ffe.lang
Class Atom

java.lang.Object
  javax.swing.tree.DefaultMutableTreeNode
      ffe.lang.FNode
          ffe.lang.Atom

All Implemented Interfaces:

java.lang.Cloneable, javax.swing.tree.MutableTreeNode, java.io.Serializable, javax.swing.tree.TreeNode

public final class Atom

extends FNode

The Atom class represents a single atom.

See Also:

Serialized Form

Nested Class Summary

Nested classes inherited from class javax.swing.tree.DefaultMutableTreeNode

Field Summary

static java.util.ArrayList	atompool
static java.util.Hashtable	hybridTable
int	xyzindex

Fields inherited from class ffe.lang.FNode

selected

Fields inherited from class javax.swing.tree.DefaultMutableTreeNode

allowsChildren, children, EMPTY_ENUMERATION, parent, userObject

Constructor Summary

Atom(int xyznum, java.lang.String id, MMAtom mmdata, double[] d)
Constructor used when parsing XYZ files

Atom(int xyznum, java.lang.String id, MMAtom mmdata, double[] d, java.lang.String r, int n, java.lang.String c)

Atom(java.lang.String s)
Constructor

Atom(java.lang.String id, MMAtom mmdata, double[] d)

Method Summary

void	addTrajectoryCoords(javax.vecmath.Vector3d coords, int position)
void	destroy()
void	drawLabel(Graphics3D graphics, javax.media.j3d.J3DGraphics2D g2d, javax.media.j3d.Node node, boolean labelAtoms, boolean labelResidues)
boolean	equals(java.lang.Object object) Overidden equals method
void	getAcceleration(double[] t)
java.util.ArrayList	getAngles()
javax.media.j3d.Appearance	getAppearance()
int	getAtomicNum() Gets the Atomic Number
java.util.List	getAtomList() Returns an ArrayList of all Atoms below the present FNode.
java.lang.String	getAtomType()
Bond	getBond(Atom a)
int	getBondCount()
java.util.ArrayList	getBonds() Gets the list of the Bonds this Atom helps to form
java.lang.String	getChain() Get the chain name
float	getCharge() Gets the partial atomic charge
javax.vecmath.Color3f	getColor()
java.util.ArrayList	getDihedrals()
float	getEpsilon() Gets the Epsilon value
void	getForce(double[] t)
int	getHybridization() Gets the Atomic Hybridization
java.lang.String	getID() Gets the ID
java.lang.String	getIdent() Gets the atom ID
void	getInducedDipole(double[] t)
javax.media.j3d.Group	getJ3D()
java.lang.String	getKey() Gets the atom Key
double	getMagnitude(boolean relative)
float	getMass() Gets the Atomic Mass
static double	getMaxAcceleration()
static double	getMaxForce()
static double	getMaxInduced()
static double	getMaxVelocity()
int	getNumAngles()
int	getNumBonds() Gets the number of atoms bonded to Atom
int	getNumDihedrals()
java.lang.String	getResidueName() Get the residue name
int	getResidueNumber()
float	getSigma() Gets the Sigma value
javax.vecmath.Vector3f	getTrajectoryCoords(int position)
int	getTrajectoryLength()
void	getV3D(javax.vecmath.Vector3d temp) Gets the Atom's Cartesian Coordinates return The Cartesian Coordinates
float	getVDWR() Gets the van der Waals radius return van der Waals radius
void	getVelocity(double[] t)
double	getX() Gets the x coordinate
void	getXYZ(double[] xyz) Gets the Atom's Cartesian Coordinates return The Cartesian Coordinates
int	getXYZIndex() Gets the XYZ Index
double	getY() Gets the y coordinate
double	getZ() Gets the z coordinate
boolean	initJ3D()
void	initVec()
boolean	isBonded(Atom a) Checks to see if an Atom is bonded to this Atom
boolean	isBondVisible()
boolean	isDangeling() Gets whether or not the Atom is under-constrained
boolean	isVisible()
void	move(double[] d) Add a vector to the Atom's current position vector
void	moveto(double[] d) Moves the atom to the specified location
void	moveto(double x, double y, double z)
void	print() Prints the atom identity and Cartesian coordinates to stout
void	reInit(int index, java.lang.String i, MMAtom mmdata, double[] d)
void	setAcceleration(double x, double y, double z)
void	setAngle(Angle a)
void	setBond(Bond b) Specify that this Atom is part of a Bond
void	setCurrentCycle(int cycle)
void	setDihedral(Dihedral d)
void	setForce(double x, double y, double z)
void	setInducedDipole(double x, double y, double z)
static void	setMaxAcceleration(double f)
static void	setMaxForce(double f)
static void	setMaxInduced(double f)
static void	setMaxVelocity(double f)
void	setSelected(boolean b)
void	setVeclocity(double x, double y, double z)
void	setVectorTransform3d(double[] orient, double mag)
void	setVisible(boolean v)
void	setXYZIndex(int index)
boolean	showHydrogen()
void	switchColor(int ctype, javax.vecmath.Color3f newCol, javax.media.j3d.Material newMat)
void	switchView(int viewtype)
java.lang.String	toShortString()
java.lang.String	toString() Overidden toString method returns the FNode's name
void	update() Atomic Positions are not updated unless the atom is visible -> this allows better performance for rendering partial structures during an interactive dynamics run or during trajectory playback.
void	updateTransforms()

Methods inherited from class ffe.lang.FNode

findCenter, getBondList, getFSystemNode, getList, getListIterator, getMoleculeNode, getMW, getName, getPolymerNode, getResidueNode, getTermList, isSelected, setName

Methods inherited from class javax.swing.tree.DefaultMutableTreeNode

add, breadthFirstEnumeration, children, clone, depthFirstEnumeration, getAllowsChildren, getChildAfter, getChildAt, getChildBefore, getChildCount, getDepth, getFirstChild, getFirstLeaf, getIndex, getLastChild, getLastLeaf, getLeafCount, getLevel, getNextLeaf, getNextNode, getNextSibling, getParent, getPath, getPathToRoot, getPreviousLeaf, getPreviousNode, getPreviousSibling, getRoot, getSharedAncestor, getSiblingCount, getUserObject, getUserObjectPath, insert, isLeaf, isNodeAncestor, isNodeChild, isNodeDescendant, isNodeRelated, isNodeSibling, isRoot, pathFromAncestorEnumeration, postorderEnumeration, preorderEnumeration, remove, remove, removeAllChildren, removeFromParent, setAllowsChildren, setParent, setUserObject

Methods inherited from class java.lang.Object

finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

xyzindex

public int xyzindex

atompool

public static java.util.ArrayList atompool

hybridTable

public static final java.util.Hashtable hybridTable

Constructor Detail

Atom

public Atom(java.lang.String s)

Constructor

Atom

public Atom(java.lang.String id,
            MMAtom mmdata,
            double[] d)

Atom

public Atom(int xyznum,
            java.lang.String id,
            MMAtom mmdata,
            double[] d)

Constructor used when parsing XYZ files

Atom

public Atom(int xyznum,
            java.lang.String id,
            MMAtom mmdata,
            double[] d,
            java.lang.String r,
            int n,
            java.lang.String c)

Method Detail

addTrajectoryCoords

public final void addTrajectoryCoords(javax.vecmath.Vector3d coords,
                                      int position)

destroy

public final void destroy()

Overrides:

destroy in class FNode

equals

public final boolean equals(java.lang.Object object)

Overidden equals method

Overrides:

equals in class FNode

Parameters:

object - The Object to compare with this

Returns:

True if this atom and object do not reference the same object, are of the same class, and have the same id

getVelocity

public void getVelocity(double[] t)

getAcceleration

public void getAcceleration(double[] t)

getForce

public void getForce(double[] t)

setMaxForce

public static void setMaxForce(double f)

setMaxVelocity

public static void setMaxVelocity(double f)

setMaxAcceleration

public static void setMaxAcceleration(double f)

setMaxInduced

public static void setMaxInduced(double f)

getMaxForce

public static double getMaxForce()

getMaxVelocity

public static double getMaxVelocity()

getMaxAcceleration

public static double getMaxAcceleration()

getMaxInduced

public static double getMaxInduced()

getInducedDipole

public void getInducedDipole(double[] t)

setVeclocity

public void setVeclocity(double x,
                         double y,
                         double z)

setAcceleration

public void setAcceleration(double x,
                            double y,
                            double z)

setForce

public void setForce(double x,
                     double y,
                     double z)

setInducedDipole

public void setInducedDipole(double x,
                             double y,
                             double z)

getAngles

public final java.util.ArrayList getAngles()

getAppearance

public final javax.media.j3d.Appearance getAppearance()

getAtomicNum

public final int getAtomicNum()

Gets the Atomic Number

Returns:

Atomic Number

getAtomList

public final java.util.List getAtomList()

Description copied from class: FNode

Returns an ArrayList of all Atoms below the present FNode.

Overrides:

getAtomList in class FNode

getAtomType

public final java.lang.String getAtomType()

getBond

public final Bond getBond(Atom a)

getBondCount

public final int getBondCount()

getBonds

public final java.util.ArrayList getBonds()

Gets the list of the Bonds this Atom helps to form

Returns:

A list of the bonds this atom helps to form

getCharge

public final float getCharge()

Gets the partial atomic charge

Returns:

partial atomic charge

getColor

public final javax.vecmath.Color3f getColor()

getDihedrals

public final java.util.ArrayList getDihedrals()

getEpsilon

public final float getEpsilon()

Gets the Epsilon value

Returns:

Epsilon value

getHybridization

public final int getHybridization()

Gets the Atomic Hybridization

Returns:

Atomic Hybridization

getID

public final java.lang.String getID()

Gets the ID

Returns:

ID

getResidueName

public final java.lang.String getResidueName()

Get the residue name

Returns:

String

getResidueNumber

public final int getResidueNumber()

getChain

public final java.lang.String getChain()

Get the chain name

Returns:

String

getIdent

public final java.lang.String getIdent()

Gets the atom ID

Returns:

atom ID

getJ3D

public final javax.media.j3d.Group getJ3D()

getKey

public final java.lang.String getKey()

Gets the atom Key

Returns:

atom Key

getMass

public final float getMass()

Gets the Atomic Mass

Returns:

Atomic Mass

getNumAngles

public final int getNumAngles()

getNumBonds

public final int getNumBonds()

Gets the number of atoms bonded to Atom

Returns:

Number of atoms bonded to this atom

getNumDihedrals

public final int getNumDihedrals()

getSigma

public float getSigma()

Gets the Sigma value

Returns:

Sigma value

getTrajectoryCoords

public javax.vecmath.Vector3f getTrajectoryCoords(int position)

getTrajectoryLength

public int getTrajectoryLength()

getV3D

public void getV3D(javax.vecmath.Vector3d temp)

Gets the Atom's Cartesian Coordinates return The Cartesian Coordinates

getVDWR

public float getVDWR()

Gets the van der Waals radius return van der Waals radius

getX

public double getX()

Gets the x coordinate

Returns:

x coordinate

getXYZ

public void getXYZ(double[] xyz)

Gets the Atom's Cartesian Coordinates return The Cartesian Coordinates

getXYZIndex

public final int getXYZIndex()

Gets the XYZ Index

Returns:

XYZ Index

getY

public final double getY()

Gets the y coordinate

Returns:

y coordinate

getZ

public final double getZ()

Gets the z coordinate

Returns:

z coordinate

isBonded

public final boolean isBonded(Atom a)

Checks to see if an Atom is bonded to this Atom

Parameters:

a - Atom to check

Returns:

True is Atom a is bonded to thisthis atom

isVisible

public boolean isVisible()

isBondVisible

public boolean isBondVisible()

showHydrogen

public boolean showHydrogen()

isDangeling

public boolean isDangeling()

Gets whether or not the Atom is under-constrained

Returns:

True if the atom is under-constrained (ie has can accept bonds)

initJ3D

public boolean initJ3D()

initVec

public void initVec()

move

public final void move(double[] d)

Add a vector to the Atom's current position vector

Parameters:

d - Vector to add to the current position

moveto

public final void moveto(double[] d)

Moves the atom to the specified location

Parameters:

d - Location to move this Atom to

moveto

public final void moveto(double x,
                         double y,
                         double z)

print

public final void print()

Prints the atom identity and Cartesian coordinates to stout

Overrides:

print in class FNode

reInit

public final void reInit(int index,
                         java.lang.String i,
                         MMAtom mmdata,
                         double[] d)

setAngle

public final void setAngle(Angle a)

setBond

public final void setBond(Bond b)

Specify that this Atom is part of a Bond

Parameters:

b - Bond that this Atom is part of

setCurrentCycle

public final void setCurrentCycle(int cycle)

setDihedral

public final void setDihedral(Dihedral d)

setXYZIndex

public final void setXYZIndex(int index)

setSelected

public void setSelected(boolean b)

Overrides:

setSelected in class FNode

switchColor

public final void switchColor(int ctype,
                              javax.vecmath.Color3f newCol,
                              javax.media.j3d.Material newMat)

Overrides:

switchColor in class FNode

switchView

public final void switchView(int viewtype)

Overrides:

switchView in class FNode

drawLabel

public void drawLabel(Graphics3D graphics,
                      javax.media.j3d.J3DGraphics2D g2d,
                      javax.media.j3d.Node node,
                      boolean labelAtoms,
                      boolean labelResidues)

Overrides:

drawLabel in class FNode

getMagnitude

public double getMagnitude(boolean relative)

setVisible

public final void setVisible(boolean v)

toString

public java.lang.String toString()

Description copied from class: FNode

Overidden toString method returns the FNode's name

Overrides:

toString in class FNode

toShortString

public java.lang.String toShortString()

update

public void update()

Atomic Positions are not updated unless the atom is visible -> this allows better performance for rendering partial structures during an interactive dynamics run or during trajectory playback.

updateTransforms

public void updateTransforms()

setVectorTransform3d

public void setVectorTransform3d(double[] orient,
                                 double mag)