cct.modelling
Class gAtom

java.lang.Object
  cct.vecmath.vPoint3f
      cct.modelling.vAtom
          cct.modelling.gAtom

All Implemented Interfaces:

AtomInterface, Point3fInterface, java.lang.Cloneable

public class gAtom
extends vAtom
implements AtomInterface

Title:

Description:

Copyright: Copyright (c) 2006

Company: ANU

Field Summary

Fields inherited from class cct.modelling.vAtom

bondedToAtoms, bondsIndex, dynamic, element, mass, monomer_id, name, properties, selected

Fields inherited from class cct.vecmath.vPoint3f

DEGREES_TO_RADIANS, PI_FLOAT, RADIANS_TO_DEGREES, x, y, z

Fields inherited from interface cct.interfaces.AtomInterface

AMBER_NAME, AMBER_TYPE_INDEX, AMBIENT_RGB_COLOR, ATOMIC_CHARGE, CCT_ATOM_TYPE, COVALENT_TO_GRADIUS_FACTOR, DIFFUSE_RGB_COLOR, GR_RADIUS, NAME, PICKABILITY, RENDER_POINT, RENDER_SMART_POINT, RENDER_SPHERE, RENDERING_STYLE, RGB_COLOR, SPECULAR_RGB_COLOR, SYBYL_TYPE, VISIBLE

Constructor Summary

gAtom()

gAtom(AtomInterface a)

gAtom(gAtom a)

gAtom(int element, float x, float y, float z)

Method Summary

gAtom	clone()
float	distanceTo(gAtom a)
java.util.HashMap	getAtomProperties()
float[]	getCoordinates()
float[]	getDirectionTo(vPoint3f a)
AtomInterface	getNewAtom()
AtomInterface	getNewAtomInstance()
AtomInterface	getNewAtomInstance(AtomInterface a)
float	getX()
float	getY()
float	getZ()
boolean	IsSelected()
void	setX(float x)
void	setXYZ(float x, float y, float z)
void	setXYZ(vPoint3f xyz)
void	setY(float x)
void	setZ(float x)
void	translateAtom(float[] dir, float increment)
void	translateAtom(vPoint3f dir, float increment)
float	vectorNorm()

Methods inherited from class cct.modelling.vAtom

distanceTo, distanceTo, getAtomicMass, getAtomicNumber, getBondedToAtoms, getBondIndex, getBondToAtom, getName, getNumberOfBondedAtoms, getProperties, getProperty, getSubstructureNumber, isBondedTo, isDynamic, isSelected, removeBond, setAtomicMass, setAtomicNumber, setBondedTo, setBondedTo, setBondIndex, setName, setProperty, setSelected, setSubstructureNumber, setUnbondedTo

Methods inherited from class cct.vecmath.vPoint3f

add, add, add, angleBetween, angleBetween, angleBetween, crossProduct, crossProduct, crossProduct, crossProduct, dihedralAngle, distance, distanceSquared, distanceTo, distanceTo, distanceTo, distanceToLine, getInstance, getInstance, getInstance, getXYZ, multiply, multiply, norm, norm, norm, normalize, normalize, product, product, product, setXYZ, setXYZ, squaredNorm, squaredNorm, substract, subtract, translatePoint, vectorNorm, vectorSquaredNorm

Methods inherited from class java.lang.Object

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

Methods inherited from interface cct.interfaces.AtomInterface

getAtomicMass, getAtomicNumber, getBondedToAtoms, getBondIndex, getBondToAtom, getName, getNumberOfBondedAtoms, getProperties, getProperty, getSubstructureNumber, isBondedTo, isDynamic, isSelected, removeBond, setAtomicMass, setAtomicNumber, setBondedTo, setBondIndex, setName, setProperty, setSelected, setSubstructureNumber

Methods inherited from interface cct.interfaces.Point3fInterface

distanceTo, getInstance, getInstance, getInstance, setXYZ, subtract

Constructor Detail

gAtom

public gAtom()

gAtom

gAtom(gAtom a)

gAtom

gAtom(AtomInterface a)

gAtom

public gAtom(int element,
             float x,
             float y,
             float z)

Method Detail

getNewAtom

public AtomInterface getNewAtom()

getNewAtomInstance

public AtomInterface getNewAtomInstance()

Specified by:

getNewAtomInstance in interface AtomInterface

Overrides:

getNewAtomInstance in class vAtom

getNewAtomInstance

public AtomInterface getNewAtomInstance(AtomInterface a)

Specified by:

getNewAtomInstance in interface AtomInterface

Overrides:

getNewAtomInstance in class vAtom

distanceTo

public float distanceTo(gAtom a)

getAtomProperties

public java.util.HashMap getAtomProperties()

getX

public float getX()

Specified by:

getX in interface Point3fInterface

Overrides:

getX in class vPoint3f

getY

public float getY()

Specified by:

getY in interface Point3fInterface

Overrides:

getY in class vPoint3f

getZ

public float getZ()

Specified by:

getZ in interface Point3fInterface

Overrides:

getZ in class vPoint3f

getCoordinates

public float[] getCoordinates()

IsSelected

public boolean IsSelected()

setXYZ

public void setXYZ(float x,
                   float y,
                   float z)

Specified by:

setXYZ in interface Point3fInterface

Overrides:

setXYZ in class vPoint3f

setXYZ

public void setXYZ(vPoint3f xyz)

Overrides:

setXYZ in class vPoint3f

setX

public void setX(float x)

Specified by:

setX in interface Point3fInterface

Overrides:

setX in class vPoint3f

setY

public void setY(float x)

Specified by:

setY in interface Point3fInterface

Overrides:

setY in class vPoint3f

setZ

public void setZ(float x)

Specified by:

setZ in interface Point3fInterface

Overrides:

setZ in class vPoint3f

vectorNorm

public float vectorNorm()

Overrides:

vectorNorm in class vPoint3f

getDirectionTo

public float[] getDirectionTo(vPoint3f a)

translateAtom

public void translateAtom(float[] dir,
                          float increment)

translateAtom

public void translateAtom(vPoint3f dir,
                          float increment)

clone

public gAtom clone()

Overrides:

clone in class vAtom