showHybrid
Class ShowHybrid

java.lang.Object
  java.awt.Component
      java.awt.Container
          java.awt.Panel
              java.applet.Applet
                  showHybrid.ShowHybrid

All Implemented Interfaces:

java.awt.image.ImageObserver, java.awt.MenuContainer, java.io.Serializable, javax.accessibility.Accessible

public class ShowHybrid
extends java.applet.Applet

Displays orbital isosurfaces given a point set.

Applet Parameters

NAME	Variable Type	Default	Description
CreateAxes	Boolean	False	Determines whether coordinate axes will be created.
EnableRotate	Boolean	True	Allows orbital to be individually rotated.
IsReady	String		JavaScript variable that will be set to true when applet has initialized. Must use MAYSCRIPT in APPLET tag to use this feature.
Path	String		Path from the current directory to the orbital VRML files
Set	int	1	Each set bit represents an orbital set to be loaded. bit 0 2s and 2p orbitals bit 1 sp, 2px, and 2py orbitals bit 2 sp2 and 2pz orbitals bit 3 sp3 orbitals bit 4 3d orbitals
Radius	float	1.0	Radius of spheres.

Version:

1.0

Author:

David N. Blauch

See Also:

Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from class java.awt.Component

java.awt.Component.BaselineResizeBehavior

Field Summary

Fields inherited from class java.awt.Component

BOTTOM_ALIGNMENT, CENTER_ALIGNMENT, LEFT_ALIGNMENT, RIGHT_ALIGNMENT, TOP_ALIGNMENT

Fields inherited from interface java.awt.image.ImageObserver

ABORT, ALLBITS, ERROR, FRAMEBITS, HEIGHT, PROPERTIES, SOMEBITS, WIDTH

Constructor Summary

ShowHybrid()

Method Summary

void	alignOrbitals() For matched sphere geometries and orbitals sets, rotates the orbitals to place the z-axis along the highest axis of symmetry for the sphere geometry.
void	destroy()
java.lang.String	getAppletInfo()
java.lang.String	getParameter(java.lang.String key, java.lang.String def)
java.lang.String[][]	getParameterInfo()
javax.vecmath.AxisAngle4d	getRotation() Provides the current setting for the system TransformGroup.
double	getRotationAngle() Returns the x component of the axis of rotation for the current transform
double	getRotationX() Returns the x component of the axis of rotation for the current transform
double	getRotationY() Returns the y component of the axis of rotation for the current transform
double	getRotationZ() Returns the z component of the axis of rotation for the current transform
void	init()
void	rotateSpheres(double x, double y, double z, double a) Rotates the spheres.
void	setAtomView(double x, double y, double z, double xa, double ya, double za, double a) Sets the rotation for a specific atom to view down the x axis.
void	setAxesLength(float r) Sets the range of all axes from -r to r.
void	setAxesLength(float xL, float xU, float yL, float yU, float zL, float zU) Sets the lengths of the axes.
void	setAxesVisible(boolean s) Indicates whether axes are visible
void	setFontSize(int s) Sets the font size for the axes labels
void	setGeometry(int g, double r) Orients the spheres for a specific geometry: g = 2 linear g = 3 trigonal planar g = 4 tetrahedral g = 5 trigonal bipyramidal g = 6 octahedral g = 7 square planar
void	setOrbital(int n) Determines which arrows or orbitals are displayed.
void	setOrbitalSet(int n) Determines which orbital set is active.
void	setRadius(double r) Sets the radius for the spheres.
void	setRotation(double x, double y, double z, double a) Set the rotation for the display.
void	setShowArrow(java.lang.Boolean s) Determines whether arrows or orbitals are displayed
void	setShowOverlay(java.lang.Boolean s) Determines whether arrows/orbitals are overlaid.
void	setSphereDistance(double r) Sets the distance of the spheres from the origin.
void	setView(double x, double y, double z, double a) Sets the orbital orientation to a specific value.
void	setViewDistance(float r) Sets the viewing distance.
void	setXView() Sets the orbital orientation to view down the orbital x axis.
void	setYView() Sets the orbital orientation to view down the orbital y axis.
void	setZView() Sets the orbital orientation to view down the orbital z axis.
void	start()
void	stop()

Methods inherited from class java.applet.Applet

getAccessibleContext, getAppletContext, getAudioClip, getAudioClip, getCodeBase, getDocumentBase, getImage, getImage, getLocale, getParameter, isActive, newAudioClip, play, play, resize, resize, setStub, showStatus

Methods inherited from class java.awt.Panel

addNotify

Methods inherited from class java.awt.Container

add, add, add, add, add, addContainerListener, addPropertyChangeListener, addPropertyChangeListener, applyComponentOrientation, areFocusTraversalKeysSet, countComponents, deliverEvent, doLayout, findComponentAt, findComponentAt, getAlignmentX, getAlignmentY, getComponent, getComponentAt, getComponentAt, getComponentCount, getComponents, getComponentZOrder, getContainerListeners, getFocusTraversalKeys, getFocusTraversalPolicy, getInsets, getLayout, getListeners, getMaximumSize, getMinimumSize, getMousePosition, getPreferredSize, insets, invalidate, isAncestorOf, isFocusCycleRoot, isFocusCycleRoot, isFocusTraversalPolicyProvider, isFocusTraversalPolicySet, layout, list, list, locate, minimumSize, paint, paintComponents, preferredSize, print, printComponents, remove, remove, removeAll, removeContainerListener, removeNotify, setComponentZOrder, setFocusCycleRoot, setFocusTraversalKeys, setFocusTraversalPolicy, setFocusTraversalPolicyProvider, setFont, setLayout, transferFocusBackward, transferFocusDownCycle, update, validate

Methods inherited from class java.awt.Component

action, add, addComponentListener, addFocusListener, addHierarchyBoundsListener, addHierarchyListener, addInputMethodListener, addKeyListener, addMouseListener, addMouseMotionListener, addMouseWheelListener, bounds, checkImage, checkImage, contains, contains, createImage, createImage, createVolatileImage, createVolatileImage, disable, dispatchEvent, enable, enable, enableInputMethods, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, getBackground, getBaseline, getBaselineResizeBehavior, getBounds, getBounds, getColorModel, getComponentListeners, getComponentOrientation, getCursor, getDropTarget, getFocusCycleRootAncestor, getFocusListeners, getFocusTraversalKeysEnabled, getFont, getFontMetrics, getForeground, getGraphics, getGraphicsConfiguration, getHeight, getHierarchyBoundsListeners, getHierarchyListeners, getIgnoreRepaint, getInputContext, getInputMethodListeners, getInputMethodRequests, getKeyListeners, getLocation, getLocation, getLocationOnScreen, getMouseListeners, getMouseMotionListeners, getMousePosition, getMouseWheelListeners, getName, getParent, getPeer, getPropertyChangeListeners, getPropertyChangeListeners, getSize, getSize, getToolkit, getTreeLock, getWidth, getX, getY, gotFocus, handleEvent, hasFocus, hide, imageUpdate, inside, isBackgroundSet, isCursorSet, isDisplayable, isDoubleBuffered, isEnabled, isFocusable, isFocusOwner, isFocusTraversable, isFontSet, isForegroundSet, isLightweight, isMaximumSizeSet, isMinimumSizeSet, isOpaque, isPreferredSizeSet, isShowing, isValid, isVisible, keyDown, keyUp, list, list, list, location, lostFocus, mouseDown, mouseDrag, mouseEnter, mouseExit, mouseMove, mouseUp, move, nextFocus, paintAll, postEvent, prepareImage, prepareImage, printAll, remove, removeComponentListener, removeFocusListener, removeHierarchyBoundsListener, removeHierarchyListener, removeInputMethodListener, removeKeyListener, removeMouseListener, removeMouseMotionListener, removeMouseWheelListener, removePropertyChangeListener, removePropertyChangeListener, repaint, repaint, repaint, repaint, requestFocus, requestFocusInWindow, reshape, setBackground, setBounds, setBounds, setComponentOrientation, setCursor, setDropTarget, setEnabled, setFocusable, setFocusTraversalKeysEnabled, setForeground, setIgnoreRepaint, setLocale, setLocation, setLocation, setMaximumSize, setMinimumSize, setName, setPreferredSize, setSize, setSize, setVisible, show, show, size, toString, transferFocus, transferFocusUpCycle

Methods inherited from class java.lang.Object

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

Constructor Detail

ShowHybrid

public ShowHybrid()

Method Detail

getAppletInfo

public java.lang.String getAppletInfo()

Overrides:

getAppletInfo in class java.applet.Applet

getParameterInfo

public java.lang.String[][] getParameterInfo()

Overrides:

getParameterInfo in class java.applet.Applet

getParameter

public java.lang.String getParameter(java.lang.String key,
                                     java.lang.String def)

init

public void init()

Overrides:

init in class java.applet.Applet

start

public void start()

Overrides:

start in class java.applet.Applet

stop

public void stop()

Overrides:

stop in class java.applet.Applet

destroy

public void destroy()

Overrides:

destroy in class java.applet.Applet

alignOrbitals

public void alignOrbitals()

For matched sphere geometries and orbitals sets, rotates the orbitals to place the z-axis along the highest axis of symmetry for the sphere geometry. Otherwise one orbital is aligned with one sphere.

getRotation

public javax.vecmath.AxisAngle4d getRotation()

Provides the current setting for the system TransformGroup.

Returns:

AxisAngle4d object for the current transform

getRotationX

public double getRotationX()

Returns the x component of the axis of rotation for the current transform

Returns:

x-component of axis of rotation

getRotationY

public double getRotationY()

Returns the y component of the axis of rotation for the current transform

Returns:

y-component of axis of rotation

getRotationZ

public double getRotationZ()

Returns the z component of the axis of rotation for the current transform

Returns:

z-component of axis of rotation

getRotationAngle

public double getRotationAngle()

Returns the x component of the axis of rotation for the current transform

Returns:

angle of rotation

rotateSpheres

public void rotateSpheres(double x,
                          double y,
                          double z,
                          double a)

Rotates the spheres.

Parameters:

x - x component of axis of rotation

y - y component of axis of rotation

z - z component of axis of rotation

a - angle of rotation

setAtomView

public void setAtomView(double x,
                        double y,
                        double z,
                        double xa,
                        double ya,
                        double za,
                        double a)

Sets the rotation for a specific atom to view down the x axis.

Parameters:

x - x position

y - y position

z - z position

xa - x-component of the axis of rotation

ya - y-component of the axis of rotation

za - z-component of the axis of rotation

a - angle of rotation

setAxesLength

public void setAxesLength(float r)

Sets the range of all axes from -r to r.

Parameters:

r - limits of each axis

setAxesLength

public void setAxesLength(float xL,
                          float xU,
                          float yL,
                          float yU,
                          float zL,
                          float zU)

Sets the lengths of the axes.

Parameters:

xL - lower limit of x axis

xU - upper limit of x axis

yL - lower limit of y axis

yU - upper limit of y axis

zL - lower limit of z axis

zU - upper limit of z axis

setAxesVisible

public void setAxesVisible(boolean s)

Indicates whether axes are visible

Parameters:

s - visibility state

setFontSize

public void setFontSize(int s)

Sets the font size for the axes labels

Parameters:

s - font size for the axes labels

setGeometry

public void setGeometry(int g,
                        double r)

Orients the spheres for a specific geometry:
g = 2 linear
g = 3 trigonal planar
g = 4 tetrahedral
g = 5 trigonal bipyramidal
g = 6 octahedral
g = 7 square planar

Parameters:

g - geometry indicator

r - distance of spheres from origin

setOrbital

public void setOrbital(int n)

Determines which arrows or orbitals are displayed. Index is keyed to the orbitals sequence. If n < 0, no orbital is displayed.

Parameters:

n - index of item to be displayed

setOrbitalSet

public void setOrbitalSet(int n)

Determines which orbital set is active. The orbital set index is based upon the sequence of loaded orbital sets.

Parameters:

n - index of orbital set

setRadius

public void setRadius(double r)

Sets the radius for the spheres. Preserves existing geometry.

Parameters:

r - radius

setRotation

public void setRotation(double x,
                        double y,
                        double z,
                        double a)

Set the rotation for the display.

Parameters:

x - x component of axis of rotation

y - y component of axis of rotation

z - z component of axis of rotation

a - angle of rotation

setShowArrow

public void setShowArrow(java.lang.Boolean s)

Determines whether arrows or orbitals are displayed

Parameters:

s - displays arrows if true

setShowOverlay

public void setShowOverlay(java.lang.Boolean s)

Determines whether arrows/orbitals are overlaid.

Parameters:

s - overlays if true

setSphereDistance

public void setSphereDistance(double r)

Sets the distance of the spheres from the origin.

Parameters:

r - distance from origin

setView

public void setView(double x,
                    double y,
                    double z,
                    double a)

Sets the orbital orientation to a specific value.

Parameters:

x - x-component of the axis of rotation

y - y-component of the axis of rotation

z - z-component of the axis of rotation

a - angle of rotation (right hand rule)

setViewDistance

public void setViewDistance(float r)

Sets the viewing distance.

Parameters:

r - new viewing distance (along z axis)

See Also:

setBoundsRadius

setXView

public void setXView()

Sets the orbital orientation to view down the orbital x axis.

setYView

public void setYView()

Sets the orbital orientation to view down the orbital y axis.

setZView

public void setZView()

Sets the orbital orientation to view down the orbital z axis. (This is the original orientation.)