentCell::currentTime [protected]

int AgentCell::currentMovement [protected]

int AgentCell::lastMovement [protected]

double AgentCell::currentLigConc [protected]

const double AgentCell::DefaultGammaAlpha = 4. [static, protected]

const double AgentCell::DefaultGammaBeta = 1./18.32045567939674 [static, protected]

const double AgentCell::DefaultGammaOffset = -4.606176605609249 [static, protected]

const double AgentCell::DefaultSpeed = 20 [static, protected]

const double AgentCell::DefaultRotDifConst = 0.06205 [static, protected]

System* AgentCell::system [protected]

Environment* AgentCell::env [protected]

ofstream AgentCell::motorFileStream [protected]

ofstream AgentCell::outputFileStream [protected]

double AgentCell::runTimeSpent [protected]

string AgentCell::fileName [protected]

unsigned int AgentCell::binaryFileOutputCounter [protected]

const int AgentCell::CW = 1 [static, protected]

const int AgentCell::CCW = 0 [static, protected]

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

• /home/msneddon/eclipse/galileoSR1_cpp/workspace/NFsim/src/NFtest/agentcell/cell/cell.hh
• /home/msneddon/eclipse/galileoSR1_cpp/workspace/NFsim/src/NFtest/agentcell/cell/cell.cpp

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