Class SubunitGraphic

java.lang.Object
  javax.media.j3d.SceneGraphObject
      javax.media.j3d.Node
          javax.media.j3d.Group
              javax.media.j3d.BranchGroup
                  SubunitGraphic

public class SubunitGraphic

extends javax.media.j3d.BranchGroup

extends branchGroup to make a complete Subunit graphic using BindingSiteGraphic components: SubunitGraphic / | Lights TRansformGroup | protein / \ ... sphere TransformGroup ... | ... cone ...

Field Summary

Fields inherited from class javax.media.j3d.BranchGroup

ALLOW_DETACH

Fields inherited from class javax.media.j3d.Group

ALLOW_CHILDREN_EXTEND, ALLOW_CHILDREN_READ, ALLOW_CHILDREN_WRITE, ALLOW_COLLISION_BOUNDS_READ, ALLOW_COLLISION_BOUNDS_WRITE

Fields inherited from class javax.media.j3d.Node

ALLOW_AUTO_COMPUTE_BOUNDS_READ, ALLOW_AUTO_COMPUTE_BOUNDS_WRITE, ALLOW_BOUNDS_READ, ALLOW_BOUNDS_WRITE, ALLOW_COLLIDABLE_READ, ALLOW_COLLIDABLE_WRITE, ALLOW_LOCAL_TO_VWORLD_READ, ALLOW_PICKABLE_READ, ALLOW_PICKABLE_WRITE, ENABLE_COLLISION_REPORTING, ENABLE_PICK_REPORTING

Constructor Summary

SubunitGraphic()
Constructs a SubunitGraphic with a default BranchGroup leading to the main TransformGroup and a sphere for the basic Subunit

SubunitGraphic(Subunit sub)
Constructs a SubunitGraphic based on sub.

Method Summary

javax.media.j3d.BranchGroup	branchGroup() Return SubunitGraphic as a BranchGroup
void	changeConformation(Conformation oldConf, Conformation newConf)
javax.vecmath.Vector3d	getBindingSitePos(BindingSite bs) Returns the position of the BindingSite bs in relation to the Assembly
javax.vecmath.Quat4d	getBindingSiteRot(BindingSite bs) Returns the actual rotation of the binding site bs in relation to the Assembly
javax.vecmath.Vector3d	getPos()
javax.vecmath.Quat4d	getRot()
javax.media.j3d.Transform3D	getTransform() Gets the Transform3D of this SubunitGraphic
void	realRotate(javax.vecmath.Quat4d rot)
void	rotate(javax.vecmath.Quat4d q) Rotates this SubunitGraphic by q
void	translate(javax.vecmath.Vector3d v) Translates this SubunitGraphic by v
void	updateLocation(javax.vecmath.Quat4d rot, javax.vecmath.Vector3d pos) Sets the location of this SubunitGraphic to specified rotation and position
void	updateLocation(javax.media.j3d.Transform3D t) Sets location of this SubunitGraphic to Transform3D t

Methods inherited from class javax.media.j3d.BranchGroup

cloneNode, compile, detach, pickAll, pickAllSorted, pickAny, pickClosest

Methods inherited from class javax.media.j3d.Group

addChild, getAllChildren, getAlternateCollisionTarget, getChild, getCollisionBounds, indexOfChild, insertChild, moveTo, numChildren, removeAllChildren, removeChild, removeChild, setAlternateCollisionTarget, setChild, setCollisionBounds

Methods inherited from class javax.media.j3d.Node

cloneTree, cloneTree, cloneTree, cloneTree, cloneTree, cloneTree, duplicateNode, getBounds, getBoundsAutoCompute, getCollidable, getLocalToVworld, getLocalToVworld, getParent, getPickable, setBounds, setBoundsAutoCompute, setCollidable, setPickable

Methods inherited from class javax.media.j3d.SceneGraphObject

clearCapability, clearCapabilityIsFrequent, duplicateSceneGraphObject, getCapability, getCapabilityIsFrequent, getUserData, isCompiled, isLive, setCapability, setCapabilityIsFrequent, setUserData, updateNodeReferences

Methods inherited from class java.lang.Object

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

Constructor Detail

SubunitGraphic

public SubunitGraphic()

Constructs a SubunitGraphic with a default BranchGroup leading to the main TransformGroup and a sphere for the basic Subunit

SubunitGraphic

public SubunitGraphic(Subunit sub)

Constructs a SubunitGraphic based on sub. the main TransformGroup is parent to the Subunit sphere and graphics for all the BindingSites found in sub.

Parameters:

sub - Subunit

Method Detail

updateLocation

public void updateLocation(javax.vecmath.Quat4d rot,
                           javax.vecmath.Vector3d pos)

Sets the location of this SubunitGraphic to specified rotation and position

Parameters:

rot - Quat4d

pos - Vector3d

changeConformation

public void changeConformation(Conformation oldConf,
                               Conformation newConf)

updateLocation

public void updateLocation(javax.media.j3d.Transform3D t)

Sets location of this SubunitGraphic to Transform3D t

Parameters:

t -

realRotate

public void realRotate(javax.vecmath.Quat4d rot)

rotate

public void rotate(javax.vecmath.Quat4d q)

Rotates this SubunitGraphic by q

Parameters:

q - Quat4d

getRot

public javax.vecmath.Quat4d getRot()

getPos

public javax.vecmath.Vector3d getPos()

translate

public void translate(javax.vecmath.Vector3d v)

Translates this SubunitGraphic by v

Parameters:

v - Vector3d

branchGroup

public javax.media.j3d.BranchGroup branchGroup()

Return SubunitGraphic as a BranchGroup

Returns:

BranchGroup

getTransform

public javax.media.j3d.Transform3D getTransform()

Gets the Transform3D of this SubunitGraphic

Returns:

Transform3D

getBindingSitePos

public javax.vecmath.Vector3d getBindingSitePos(BindingSite bs)

Returns the position of the BindingSite bs in relation to the Assembly

Parameters:

bs - BindingSite

Returns:

Vector3d

getBindingSiteRot

public javax.vecmath.Quat4d getBindingSiteRot(BindingSite bs)

Returns the actual rotation of the binding site bs in relation to the Assembly

Parameters:

bs -

Returns:

Quat4d