showMol
Class ShowMol

java.lang.Object
  java.awt.Component
      java.awt.Container
          java.awt.Panel
              java.applet.Applet
                  showMol.ShowMol

All Implemented Interfaces:

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

public class ShowMol
extends java.applet.Applet

ShowMol is a molecular viewer for the following file types:

PDB (Brookhaven Protein Database format)

Applet Parameters

NAME	Variable Type	Default	Description
BackgroundColor	String	000000	Sets the background color for the display. By default the background is black. Color is specified by six digit hexadecimal RGB value.
Center	Boolean	true	If true, the molecule is positioned at the center of the display. Applies only to the file specified by the File parameter.
Display	Integer	1	Display format. See documentation for codes.
File	String		Name of file to be loaded.
Format	String	PDB	Format of the molecular structure file. PDB Brookhave Protein Database (recognizes only ATOM, HETATM, and CONECT keywords) XYZ List of atoms with x,y,z positions COM Gaussian job file CUBE Gaussian cube file <\UL>
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
ViewDistance	float	20.0	Distance of view from origin. Set to keep entire molecule in view.

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

static int	BALL
static int	BALLANDSTICK
static int	CENTERED
static int	COM
static int	CREATEBONDS
static int	CUBE
static int	PDB
static int	SPACEFILLING
static int	WIREFRAME
static int	XYZ

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

ShowMol()

Method Summary

void	addLine(double x1, double y1, double z1, double x2, double y2, double z2) Creates a line between two points with the pre-defined emissive color.
void	addMolecule(java.lang.String filename) Adds a molecule to the display.
void	addMolecule(java.lang.String filename, int dFormat) Adds a molecule to the display.
void	addMolecule(java.lang.String filename, int dFormat, int fFormat) Adds a molecule to the display.
void	addMoleculeRotation(int n, double x, double y, double z, double a) Rotates the selected molecule.
void	addSpecial(int s) Adds a Molecule based upon one of the special, pre-defined settings.
void	addSphere(float r, float x, float y, float z) Adds a sphere to the display.
void	centerMolecule(int idx) Centers the specified molecule.
void	centerMoleculeOnAtom(int idx, int a) Translates the indicated molecule so that the specified atom is at the origin.
void	centerSpheres() Translates all spheres so that the center of the set lies at the origin.
void	clearMouse() Clears the mouse transformations.
void	clearRotation(int idx) Clears the rotation component of the transform for this specified molecule.
void	destroy()
java.lang.String	getAppletInfo()
java.lang.String	getParameter(java.lang.String key, java.lang.String def)
java.lang.String[][]	getParameterInfo()
void	init()
void	setDiffuseColor(float r, float g, float b) Sets the diffuse color for new spheres and lines.
void	setDisplayFormat(int d) Sets the display format for molecules that will be loaded.
void	setDisplayFormat(int n, int d) Sets the display format for the indicated molecule, which must have previously been loaded.
void	setDisplayFormats(int d) Sets the display format for all molecules currently loaded.
void	setEmissiveColor(float r, float g, float b) Sets the emissive color for new spheres and lines.
void	setFileFormat(int format) Sets the default format for molecular structure files.
void	setMoleculeRotation(int n, double x, double y, double z, double a) Rotates the selected molecule.
void	setMoleculeRotationOnAtom(int n, int idx, double x, double y, double z, double a) Rotates the selected molecule.
void	setMoleculesVisible(boolean s) Sets all or none of the molecules to be visible
void	setMoleculeTranslation(int n, double x, double y, double z) Sets the location of the selected molecule.
void	setMoleculeVisible(int n, boolean s) Determines whether the specified molecule is displayed.
void	setPath(java.lang.String filePath) Sets the default path for files.
void	setRotation(double x, double y, double z, double a) Rotates the scene.
void	setTranslation(double x, double y, double z) Shifts the position of the scene.
void	setViewDistance(float r) Sets the viewing distance.
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

Field Detail

PDB

public static int PDB

XYZ

public static int XYZ

COM

public static int COM

CUBE

public static int CUBE

BALLANDSTICK

public static int BALLANDSTICK

BALL

public static int BALL

SPACEFILLING

public static int SPACEFILLING

WIREFRAME

public static int WIREFRAME

CENTERED

public static int CENTERED

CREATEBONDS

public static int CREATEBONDS

Constructor Detail

ShowMol

public ShowMol()

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

addMolecule

public void addMolecule(java.lang.String filename)

Adds a molecule to the display. The file must be of the default file format (PDB) or the format specified by the setFileFormat method. The default or user-defined display format is shown.

Parameters:

filename - name of file to be loaded

See Also:

setDisplayFormat, setFileFormat

addMolecule

public void addMolecule(java.lang.String filename,
                        int dFormat)

Adds a molecule to the display. The file format must be the default (PDB) or user-specified (setFileFormat) format. The available display formats are

ShowMol.BALLANDSTICK (1) (default)
ShowMol.BALL (2) balls only, no sticks
ShowMol.SPACEFILLING (4)
ShowMol.WIREFRAME (8)

The display format may be combined (via a logical OR) with the following options

ShowMol.CENTERED (128)
ShowMol.CREATEBONDS (256) Bonds will be created based upon atom proximity.

Parameters:

filename - name of file to be loaded

dFormat - index for display format

See Also:

setFileFormat

addMolecule

public void addMolecule(java.lang.String filename,
                        int dFormat,
                        int fFormat)

Adds a molecule to the display. The file format is specified by

ShowMol.PDB (1) Brookhaven Protein Database
ShowMol.XYZ (2) Text file listing atomic symbol and x,y,z coordinates
ShowMol.COM (4) Gaussian job file
ShowMol.CUBE (8) Gaussian cube file

The available display formats are

ShowMol.BALLANDSTICK (1) (default)
ShowMol.BALL (2) balls only, no sticks
ShowMol.SPACEFILLING (4)
ShowMol.WIREFRAME (8)

The display format may be combined (via a logical OR) with the following options

ShowMol.CENTERED (128)
ShowMol.CREATEBONDS (256) Bonds will be created based upon atom proximity.

Parameters:

filename - name of file to be loaded

dFormat - index for the display format

fFormat - index for file format

addSpecial

public void addSpecial(int s)

Adds a Molecule based upon one of the special, pre-defined settings. 1 graphite 2 cristobalite

Parameters:

s - index of special molecule

addMoleculeRotation

public void addMoleculeRotation(int n,
                                double x,
                                double y,
                                double z,
                                double a)

Rotates the selected molecule. Rotation is applied to existing transform.

Parameters:

n - index of molecule to be rotated

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

addSphere

public void addSphere(float r,
                      float x,
                      float y,
                      float z)

Adds a sphere to the display. The diffuse and emissive colors must be previously defined.

Parameters:

r - radius of sphere

x - x coordinate for center of sphere

y - y coordinate for center of sphere

z - z coordinate for center of sphere

See Also:

setDiffuseColor, setEmissiveColor

addLine

public void addLine(double x1,
                    double y1,
                    double z1,
                    double x2,
                    double y2,
                    double z2)

Creates a line between two points with the pre-defined emissive color.

Parameters:

x1 -

y1 -

z1 -

x2 -

y2 -

z2 -

See Also:

setEmissiveColor

centerMolecule

public void centerMolecule(int idx)

Centers the specified molecule.

Parameters:

idx - index of molecule to be centered

centerMoleculeOnAtom

public void centerMoleculeOnAtom(int idx,
                                 int a)

Translates the indicated molecule so that the specified atom is at the origin.

Parameters:

idx - index of molecule to be centered

a - index of atom to place at the origin

centerSpheres

public void centerSpheres()

Translates all spheres so that the center of the set lies at the origin.

clearMouse

public void clearMouse()

Clears the mouse transformations.

clearRotation

public void clearRotation(int idx)

Clears the rotation component of the transform for this specified molecule.

Parameters:

idx - index of molecule to be centered

setDiffuseColor

public void setDiffuseColor(float r,
                            float g,
                            float b)

Sets the diffuse color for new spheres and lines. Does not affect existing shapes.

Parameters:

r - red component

g - green component

b - blue component

setEmissiveColor

public void setEmissiveColor(float r,
                             float g,
                             float b)

Sets the emissive color for new spheres and lines. Does not affect existing shapes.

Parameters:

r - red component

g - green component

b - blue component

setDisplayFormat

public void setDisplayFormat(int d)

Sets the display format for molecules that will be loaded. The display index is specified with

ShowMol.BALLANDSTICK (1) (default)
ShowMol.BALL (2)
ShowMol.SPACEFILLING (4)
ShowMol.WIREFRAME (8)

. The display format may be combined (via a logical OR) with the following options, which do not apply to molecules already loaded.

ShowMol.CENTERED (128)
ShowMol.CREATEBONDS (256) Bonds will be created based upon atom proximity.

Parameters:

n - index for the molecule

d - index for display

setDisplayFormat

public void setDisplayFormat(int n,
                             int d)

Sets the display format for the indicated molecule, which must have previously been loaded. The display index is specified with

ShowMol.BALLANDSTICK (1)
ShowMol.BALL (2)
ShowMol.SPACEFILLING (4)
ShowMol.WIREFRAME (8)
.

Parameters:

n - index for the molecule

d - index for display

setDisplayFormats

public void setDisplayFormats(int d)

Sets the display format for all molecules currently loaded. The display index is specified with

ShowMol.BALLANDSTICK (1)
ShowMol.BALL (2)
ShowMol.SPACEFILLING (4)
ShowMol.WIREFRAME (8)
.

Parameters:

d - index for display

setFileFormat

public void setFileFormat(int format)

Sets the default format for molecular structure files.

ShowMol.PDB (1) Brookhaven Protein Database
ShowMol.XYZ (2) Text file listing atomic symbol and x,y,z coordinates
ShowMol.COM (4) Gaussian job file
ShowMol.CUBE (8) Gaussian cube file

Parameters:

format - format index

setMoleculeRotation

public void setMoleculeRotation(int n,
                                double x,
                                double y,
                                double z,
                                double a)

Rotates the selected molecule. Molecule is rotated about its center.

Parameters:

n - index of molecule to be rotated

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

setMoleculeRotationOnAtom

public void setMoleculeRotationOnAtom(int n,
                                      int idx,
                                      double x,
                                      double y,
                                      double z,
                                      double a)

Rotates the selected molecule. Molecule is rotated about the indicated atom.

Parameters:

n - index of molecule to be rotated

idx - index of atom about which rotation occurs

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

setMoleculeTranslation

public void setMoleculeTranslation(int n,
                                   double x,
                                   double y,
                                   double z)

Sets the location of the selected molecule. Overrides previous transformations.

Parameters:

n - index of molecule to be moved

x - x component of translation

y - y component of translation

z - z component of translation

setMoleculeVisible

public void setMoleculeVisible(int n,
                               boolean s)

Determines whether the specified molecule is displayed.

Parameters:

n - index of molecule

s - visibility state

setMoleculesVisible

public void setMoleculesVisible(boolean s)

Sets all or none of the molecules to be visible

Parameters:

s - visibility state

setPath

public void setPath(java.lang.String filePath)

Sets the default path for files.

Parameters:

filePath - path to files

setRotation

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

Rotates the scene.

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

setTranslation

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

Shifts the position of the scene.

Parameters:

x - x component of translation

y - y component of translation

z - z component of translation

setViewDistance

public void setViewDistance(float r)

Sets the viewing distance.

Parameters:

r - new viewing distance (along z axis)

See Also:

setBoundsRadius