Class Assembly

java.lang.Object
  Assembly

public class Assembly

extends java.lang.Object

Assembly holds an Assembly of Subunits and the AssemblyGraphic. It also tracks the next Event for this Assembly and its validity. Assemblies can be bonded, split, or relaxed.

Constructor Summary

Assembly()
Constructs an default Assembly with no Subunits and no valid Events

Assembly(java.util.Vector s, java.lang.String name)
Constructs an Assembly named name with Subunits from s

Method Summary

Assembly	bindAssemblies(Assembly bindasm, FormBondEvent e, Subunit bsSub1, Subunit bsSub2) Carries out the FormBondEvent e by binding bindasm to this through a bond between bsSub1 in this Assembly and bsSub2 in bindasm.Both Assembly(s) should be different.
void	compoundTransforms() Composes Assembly and Subunit transforms so that the Subunits hold all the significant location information and the Assembly location information is all the identity function
boolean	containsSubunit(Subunit s) Returns true if s is in this Assembly
boolean	equals(Assembly a) Returns this true if this Assembly is the same object as Assembly a
void	fastBind(FormBondEvent e) bind an broken bond which breaks a loop in an assembly
AssemblyGraphic	getAssemblyGraphic() Returns this Assembly's AssemblyGraphic
javax.vecmath.Vector3d	getBindingSitePos(Subunit sub, BindingSite bs) Returns the position of the binding site relative to the real axis system
javax.vecmath.Quat4d	getBindingSiteRot(Subunit sub, BindingSite bs) Returns the rotation of the binding site relative to the real axis system
javax.vecmath.Vector3d	getBindingSiteTipPos(Subunit sub, BindingSite bs)
int[]	getBSCounts() get the amounts of different types of free BindingSite(s) in an assembly
java.util.Vector	getFreebss() Gets all the free BindingSite(s) in an assembly, and put them in an vector
java.lang.String	getName() Returns this Assembly's name
javax.vecmath.Vector3d	getPos() Returns this Assembly's position
javax.vecmath.Quat4d	getRot() Returns this Assembly's rotation
Subunit	getSubunit(BindingSite bs) Returns the Subunit in this Assembly that holds bs, if that's not found returns a new blank Subunit
java.util.Vector	getSubunits() Returns a Vector of this Assembly's Subunits
javax.media.j3d.Transform3D	getTransform() Returns this Assembly's transform
Event	nextEvent() Returns this Assembly's next Event
double	nextEventEndTime() Returns this Assembly's next Event's end time
int	numSubunits() public boolean containsSubunit(Subunit s) { return mysubs.contains(s); } /** Returns number of subunits in this Assembly
void	rotate(javax.vecmath.Quat4d rot)
void	setNextEvent(Event ev) Sets the next event for this Assembly to ev
void	setPos(javax.vecmath.Vector3d v) Sets this Assembly's position to v
void	setValidTime(double time) Sets the valid time for this Assembly to time
Assembly	splitAssembly(BreakBondEvent e, int newasmnum) Used to split this Assembly when indicated by a BreakBondEvent.
java.lang.String	toString() Returns a String version of this Assembly
void	updateLocation(javax.vecmath.Quat4d q, javax.vecmath.Vector3d v) Sets this Assembly's position to v and rotation to q
void	updateLocation(javax.media.j3d.Transform3D tr) Sets this Assembly's transform to tr
double	validTime() Returns this Assembly's valid time

Methods inherited from class java.lang.Object

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

Constructor Detail

Assembly

public Assembly()

Constructs an default Assembly with no Subunits and no valid Events

Assembly

public Assembly(java.util.Vector s,
                java.lang.String name)

Constructs an Assembly named name with Subunits from s

Parameters:

s - Vector, all the Subunits to be in this Assembly

name - String, the name of this Assembly

Method Detail

getFreebss

public java.util.Vector getFreebss()

Gets all the free BindingSite(s) in an assembly, and put them in an vector

Returns:

Vector

getSubunit

public Subunit getSubunit(BindingSite bs)

Returns the Subunit in this Assembly that holds bs, if that's not found returns a new blank Subunit

Parameters:

bs - BindingSite

Returns:

Subunit

fastBind

public void fastBind(FormBondEvent e)

bind an broken bond which breaks a loop in an assembly

Parameters:

e - void

getBSCounts

public int[] getBSCounts()

get the amounts of different types of free BindingSite(s) in an assembly

Returns:

int[]

splitAssembly

public Assembly splitAssembly(BreakBondEvent e,
                              int newasmnum)

Used to split this Assembly when indicated by a BreakBondEvent. Returns the newly split off Assembly, or null if the split didn't make a new Assembly (rather, it broke a loop)

Parameters:

e - BreakBondEvent, the event that causes the split

newasmnum - int, the number of the Assembly to be split off

Returns:

Assembly

bindAssemblies

public Assembly bindAssemblies(Assembly bindasm,
                               FormBondEvent e,
                               Subunit bsSub1,
                               Subunit bsSub2)

Carries out the FormBondEvent e by binding bindasm to this through a bond between bsSub1 in this Assembly and bsSub2 in bindasm.Both Assembly(s) should be different. If the binding can not occur (because of steric hindrance), returns a modified version of bindasm, otherwise returns null.

Parameters:

bindasm - Assembly, assembly to be bound

e - FormBondEvent, the event that causes the binding

bsSub1 - Subunit, the Subunit on this Assembly that holds the BindingSite which forms the bond

bsSub2 - Subunit, the Subunit on bindasm that holds the BindingSite which forms the bond

Returns:

Assembly

compoundTransforms

public void compoundTransforms()

Composes Assembly and Subunit transforms so that the Subunits hold all the significant location information and the Assembly location information is all the identity function

rotate

public void rotate(javax.vecmath.Quat4d rot)

getBindingSitePos

public javax.vecmath.Vector3d getBindingSitePos(Subunit sub,
                                                BindingSite bs)

Returns the position of the binding site relative to the real axis system

Parameters:

sub - Subunit, holds bs

bs - BindingSite

Returns:

Vector3d

getBindingSiteTipPos

public javax.vecmath.Vector3d getBindingSiteTipPos(Subunit sub,
                                                   BindingSite bs)

getBindingSiteRot

public javax.vecmath.Quat4d getBindingSiteRot(Subunit sub,
                                              BindingSite bs)

Returns the rotation of the binding site relative to the real axis system

Parameters:

sub - Subunit, holds bs

bs - BindingSite

Returns:

Quat4d

getAssemblyGraphic

public AssemblyGraphic getAssemblyGraphic()

Returns this Assembly's AssemblyGraphic

Returns:

AssemblyGraphic

getTransform

public javax.media.j3d.Transform3D getTransform()

Returns this Assembly's transform

Returns:

Transform3D

getRot

public javax.vecmath.Quat4d getRot()

Returns this Assembly's rotation

Returns:

Quat4d

getPos

public javax.vecmath.Vector3d getPos()

Returns this Assembly's position

Returns:

Vector3d

getName

public java.lang.String getName()

Returns this Assembly's name

Returns:

String

getSubunits

public java.util.Vector getSubunits()

Returns a Vector of this Assembly's Subunits

Returns:

Vector

setPos

public void setPos(javax.vecmath.Vector3d v)

Sets this Assembly's position to v

Parameters:

v - Vector3d

updateLocation

public void updateLocation(javax.vecmath.Quat4d q,
                           javax.vecmath.Vector3d v)

Sets this Assembly's position to v and rotation to q

Parameters:

q - Quat4d

v - Vector3d

updateLocation

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

Sets this Assembly's transform to tr

Parameters:

tr - Transform3D

containsSubunit

public boolean containsSubunit(Subunit s)

Returns true if s is in this Assembly

Parameters:

s - Subunit

Returns:

boolean

numSubunits

public int numSubunits()

public boolean containsSubunit(Subunit s) { return mysubs.contains(s); } /** Returns number of subunits in this Assembly

Returns:

int

setNextEvent

public void setNextEvent(Event ev)

Sets the next event for this Assembly to ev

Parameters:

ev - Event

nextEvent

public Event nextEvent()

Returns this Assembly's next Event

Returns:

Event

nextEventEndTime

public double nextEventEndTime()

Returns this Assembly's next Event's end time

Returns:

double

setValidTime

public void setValidTime(double time)

Sets the valid time for this Assembly to time

Parameters:

time - double

validTime

public double validTime()

Returns this Assembly's valid time

Returns:

double

equals

public boolean equals(Assembly a)

Returns this true if this Assembly is the same object as Assembly a

Parameters:

a - Assembly

Returns:

boolean

toString

public java.lang.String toString()

Returns a String version of this Assembly

Returns:

String