org.concord.molecular.engine
Class DefaultMolecularModel

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

All Implemented Interfaces:

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

public class DefaultMolecularModel

extends DefaultAtomicModel

implements org.concord.oslet.models.MolecularModel

Field Summary

protected org.concord.oslet.models.AngularBondCollection	bends
protected org.concord.oslet.models.RadialBondCollection	bonds
protected java.awt.Rectangle	boundBox
protected java.awt.Point	centerOfMass
protected org.concord.oslet.models.MoleculeCollection	molecules
protected int	numberOfAtomsPerMolecules
protected int	numberOfBends
protected int	numberOfBonds
protected int	numberOfMolecules
protected org.concord.oslet.models.ObstacleCollection	obstacles

Fields inherited from class org.concord.molecular.engine.DefaultAtomicModel

assign, atomicDataEvent, bound, boundary, boundaryType, DEFAULT_CUTOFF, DEFAULT_DELAY, DEFAULT_DELTA, DEFAULT_DESCENT, DEFAULT_HEIGHT, DEFAULT_INTERVAL, DEFAULT_SKIN, DEFAULT_TEMPERATURE, DEFAULT_WIDTH, delay, delta, descent, dynamics, ELASTIC_MODEL, epsilon1, epsilon2, epsilon3, epsilon4, FULL_MODEL, interval, io, kineticEnergy, listeners, mass1, mass2, mass3, mass4, mml, MODEL_UPDATE, modelType, name, numberOfAtoms, pause, paused, potentialEnergy, running, sigma1, sigma2, sigma3, sigma4, temperature, thread

Constructor Summary

DefaultMolecularModel()

DefaultMolecularModel(int width, int height)

Method Summary

java.awt.Rectangle	box(org.concord.oslet.models.Atom[] atom, int skin)
java.awt.Point	centerOfMass(org.concord.oslet.models.Atom[] atom)
org.concord.oslet.models.AngularBondCollection	getBends()
org.concord.oslet.models.RadialBondCollection	getBonds()
org.concord.oslet.models.MoleculeCollection	getMolecules()
int	getNumberOfAtomsPerMolecule()
int	getNumberOfBends()
int	getNumberOfBonds()
int	getNumberOfMolecules()
org.concord.oslet.models.ObstacleCollection	getObstacles()
void	moveTo(int x, int y, org.concord.oslet.models.Atom[] atom)
void	setNumberOfBends(int n)
void	setNumberOfBonds(int n)
void	setNumberOfMolecules(int n)
void	setObstacles(org.concord.oslet.models.ObstacleCollection o)

Methods inherited from class org.concord.molecular.engine.DefaultAtomicModel

addAtom, addAtomicDataListener, build, build, callAtomicDataListeners, checkPause, clearAtoms, defineElementA, defineElementB, defineElementC, defineElementD, elasticModel, fullModel, getAssignVelocities, getAtoms, getBoundaries, getBoundary, getBoundaryType, getDelay, getDelta, getDynamics, getHeight, getInterval, getKineticEnergy, getModelType, getName, getNumberOfAtoms, getPause, getPotentialEnergy, getRunning, getTemperature, getWidth, getX, getY, initialize, removeAtomicDataListener, run, setAssignVelocities, setBoundary, setBoundaryType, setDelay, setDelta, setHeight, setInterval, setModelType, setName, setNumberOfAtoms, setPause, setRunning, setSize, setTemperature, setTimeStep, setWidth, setX, setY, sleep, waitForPause, zeroAllCharges, zeroAllRestraints

Methods inherited from class java.lang.Object

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

Methods inherited from interface org.concord.oslet.models.MolecularModel

build, getNumberOfAtoms, setNumberOfAtoms

Methods inherited from interface org.concord.oslet.models.AtomicModel

defineElementA, defineElementB, defineElementC, defineElementD, getBoundary, getHeight, getName, getWidth, getX, getY, setBoundary, setHeight, setName, setWidth, setX, setY, zeroAllCharges, zeroAllRestraints

Field Detail

numberOfBonds

protected int numberOfBonds

numberOfBends

protected int numberOfBends

numberOfMolecules

protected int numberOfMolecules

numberOfAtomsPerMolecules

protected int numberOfAtomsPerMolecules

bonds

protected org.concord.oslet.models.RadialBondCollection bonds

bends

protected org.concord.oslet.models.AngularBondCollection bends

molecules

protected org.concord.oslet.models.MoleculeCollection molecules

obstacles

protected org.concord.oslet.models.ObstacleCollection obstacles

centerOfMass

protected java.awt.Point centerOfMass

boundBox

protected java.awt.Rectangle boundBox

Constructor Detail

DefaultMolecularModel

public DefaultMolecularModel()

DefaultMolecularModel

public DefaultMolecularModel(int width,
                             int height)

Method Detail

getBonds

public org.concord.oslet.models.RadialBondCollection getBonds()

Specified by:

getBonds in interface org.concord.oslet.models.MolecularModel

getBends

public org.concord.oslet.models.AngularBondCollection getBends()

Specified by:

getBends in interface org.concord.oslet.models.MolecularModel

getMolecules

public org.concord.oslet.models.MoleculeCollection getMolecules()

getObstacles

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

Overrides:

getObstacles in class DefaultAtomicModel

setObstacles

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

Overrides:

setObstacles in class DefaultAtomicModel

getNumberOfBonds

public int getNumberOfBonds()

Specified by:

getNumberOfBonds in interface org.concord.oslet.models.MolecularModel

getNumberOfBends

public int getNumberOfBends()

Specified by:

getNumberOfBends in interface org.concord.oslet.models.MolecularModel

setNumberOfBonds

public void setNumberOfBonds(int n)

Specified by:

setNumberOfBonds in interface org.concord.oslet.models.MolecularModel

setNumberOfBends

public void setNumberOfBends(int n)

Specified by:

setNumberOfBends in interface org.concord.oslet.models.MolecularModel

getNumberOfAtomsPerMolecule

public int getNumberOfAtomsPerMolecule()

Specified by:

getNumberOfAtomsPerMolecule in interface org.concord.oslet.models.MolecularModel

getNumberOfMolecules

public int getNumberOfMolecules()

Specified by:

getNumberOfMolecules in interface org.concord.oslet.models.MolecularModel

setNumberOfMolecules

public void setNumberOfMolecules(int n)

Specified by:

setNumberOfMolecules in interface org.concord.oslet.models.MolecularModel

centerOfMass

public java.awt.Point centerOfMass(org.concord.oslet.models.Atom[] atom)

Specified by:

centerOfMass in interface org.concord.oslet.models.MolecularModel

box

public java.awt.Rectangle box(org.concord.oslet.models.Atom[] atom,
                              int skin)

Specified by:

box in interface org.concord.oslet.models.MolecularModel

moveTo

public void moveTo(int x,
                   int y,
                   org.concord.oslet.models.Atom[] atom)

Specified by:

moveTo in interface org.concord.oslet.models.MolecularModel