showIsosurface
Class Atom

java.lang.Object
  showIsosurface.Atom

public class Atom
extends java.lang.Object

The Atom class creates a TransformGroup object that locates the position of the atom and a Switch object that contains one or more Orbital Representations.

Version:

1.0

Author:

David N. Blauch

Constructor Summary

Atom()
Creates an Atom object with the atom located at the origin.

Atom(double x, double y, double z)
Creates an Atom object with the atom located at the specified position.

Method Summary

void	createOrbital(int n) Creates a new Orbital object containing no isosurfaces
void	createOrbital(int n, java.net.URL url) Creates a new Orbital object containing one isosurface, which is loaded from the specified VRML file
void	createOrbital(int n, java.net.URL url, int nSurf) Creates a new Orbital object containing multiple isosurfaces, which are loaded from the specified VRML files
void	destroy() Destroys the objects associated with this atom
java.util.BitSet	getChildMask() Returns the ChildMask for the atom SwitchGroup.
java.lang.String	getInfo() Returns name, version, copyright, and author information about this class.
java.lang.String	getName() Provides the name of the atom
Orbital	getOrbital(int n) Provides the indicated Orbital object
javax.media.j3d.Transform3D	getTransform3D() Method for obtaining the atom's TransformGroup transform
javax.media.j3d.TransformGroup	getTransformGroup() Method for obtaining the atom's TransformGroup
void	loadIsosurface(int n, java.net.URL url) Loads an isosurface in the specified orbital
void	loadIsosurfaces(int n, java.net.URL url, int nSurf) Loads multiple isosurfaces in the specified orbital
void	setAllIsosurfacesVisible(int nOrb, boolean s) Determines whether all isosurfaces in the specified orbital are visible
void	setChildMask(java.util.BitSet b) Sets the ChildMask option to indicate which orbitals are displayed.
void	setIsosurfaceVisible(int nOrb, int nIso, boolean s) Determines whether the specified isosurface in the specified orbital is visible
void	setName(java.lang.String name) Sets the name of the atom
void	setNucleusColor(float x, float y, float z) Sets the emissive color of the nucleus and sets the nucleus to be visible
void	setNucleusVisible(boolean s) Determines whether the nucleus is visible as a small where sphere
void	setOrbitalActive(int n) The orbital's BranchGroup is compiled and added to the atom's Switch node.
void	setPosition(double x, double y, double z) Sets the position of the atom
void	setScale(double s) Sets the transform scale
void	setTransform(javax.media.j3d.Transform3D trans) Sets the transform of the atom
void	setTransparency(int n, float t) Sets the transparency of the specified orbital
void	setWhichOrbital(int n) Indicates which orbital is to be displayed May also specify Switch.CHILD_ALL, Switch.CHILD_NONE, or Switch.CHILD_MASK.

Methods inherited from class java.lang.Object

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

Constructor Detail

Atom

public Atom()

Creates an Atom object with the atom located at the origin.

Atom

public Atom(double x,
            double y,
            double z)

Creates an Atom object with the atom located at the specified position.

Parameters:

x - position of atom along x axis

y - position of atom along y axis

z - position of atom along z axis

Method Detail

createOrbital

public void createOrbital(int n)

Creates a new Orbital object containing no isosurfaces

Parameters:

n - number of isosurfaces for the orbital

createOrbital

public void createOrbital(int n,
                          java.net.URL url)

Creates a new Orbital object containing one isosurface, which is loaded from the specified VRML file

Parameters:

n - number of isosurfaces for the orbital

fname - file name of the VRML file describing an isosurface

createOrbital

public void createOrbital(int n,
                          java.net.URL url,
                          int nSurf)

Creates a new Orbital object containing multiple isosurfaces, which are loaded from the specified VRML files

Parameters:

n - number of isosurfaces for the orbital

fname - base file name of the VRML files describing isosurfaces

nSurf - number of isosurfaces to be loaded

destroy

public void destroy()

Destroys the objects associated with this atom

getInfo

public java.lang.String getInfo()

Returns name, version, copyright, and author information about this class.

getName

public java.lang.String getName()

Provides the name of the atom

Returns:

atom name

getOrbital

public Orbital getOrbital(int n)

Provides the indicated Orbital object

Parameters:

n - index of the orbital

Returns:

Orbital object

getTransform3D

public javax.media.j3d.Transform3D getTransform3D()

Method for obtaining the atom's TransformGroup transform

Returns:

Transform3D object for the atom

getTransformGroup

public javax.media.j3d.TransformGroup getTransformGroup()

Method for obtaining the atom's TransformGroup

Returns:

TransformGroup for the atom

loadIsosurface

public void loadIsosurface(int n,
                           java.net.URL url)

Loads an isosurface in the specified orbital

Parameters:

n - orbital index

fname - file name of VRML file used to create the isosurface

loadIsosurfaces

public void loadIsosurfaces(int n,
                            java.net.URL url,
                            int nSurf)

Loads multiple isosurfaces in the specified orbital

Parameters:

n - orbital index

fname - base file name of VRML files used to create the isosurfaces

nSurf - number of isosurfaces to be loaded

setAllIsosurfacesVisible

public void setAllIsosurfacesVisible(int nOrb,
                                     boolean s)

Determines whether all isosurfaces in the specified orbital are visible

Parameters:

nOrb - index of Orbital

s - visibility state

setIsosurfaceVisible

public void setIsosurfaceVisible(int nOrb,
                                 int nIso,
                                 boolean s)

Determines whether the specified isosurface in the specified orbital is visible

Parameters:

nOrb - index of Orbital

nIso - index of Isosurface

s - visibility state

setName

public void setName(java.lang.String name)

Sets the name of the atom

Parameters:

name - atom name

setNucleusColor

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

Sets the emissive color of the nucleus and sets the nucleus to be visible

Parameters:

x - x component

y - y component

z - z component

setNucleusVisible

public void setNucleusVisible(boolean s)

Determines whether the nucleus is visible as a small where sphere

Parameters:

s - visibility state

setOrbitalActive

public void setOrbitalActive(int n)

The orbital's BranchGroup is compiled and added to the atom's Switch node.

Parameters:

n - index of orbital to be made active

setPosition

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

Sets the position of the atom

Parameters:

x - position of atom along x axis

y - position of atom along y axis

z - position of atom along z axis

setScale

public void setScale(double s)

Sets the transform scale

Parameters:

s - scale

setTransform

public void setTransform(javax.media.j3d.Transform3D trans)

Sets the transform of the atom

Parameters:

trans - orientation and position of the atom

setTransparency

public void setTransparency(int n,
                            float t)

Sets the transparency of the specified orbital

Parameters:

n - orbital index

t - transparency

setWhichOrbital

public void setWhichOrbital(int n)

Indicates which orbital is to be displayed May also specify Switch.CHILD_ALL, Switch.CHILD_NONE, or Switch.CHILD_MASK. If CHILD_MASK is specified, setChildMask() is employed to identify the orbitals to be displayed.

Parameters:

n - orbital index

See Also:

setChildMask, getChildMask

getChildMask

public java.util.BitSet getChildMask()

Returns the ChildMask for the atom SwitchGroup. This value indicates which orbitals are being displayed.

Returns:

ChildMask value

setChildMask

public void setChildMask(java.util.BitSet b)

Sets the ChildMask option to indicate which orbitals are displayed. Use with setWhichOrbital(Switch.CHILD_MASK)

Parameters:

b - BitSet indicating which orbitals are displayed

See Also:

setWhichOrbital