chemaxon.marvin.applet

Class MSpaceApplet

java.lang.Object

java.awt.Component

java.awt.Container

java.awt.Panel

java.applet.Applet

javax.swing.JApplet

chemaxon.marvin.applet.MSpaceApplet

All Implemented Interfaces:

chemaxon.marvin.util.ParentPanelIface, ImageObserver, MenuContainer, Serializable, Accessible, RootPaneContainer

public class MSpaceApplet
extends JApplet
implements chemaxon.marvin.util.ParentPanelIface

MarvinSpace applet support.

Since:

MarvinSpace 1.0

Author:

Judit Vasko-Szedlar, Miklos Vargyas

See Also:

Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from class javax.swing.JApplet

JApplet.AccessibleJApplet

Nested classes/interfaces inherited from class java.applet.Applet

Applet.AccessibleApplet

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

Panel.AccessibleAWTPanel

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

Container.AccessibleAWTContainer

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

Component.AccessibleAWTComponent, Component.BaselineResizeBehavior, Component.BltBufferStrategy, Component.FlipBufferStrategy

Field Summary

Fields inherited from class javax.swing.JApplet

accessibleContext, rootPane, rootPaneCheckingEnabled

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

Constructors

Constructor and Description
MSpaceApplet() Creates a new instance of MSpaceApplet

Method Summary

Methods

Modifier and Type	Method and Description
void	addMolecule(String fileName) Adds a molecule to the active cell without removing components from it.
void	addMolecules(String mols, String separator) Adds molecules to display without removing existing components from the viewer.
void	addMoleculeString(String smiles) Adds a molecule to the active cell without removing components from it.
void	addPDB(String pdbId) Loads a pdb file from the RCSB Protein Data Bank (http://www.rcsb.org/)
chemaxon.marvin.space.SlabComponent	createSlabComponent() Creates a SlabComponent, that can be initailized by SlabComponent.beginSlab(), vertices can be set by the SlabComponent.addVertex(float, float, float) method, and finally SlabComponent.endSlab() should be invoked.
chemaxon.marvin.space.SlabComponent	createSlabComponent(float[] vertices) Creates a SlabComponent with the given vertices.
chemaxon.marvin.space.SlabComponent	createSlabComponent(float[][] vertices) Creates a SlabComponent with the given vertices.
chemaxon.marvin.space.SlabComponent	createSlabComponent(String name) Creates a SlabComponent, that can be initailized by SlabComponent.beginSlab(), vertices can be set by the SlabComponent.addVertex(float, float, float) method, and finally SlabComponent.endSlab() should be invoked.
chemaxon.marvin.space.SlabComponent	createSlabComponent(String name, int r, int g, int b) Creates a SlabComponent, that can be initailized by SlabComponent.beginSlab(), vertices can be set by the SlabComponent.addVertex(float, float, float) method, and finally SlabComponent.endSlab() should be invoked.
chemaxon.marvin.space.MSpaceEasy	getMSpaceEasy() Returns MSpaceEasy which offers some more API calls.
String	getProgName() See ParentPanelIface.getProgName() for details.
String	getVersion() See ParentPanelIface.getVersion() for details.
void	hideWindow(Window f) See ParentPanelIface.hideWindow(java.awt.Window) for details.
void	init() Initializes the applet by loading necessary natives and processing parameters.
void	mapPropertyFile(String filename, float min, float max) Computes a Connolly molecular surface, loads the given property file, colors the surface by it, and sets minimum and maximum values that affect coloring the surface.
void	mapPropertyFile(String filename, float min, float max, float surfacePrecision) Computes a Connolly molecular surface by the given precision, loads the given property file, colors the surface by it, and sets minimum and maximum values that affect coloring the surface.
void	mapPropertyFile(String filename, String surfacetype, float min, float max) Computes an arbitrary type molecular surface, loads the given property file, colors the surface by it, and sets minimum and maximum values that affect coloring the surface.
void	mapPropertyFile(String filename, String surfacetype, float min, float max, float surfacePrecision) Computes a Connolly molecular surfaces by the given precision, loads the given property file, colors the surface by it, and sets minimum and maximum values that affect coloring the surface.
void	processLog(String filename) Processes the given log file.
void	readPropertyFile(String filename, float isoValue) Reads a property file (Charmm format), and creates isocontour surfaces.
void	refresh() Quick refresh of the graphic canvas.
void	setMolecule(String fileName) Removes all components from the active cell and adds a molecule.
void	setMoleculeString(String smiles) Removes all components from the active cell and adds a molecule.
void	setPDB(String pdbId) Loads a pdb file from the RCSB Protein Data Bank (http://www.rcsb.org/)
void	setProperty(String propertyName, String propertyValue) Sets a draw property of MarvinSpace.
void	showWindow(Window f) See ParentPanelIface.showWindow(java.awt.Window) for details.
void	unregWindow(Window f) See ParentPanelIface.unregWindow(java.awt.Window) for details.

Methods inherited from class javax.swing.JApplet

addImpl, createRootPane, getAccessibleContext, getContentPane, getGlassPane, getGraphics, getJMenuBar, getLayeredPane, getRootPane, getTransferHandler, isRootPaneCheckingEnabled, paramString, remove, repaint, setContentPane, setGlassPane, setJMenuBar, setLayeredPane, setLayout, setRootPane, setRootPaneCheckingEnabled, setTransferHandler, update

Methods inherited from class java.applet.Applet

destroy, getAppletContext, getAppletInfo, getAudioClip, getAudioClip, getCodeBase, getDocumentBase, getImage, getImage, getLocale, getParameter, getParameterInfo, isActive, isValidateRoot, newAudioClip, play, play, resize, resize, setStub, showStatus, start, stop

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, processContainerEvent, processEvent, remove, removeAll, removeContainerListener, removeNotify, setComponentZOrder, setFocusCycleRoot, setFocusTraversalKeys, setFocusTraversalPolicy, setFocusTraversalPolicyProvider, setFont, transferFocusDownCycle, validate, validateTree

Methods inherited from class java.awt.Component

action, add, addComponentListener, addFocusListener, addHierarchyBoundsListener, addHierarchyListener, addInputMethodListener, addKeyListener, addMouseListener, addMouseMotionListener, addMouseWheelListener, bounds, checkImage, checkImage, coalesceEvents, contains, contains, createImage, createImage, createVolatileImage, createVolatileImage, disable, disableEvents, dispatchEvent, enable, enable, enableEvents, enableInputMethods, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, getBackground, getBaseline, getBaselineResizeBehavior, getBounds, getBounds, getColorModel, getComponentListeners, getComponentOrientation, getCursor, getDropTarget, getFocusCycleRootAncestor, getFocusListeners, getFocusTraversalKeysEnabled, getFont, getFontMetrics, getForeground, 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, processComponentEvent, processFocusEvent, processHierarchyBoundsEvent, processHierarchyEvent, processInputMethodEvent, processKeyEvent, processMouseEvent, processMouseMotionEvent, processMouseWheelEvent, remove, removeComponentListener, removeFocusListener, removeHierarchyBoundsListener, removeHierarchyListener, removeInputMethodListener, removeKeyListener, removeMouseListener, removeMouseMotionListener, removeMouseWheelListener, removePropertyChangeListener, removePropertyChangeListener, repaint, repaint, repaint, requestFocus, requestFocus, requestFocusInWindow, requestFocusInWindow, reshape, revalidate, 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, transferFocusBackward, transferFocusUpCycle

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Detail

MSpaceApplet

public MSpaceApplet()

Creates a new instance of MSpaceApplet

Method Detail

init

public void init()

Initializes the applet by loading necessary natives and processing parameters.

Overrides:

init in class Applet

setProperty

public void setProperty(String propertyName,
               String propertyValue)

Sets a draw property of MarvinSpace. To see available properties, value ranges and default values, please visit

Parameters:

propertyName - identifier of a draw property

propertyValue - value of the property to be set given as a String

getMSpaceEasy

public chemaxon.marvin.space.MSpaceEasy getMSpaceEasy()

Returns MSpaceEasy which offers some more API calls.

Returns:

See MSpaceEasy class.

addPDB

public void addPDB(String pdbId)
            throws Exception

Loads a pdb file from the RCSB Protein Data Bank (http://www.rcsb.org/)

Parameters:

pdbId - PDB ID used by the RSCB PDB

Throws:

Exception - when reading file or adding component fails

setPDB

public void setPDB(String pdbId)
            throws Exception

Loads a pdb file from the RCSB Protein Data Bank (http://www.rcsb.org/)

Parameters:

pdbId - PDB ID used by the RSCB PDB

Throws:

Exception - when reading file or adding component fails

addMolecules

public void addMolecules(String mols,
                String separator)
                  throws Exception

Adds molecules to display without removing existing components from the viewer.

Parameters:

mols - list of molecules separated by the separator character in a String

separator - character in the mols string delimiting each molecules

Throws:

Exception - when reading file or adding component fails

addMolecule

public void addMolecule(String fileName)
                 throws Exception

Adds a molecule to the active cell without removing components from it.

Parameters:

fileName - url or path relative to applet codebase

Throws:

Exception - when reading file or adding component fails

addMoleculeString

public void addMoleculeString(String smiles)
                       throws Exception

Adds a molecule to the active cell without removing components from it.

Parameters:

smiles - the molecule data in smiles

Throws:

Exception - when reading smiles or adding component fails

setMolecule

public void setMolecule(String fileName)
                 throws Exception

Removes all components from the active cell and adds a molecule.

Parameters:

fileName - url or path relative to applet codebase

Throws:

Exception - when reading file or adding component fails

setMoleculeString

public void setMoleculeString(String smiles)
                       throws Exception

Removes all components from the active cell and adds a molecule.

Parameters:

smiles - the molecule in smiles

Throws:

Exception - when reading smiles or adding component fails

refresh

public void refresh()

Quick refresh of the graphic canvas. Note that setProperty refreshes automatically after the property setting.

processLog

public void processLog(String filename)
                throws IOException

Processes the given log file.

Parameters:

filename - url or path relative to applet codebase

Throws:

IOException - if an I/O exception occurs

readPropertyFile

public void readPropertyFile(String filename,
                    float isoValue)

Reads a property file (Charmm format), and creates isocontour surfaces. The isocontour surface representing negative values will be colored red, while the other surface representing positive values will be blue.

Parameters:

filename - file, url or relative location to the codebase

isoValue - initial threshold value to create isocontour surfaces

mapPropertyFile

public void mapPropertyFile(String filename,
                   String surfacetype,
                   float min,
                   float max)

Computes an arbitrary type molecular surface, loads the given property file, colors the surface by it, and sets minimum and maximum values that affect coloring the surface.

Parameters:

filename - file, url or relative location to the codebase

surfacetype - one of the following strings: "van der Waals", "Solvent-accessible", "Connolly", "Blobby"

min - vertices having equal or lesser values will be colored as minimum

max - vertices having equal or greater values will be colored as maximum

mapPropertyFile

public void mapPropertyFile(String filename,
                   String surfacetype,
                   float min,
                   float max,
                   float surfacePrecision)

Computes a Connolly molecular surfaces by the given precision, loads the given property file, colors the surface by it, and sets minimum and maximum values that affect coloring the surface.

Parameters:

filename - file, url or relative location to the codebase

surfacetype - one of the following strings: "van der Waals", "Solvent-accessible", "Connolly", "Blobby"

min - vertices having equal or lesser values will be colored as minimum

max - vertices having equal or greater values will be colored as maximum

surfacePrecision - grid spacing of surface in Angstroms, default value is 0.55

mapPropertyFile

public void mapPropertyFile(String filename,
                   float min,
                   float max)

Computes a Connolly molecular surface, loads the given property file, colors the surface by it, and sets minimum and maximum values that affect coloring the surface.

Parameters:

filename - file, url or relative location to the codebase

min - vertices having equal or lesser values will be colored as minimum

max - vertices having equal or greater values will be colored as maximum

mapPropertyFile

public void mapPropertyFile(String filename,
                   float min,
                   float max,
                   float surfacePrecision)

Computes a Connolly molecular surface by the given precision, loads the given property file, colors the surface by it, and sets minimum and maximum values that affect coloring the surface.

Parameters:

filename - file, url or relative location to the codebase

min - vertices having equal or lesser values will be colored as minimum

max - vertices having equal or greater values will be colored as maximum

surfacePrecision - grid spacing of surface in Angstroms, default value is 0.55

createSlabComponent

public chemaxon.marvin.space.SlabComponent createSlabComponent()

Creates a SlabComponent, that can be initailized by SlabComponent.beginSlab(), vertices can be set by the SlabComponent.addVertex(float, float, float) method, and finally SlabComponent.endSlab() should be invoked.

Returns:

the created component

createSlabComponent

public chemaxon.marvin.space.SlabComponent createSlabComponent(String name)

Creates a SlabComponent, that can be initailized by SlabComponent.beginSlab(), vertices can be set by the SlabComponent.addVertex(float, float, float) method, and finally SlabComponent.endSlab() should be invoked.

Parameters:

name - name of the component

Returns:

the created component

createSlabComponent

public chemaxon.marvin.space.SlabComponent createSlabComponent(String name,
                                                      int r,
                                                      int g,
                                                      int b)

Creates a SlabComponent, that can be initailized by SlabComponent.beginSlab(), vertices can be set by the SlabComponent.addVertex(float, float, float) method, and finally SlabComponent.endSlab() should be invoked.

Parameters:

name - name of the component

r - red component of the color

g - green component of the color

b - blue component of the color

Returns:

the created component

createSlabComponent

public chemaxon.marvin.space.SlabComponent createSlabComponent(float[][] vertices)

Creates a SlabComponent with the given vertices. Warning: this function is not working with JavaScript and certain browsers. It is suggested to use the createSlabComponent() method.

Parameters:

vertices - array of xyz coordinate arrays

Returns:

the component that is created

createSlabComponent

public chemaxon.marvin.space.SlabComponent createSlabComponent(float[] vertices)

Creates a SlabComponent with the given vertices. Warning: this function is not working with JavaScript and certain browsers. It is suggested to use the createSlabComponent() method.

Parameters:

vertices - array of x, y, z coordinates

Returns:

the component that is created

showWindow

public void showWindow(Window f)

See ParentPanelIface.showWindow(java.awt.Window) for details. Warning: for internal usage only MarvinSpace needs this interface to be able to control Help windows.

Specified by:

showWindow in interface chemaxon.marvin.util.ParentPanelIface

hideWindow

public void hideWindow(Window f)

See ParentPanelIface.hideWindow(java.awt.Window) for details. Warning: for internal usage only MarvinSpace needs this interface to be able to control Help windows.

Specified by:

hideWindow in interface chemaxon.marvin.util.ParentPanelIface

unregWindow

public void unregWindow(Window f)

See ParentPanelIface.unregWindow(java.awt.Window) for details. Warning: for internal usage only MarvinSpace needs this interface to be able to control Help windows.

Specified by:

unregWindow in interface chemaxon.marvin.util.ParentPanelIface

getProgName

public String getProgName()

See ParentPanelIface.getProgName() for details. Warning: for internal usage only MarvinSpace needs this interface to be able to control Help windows.

Specified by:

getProgName in interface chemaxon.marvin.util.ParentPanelIface

getVersion

public String getVersion()

See ParentPanelIface.getVersion() for details. Warning: for internal usage only MarvinSpace needs this interface to be able to control Help windows.

Specified by:

getVersion in interface chemaxon.marvin.util.ParentPanelIface