org.concord.molecular.engine
Class DefaultAtomicModel

java.lang.Object
  |
  +--org.concord.molecular.engine.DefaultAtomicModel

All Implemented Interfaces:

org.concord.oslet.models.AtomicModel, java.lang.Runnable

Direct Known Subclasses:

DefaultMolecularModel

public class DefaultAtomicModel

extends java.lang.Object

implements org.concord.oslet.models.AtomicModel, java.lang.Runnable

This class is a convenience class for using the Oslet AtomicModel It attempts to simplify the use of this view in activity by providing a specific set of methods for parameterizing the model.

Version:

$Revision: 1.24 $ $Date: 2002/03/01 20:41:17 $

Author:

$Author: dima $

Field Summary

protected boolean	assign
protected AtomicDataEvent	atomicDataEvent
protected org.concord.pseudojava2.awt.geom.Rectangle2D.Float	bound
protected org.concord.oslet.models.Boundaries	boundary
protected java.lang.String	boundaryType
static int	DEFAULT_CUTOFF
static int	DEFAULT_DELAY
static double	DEFAULT_DELTA
static double	DEFAULT_DESCENT
static int	DEFAULT_HEIGHT
static int	DEFAULT_INTERVAL
static int	DEFAULT_SKIN
static int	DEFAULT_TEMPERATURE
static int	DEFAULT_WIDTH
protected int	delay
protected double	delta
protected double	descent
protected org.concord.oslet.dynamics.Dynamics	dynamics
static java.lang.String	ELASTIC_MODEL
protected double	epsilon1
protected double	epsilon2
protected double	epsilon3
protected double	epsilon4
static java.lang.String	FULL_MODEL
protected int	interval
protected org.concord.oslet.IO	io
protected double	kineticEnergy
protected java.util.Vector	listeners
protected double	mass1
protected double	mass2
protected double	mass3
protected double	mass4
protected org.concord.oslet.IO.MML	mml
static java.lang.String	MODEL_UPDATE
protected java.lang.String	modelType
protected java.lang.String	name
protected int	numberOfAtoms
protected org.concord.oslet.models.ObstacleCollection	obstacles
protected boolean	pause
protected boolean	paused
protected double	potentialEnergy
protected boolean	running
protected double	sigma1
protected double	sigma2
protected double	sigma3
protected double	sigma4
protected int	temperature
protected java.lang.Thread	thread

Constructor Summary

DefaultAtomicModel()

DefaultAtomicModel(int width, int height)

Method Summary

void	addAtom()
void	addAtomicDataListener(AtomicDataListener listener)
int	build()
int	build(org.concord.oslet.models.Atom[] atom)
protected void	callAtomicDataListeners()
protected boolean	checkPause()
void	clearAtoms()
void	defineElementA(double mass, double sigma, double epsilon)
void	defineElementB(double mass, double sigma, double epsilon)
void	defineElementC(double mass, double sigma, double epsilon)
void	defineElementD(double mass, double sigma, double epsilon)
void	elasticModel()
void	fullModel()
boolean	getAssignVelocities()
org.concord.oslet.models.Atom[]	getAtoms()
org.concord.oslet.models.Boundaries	getBoundaries()
java.lang.String	getBoundary()
java.lang.String	getBoundaryType()
int	getDelay()
double	getDelta()
org.concord.oslet.dynamics.Dynamics	getDynamics()
float	getHeight()
int	getInterval()
double	getKineticEnergy()
java.lang.String	getModelType()
java.lang.String	getName()
int	getNumberOfAtoms()
org.concord.oslet.models.ObstacleCollection	getObstacles()
boolean	getPause()
double	getPotentialEnergy()
boolean	getRunning()
int	getTemperature()
float	getWidth()
float	getX()
float	getY()
void	initialize()
void	removeAtomicDataListener(AtomicDataListener listener)
void	run()
void	setAssignVelocities(boolean value)
void	setBoundary(java.lang.String boundaryType)
void	setBoundaryType(java.lang.String boundaryType)
void	setDelay(int value)
void	setDelta(double value)
void	setHeight(float height)
void	setInterval(int interval)
void	setModelType(java.lang.String type)
void	setName(java.lang.String name)
void	setNumberOfAtoms(int n)
void	setObstacles(org.concord.oslet.models.ObstacleCollection o)
void	setPause(boolean value)
void	setRunning(boolean value)
void	setSize(int width, int height)
void	setTemperature(int value)
void	setTimeStep(double time)
void	setWidth(float width)
void	setX(float x)
void	setY(float y)
void	sleep()
boolean	waitForPause()
void	zeroAllCharges(org.concord.oslet.models.Atom[] atom)
void	zeroAllRestraints(org.concord.oslet.models.Atom[] atom)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

DEFAULT_TEMPERATURE

public static final int DEFAULT_TEMPERATURE

DEFAULT_INTERVAL

public static final int DEFAULT_INTERVAL

DEFAULT_DELAY

public static final int DEFAULT_DELAY

DEFAULT_WIDTH

public static final int DEFAULT_WIDTH

DEFAULT_HEIGHT

public static final int DEFAULT_HEIGHT

DEFAULT_DELTA

public static final double DEFAULT_DELTA

DEFAULT_DESCENT

public static final double DEFAULT_DESCENT

MODEL_UPDATE

public static final java.lang.String MODEL_UPDATE

FULL_MODEL

public static final java.lang.String FULL_MODEL

ELASTIC_MODEL

public static final java.lang.String ELASTIC_MODEL

name

protected java.lang.String name

mass1

protected double mass1

sigma1

protected double sigma1

epsilon1

protected double epsilon1

mass2

protected double mass2

sigma2

protected double sigma2

epsilon2

protected double epsilon2

mass3

protected double mass3

sigma3

protected double sigma3

epsilon3

protected double epsilon3

mass4

protected double mass4

sigma4

protected double sigma4

epsilon4

protected double epsilon4

temperature

protected int temperature

kineticEnergy

protected double kineticEnergy

potentialEnergy

protected double potentialEnergy

boundaryType

protected java.lang.String boundaryType

boundary

protected org.concord.oslet.models.Boundaries boundary

DEFAULT_CUTOFF

public static final int DEFAULT_CUTOFF

DEFAULT_SKIN

public static final int DEFAULT_SKIN

descent

protected double descent

numberOfAtoms

protected int numberOfAtoms

dynamics

protected org.concord.oslet.dynamics.Dynamics dynamics

atomicDataEvent

protected AtomicDataEvent atomicDataEvent

listeners

protected java.util.Vector listeners

thread

protected java.lang.Thread thread

running

protected boolean running

pause

protected boolean pause

paused

protected boolean paused

assign

protected boolean assign

delta

protected double delta

delay

protected int delay

interval

protected int interval

modelType

protected java.lang.String modelType

bound

protected org.concord.pseudojava2.awt.geom.Rectangle2D.Float bound

io

protected org.concord.oslet.IO io

mml

protected org.concord.oslet.IO.MML mml

obstacles

protected org.concord.oslet.models.ObstacleCollection obstacles

Constructor Detail

DefaultAtomicModel

public DefaultAtomicModel()

DefaultAtomicModel

public DefaultAtomicModel(int width,
                          int height)

Method Detail

setSize

public void setSize(int width,
                    int height)

getName

public java.lang.String getName()

Specified by:

getName in interface org.concord.oslet.models.AtomicModel

setName

public void setName(java.lang.String name)

Specified by:

setName in interface org.concord.oslet.models.AtomicModel

getX

public float getX()

Specified by:

getX in interface org.concord.oslet.models.AtomicModel

setX

public void setX(float x)

Specified by:

setX in interface org.concord.oslet.models.AtomicModel

getY

public float getY()

Specified by:

getY in interface org.concord.oslet.models.AtomicModel

setY

public void setY(float y)

Specified by:

setY in interface org.concord.oslet.models.AtomicModel

getWidth

public float getWidth()

Specified by:

getWidth in interface org.concord.oslet.models.AtomicModel

setWidth

public void setWidth(float width)

Specified by:

setWidth in interface org.concord.oslet.models.AtomicModel

getHeight

public float getHeight()

Specified by:

getHeight in interface org.concord.oslet.models.AtomicModel

setHeight

public void setHeight(float height)

Specified by:

setHeight in interface org.concord.oslet.models.AtomicModel

getInterval

public int getInterval()

setInterval

public void setInterval(int interval)

getDelay

public int getDelay()

setDelay

public void setDelay(int value)

getDelta

public double getDelta()

setDelta

public void setDelta(double value)

getModelType

public java.lang.String getModelType()

setModelType

public void setModelType(java.lang.String type)

defineElementA

public void defineElementA(double mass,
                           double sigma,
                           double epsilon)

Specified by:

defineElementA in interface org.concord.oslet.models.AtomicModel

defineElementB

public void defineElementB(double mass,
                           double sigma,
                           double epsilon)

Specified by:

defineElementB in interface org.concord.oslet.models.AtomicModel

defineElementC

public void defineElementC(double mass,
                           double sigma,
                           double epsilon)

Specified by:

defineElementC in interface org.concord.oslet.models.AtomicModel

defineElementD

public void defineElementD(double mass,
                           double sigma,
                           double epsilon)

Specified by:

defineElementD in interface org.concord.oslet.models.AtomicModel

zeroAllRestraints

public void zeroAllRestraints(org.concord.oslet.models.Atom[] atom)

Specified by:

zeroAllRestraints in interface org.concord.oslet.models.AtomicModel

zeroAllCharges

public void zeroAllCharges(org.concord.oslet.models.Atom[] atom)

Specified by:

zeroAllCharges in interface org.concord.oslet.models.AtomicModel

initialize

public void initialize()

getDynamics

public org.concord.oslet.dynamics.Dynamics getDynamics()

setBoundary

public void setBoundary(java.lang.String boundaryType)

Specified by:

setBoundary in interface org.concord.oslet.models.AtomicModel

setBoundaryType

public void setBoundaryType(java.lang.String boundaryType)

getBoundaryType

public java.lang.String getBoundaryType()

getBoundary

public java.lang.String getBoundary()

Specified by:

getBoundary in interface org.concord.oslet.models.AtomicModel

getBoundaries

public org.concord.oslet.models.Boundaries getBoundaries()

getNumberOfAtoms

public int getNumberOfAtoms()

setNumberOfAtoms

public void setNumberOfAtoms(int n)

build

public int build(org.concord.oslet.models.Atom[] atom)

Specified by:

build in interface org.concord.oslet.models.AtomicModel

build

public int build()

getAtoms

public org.concord.oslet.models.Atom[] getAtoms()

addAtom

public void addAtom()

clearAtoms

public void clearAtoms()

getTemperature

public int getTemperature()

setTemperature

public void setTemperature(int value)

setTimeStep

public void setTimeStep(double time)

getAssignVelocities

public boolean getAssignVelocities()

setAssignVelocities

public void setAssignVelocities(boolean value)

checkPause

protected boolean checkPause()

waitForPause

public boolean waitForPause()

setRunning

public void setRunning(boolean value)

getRunning

public boolean getRunning()

setPause

public void setPause(boolean value)

getPause

public boolean getPause()

getPotentialEnergy

public double getPotentialEnergy()

getKineticEnergy

public double getKineticEnergy()

sleep

public void sleep()

run

public void run()

Specified by:

run in interface java.lang.Runnable

fullModel

public void fullModel()

elasticModel

public void elasticModel()

addAtomicDataListener

public void addAtomicDataListener(AtomicDataListener listener)

removeAtomicDataListener

public void removeAtomicDataListener(AtomicDataListener listener)

callAtomicDataListeners

protected void callAtomicDataListeners()

getObstacles

public org.concord.oslet.models.ObstacleCollection getObstacles()

setObstacles

public void setObstacles(org.concord.oslet.models.ObstacleCollection o)