AgentCell Class Reference

#include <cell.hh>

List of all members.

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
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

Constructor & Destructor Documentation

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

AgentCell::~AgentCell (  ) 

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]

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]

The documentation for this class was generated from the following files:
Generated on Thu Dec 9 11:02:48 2010 for NFsim by  doxygen 1.5.4