cct.modelling
Class vAtom

java.lang.Object
  extended by cct.vecmath.vPoint3f
      extended by cct.modelling.vAtom
All Implemented Interfaces:
AtomInterface, Point3fInterface, java.lang.Cloneable
Direct Known Subclasses:
gAtom

public class vAtom
extends vPoint3f
implements AtomInterface

Title:

Description:

Copyright: Copyright (c) 2004

Company:


Field Summary
protected  java.util.ArrayList bondedToAtoms
           
protected  java.util.ArrayList bondsIndex
           
protected  boolean dynamic
           
protected  int element
           
protected  float mass
           
protected  int monomer_id
           
protected  java.lang.String name
           
protected  java.util.HashMap properties
           
protected  boolean 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
vAtom()
           
vAtom(AtomInterface atom)
           
vAtom(int el)
           
vAtom(int el, java.lang.String aName)
           
vAtom(vAtom atom)
           
 
Method Summary
 vAtom clone()
           
 float distanceTo(AtomInterface a)
           
 float distanceTo(vPoint3f a)
           
 float getAtomicMass()
           
 int getAtomicNumber()
           
 java.util.ArrayList getBondedToAtoms()
           
 java.util.ArrayList getBondIndex()
           
 BondInterface getBondToAtom(AtomInterface a)
           
 java.lang.String getName()
           
 AtomInterface getNewAtomInstance()
           
 AtomInterface getNewAtomInstance(AtomInterface a)
           
 int getNumberOfBondedAtoms()
           
 java.util.HashMap getProperties()
           
 java.lang.Object getProperty(java.lang.String key)
           
 int getSubstructureNumber()
           
 boolean isBondedTo(AtomInterface a)
           
 boolean isDynamic()
           
 boolean isSelected()
           
 boolean removeBond(BondInterface bond)
          Used internally !!!
 void setAtomicMass(float mass)
           
 void setAtomicNumber(int anumber)
           
 void setBondedTo(AtomInterface a)
           
 void setBondedTo(AtomInterface a, boolean set_bond)
           
 void setBondIndex(BondInterface a)
           
 void setName(java.lang.String aName)
           
 void setProperty(java.lang.Object prop, java.lang.Object value)
           
 void setSelected(boolean select)
           
 void setSubstructureNumber(int n)
           
 void setUnbondedTo(AtomInterface a)
           
 
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, getX, getXYZ, getY, getZ, multiply, multiply, norm, norm, norm, normalize, normalize, product, product, product, setX, setXYZ, setXYZ, setXYZ, setXYZ, setY, setZ, squaredNorm, squaredNorm, substract, subtract, translatePoint, vectorNorm, 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.Point3fInterface
distanceTo, getInstance, getInstance, getInstance, getX, getY, getZ, setX, setXYZ, setXYZ, setY, setZ, subtract
 

Field Detail

element

protected int element

mass

protected float mass

name

protected java.lang.String name

monomer_id

protected int monomer_id

selected

protected boolean selected

dynamic

protected boolean dynamic

properties

protected java.util.HashMap properties

bondedToAtoms

protected java.util.ArrayList bondedToAtoms

bondsIndex

protected java.util.ArrayList bondsIndex
Constructor Detail

vAtom

public vAtom()

vAtom

public vAtom(vAtom atom)

vAtom

public vAtom(AtomInterface atom)

vAtom

public vAtom(int el)

vAtom

public vAtom(int el,
             java.lang.String aName)
Method Detail

getNewAtomInstance

public AtomInterface getNewAtomInstance()
Specified by:
getNewAtomInstance in interface AtomInterface

getNewAtomInstance

public AtomInterface getNewAtomInstance(AtomInterface a)
Specified by:
getNewAtomInstance in interface AtomInterface

getAtomicMass

public float getAtomicMass()
Specified by:
getAtomicMass in interface AtomInterface

setAtomicMass

public void setAtomicMass(float mass)
Specified by:
setAtomicMass in interface AtomInterface

setProperty

public void setProperty(java.lang.Object prop,
                        java.lang.Object value)
Specified by:
setProperty in interface AtomInterface

getProperty

public java.lang.Object getProperty(java.lang.String key)
Specified by:
getProperty in interface AtomInterface

getProperties

public java.util.HashMap getProperties()
Specified by:
getProperties in interface AtomInterface

getAtomicNumber

public int getAtomicNumber()
Specified by:
getAtomicNumber in interface AtomInterface

setAtomicNumber

public void setAtomicNumber(int anumber)
Specified by:
setAtomicNumber in interface AtomInterface

getName

public java.lang.String getName()
Specified by:
getName in interface AtomInterface

setName

public void setName(java.lang.String aName)
Specified by:
setName in interface AtomInterface

setSubstructureNumber

public void setSubstructureNumber(int n)
Specified by:
setSubstructureNumber in interface AtomInterface

setSelected

public void setSelected(boolean select)
Specified by:
setSelected in interface AtomInterface

getSubstructureNumber

public int getSubstructureNumber()
Specified by:
getSubstructureNumber in interface AtomInterface

distanceTo

public float distanceTo(vPoint3f a)

distanceTo

public float distanceTo(AtomInterface a)

getBondedToAtoms

public java.util.ArrayList getBondedToAtoms()
Specified by:
getBondedToAtoms in interface AtomInterface

getNumberOfBondedAtoms

public int getNumberOfBondedAtoms()
Specified by:
getNumberOfBondedAtoms in interface AtomInterface

removeBond

public boolean removeBond(BondInterface bond)
Used internally !!!

Specified by:
removeBond in interface AtomInterface
Parameters:
bond - BondInterface
Returns:
BondInterface

getBondIndex

public java.util.ArrayList getBondIndex()
Specified by:
getBondIndex in interface AtomInterface

getBondToAtom

public BondInterface getBondToAtom(AtomInterface a)
Specified by:
getBondToAtom in interface AtomInterface

setBondedTo

public void setBondedTo(AtomInterface a)

setBondedTo

public void setBondedTo(AtomInterface a,
                        boolean set_bond)
Specified by:
setBondedTo in interface AtomInterface

setUnbondedTo

public void setUnbondedTo(AtomInterface a)

setBondIndex

public void setBondIndex(BondInterface a)
Specified by:
setBondIndex in interface AtomInterface

isSelected

public boolean isSelected()
Specified by:
isSelected in interface AtomInterface

isDynamic

public boolean isDynamic()
Specified by:
isDynamic in interface AtomInterface

clone

public vAtom clone()
Overrides:
clone in class java.lang.Object

isBondedTo

public boolean isBondedTo(AtomInterface a)
Specified by:
isBondedTo in interface AtomInterface