cct.modelling
Class gAtom

java.lang.Object
  extended by cct.vecmath.vPoint3f
      extended by cct.modelling.vAtom
          extended by 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