Class Subunit

java.lang.Object
  Subunit

public class Subunit

extends java.lang.Object

Subunit holds information about a specific Subunit including its SubunitType, current Conformations, ID, Solution, location/velocity mass, radius, bound Subunits, and graphic.

Field Summary

javax.vecmath.Vector3d	mypos
javax.vecmath.Quat4d	myrot

Constructor Summary

Subunit()
Constructs a Subunit with default SubunitType, and other default parameters

Subunit(SubunitType st, java.util.Vector doms, Solution soln, int id, javax.vecmath.Vector3d p, javax.vecmath.Quat4d r, javax.vecmath.Vector3d v, javax.vecmath.Quat4d rv)
Constructs a Subunit with the specified SubunitType, current Conformations, Solution, ID, position, rotation, velocity, angular velocity, mass, and radius.

Method Summary

void	addPartner(Subunit s) Add Subunit s to this Subunit's list of bound partner Subunits
boolean	changeConf(int dmid, Conformation newConf) Changes the Conformation of Domain number domain to newconf.
void	detachGraphic() Detaches this Subunit's graphic from its parent Assembly graphic
boolean	equals(Subunit s) Returns true if this Subunit is Subunit s
javax.vecmath.Vector3d	getBindingSitePos(BindingSite bs) Returns the position of bs in relation to the parent Assembly
javax.vecmath.Quat4d	getBindingSiteRot(BindingSite bs) Returns the rotation of bs in relation to the parent Assembly
java.util.Vector	getBindSiteOrs() Returns a Vector of the rotations of this Subunit's current BindingSites
java.util.Vector	getBindSitePoses() Returns a Vector of the positions of this Subunit's current BindingSites
java.util.Vector	getBindSites() Returns a Vector of the Subunit's current BindingSites and resets the BindingSites' Domain ID's
java.util.Vector	getBoundSubunits() Returns a Vector of Subunits bound to this Subunit
javax.vecmath.Vector3d	getBSPos(BindingSite bs) Returns the position of bs in relation to this Subunit
javax.vecmath.Quat4d	getBSRot(BindingSite bs) Returns the rotation of bs in relation to this Subunit
javax.media.j3d.Transform3D	getBStoSubTransform(BindingSite bs) Returns the transform of bs in relation to this Subunit
javax.vecmath.Vector3d	getBSUptoSub(BindingSite bs) Returns the up vector of bs in relation to this Subunit
java.util.Vector	getConfs() Returns a Vector of current Conformations (one for each Domain)
java.util.Vector	getConnectingBSs(Subunit s) Returns a Vector of all the BindingSites that bind this Subunit to s.
java.util.Vector	getDomains()
int	getid() Returns this Subunit's ID
double	getMass() Returns this Subunit's mass
javax.vecmath.Vector3d	getPos() Returns this Subunit's position in relation to its Assembly
double	getRadius() Returns this Subunit's radius
javax.vecmath.Quat4d	getRot() Returns this Subunit's rotation in relation to its Assembly
javax.vecmath.Quat4d	getRotV() Returns this Subunit's rotational velocity in relation to its Assembly
Solution	getSoln() Returns this Subunit's Solution
SubunitType	getST() Returns this Subunit's SubunitType
SubunitGraphic	getSubunitGraphic() Returns this Subunit's SubunitGraphic
javax.media.j3d.Transform3D	getTransform()
javax.vecmath.Vector3d	getV() Returns this Subunit's velocity in relation to its Assembly
boolean	isBoundSubunit(Subunit s) Returns true if this Subunit is bound to s, false otherwise
boolean	isUnbound() Returns true if this Subunit is not bound to any other Subunit, false otherwise
boolean	removePartner(Subunit s) Removes the specified Subunit from the vector of bound partner Subunits.
void	setid(int i) Sets this Subunit's ID to i
void	setTrans(javax.media.j3d.Transform3D t) Sets this Subunit's transformation in relation to its Assembly to t
java.lang.String	toString() Returns a String version of this Subunit

Methods inherited from class java.lang.Object

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

Field Detail

mypos

public javax.vecmath.Vector3d mypos

myrot

public javax.vecmath.Quat4d myrot

Constructor Detail

Subunit

public Subunit()

Constructs a Subunit with default SubunitType, and other default parameters

Subunit

public Subunit(SubunitType st,
               java.util.Vector doms,
               Solution soln,
               int id,
               javax.vecmath.Vector3d p,
               javax.vecmath.Quat4d r,
               javax.vecmath.Vector3d v,
               javax.vecmath.Quat4d rv)

Constructs a Subunit with the specified SubunitType, current Conformations, Solution, ID, position, rotation, velocity, angular velocity, mass, and radius. A graphic is construced according to the parameters given

Parameters:

st - SubunitType

doms - Vector of Domains in this Subunit

soln - Solution this Simulation takes place in

id - int, this Subunit's ID

p - Vector3d, this Subunit's position relative to its Assembly

r - Quat4d, this Subunit's rotation relative to its Assembly

v - Vector3d, this Subunit's velocity relative to its Assembly

rv - Quat4d, this Subunit's rotational velocity relative to its Assembly

Method Detail

changeConf

public boolean changeConf(int dmid,
                          Conformation newConf)

Changes the Conformation of Domain number domain to newconf. If the conformation change failed, returns false, returns true otherwise.

Parameters:

dmid - int, ID of the Domain in question

Returns:

boolean

getBSPos

public javax.vecmath.Vector3d getBSPos(BindingSite bs)

Returns the position of bs in relation to this Subunit

Parameters:

bs - BindingSite off of this Subunit

Returns:

Vector3d

getBSRot

public javax.vecmath.Quat4d getBSRot(BindingSite bs)

Returns the rotation of bs in relation to this Subunit

Parameters:

bs - BindingSite off of this Subunit

Returns:

Quat4d

detachGraphic

public void detachGraphic()

Detaches this Subunit's graphic from its parent Assembly graphic

getSubunitGraphic

public SubunitGraphic getSubunitGraphic()

Returns this Subunit's SubunitGraphic

Returns:

SubunitGraphic

getPos

public javax.vecmath.Vector3d getPos()

Returns this Subunit's position in relation to its Assembly

Returns:

Vector3d

getRot

public javax.vecmath.Quat4d getRot()

Returns this Subunit's rotation in relation to its Assembly

Returns:

Quat4d

getRotV

public javax.vecmath.Quat4d getRotV()

Returns this Subunit's rotational velocity in relation to its Assembly

Returns:

Quat4d

getV

public javax.vecmath.Vector3d getV()

Returns this Subunit's velocity in relation to its Assembly

Returns:

Vector3d

getRadius

public double getRadius()

Returns this Subunit's radius

Returns:

double

getMass

public double getMass()

Returns this Subunit's mass

Returns:

double

getSoln

public Solution getSoln()

Returns this Subunit's Solution

Returns:

Solution

getST

public SubunitType getST()

Returns this Subunit's SubunitType

Returns:

SubunitType

getBoundSubunits

public java.util.Vector getBoundSubunits()

Returns a Vector of Subunits bound to this Subunit

Returns:

Vector of Subunits

setTrans

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

Sets this Subunit's transformation in relation to its Assembly to t

Parameters:

t - Transform3D

isBoundSubunit

public boolean isBoundSubunit(Subunit s)

Returns true if this Subunit is bound to s, false otherwise

Parameters:

s - Subunit

Returns:

boolean

getConnectingBSs

public java.util.Vector getConnectingBSs(Subunit s)

Returns a Vector of all the BindingSites that bind this Subunit to s. The Vector is arranged as: [this Subunit's bs, s's bound bs, this Subunit's bs2, s's bound bs2, ...]

Parameters:

s - Subunit

Returns:

Vector

isUnbound

public boolean isUnbound()

Returns true if this Subunit is not bound to any other Subunit, false otherwise

Returns:

boolean

addPartner

public void addPartner(Subunit s)

Add Subunit s to this Subunit's list of bound partner Subunits

Parameters:

s - Subunit to add

removePartner

public boolean removePartner(Subunit s)

Removes the specified Subunit from the vector of bound partner Subunits. Returns true if the removal was sucessful, false otherwise

Parameters:

s - Subunit to be removed

Returns:

boolean

getid

public int getid()

Returns this Subunit's ID

Returns:

int

setid

public void setid(int i)

Sets this Subunit's ID to i

Parameters:

i - int

equals

public boolean equals(Subunit s)

Returns true if this Subunit is Subunit s

Parameters:

s - Subunit

Returns:

boolean

getConfs

public java.util.Vector getConfs()

Returns a Vector of current Conformations (one for each Domain)

Returns:

Vector

getDomains

public java.util.Vector getDomains()

getBindSites

public java.util.Vector getBindSites()

Returns a Vector of the Subunit's current BindingSites and resets the BindingSites' Domain ID's

Returns:

Vector

getBindSitePoses

public java.util.Vector getBindSitePoses()

Returns a Vector of the positions of this Subunit's current BindingSites

Returns:

Vector

getBindSiteOrs

public java.util.Vector getBindSiteOrs()

Returns a Vector of the rotations of this Subunit's current BindingSites

Returns:

Vector

getBStoSubTransform

public javax.media.j3d.Transform3D getBStoSubTransform(BindingSite bs)

Returns the transform of bs in relation to this Subunit

Parameters:

bs - BindingSite

Returns:

Transform3D

getBSUptoSub

public javax.vecmath.Vector3d getBSUptoSub(BindingSite bs)

Returns the up vector of bs in relation to this Subunit

Parameters:

bs - BindingSite

Returns:

Vector3d

getTransform

public javax.media.j3d.Transform3D getTransform()

getBindingSitePos

public javax.vecmath.Vector3d getBindingSitePos(BindingSite bs)

Returns the position of bs in relation to the parent Assembly

Parameters:

bs - BindingSite

Returns:

Vector3d

getBindingSiteRot

public javax.vecmath.Quat4d getBindingSiteRot(BindingSite bs)

Returns the rotation of bs in relation to the parent Assembly

Parameters:

bs - BindingSite

Returns:

Quat4d

toString

public java.lang.String toString()

Returns a String version of this Subunit

Returns:

String