chemaxon.struc
Class MDocument

java.lang.Object
  chemaxon.struc.MDocument

All Implemented Interfaces:

MTransformable, java.io.Serializable

Direct Known Subclasses:

MSelectionDocument

public class MDocument

extends java.lang.Object

implements MTransformable, java.io.Serializable

Marvin document. Stores molecules and graphics objects.

Since:

Marvin 3.1.4

Version:

4.1.1, 08/23/2006

Author:

Peter Csizmadia, Eva Hollo, Erika Biro

See Also:

Serialized Form

Nested Class Summary

class

MDocument.Prop Property that stores an MDocument.

Field Summary

protected MChemicalStruct	mainMChemicalStruct
protected chemaxon.struc.graphics.MMoleculeMovie	mainMMoleculeMovie
protected MObject	objectContainingSelection
protected java.util.ArrayList	objects
static int	SETCOLOR_COLORLESS The atom/bond set is colorless, normal (CPK, Monochrome etc.) colors are used.
static int	SETCOLOR_DEFAULT Default set colors should are used for coloring the atom/bond set.
static int	SETCOLOR_SPECIFIED The user specified set colors are used for coloring the atom/bond set.

Constructor Summary

	MDocument(MDocument doc) Copy constructor.
protected	MDocument(MDocument doc, boolean cloneobjs) Copy constructor.
	MDocument(Molecule[] mols) Creates a document for the specified molecule animation.
	MDocument(MoleculeGraph m) Creates a document for the specified molecule graph.

Method Summary

void	addObject(MObject o) Adds an object to the document.
DPoint3	calcCenter() Calculates the geometrical center.
DPoint3	calcCenter(CTransform3D t) Calculates the geometrical center.
void	clear() Clears the document.
void	clearSets() Clears the atomSets and the bondSets.
java.lang.Object	clone() Creates a clone.
MDocument	cloneDocument() Creates a clone.
Molecule	cloneMainMolecule() Creates a clone.
MoleculeGraph	cloneMainMoleculeGraph() Creates a clone.
void	cloneSets(MDocument doc) Clones the atom/bond sets from doc.
boolean	contains(MDocument doc) Tests whether the document contains all objects of another document.
boolean	contains(MObject o) Searches an object in the document.
boolean	containsOnlyOne(java.lang.Class cl) Tests whether the document contains only one object of the specified class.
byte[]	exportToBinFormat(java.lang.String fmt) Creates a binary representation of the document.
java.lang.String	exportToFormat(java.lang.String fmt) Creates a string representation of the document.
java.lang.Object	exportToObject(java.lang.String fmt) Creates a String, byte[] array or Image representation of the molecule.
Molecule[]	getAllMolecules() Gets an array containing all molecule objects.
Molecule[]	getAllNonEmptyMolecules() Gets an array containing all non-empty molecule objects.
java.awt.Color	getAtomSetColor(int seq) Gets an atom set color.
int	getAtomSetColorMode(int seq) Gets the atom set coloring mode.
MFont	getAtomSetFont(int seq) Gets an atom set font.
int	getAtomSetRGB(int seq) Gets an atom set color.
int	getAtomSetSize() Gets the size of the atom set.
java.awt.Color	getBondSetColor(int seq) Gets a bond set color.
int	getBondSetColorMode(int seq) Gets the bond set coloring mode.
int	getBondSetRGB(int seq) Gets a bond set color.
int	getBondSetSize() Gets the bond set size.
double	getBondSetThickness(int seq) Gets a bond set thickness.
MObject	getDraggedObject() Gets the dragged object
long	getEndPosition() Gets the end position of this document in the input file.
java.awt.Color	getExtraLabelSetColor(int seq)
int	getExtraLabelSetColorMode(int seq) Gets the coloring mode of extra label set sequences.
MFont	getExtraLabelSetFont(int seq)
long	getExtraLabelSetRGBs(int seq)
int	getExtraLabelSetSize()
MObject	getFocus() Gets the focused object
MPropertyContainer	getGUIPropertyContainer()
java.lang.String	getInputFormat() Gets the input file format.
MoleculeGraph	getMainMoleculeGraph() Gets the main molecule graph.
chemaxon.struc.graphics.MMoleculeMovie	getMoleculeMovie() Gets the molecule movie.
chemaxon.struc.MProp	getMProp() Gets the document as a property.
MObject	getObject(int i) Gets an object
MObject	getObjectContainingSelection() Gets the object that contains the selection.
int	getObjectCount() Gets the number of objects in this document.
chemaxon.struc.PageSettings	getPageSettings() Gets the page settings of multipage molecular document.
Molecule	getPrimaryMolecule() Gets the primary molecule object.
Molecule[]	getPrimaryMolecules() Gets an array containing the primary molecule objects.
long	getStartPosition() Gets the starting position of this document in the input file.
void	highlight(MObject o) Highlight an object.
int	indexOf(MObject o) Searches an object in the document.
boolean	isEmpty() Tests whether the document is empty.
boolean	isHighlighted(MObject o) Is the specified object currently highlighted?
boolean	isSimpleMolecule() Tests whether the document is equivalent to a simple molecule.
void	moveMainMoleculeGraphToFront() Move the main molecule graph to the top of stack.
void	moveMoleculeMovieToFront() Move the molecule movie (if exists) to the top of stack.
void	moveObject(MObject o, int i) Move an object to another place in the stack.
static MDocument	parseMRV(java.lang.String sval) Parses a document from a string in Marvin Document (MRV) format.
MPropertyContainer	properties() Gets the property container.
void	removeAtom(MolAtom a) Removes an atom from all the chemical graphs and removes all graphics objects that contain its reference.
void	removeAtom(MolAtom a, int cleanupFlags) Removes an atom from all the chemical graphs and removes all graphics objects that contain its reference.
void	removeNodeFromGraphs(CNode node) Removes the specified node from all molecule graphs.
void	removeObject(int i) Removes an object from the document.
void	removeObject(MObject o) Removes an object from the document.
void	selectAllObjects(boolean s) Selects or unselects all objects.
void	setAtomSetColorMode(int seq, int m) Sets the atom set coloring mode.
void	setAtomSetFont(int seq, MFont font) Sets the font of an atom set.
void	setAtomSetRGB(int seq, int rgb) Sets the color of an atom set.
void	setBondSetColorMode(int seq, int m) Sets the bond set coloring mode.
void	setBondSetRGB(int seq, int rgb) Sets the color of a bond set.
void	setBondSetThickness(int seq, double thickness) Sets the thickness of a bond set.
void	setDraggedObject(MObject o) Sets the dragged object.
void	setEndPosition(long off) Sets the end position of this document in the input file.
void	setExtraLabelColorsForDocument(Molecule mol) Sets the coloring mode sets and colors of extra labels
void	setExtraLabelSetColorMode(int seq, int mode)
void	setExtraLabelSetRGBs(int seq, int rgb)
void	setFocus(MObject o) Focus to the specified object.
void	setGUIProperyContainer(MPropertyContainer gpc) Sets the property container storing MarvinPane settings
void	setInputFormat(java.lang.String format) Sets the input file format.
void	setMainMoleculeGraph(MoleculeGraph m) Sets the main molecule graph.
void	setMoleculeMovie(chemaxon.struc.graphics.MMoleculeMovie mmm) Sets the molecule movie.
void	setObject(MObject o, int i) Sets an object
void	setObjectContainingSelection(MObject o) Sets the object that contains the selection.
void	setPageSettings(chemaxon.struc.PageSettings pageSettings) Sets the page settings of multipage molecular document.
void	setStartPosition(long off) Sets the starting position of this document in the input file.
java.lang.String	toString() Overrides Object.toString() to ease debugging.
void	transform(CTransform3D t) Transforms all object's coordinates.
void	transform(CTransform3D t, int opts) Transforms all object's coordinates.
void	transform(CTransform3D t, int opts, CTransform3D trot) Transforms all object's coordinates.
void	unhighlight(MObject o) Unhighlights an object.
void	unhighlightAll() Unhighlights all objects.

Methods inherited from class java.lang.Object

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

Field Detail

SETCOLOR_DEFAULT

public static final int SETCOLOR_DEFAULT

Default set colors should are used for coloring the atom/bond set.

Since:

Marvin 4.1, 05/31/2006

See Also:

getAtomSetColorMode(int), getBondSetColorMode(int), Constant Field Values

SETCOLOR_SPECIFIED

public static final int SETCOLOR_SPECIFIED

The user specified set colors are used for coloring the atom/bond set.

Since:

Marvin 4.1, 05/31/2006

See Also:

getAtomSetColorMode(int), getBondSetColorMode(int), Constant Field Values

SETCOLOR_COLORLESS

public static final int SETCOLOR_COLORLESS

The atom/bond set is colorless, normal (CPK, Monochrome etc.) colors are used.

Since:

Marvin 4.1, 05/31/2006

See Also:

getAtomSetColorMode(int), getBondSetColorMode(int), Constant Field Values

objects

protected transient java.util.ArrayList objects

mainMChemicalStruct

protected transient MChemicalStruct mainMChemicalStruct

mainMMoleculeMovie

protected transient chemaxon.struc.graphics.MMoleculeMovie mainMMoleculeMovie

objectContainingSelection

protected transient MObject objectContainingSelection

Constructor Detail

MDocument

public MDocument(MoleculeGraph m)

Creates a document for the specified molecule graph.

Parameters:

m - the main molecule graph

MDocument

public MDocument(Molecule[] mols)

Creates a document for the specified molecule animation.

Parameters:

mols - the molecule animation

Since:

Marvin 4.0, 06/30/2005

MDocument

public MDocument(MDocument doc)

Copy constructor.

Parameters:

doc - the source

MDocument

protected MDocument(MDocument doc,
                    boolean cloneobjs)

Copy constructor.

Parameters:

doc - the source

cloneobjs - whether to clone objects

Since:

Marvin 3.5, 11/06/2004

Method Detail

cloneSets

public void cloneSets(MDocument doc)

Clones the atom/bond sets from doc.

Parameters:

doc - the document to clone from.

parseMRV

public static MDocument parseMRV(java.lang.String sval)
                          throws chemaxon.formats.MolFormatException

Parses a document from a string in Marvin Document (MRV) format.

Parameters:

sval - the string

Throws:

chemaxon.formats.MolFormatException

Since:

Marvin 4.1, 11/20/2005

cloneDocument

public MDocument cloneDocument()

Creates a clone.

Returns:

the clone

Since:

Marvin 3.5.1, 11/20/2004

cloneMainMolecule

public final Molecule cloneMainMolecule()

Creates a clone.

Returns:

the main molecule of the clone

Throws:

java.lang.ClassCastException - if the main molecule graph is not a Molecule instance

Since:

Marvin 3.5.1, 11/20/2004

cloneMainMoleculeGraph

public final MoleculeGraph cloneMainMoleculeGraph()

Creates a clone.

Returns:

the main molecule graph of the clone

Since:

Marvin 3.5.1, 11/20/2004

clone

public final java.lang.Object clone()

Creates a clone.

Returns:

the clone

removeNodeFromGraphs

public void removeNodeFromGraphs(CNode node)

Removes the specified node from all molecule graphs.

Parameters:

node - the node to remove

selectAllObjects

public void selectAllObjects(boolean s)

Selects or unselects all objects.

getObjectContainingSelection

public MObject getObjectContainingSelection()

Gets the object that contains the selection.

Returns:

the object or null

setObjectContainingSelection

public void setObjectContainingSelection(MObject o)

Sets the object that contains the selection. All other objects's contents are unselected.

Parameters:

o - the object or null

isHighlighted

public boolean isHighlighted(MObject o)

Is the specified object currently highlighted?

Returns:

true if it is highlighted, false otherwise

highlight

public void highlight(MObject o)

Highlight an object.

Parameters:

o - the object to highlight

unhighlight

public void unhighlight(MObject o)

Unhighlights an object.

Parameters:

o - the object to unhighlight

unhighlightAll

public void unhighlightAll()

Unhighlights all objects.

getDraggedObject

public MObject getDraggedObject()

Gets the dragged object

Returns:

the dragged object or null

setDraggedObject

public void setDraggedObject(MObject o)

Sets the dragged object.

Parameters:

o - the object

getFocus

public MObject getFocus()

Gets the focused object

Returns:

the focused object or null

setFocus

public void setFocus(MObject o)

Focus to the specified object.

Parameters:

o - the object

getMainMoleculeGraph

public MoleculeGraph getMainMoleculeGraph()

Gets the main molecule graph.

Returns:

the molecule graph

setMainMoleculeGraph

public void setMainMoleculeGraph(MoleculeGraph m)

Sets the main molecule graph.

Parameters:

m - the molecule graph

getMoleculeMovie

public chemaxon.struc.graphics.MMoleculeMovie getMoleculeMovie()

Gets the molecule movie.

Returns:

the molecule movie or null

Since:

Marvin 4.0, 06/30/2005

getPrimaryMolecule

public Molecule getPrimaryMolecule()

Gets the primary molecule object. The main molecule graph is returned if it is a molecule, unless it is empty and a molecule movie is also present. In that case, the current molecule of the movie is returned. WARNING! Do not change the returned molecule object! The document may become corrupted.

Returns:

the array of molecules

Since:

Marvin 4.0, 06/30/2005

getPrimaryMolecules

public Molecule[] getPrimaryMolecules()

Gets an array containing the primary molecule objects. The main molecule graph is returned if it is a molecule, unless it is empty and a molecule movie is also present. In that case, the molecules of the movie are returned. WARNING! Do not change the returned molecule objects! The document may become corrupted.

Returns:

the array of molecules

Since:

Marvin 4.0, 06/30/2005

getAllMolecules

public Molecule[] getAllMolecules()

Gets an array containing all molecule objects. WARNING! Do not change the returned molecule objects! The document may become corrupted.

Returns:

the array of molecules

Since:

Marvin 4.0, 06/30/2005

getAllNonEmptyMolecules

public Molecule[] getAllNonEmptyMolecules()

Gets an array containing all non-empty molecule objects. WARNING! Do not change the returned molecule objects! The document may become corrupted.

Returns:

the array of molecules

Since:

Marvin 4.0, 06/30/2005

setMoleculeMovie

public void setMoleculeMovie(chemaxon.struc.graphics.MMoleculeMovie mmm)

Sets the molecule movie.

Parameters:

mmm - the molecule movie

Since:

Marvin 4.0, 06/30/2005

indexOf

public int indexOf(MObject o)

Searches an object in the document.

Parameters:

o - the object

Returns:

the object's index if found, -1 otherwise

moveObject

public void moveObject(MObject o,
                       int i)

Move an object to another place in the stack.

Parameters:

o - the object

i - the new position

moveMainMoleculeGraphToFront

public void moveMainMoleculeGraphToFront()

Move the main molecule graph to the top of stack.

moveMoleculeMovieToFront

public void moveMoleculeMovieToFront()

Move the molecule movie (if exists) to the top of stack.

Since:

Marvin 4.0, 06/30/2005

contains

public boolean contains(MObject o)

Searches an object in the document.

Parameters:

o - the object

Returns:

true if the document contains the object, false otherwise

contains

public boolean contains(MDocument doc)

Tests whether the document contains all objects of another document.

Parameters:

doc - the other document

Returns:

true if the document contains the objects of the other document, false otherwise

Since:

Marvin 3.4

containsOnlyOne

public boolean containsOnlyOne(java.lang.Class cl)

Tests whether the document contains only one object of the specified class.

Parameters:

cl - MObject.class or a derived class

Returns:

true if no more and not less than one non-empty object is instance of the specified class

Since:

Marvin 3.5, 07/12/2004

addObject

public void addObject(MObject o)

Adds an object to the document.

Parameters:

o - the object

removeObject

public void removeObject(MObject o)

Removes an object from the document.

Parameters:

o - the object

removeObject

public void removeObject(int i)

Removes an object from the document.

Parameters:

i - the object index

getObjectCount

public int getObjectCount()

Gets the number of objects in this document.

Returns:

the number of objects

getObject

public MObject getObject(int i)

Gets an object

Parameters:

i - the line number

Returns:

two-element array containing the two endpoints

setObject

public void setObject(MObject o,
                      int i)

Sets an object

Parameters:

o - the object

i - the index

removeAtom

public void removeAtom(MolAtom a)

Removes an atom from all the chemical graphs and removes all graphics objects that contain its reference.

Parameters:

a - the atom to remove

Since:

Marvin 3.5, 07/05/2004

removeAtom

public void removeAtom(MolAtom a,
                       int cleanupFlags)

Removes an atom from all the chemical graphs and removes all graphics objects that contain its reference.

Parameters:

a - the atom to remove

cleanupFlags - cleanup options

Since:

Marvin 4.1, 03/07/2006

clear

public void clear()

Clears the document. Removes all objects except the main molecule graph, from which all atoms, bonds and other objects are removed.

clearSets

public void clearSets()

Clears the atomSets and the bondSets.

isEmpty

public boolean isEmpty()

Tests whether the document is empty.

Returns:

true if the document is empty, false otherwise

isSimpleMolecule

public boolean isSimpleMolecule()

Tests whether the document is equivalent to a simple molecule.

Returns:

true if the document does not have extra properties, false otherwise

Since:

Marvin 4.1, 11/19/2005

transform

public void transform(CTransform3D t)

Transforms all object's coordinates.

Specified by:

transform in interface MTransformable

Parameters:

t - the transformation matrix

transform

public void transform(CTransform3D t,
                      int opts)

Transforms all object's coordinates.

Parameters:

t - the transformation matrix

opts - the transformation options

See Also:

MObject.transform(CTransform3D, int, CTransform3D)

transform

public void transform(CTransform3D t,
                      int opts,
                      CTransform3D trot)

Transforms all object's coordinates.

Parameters:

t - the transformation matrix

opts - the transformation options

trot - the viewing transformation

Since:

Marvin 4.1, 04/28/2006

See Also:

MObject.transform(CTransform3D, int, CTransform3D)

calcCenter

public DPoint3 calcCenter()

Calculates the geometrical center.

Returns:

the center in `absolute' coordinates

calcCenter

public DPoint3 calcCenter(CTransform3D t)

Calculates the geometrical center.

Parameters:

t - the viewing transformation or null

Returns:

the center in transformed coordinates

Since:

Marvin 4.1, 04/28/2006

getStartPosition

public long getStartPosition()

Gets the starting position of this document in the input file.

Returns:

the starting position

setStartPosition

public void setStartPosition(long off)

Sets the starting position of this document in the input file.

Parameters:

off - the starting position

getEndPosition

public long getEndPosition()

Gets the end position of this document in the input file.

Returns:

the end position

setEndPosition

public void setEndPosition(long off)

Sets the end position of this document in the input file.

Parameters:

off - the end position

getInputFormat

public final java.lang.String getInputFormat()

Gets the input file format. Set by the import module if the molecule is from a file.

Returns:

the input file format for the document

setInputFormat

public void setInputFormat(java.lang.String format)

Sets the input file format.

Parameters:

format - the input format

exportToFormat

public final java.lang.String exportToFormat(java.lang.String fmt)
                                      throws MolExportException

Creates a string representation of the document. 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 = doc.exportToFormat("mol");
 s2 = doc.exportToFormat("smiles:a-H"); // aromatize and remove Hydrogens
 

Parameters:

fmt - the format descriptor string

Returns:

string representation of the document in the specified format

Throws:

MolExportException - Export error

java.lang.IllegalArgumentException - Invalid format string.

java.lang.SecurityException - Export module cannot be loaded because of security reasons (firewall).

Since:

Marvin 4.0, 07/01/2005

See Also:

exportToBinFormat(java.lang.String), exportToObject(java.lang.String), Molecule.exportToFormat(java.lang.String)

exportToBinFormat

public final byte[] exportToBinFormat(java.lang.String fmt)
                               throws MolExportException

Creates a binary representation of the document. Works with all the text formats that are supported by the exportToFormat method, and also with the binary image formats (jpeg, msbmp, png, ppm). When creating an image, display options can also be specified in the format descriptor string. Format and options are separated by a colon, multiple options can be separated by commas. See the possible formats and their options on the File Formats in Marvin page. Examples:

 byte[] d1 = doc.exportToBinFormat("mrv");
 byte[] d2 = doc.exportToBinFormat("smiles:a-H"); // aromatize and remove H
 byte[] d3 = doc.exportToBinFormat("ppm:w300,h300,#ffff00");
 byte[] d4 = doc.exportToBinFormat("png:w300,h300,b32,#00ffff00");
 byte[] d5 = doc.exportToBinFormat("jpeg:w300,h300,Q95,#ffff00,spacefill");
 

Parameters:

fmt - the format descriptor string

Returns:

a binary representation of the document in the specified format

Throws:

MolExportException - Export error.

java.lang.IllegalArgumentException - Invalid format string.

java.lang.SecurityException - Export module cannot be loaded because of security reasons (firewall).

Since:

Marvin 4.0, 07/01/2005

See Also:

exportToFormat(java.lang.String), exportToObject(java.lang.String), Molecule.exportToBinFormat(java.lang.String)

exportToObject

public java.lang.Object exportToObject(java.lang.String fmt)
                                throws MolExportException

Creates a String, byte[] array or Image representation of the molecule. When creating an image, display options can also be specified in the format descriptor string. Format and options are separated by a colon, multiple options can be separated by commas. See the possible formats and their options on the File Formats in Marvin page. Examples:

 import java.awt.Image;
 ...
 String s1 = (String)doc.exportToObject("mol");
 String s2 = (String)doc.exportToObject("smiles:a-H"); // aromatize, remove H
 Image img = (Image)doc.exportToObject("image:w300,h300,#ffff00");
 byte[] d3 = (byte[])doc.exportToObject("ppm:w300,h300,#ffff00");
 byte[] d4 = (byte[])doc.exportToObject("png:w300,h300,b32,#00ffff00");
 byte[] d5 = (byte[])doc.exportToObject("jpeg:w300,h300,Q95,#ffff00,spacefill");
 

Parameters:

fmt - the format descriptor string

Returns:

a String, a byte[] array or an Image

Throws:

MolExportException - Export error.

java.lang.IllegalArgumentException - Invalid format string.

java.lang.SecurityException - Export module cannot be loaded because of security reasons (firewall).

Since:

Marvin 4.0, 07/01/2005

See Also:

exportToFormat(java.lang.String), exportToBinFormat(java.lang.String), Molecule.exportToObject(java.lang.String)

getMProp

public chemaxon.struc.MProp getMProp()

Gets the document as a property.

Since:

Marvin 4.1, 08/01/2006

properties

public MPropertyContainer properties()

Gets the property container.

Since:

Marvin 4.0, 06/18/2005

getAtomSetFont

public MFont getAtomSetFont(int seq)

Gets an atom set font.

Parameters:

seq - the atom set sequence number

Returns:

the font

Since:

Marvin 4.0.3, 06/10/2005

setAtomSetFont

public void setAtomSetFont(int seq,
                           MFont font)

Sets the font of an atom set.

Parameters:

seq - atom set sequence number (0, ..., MolAtom.SETSEQ_MAX)

font -

Since:

Marvin 4.0.3, 06/10/2005

getAtomSetColorMode

public int getAtomSetColorMode(int seq)

Gets the atom set coloring mode.

Parameters:

seq - the atom set sequence number

Returns:

the mode

Since:

Marvin 4.1, 05/31/2006

See Also:

SETCOLOR_DEFAULT, SETCOLOR_SPECIFIED, SETCOLOR_COLORLESS

setAtomSetColorMode

public void setAtomSetColorMode(int seq,
                                int m)

Sets the atom set coloring mode.

Parameters:

seq - the atom set sequence number

m - the mode

Since:

Marvin 4.1, 05/31/2006

See Also:

SETCOLOR_DEFAULT, SETCOLOR_SPECIFIED, SETCOLOR_COLORLESS

setExtraLabelSetColorMode

public void setExtraLabelSetColorMode(int seq,
                                      int mode)

getAtomSetSize

public int getAtomSetSize()

Gets the size of the atom set.

Returns:

the atom set size

getExtraLabelSetSize

public int getExtraLabelSetSize()

getAtomSetRGB

public int getAtomSetRGB(int seq)

Gets an atom set color.

Parameters:

seq - the atom set sequence number

Returns:

the RGB values or -1 if unset or default atom coloring is used

Since:

Marvin 4.0, 03/02/2005

getExtraLabelSetRGBs

public long getExtraLabelSetRGBs(int seq)

getExtraLabelSetColorMode

public int getExtraLabelSetColorMode(int seq)

Gets the coloring mode of extra label set sequences.

Parameters:

seq - the atom sequence number

Returns:

the coloring mode

Since:

Marvin 4.1, 07/06/2006

See Also:

SETCOLOR_DEFAULT, SETCOLOR_SPECIFIED, SETCOLOR_COLORLESS

getExtraLabelSetFont

public MFont getExtraLabelSetFont(int seq)

setExtraLabelColorsForDocument

public void setExtraLabelColorsForDocument(Molecule mol)

Sets the coloring mode sets and colors of extra labels

Parameters:

mol - the graph union in the document

setAtomSetRGB

public void setAtomSetRGB(int seq,
                          int rgb)

Sets the color of an atom set. It also sets the color mode of the set to SETCOLOR_SPECIFIED.

Parameters:

seq - atom set sequence number (0, ..., MolAtom.SETSEQ_MAX)

rgb - the RGB values

Since:

Marvin 4.0, 03/02/2005

setExtraLabelSetRGBs

public void setExtraLabelSetRGBs(int seq,
                                 int rgb)

getAtomSetColor

public java.awt.Color getAtomSetColor(int seq)

Gets an atom set color.

Parameters:

seq - the atom set sequence number

Returns:

the color or null if unset or default bond coloring is used

Since:

Marvin 4.0, 03/02/2005

getExtraLabelSetColor

public java.awt.Color getExtraLabelSetColor(int seq)

getBondSetSize

public int getBondSetSize()

Gets the bond set size.

Returns:

the bond set size

getBondSetThickness

public double getBondSetThickness(int seq)

Gets a bond set thickness.

Parameters:

seq - the atom set sequence number

Returns:

the thickness

Since:

Marvin 4.0.3, 10/14/2005

setBondSetThickness

public void setBondSetThickness(int seq,
                                double thickness)

Sets the thickness of a bond set.

Parameters:

seq - bond set sequence number (0, ..., MolAtom.SETSEQ_MAX)

thickness -

Since:

Marvin 4.0.3, 10/14/2005

getBondSetColorMode

public int getBondSetColorMode(int seq)

Gets the bond set coloring mode.

Parameters:

seq - the bond set sequence number

Returns:

the mode

Since:

Marvin 4.1, 05/31/2006

See Also:

SETCOLOR_DEFAULT, SETCOLOR_SPECIFIED, SETCOLOR_COLORLESS

setBondSetColorMode

public void setBondSetColorMode(int seq,
                                int m)

Sets the bond set coloring mode.

Parameters:

seq - the bond set sequence number

m - the mode

Since:

Marvin 4.1, 05/31/2006

See Also:

SETCOLOR_DEFAULT, SETCOLOR_SPECIFIED, SETCOLOR_COLORLESS

getBondSetRGB

public int getBondSetRGB(int seq)

Gets a bond set color.

Parameters:

seq - the bond set sequence number

Returns:

the RGB values or -1 if unset or default coloring is used

Since:

Marvin 4.0, 03/02/2005

setBondSetRGB

public void setBondSetRGB(int seq,
                          int rgb)

Sets the color of a bond set. It also sets the color mode of the set to SETCOLOR_SPECIFIED.

Parameters:

seq - bond set sequence number (1, ..., MolBond.SETSEQ_MAX)

rgb - the RGB values

Since:

Marvin 4.0, 03/02/2005

getBondSetColor

public java.awt.Color getBondSetColor(int seq)

Gets a bond set color.

Parameters:

seq - the bond set sequence number

Returns:

the color or null if unset or default bond coloring is used

Since:

Marvin 4.0, 03/02/2005

toString

public java.lang.String toString()

Overrides Object.toString() to ease debugging. Returns a string consisting of the classname (without the package name!), the at-sign character `@', and the unsigned hexadecimal representation of the hash code of the object. If the main molecule graph is not empty, then the string also contains the number of nodes and edges in "[Na,Mb]" form.

Returns:

a string representation of the object

Since:

Marvin 4.1, 04/18/2006

getPageSettings

public chemaxon.struc.PageSettings getPageSettings()

Gets the page settings of multipage molecular document.

Returns:

the page settings

Since:

Marvin 4.1, 01/09/2006

setPageSettings

public void setPageSettings(chemaxon.struc.PageSettings pageSettings)

Sets the page settings of multipage molecular document.

Parameters:

pageSettings - the page settings

Since:

Marvin 4.1, 01/09/2006

setGUIProperyContainer

public void setGUIProperyContainer(MPropertyContainer gpc)

Sets the property container storing MarvinPane settings

Parameters:

gpc -

Since:

4.1 11/04/2006

getGUIPropertyContainer

public MPropertyContainer getGUIPropertyContainer()

Returns:

the property container storing GUI settings or null

Since:

4.1 11/04/2006