Class JMSketch

java.lang.Object
  java.awt.Component
      java.awt.Container
          java.awt.Panel
              java.applet.Applet
                  javax.swing.JApplet
                      JMSketch

All Implemented Interfaces:

java.awt.event.MouseListener, java.awt.image.ImageObserver, java.awt.MenuContainer, java.beans.PropertyChangeListener, java.io.Serializable, java.util.EventListener, javax.accessibility.Accessible, javax.swing.RootPaneContainer, JMSketchIface, MAppletIface

public class JMSketch
extends javax.swing.JApplet
implements java.awt.event.MouseListener, java.beans.PropertyChangeListener, JMSketchIface

Swing version of the MarvinSketch Applet.

Since:

Marvin 2.0

Version:

5.2.3, 06/20/2009

Author:

Peter Csizmadia, Nora Mate, Zsolt Mohacsi, Istvan Fajth, Tamas Vertse

See Also:

Serialized Form

Nested Class Summary

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

javax.swing.JApplet.AccessibleJApplet

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

java.applet.Applet.AccessibleApplet

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

java.awt.Panel.AccessibleAWTPanel

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

java.awt.Container.AccessibleAWTContainer

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

java.awt.Component.AccessibleAWTComponent, java.awt.Component.BltBufferStrategy, java.awt.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

JMSketch()

Method Summary

void	destroy() Disposes all the frames and removes references to the sketcher.
java.lang.String	evaluateChemicalTerms(java.lang.String expression) Evaluates a Chemical Terms expression on the molecule in MarvinSketch, and returns the result in string format.
java.lang.String	getAppletInfo() Returns a string containing the version and the author.
java.lang.String	getAtomAlias(int i) Gets atom alias.
int	getAtomCount() Returns the number of atoms.
java.lang.String	getAtomExtraLabel(int i) Gets extra atom label.
boolean	getAutoScale() Returns the autoscale property.
java.lang.String	getImageShowURL() Gets the show image URL.
java.lang.String	getMol(java.lang.String fmt) Gets the molecule in a text format.
double	getMolExactMass() Gets the exact molecule weight.
java.lang.String	getMolFormula() Gets the molecule formula.
double	getMolMass() Gets the molecule weight.
java.lang.String	getMolProperty(java.lang.String key) Gets an RDfile/SDfile property.
int	getMolPropertyCount() Gets the number of RDfile/SDfile properties.
java.lang.String	getMolPropertyKey(int i) Gets an RDfile/SDfile property key.
java.lang.String	getPiece(java.lang.String fmt) Gets the current molecule piece in the specified format.
double	getScale() Gets the magnification.
java.lang.String	getSelectedMol(java.lang.String fmt) Gets the selected molecule part in a text format.
boolean	hasValenceError() Determines if this molecule has a valence error on any of its atoms.
void	init() Initializes the applet.
boolean	isAtomSelected(int i) Returns true if atom is selected.
boolean	isChemicalTermsExpressionSyntaxError() Returns true, if the last Chemical Terms expression evaluated by the JMSketchIface.evaluateChemicalTerms(String) method is a syntactically not correct expression.
boolean	isEmpty() Returns true sketcher canvas is empty.
void	mouseClicked(java.awt.event.MouseEvent ev) Does nothing.
void	mouseEntered(java.awt.event.MouseEvent ev) Does nothing.
void	mouseExited(java.awt.event.MouseEvent ev) Does nothing.
void	mousePressed(java.awt.event.MouseEvent ev) Does nothing.
void	mouseReleased(java.awt.event.MouseEvent ev) Handles the viewer button press events.
void	postImage(java.lang.String fmt, java.lang.String where) Posts image to CGI script.
void	propertyChange(java.beans.PropertyChangeEvent ev) Invoke propertyChange(prop) JavaScript method on applet's page.
void	redo() Invokes the Redo command.
void	selectAllAtoms(boolean v) Select or unselect all atoms in the specified molecule.
void	selectAtom(int atom, boolean v) Select or unselect an atom in the specified molecule.
void	setAtomAlias(int i, java.lang.String alias) Sets atom alias.
void	setAtomExtraLabel(int i, java.lang.String label) Sets extra atom label.
void	setAutoScale(boolean as) Sets the autoscale property.
void	setMol(java.lang.String s) Starts loading a molecule into the sketcher in a separate thread.
void	setMol(java.lang.String s, java.lang.String opts) Starts loading a molecule into the sketcher in a separate thread.
void	setMolProperty(java.lang.String key, java.lang.String value) Sets an RDfile/SDfile property.
void	setParentApplet(javax.swing.JApplet parent)
void	setPiece(java.lang.String s) Sets the current piece.
void	setScale(double m) Sets the magnification.
void	start() Starts the applet.
void	stop() Hide the frames when stopped.
void	undo() Invokes the Undo command.

Methods inherited from class javax.swing.JApplet

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

Methods inherited from class java.applet.Applet

getAppletContext, getAudioClip, getAudioClip, getCodeBase, getDocumentBase, getImage, getImage, getLocale, getParameter, getParameterInfo, 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, processContainerEvent, processEvent, remove, removeAll, removeContainerListener, removeNotify, setComponentZOrder, setFocusCycleRoot, setFocusTraversalKeys, setFocusTraversalPolicy, setFocusTraversalPolicyProvider, setFont, transferFocusBackward, 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, 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, processComponentEvent, processFocusEvent, processHierarchyBoundsEvent, processHierarchyEvent, processInputMethodEvent, processKeyEvent, processMouseEvent, processMouseMotionEvent, processMouseWheelEvent, remove, removeComponentListener, removeFocusListener, removeHierarchyBoundsListener, removeHierarchyListener, removeInputMethodListener, removeKeyListener, removeMouseListener, removeMouseMotionListener, removeMouseWheelListener, removePropertyChangeListener, removePropertyChangeListener, repaint, repaint, repaint, repaint, requestFocus, requestFocus, requestFocusInWindow, 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

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

Constructor Detail

JMSketch

public JMSketch()

Method Detail

init

public void init()

Initializes the applet.

Overrides:

init in class java.applet.Applet

start

public void start()

Starts the applet.

Overrides:

start in class java.applet.Applet

propertyChange

public void propertyChange(java.beans.PropertyChangeEvent ev)

Invoke propertyChange(prop) JavaScript method on applet's page. Only for internal usage.

Specified by:

propertyChange in interface java.beans.PropertyChangeListener

Since:

Marvin 5.0 08/29/2007

stop

public void stop()

Hide the frames when stopped.

Overrides:

stop in class java.applet.Applet

destroy

public void destroy()

Disposes all the frames and removes references to the sketcher.

Overrides:

destroy in class java.applet.Applet

getAppletInfo

public java.lang.String getAppletInfo()

Returns a string containing the version and the author.

Overrides:

getAppletInfo in class java.applet.Applet

Returns:

the information

isEmpty

public boolean isEmpty()

Returns true sketcher canvas is empty.

Specified by:

isEmpty in interface JMSketchIface

Returns:

true if sketcher canvas is empty

Since:

Marvin 3.5.1

getSelectedMol

public java.lang.String getSelectedMol(java.lang.String fmt)

Gets the selected molecule part in a text format. Should be called after the molecule has been loaded. The format descriptor string can also contain export options. Format and options are separated by a colon, multiple options can be separated by commas. See the text formats and their options on the File Formats in Marvin page. Examples:

 s1 = msketch.getSelectedMol("mol");
 s2 = msketch.getSelectedMol("smiles:a-H"); // aromatize and remove Hydrogens
 

Specified by:

getSelectedMol in interface JMSketchIface

Parameters:

fmt - the format descriptor string

Returns:

string containing the molecule in a molecule file format

Since:

Marvin 4.0.2

getMol

public java.lang.String getMol(java.lang.String fmt)

Gets the molecule in a text format. Should be called after the molecule has been loaded. The format descriptor string can also contain export options. Format and options are separated by a colon, multiple options can be separated by commas. See the text formats and their options on the File Formats in Marvin page. Examples:

 s1 = msketch.getMol("mol");
 s2 = msketch.getMol("smiles:a-H"); // aromatize and remove Hydrogens
 

Specified by:

getMol in interface JMSketchIface

Parameters:

fmt - the format descriptor string

Returns:

string containing the molecule in a molecule file format

getMolProperty

public java.lang.String getMolProperty(java.lang.String key)

Gets an RDfile/SDfile property. Should be called after the molecule has been loaded.

Specified by:

getMolProperty in interface JMSketchIface

Parameters:

key - the property key

Returns:

the value of the property, or null if the key is not found

Since:

Marvin 3.4.1

setMolProperty

public void setMolProperty(java.lang.String key,
                           java.lang.String value)

Sets an RDfile/SDfile property. Setting null value removes the property. Should be called after the molecule has been loaded.

Specified by:

setMolProperty in interface JMSketchIface

Parameters:

key - the property name

value - the value or null

Since:

Marvin 3.4.1

getMolPropertyCount

public int getMolPropertyCount()

Gets the number of RDfile/SDfile properties. Should be called after the molecule has been loaded.

Specified by:

getMolPropertyCount in interface JMSketchIface

Returns:

the number of RDfile/SDfile properties

Since:

Marvin 3.5

getMolPropertyKey

public java.lang.String getMolPropertyKey(int i)

Gets an RDfile/SDfile property key. Should be called after the molecule has been loaded.

Specified by:

getMolPropertyKey in interface JMSketchIface

Parameters:

i - the property key index

Returns:

the property key

Since:

Marvin 3.5

getAtomCount

public int getAtomCount()

Returns the number of atoms. Should be called after the molecule has been loaded.

Specified by:

getAtomCount in interface JMSketchIface

Returns:

the number of atoms

Since:

Marvin 3.5.1

isAtomSelected

public boolean isAtomSelected(int i)

Returns true if atom is selected. Should be called after the molecule has been loaded.

Specified by:

isAtomSelected in interface JMSketchIface

Parameters:

i - the atom index

Returns:

true if atom is selected

Since:

Marvin 3.5.1

selectAllAtoms

public void selectAllAtoms(boolean v)

Select or unselect all atoms in the specified molecule.

Specified by:

selectAllAtoms in interface JMSketchIface

Parameters:

v - select (true) or unselect (false)

Since:

Marvin 5.0.3, 03/25/2008

selectAtom

public void selectAtom(int atom,
                       boolean v)

Select or unselect an atom in the specified molecule.

Specified by:

selectAtom in interface JMSketchIface

Parameters:

atom - atom index

v - select (true) or unselect (false)

Since:

Marvin 5.0.3, 03/25/2008

setAtomAlias

public void setAtomAlias(int i,
                         java.lang.String alias)

Sets atom alias. Should be called after the molecule has been loaded.

Specified by:

setAtomAlias in interface JMSketchIface

Parameters:

i - the atom index

alias - the alias

Since:

Marvin 3.5

getAtomAlias

public java.lang.String getAtomAlias(int i)

Gets atom alias. Should be called after the molecule has been loaded.

Specified by:

getAtomAlias in interface JMSketchIface

Parameters:

i - the atom index

Returns:

the atom alias

Since:

Marvin 3.5

setAtomExtraLabel

public void setAtomExtraLabel(int i,
                              java.lang.String label)

Sets extra atom label. Should be called after the molecule has been loaded.

Specified by:

setAtomExtraLabel in interface JMSketchIface

Parameters:

i - the atom index

label - the extra atom label

Since:

Marvin 3.5

getAtomExtraLabel

public java.lang.String getAtomExtraLabel(int i)

Gets extra atom label. Should be called after the molecule has been loaded.

Specified by:

getAtomExtraLabel in interface JMSketchIface

Parameters:

i - the atom index

Returns:

the extra atom label

Since:

Marvin 3.5

getMolMass

public double getMolMass()

Gets the molecule weight. Should be called after the molecule has been loaded.

Specified by:

getMolMass in interface JMSketchIface

Returns:

the molecule weight

Since:

Marvin 4.0.2

getMolExactMass

public double getMolExactMass()

Gets the exact molecule weight. Should be called after the molecule has been loaded.

Specified by:

getMolExactMass in interface JMSketchIface

Returns:

the exact molecule weight

Since:

Marvin 4.0.2

getMolFormula

public java.lang.String getMolFormula()

Gets the molecule formula. Should be called after the molecule has been loaded.

Specified by:

getMolFormula in interface JMSketchIface

Returns:

the molecule formula

Since:

Marvin 4.0.2

evaluateChemicalTerms

public java.lang.String evaluateChemicalTerms(java.lang.String expression)

Evaluates a Chemical Terms expression on the molecule in MarvinSketch, and returns the result in string format. Should be called after the molecule has been loaded.

Examples:

 s1 = MSketch.evaluateChemicalTerms("atomCount()");
 s2 = MSketch.evaluateChemicalTerms("logP() <= 5");
 

See the Chemical Terms Language Reference and the Chemical Terms Reference Tables for more.

Specified by:

evaluateChemicalTerms in interface JMSketchIface

Parameters:

expression - the Chemical Terms expression

Returns:

the result of the evaluation

Since:

Marvin 5.1

isChemicalTermsExpressionSyntaxError

public boolean isChemicalTermsExpressionSyntaxError()

Returns true, if the last Chemical Terms expression evaluated by the JMSketchIface.evaluateChemicalTerms(String) method is a syntactically not correct expression. Should be called after JMSketchIface.evaluateChemicalTerms(String).

Specified by:

isChemicalTermsExpressionSyntaxError in interface JMSketchIface

Returns:

true, if the last evaluated Chemical Terms expression is syntactically not correct

Since:

Marvin 5.1.2

setMol

public void setMol(java.lang.String s)

Starts loading a molecule into the sketcher in a separate thread.

Specified by:

setMol in interface JMSketchIface

Parameters:

s - molfile contents, URL or (Unix) filename

setMol

public void setMol(java.lang.String s,
                   java.lang.String opts)

Starts loading a molecule into the sketcher in a separate thread. The file format and/or import options can be specified if the second argument is in one of the following forms: "options", "format:", or "format:options". See the text formats and their options on the File Formats in Marvin page.

Specified by:

setMol in interface JMSketchIface

Parameters:

s - molfile contents, URL or (Unix) filename

opts - options or null

Since:

Marvin 3.3

getPiece

public java.lang.String getPiece(java.lang.String fmt)

Gets the current molecule piece in the specified format. Should be called after the molecule has been loaded.

Specified by:

getPiece in interface JMSketchIface

Parameters:

fmt - the format

Returns:

the molecule in a molecule file format

Since:

Marvin 2.2

See Also:

JMSketchIface.getMol(java.lang.String)

setPiece

public void setPiece(java.lang.String s)

Sets the current piece. This method makes it possible to implement the Periodic Table of elements and tables of template molecules as external JavaScript/HTML components.

Specified by:

setPiece in interface JMSketchIface

Parameters:

s - string containing the molecule in a molecule file format

postImage

public void postImage(java.lang.String fmt,
                      java.lang.String where)

Posts image to CGI script. This method is experimental. Do not use it yet!

Specified by:

postImage in interface JMSketchIface

Parameters:

fmt - image file format: "jpeg", "png" or "ppm"

Since:

Marvin 2.9.12

undo

public void undo()

Invokes the Undo command.

Specified by:

undo in interface JMSketchIface

Since:

Marvin 4.1.2

redo

public void redo()

Invokes the Redo command.

Specified by:

redo in interface JMSketchIface

Since:

Marvin 4.1.2

getImageShowURL

public java.lang.String getImageShowURL()

Gets the show image URL.

Specified by:

getImageShowURL in interface JMSketchIface

Returns:

the URL or null

setAutoScale

public void setAutoScale(boolean as)

Sets the autoscale property. If autoscale is true the molecule is sized to fit on the molecule panel.

Specified by:

setAutoScale in interface JMSketchIface

Parameters:

as - true to switch on, false to switch off autoscale

Since:

Marvin 2.9.3

getAutoScale

public boolean getAutoScale()

Returns the autoscale property.

Specified by:

getAutoScale in interface JMSketchIface

Returns:

true if autoscale is on, false if off

Since:

Marvin 2.9.3

getScale

public double getScale()

Gets the magnification.

Specified by:

getScale in interface JMSketchIface

Returns:

the scaling factor

Since:

Marvin 2.2

setScale

public void setScale(double m)

Sets the magnification. Changes the mag parameter at runtime.

Specified by:

setScale in interface JMSketchIface

Parameters:

m - the scaling factor

hasValenceError

public boolean hasValenceError()

Determines if this molecule has a valence error on any of its atoms.

Specified by:

hasValenceError in interface JMSketchIface

Returns:

true if there is an atom with valence error, false if there is no valence error

Since:

Marvin 4.1.3 11/13/2006

mouseEntered

public void mouseEntered(java.awt.event.MouseEvent ev)

Does nothing. @param ev the event object

Specified by:

mouseEntered in interface java.awt.event.MouseListener

mouseExited

public void mouseExited(java.awt.event.MouseEvent ev)

Does nothing. @param ev the event object

Specified by:

mouseExited in interface java.awt.event.MouseListener

mouseClicked

public void mouseClicked(java.awt.event.MouseEvent ev)

Does nothing. @param ev the event object

Specified by:

mouseClicked in interface java.awt.event.MouseListener

mousePressed

public void mousePressed(java.awt.event.MouseEvent ev)

Does nothing. @param ev the event object

Specified by:

mousePressed in interface java.awt.event.MouseListener

mouseReleased

public void mouseReleased(java.awt.event.MouseEvent ev)

Handles the viewer button press events.

Specified by:

mouseReleased in interface java.awt.event.MouseListener

Parameters:

ev - the event object

setParentApplet

public void setParentApplet(javax.swing.JApplet parent)

Specified by:

setParentApplet in interface MAppletIface

Since:

5.1.6 (Not included in 5.2.0)