showMol
Class Atom

java.lang.Object
  showMol.Atom

public class Atom
extends java.lang.Object

Atom contains the coordinate and display properties for an atom.

Version:

1.0

Author:

David N. Blauch

Constructor Summary

Atom()
The default constructor creates an Atom object for an unspecified element (X) located at the origin.

Atom(int Z, double xx, double yy, double zz)
The Atom object is created for the element identified by its atomic number at the specified location.

Atom(java.lang.String sym, double xx, double yy, double zz)
The Atom object is created for the element identified by its symbol at the specified location.

Method Summary

int	getAtomicNumber() Provides the atomic number of the atom.
javax.media.j3d.TransformGroup	getBallAndStickTransformGroup() Provides the TransformGroup for the Ball and Stick representation of the atom.
float	getCovalentRadius() Provides the covalent radius (in angstroms) for the atom.
javax.vecmath.Color3f	getCPKColor() Provides the Color3f object for the atom's CPK color.
javax.media.j3d.TransformGroup	getSpaceFillingTransformGroup() Provides the TransformGroup for the Space Filling representation of the atom.
java.lang.String	getSymbol() Provides the atomic symbol for this atom

Methods inherited from class java.lang.Object

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

Constructor Detail

Atom

public Atom()

The default constructor creates an Atom object for an unspecified element (X) located at the origin.

Atom

public Atom(java.lang.String sym,
            double xx,
            double yy,
            double zz)

The Atom object is created for the element identified by its symbol at the specified location. If parameters are not available for the specified atom, parameters for the generic atom (X) are used.

Parameters:

sym - symbol for the element (case insensitive)

x - position along x axis

y - position along y axis

z - position along z axis

Atom

public Atom(int Z,
            double xx,
            double yy,
            double zz)

The Atom object is created for the element identified by its atomic number at the specified location. If parameters are not available for the specified atom, parameters for the generic atom (X) are used.

Parameters:

Z - atomic number

x - position along x axis

y - position along y axis

z - position along z axis

Method Detail

getAtomicNumber

public int getAtomicNumber()

Provides the atomic number of the atom.

Returns:

atomic number

getBallAndStickTransformGroup

public javax.media.j3d.TransformGroup getBallAndStickTransformGroup()

Provides the TransformGroup for the Ball and Stick representation of the atom.

Returns:

TransformGroup for the Ball and Stick ball

getCovalentRadius

public float getCovalentRadius()

Provides the covalent radius (in angstroms) for the atom.

Returns:

covalent radius

getCPKColor

public javax.vecmath.Color3f getCPKColor()

Provides the Color3f object for the atom's CPK color.

Returns:

CPK color

getSpaceFillingTransformGroup

public javax.media.j3d.TransformGroup getSpaceFillingTransformGroup()

Provides the TransformGroup for the Space Filling representation of the atom.

Returns:

TransformGroup for the space filling sphere

getSymbol

public java.lang.String getSymbol()

Provides the atomic symbol for this atom

Returns:

atomic symbol