chemaxon.marvin.applet
Class JMSketch

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

All Implemented Interfaces:

chemaxon.marvin.applet.JMSketchIface, chemaxon.marvin.applet.MAppletIface, 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

public class JMSketch
extends AbstractMarvinApplet
implements chemaxon.marvin.applet.JMSketchIface

Swing version of the MarvinSketch Applet.

Since:

Marvin 2.0

Version:

5.3, 11/08/2009

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.BaselineResizeBehavior, java.awt.Component.BltBufferStrategy, java.awt.Component.FlipBufferStrategy

Field Summary

Fields inherited from class chemaxon.marvin.applet.AbstractMarvinApplet

debug, panel

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	clean2D() Invokes the Clean2D command.
void	clean3D() Invokes the Clean3D command.
protected void	createGUI()
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.
protected java.lang.String	evaluateChemicalTerms0(java.lang.String expression, chemaxon.struc.Molecule mol)
java.lang.String	getAtomAlias(int i) Gets atom alias.
int	getAtomCharge(int atomNum) Gets the charge of the specified atom, from the molecule currently used.
int	getAtomCount() Returns the number of atoms.
java.lang.String	getAtomExtraLabel(int i) Gets extra atom label.
int	getAtomRadicalState(int atomNum) Gets the radical state of the specified atom, from the molecule currently used.
java.lang.String	getAtomSymbol(int atomNum) Gets the atom symbol of the specified atom, from the molecule currently used.
int	getAtomValenceProperty(int atomNum) Gets the valence property of the specified atom, from the molecule currently used.
boolean	getAutoScale() Returns the autoscale property.
protected chemaxon.struc.MDocument	getDocInPanel()
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.
protected chemaxon.struc.Molecule	getMolInPanel()
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.
protected chemaxon.marvin.sketch.swing.SketchPanel	getPanel()
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.
boolean	isAtomSelected(int i) Returns true if atom is selected.
boolean	isEmpty() Returns true sketcher canvas is empty.
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	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	setAbsoluteStereoFlag(boolean stereoFlag)
void	setAbsoluteStereoFlag0(java.lang.Boolean stereoFlag)
void	setAtomAlias(int i, java.lang.String alias) Sets atom alias.
void	setAtomCharge(int atomNum, int chg) Sets the charge of the specified atom, from the molecule currently used.
void	setAtomExtraLabel(int i, java.lang.String label) Sets extra atom label.
void	setAtomRadicalState(int atomNum, int radState) Sets the radical state of the specified atom, from the molecule currently used.
void	setAtomValenceProperty(int atomNum, int value) Sets the valence property of the specified atom, from the molecule currently used.
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	setPiece(java.lang.String s) Sets the current piece.
void	setScale(double m) Sets the magnification.
void	start() Starts the applet.
void	undo() Invokes the Undo command.

Methods inherited from class chemaxon.marvin.applet.AbstractMarvinApplet

destroy, enqueueForPrivilegedProcessing, getAppletInBrowser, getAppletInfo, getCodeBase, getParameter, init, isChemicalTermsExpressionSyntaxError, mouseClicked, mouseEntered, mouseExited, mousePressed, propertyChange, setPanel, setParentApplet, stop, validateMoleculeStr, validateMoleculeStr

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

getAppletContext, getAudioClip, getAudioClip, getDocumentBase, getImage, getImage, getLocale, 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, 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, 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

Methods inherited from interface chemaxon.marvin.applet.JMSketchIface

mouseClicked, mouseEntered, mouseExited, mousePressed

Methods inherited from interface chemaxon.marvin.applet.MAppletIface

isChemicalTermsExpressionSyntaxError, setParentApplet, validateMoleculeStr, validateMoleculeStr

Constructor Detail

JMSketch

public JMSketch()

Method Detail

createGUI

protected void createGUI()

Specified by:

createGUI in class AbstractMarvinApplet

start

public void start()

Description copied from class: AbstractMarvinApplet

Starts the applet.

Overrides:

start in class AbstractMarvinApplet

getPanel

protected chemaxon.marvin.sketch.swing.SketchPanel getPanel()

Specified by:

getPanel in class AbstractMarvinApplet

getMolInPanel

protected chemaxon.struc.Molecule getMolInPanel()

getDocInPanel

protected chemaxon.struc.MDocument getDocInPanel()

isEmpty

public boolean isEmpty()

Returns true sketcher canvas is empty.

Specified by:

isEmpty in interface chemaxon.marvin.applet.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 chemaxon.marvin.applet.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 chemaxon.marvin.applet.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 chemaxon.marvin.applet.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 chemaxon.marvin.applet.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 chemaxon.marvin.applet.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 chemaxon.marvin.applet.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 chemaxon.marvin.applet.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 chemaxon.marvin.applet.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 chemaxon.marvin.applet.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 chemaxon.marvin.applet.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 chemaxon.marvin.applet.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 chemaxon.marvin.applet.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 chemaxon.marvin.applet.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 chemaxon.marvin.applet.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 chemaxon.marvin.applet.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 chemaxon.marvin.applet.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 chemaxon.marvin.applet.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 chemaxon.marvin.applet.JMSketchIface

Parameters:

expression - the Chemical Terms expression

Returns:

the result of the evaluation

Since:

Marvin 5.1

evaluateChemicalTerms0

protected java.lang.String evaluateChemicalTerms0(java.lang.String expression,
                                                  chemaxon.struc.Molecule mol)

Overrides:

evaluateChemicalTerms0 in class AbstractMarvinApplet

setMol

public void setMol(java.lang.String s)

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

Specified by:

setMol in interface chemaxon.marvin.applet.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 chemaxon.marvin.applet.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 chemaxon.marvin.applet.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 chemaxon.marvin.applet.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 chemaxon.marvin.applet.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 chemaxon.marvin.applet.JMSketchIface

Since:

Marvin 4.1.2

redo

public void redo()

Invokes the Redo command.

Specified by:

redo in interface chemaxon.marvin.applet.JMSketchIface

Since:

Marvin 4.1.2

clean2D

public void clean2D()

Invokes the Clean2D command.

Specified by:

clean2D in interface chemaxon.marvin.applet.JMSketchIface

Since:

Marvin 5.3

clean3D

public void clean3D()

Invokes the Clean3D command.

Specified by:

clean3D in interface chemaxon.marvin.applet.JMSketchIface

Since:

Marvin 5.3

getImageShowURL

public java.lang.String getImageShowURL()

Gets the show image URL.

Specified by:

getImageShowURL in interface chemaxon.marvin.applet.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 chemaxon.marvin.applet.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 chemaxon.marvin.applet.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 chemaxon.marvin.applet.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 chemaxon.marvin.applet.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 chemaxon.marvin.applet.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

mouseReleased

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

Handles the viewer button press events.

Specified by:

mouseReleased in interface java.awt.event.MouseListener

Overrides:

mouseReleased in class AbstractMarvinApplet

Parameters:

ev - the event object

getAtomSymbol

public java.lang.String getAtomSymbol(int atomNum)

Gets the atom symbol of the specified atom, from the molecule currently used.

Specified by:

getAtomSymbol in interface chemaxon.marvin.applet.JMSketchIface

Parameters:

atomNum - the specified atom's number in the molecule

Returns:

atom symbol

getAtomValenceProperty

public int getAtomValenceProperty(int atomNum)

Gets the valence property of the specified atom, from the molecule currently used.

Specified by:

getAtomValenceProperty in interface chemaxon.marvin.applet.JMSketchIface

Parameters:

atomNum - the specified atom's number in the molecule

Returns:

valence property

setAtomValenceProperty

public void setAtomValenceProperty(int atomNum,
                                   int value)

Sets the valence property of the specified atom, from the molecule currently used.

Specified by:

setAtomValenceProperty in interface chemaxon.marvin.applet.JMSketchIface

Parameters:

atomNum - the specified atom's number in the molecule

value - valence property value

getAtomCharge

public int getAtomCharge(int atomNum)

Gets the charge of the specified atom, from the molecule currently used.

Specified by:

getAtomCharge in interface chemaxon.marvin.applet.JMSketchIface

Parameters:

atomNum - the specified atom's number in the molecule

Returns:

the charge

setAtomCharge

public void setAtomCharge(int atomNum,
                          int chg)

Sets the charge of the specified atom, from the molecule currently used.

Specified by:

setAtomCharge in interface chemaxon.marvin.applet.JMSketchIface

Parameters:

atomNum - the specified atom's number in the molecule

chg - the charge

getAtomRadicalState

public int getAtomRadicalState(int atomNum)

Gets the radical state of the specified atom, from the molecule currently used.

Specified by:

getAtomRadicalState in interface chemaxon.marvin.applet.JMSketchIface

Parameters:

atomNum - the specified atom's number in the molecule

Returns:

radical state

setAtomRadicalState

public void setAtomRadicalState(int atomNum,
                                int radState)

Sets the radical state of the specified atom, from the molecule currently used.

Specified by:

setAtomRadicalState in interface chemaxon.marvin.applet.JMSketchIface

Parameters:

atomNum - the specified atom's number in the molecule

radState - radical state

setAbsoluteStereoFlag

public void setAbsoluteStereoFlag(boolean stereoFlag)

Specified by:

setAbsoluteStereoFlag in interface chemaxon.marvin.applet.JMSketchIface

setAbsoluteStereoFlag0

public void setAbsoluteStereoFlag0(java.lang.Boolean stereoFlag)