uk.ac.ed.simulator_pdb
Class SimulationJava3DController

java.lang.Object
  uk.ac.ed.simulator_pdb.Java3DController
      uk.ac.ed.simulator_pdb.SimulationJava3DController

public class SimulationJava3DController

extends Java3DController

Nested Class Summary

protected class	SimulationJava3DController.BondPositions
protected class	SimulationJava3DController.ParticlePositions

Field Summary

static double	MAX_BOND_DIST
static double	MAX_COLLISION_DIST
static double	PROBABILITY_OF_BOND_UPDATE

Fields inherited from class uk.ac.ed.simulator_pdb.Java3DController

model, view

Constructor Summary

SimulationJava3DController(Model model, Java3DView view)

Method Summary

protected void	alignForBonding(javax.vecmath.Matrix4d bond1_to_world_transform, javax.vecmath.Matrix4d bond2_to_world_transform, double ratio)
protected boolean	alignForBonding(SimBond bond1, SimBond bond2)
protected void	checkForBondUpdates(SimBond bond)
protected boolean	collide(SimCluster cluster, javax.vecmath.Matrix4d new_transformation_matrix)
protected boolean	collide(SimCluster cluster1, javax.vecmath.Matrix4d new_cluster1_transformation, SimCluster cluster2, javax.vecmath.Matrix4d new_cluster2_transformation)
protected boolean	constrain(SimCluster cluster, javax.vecmath.Matrix4d new_transformation_matrix)
protected double	getClusterEnergy(SimCluster cluster, javax.vecmath.Matrix4d transformation_matrix)
protected void	initModelEventHandler()
protected boolean	isAlignedForBonding(javax.vecmath.Matrix4d bond1_to_world_transform, javax.vecmath.Matrix4d bond2_to_world_transform)
protected boolean	isAlignedForBonding(SimBond bond1, SimBond bond2)
protected boolean	isOrientatedForBonding(javax.vecmath.Matrix4d bond1_to_world_transform, javax.vecmath.Matrix4d bond2_to_world_transform)
protected boolean	isPositionedForBonding(javax.vecmath.Matrix4d bond1_to_world_transform, javax.vecmath.Matrix4d bond2_to_world_transform)
protected boolean	moveCluster(SimCluster cluster)
protected void	orientateForBonding(javax.vecmath.Matrix4d bond1_to_world_transform, javax.vecmath.Matrix4d bond2_to_world_transform, double ratio)
protected void	positionForBonding(javax.vecmath.Matrix4d bond1_to_world_transform, javax.vecmath.Matrix4d bond2_to_world_transform, double ratio)
protected void	testBondChanges(SimBond bond, java.util.ArrayList nearby_bonds, java.util.ArrayList possible_new_bonds)
void	update()
protected void	updateBonds(SimBond bond, java.util.ArrayList possible_new_bonds)

Methods inherited from class java.lang.Object

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

Field Detail

MAX_COLLISION_DIST

public static final double MAX_COLLISION_DIST

See Also:

Constant Field Values

MAX_BOND_DIST

public static final double MAX_BOND_DIST

See Also:

Constant Field Values

PROBABILITY_OF_BOND_UPDATE

public static final double PROBABILITY_OF_BOND_UPDATE

See Also:

Constant Field Values

Constructor Detail

SimulationJava3DController

public SimulationJava3DController(Model model,
                                  Java3DView view)

Method Detail

update

public void update()

initModelEventHandler

protected void initModelEventHandler()

moveCluster

protected boolean moveCluster(SimCluster cluster)

constrain

protected boolean constrain(SimCluster cluster,
                            javax.vecmath.Matrix4d new_transformation_matrix)

getClusterEnergy

protected double getClusterEnergy(SimCluster cluster,
                                  javax.vecmath.Matrix4d transformation_matrix)

collide

protected boolean collide(SimCluster cluster,
                          javax.vecmath.Matrix4d new_transformation_matrix)

collide

protected boolean collide(SimCluster cluster1,
                          javax.vecmath.Matrix4d new_cluster1_transformation,
                          SimCluster cluster2,
                          javax.vecmath.Matrix4d new_cluster2_transformation)

checkForBondUpdates

protected void checkForBondUpdates(SimBond bond)

testBondChanges

protected void testBondChanges(SimBond bond,
                               java.util.ArrayList nearby_bonds,
                               java.util.ArrayList possible_new_bonds)

updateBonds

protected void updateBonds(SimBond bond,
                           java.util.ArrayList possible_new_bonds)

orientateForBonding

protected void orientateForBonding(javax.vecmath.Matrix4d bond1_to_world_transform,
                                   javax.vecmath.Matrix4d bond2_to_world_transform,
                                   double ratio)

positionForBonding

protected void positionForBonding(javax.vecmath.Matrix4d bond1_to_world_transform,
                                  javax.vecmath.Matrix4d bond2_to_world_transform,
                                  double ratio)

alignForBonding

protected void alignForBonding(javax.vecmath.Matrix4d bond1_to_world_transform,
                               javax.vecmath.Matrix4d bond2_to_world_transform,
                               double ratio)

alignForBonding

protected boolean alignForBonding(SimBond bond1,
                                  SimBond bond2)

isOrientatedForBonding

protected boolean isOrientatedForBonding(javax.vecmath.Matrix4d bond1_to_world_transform,
                                         javax.vecmath.Matrix4d bond2_to_world_transform)

isPositionedForBonding

protected boolean isPositionedForBonding(javax.vecmath.Matrix4d bond1_to_world_transform,
                                         javax.vecmath.Matrix4d bond2_to_world_transform)

isAlignedForBonding

protected boolean isAlignedForBonding(javax.vecmath.Matrix4d bond1_to_world_transform,
                                      javax.vecmath.Matrix4d bond2_to_world_transform)

isAlignedForBonding

protected boolean isAlignedForBonding(SimBond bond1,
                                      SimBond bond2)