chemaxon.struc.graphics

Class MChemicalStruct

java.lang.Object

chemaxon.struc.MObject

chemaxon.struc.graphics.MChemicalStruct

All Implemented Interfaces:

Serializable, Cloneable

public class MChemicalStruct
extends MObject

Molecule graph object.

Since:

Marvin 3.3

Version:

4.1, 04/28/2005

Author:

Peter Csizmadia

See Also:

Serialized Form

Field Summary

Fields inherited from class chemaxon.struc.MObject

PAINT_ANTIALIAS, PAINT_FOCUSED, TRANSFORM_DISTORT

Constructor Summary

Constructors

Modifier	Constructor and Description
protected	MChemicalStruct(MChemicalStruct mcs) Copy constructor.
	MChemicalStruct(MoleculeGraph m) Contructs a molecule graph object.

Method Summary

Methods

Modifier and Type	Method and Description
void	calcCenter(DPoint3 p, CTransform3D t) Calculates the geometrical center.
MChemicalStruct	clone() Creates a clone.
boolean	containsAtom(MolAtom a) Checks if the atom set contains the specified atom object.
double	distanceFrom(double x, double y, CTransform3D t) Gets the 2D distance from the specified point.
static double	distanceFrom(MoleculeGraph molg, double x, double y, CTransform3D t) Gets the 2D distance from the specified point.
MolAtom	getAtomOf(chemaxon.struc.graphics.MElectronContainer container)
List<chemaxon.struc.graphics.MElectronContainer>	getElectronContainersOf(MolAtom atom)
int	getMElectronContainerIndexInAtom(MolAtom atom, chemaxon.struc.graphics.MElectronContainer container)
chemaxon.struc.graphics.MElectronContainer	getMElectronContainerOf(chemaxon.struc.graphics.MElectron e)
MoleculeGraph	getMoleculeGraph() Gets the stored molecule graph.
MPoint	getPoint(int i) Gets a point of the object.
int	getPointCount() Gets the number of points (atoms).
boolean	hasElectronContainer(MolAtom atom)
boolean	hasSelection() Checks the existence of the selection.
static boolean	hasSelection(MoleculeGraph molg) Checks the existence of the selection.
boolean	isEmpty() A chemical structure object is empty if the molecule graph is empty.
void	removeElectronToAtomMapping(MolAtom atom, chemaxon.struc.graphics.MElectronContainer container)
void	setElectronToAtomMapping(MolAtom atom, chemaxon.struc.graphics.MElectronContainer container)
void	setSelected(boolean s) Selects or unselects the object.
static void	setSelected(MoleculeGraph molg, boolean s) Selects or unselects atoms in a molecule graph.
void	transform(CTransform3D t, int opts, CTransform3D trot) Transforms all points.
void	unselectContents() Unselects atoms.

Methods inherited from class chemaxon.struc.MObject

addAttributeKeys, addCdataAttributeKeys, addNotify, addNotify, checkValidity, connectToSgroupOfAtom, containsPoint, distanceFrom, finishCloning, fixClonedPoints, getAttribute, getBackground, getColor, getLineColor, getPointRef, getPointRefCount, hasBackground, hasColor, hasLineColor, isChildOf, isInternalSelectable, isReactionArrow, isSelectableNow, isSelected, isTransformable, makeColor, removeAtom, removeChild, removeNotify, removeNotify, replaceAtom, setAttribute, setBackground, setColor, setLineColor, toString, updateBoundingRect

Methods inherited from class java.lang.Object

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

Constructor Detail

MChemicalStruct

public MChemicalStruct(MoleculeGraph m)

Contructs a molecule graph object.

Parameters:

m - the molecule graph

MChemicalStruct

protected MChemicalStruct(MChemicalStruct mcs)

Copy constructor.

Parameters:

mcs - the original object

Method Detail

getMoleculeGraph

public MoleculeGraph getMoleculeGraph()

Gets the stored molecule graph.

Returns:

the molecule graph

clone

public MChemicalStruct clone()

Creates a clone.

Overrides:

clone in class MObject

Returns:

the clone

isEmpty

public boolean isEmpty()

A chemical structure object is empty if the molecule graph is empty.

Overrides:

isEmpty in class MObject

Returns:

true if empty, false otherwise

getPointCount

public int getPointCount()

Gets the number of points (atoms).

Specified by:

getPointCount in class MObject

Returns:

the number of points

getPoint

public MPoint getPoint(int i)

Gets a point of the object.

Specified by:

getPoint in class MObject

Parameters:

i - the point index

Returns:

the point's clone

containsAtom

public boolean containsAtom(MolAtom a)

Checks if the atom set contains the specified atom object.

Overrides:

containsAtom in class MObject

Returns:

true if the atom set contains the specified object, false otherwise

Since:

Marvin 3.5, 07/04/2004

transform

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

Transforms all points.

Specified by:

transform in class MObject

Parameters:

t - the transformation matrix

opts - transform options or 0

trot - the viewing transformation or null

See Also:

MObject.TRANSFORM_DISTORT

calcCenter

public void calcCenter(DPoint3 p,
              CTransform3D t)

Calculates the geometrical center.

Specified by:

calcCenter in class MObject

Parameters:

p - store the coordinates here

t - the transformation matrix or null

Since:

Marvin 4.1, 04/28/2006

distanceFrom

public double distanceFrom(double x,
                  double y,
                  CTransform3D t)

Gets the 2D distance from the specified point.

Specified by:

distanceFrom in class MObject

Parameters:

x - the x coordinate

y - the y coordinate

t - transformation or null

Since:

3.5, 11/04/2004

distanceFrom

public static double distanceFrom(MoleculeGraph molg,
                  double x,
                  double y,
                  CTransform3D t)

Gets the 2D distance from the specified point.

Parameters:

x - the x coordinate

y - the y coordinate

t - transformation or null

Since:

4.0, 06/30/2005

setSelected

public void setSelected(boolean s)

Selects or unselects the object.

Overrides:

setSelected in class MObject

Parameters:

s - use true to select, false to unselect

setSelected

public static void setSelected(MoleculeGraph molg,
               boolean s)

Selects or unselects atoms in a molecule graph.

Parameters:

s - use true to select, false to unselect

Since:

Marvin 4.0, 06/30/2005

hasSelection

public boolean hasSelection()

Checks the existence of the selection.

Returns:

true if selection exists, false otherwise

hasSelection

public static boolean hasSelection(MoleculeGraph molg)

Checks the existence of the selection.

Returns:

true if selection exists, false otherwise

Since:

Marvin 4.0, 06/30/2005

unselectContents

public void unselectContents()

Unselects atoms.

Overrides:

unselectContents in class MObject

setElectronToAtomMapping

public void setElectronToAtomMapping(MolAtom atom,
                            chemaxon.struc.graphics.MElectronContainer container)

removeElectronToAtomMapping

public void removeElectronToAtomMapping(MolAtom atom,
                               chemaxon.struc.graphics.MElectronContainer container)

getAtomOf

public MolAtom getAtomOf(chemaxon.struc.graphics.MElectronContainer container)

getElectronContainersOf

public List<chemaxon.struc.graphics.MElectronContainer> getElectronContainersOf(MolAtom atom)

hasElectronContainer

public boolean hasElectronContainer(MolAtom atom)

getMElectronContainerIndexInAtom

public int getMElectronContainerIndexInAtom(MolAtom atom,
                                   chemaxon.struc.graphics.MElectronContainer container)

getMElectronContainerOf

public chemaxon.struc.graphics.MElectronContainer getMElectronContainerOf(chemaxon.struc.graphics.MElectron e)