chemaxon.struc.graphics

Class MAtomSetPoint

java.lang.Object

chemaxon.struc.MObject

chemaxon.struc.MPoint

chemaxon.struc.graphics.MAtomSetPoint

All Implemented Interfaces:

Serializable, Cloneable

public class MAtomSetPoint
extends MPoint

Point fixed to the location of one or more atoms. The point's location is the weighted average of the atom locations. Useful for creating bond or atom pair type electron source/sink points for MEFlow.

Since:

Marvin 3.5, 07/05/2004

Version:

5.3, 09/25/2009

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

Constructor and Description
MAtomSetPoint() Contructs an empty point object.
MAtomSetPoint(MAtomSetPoint p) Copy constructor.
MAtomSetPoint(MolAtom[] a) Contructs a point object.

Method Summary

Methods

Modifier and Type	Method and Description
boolean	checkValidity(MDocument doc, Collection<MolAtom> invec) Is it a valid object in the document?
MAtomSetPoint	clone() Creates a clone.
void	connectToSgroupOfAtom(SuperatomSgroup sg, MolAtom a)
boolean	containsAtom(MolAtom a) Checks if the atom set contains the specified atom object.
boolean	equals(Object o) Two points equal if their atoms equal.
void	finishCloning(MDocument olddoc, MDocument newdoc) Finish cloning a document.
protected MolAtom[]	getAtomArray()
MolAtom[]	getAtoms() Gets the atoms.
void	getLocation(DPoint3 q, CTransform3D trot) Gets the location.
MPoint	getPoint(int i) Gets the point.
double[]	getWeights() Gets the atom weights used in average location calculation.
boolean	isTransformable() Is it a transformable object?
void	replaceAtom(MolAtom orig, MolAtom a) Replaces a contained atom with another one.
void	setAtoms(MolAtom[] a) Sets the atoms.
void	setLocation(DPoint3 p, CTransform3D trot) Sets the atom coordinates.
void	setWeights(double[] w) Sets the atom weights for location calculation.
String	toString() Overrides Object.toString() to ease debugging.
void	transform(CTransform3D t, int opts, CTransform3D trot) Does not perform any operation.

Methods inherited from class chemaxon.struc.MPoint

calcCenter, distanceFrom, getLocation, getLocation, getPointCount, getPointRef, getPointRefCount, hashCode, isChildOf, isInternalSelectable

Methods inherited from class chemaxon.struc.MObject

addAttributeKeys, addCdataAttributeKeys, addNotify, addNotify, containsPoint, distanceFrom, fixClonedPoints, getAttribute, getBackground, getColor, getLineColor, hasBackground, hasColor, hasLineColor, isEmpty, isReactionArrow, isSelectableNow, isSelected, makeColor, removeAtom, removeChild, removeNotify, removeNotify, setAttribute, setBackground, setColor, setLineColor, setSelected, unselectContents, updateBoundingRect, updateBoundingRect

Methods inherited from class java.lang.Object

finalize, getClass, notify, notifyAll, wait, wait, wait

Constructor Detail

MAtomSetPoint

public MAtomSetPoint()

Contructs an empty point object.

MAtomSetPoint

public MAtomSetPoint(MolAtom[] a)

Contructs a point object.

Parameters:

a - array of atoms

MAtomSetPoint

public MAtomSetPoint(MAtomSetPoint p)

Copy constructor.

Parameters:

p - the point

Method Detail

equals

public boolean equals(Object o)

Two points equal if their atoms equal.

Overrides:

equals in class MPoint

Parameters:

o - the other point

Returns:

true if they equal, false otherwise

clone

public MAtomSetPoint clone()

Description copied from class: MObject

Creates a clone.

Overrides:

clone in class MPoint

Returns:

the clone

setAtoms

public void setAtoms(MolAtom[] a)

Sets the atoms.

Parameters:

a - the atoms

getAtoms

public MolAtom[] getAtoms()

Gets the atoms.

Returns:

the atoms

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

connectToSgroupOfAtom

public void connectToSgroupOfAtom(SuperatomSgroup sg,
                         MolAtom a)

Overrides:

connectToSgroupOfAtom in class MObject

replaceAtom

public void replaceAtom(MolAtom orig,
               MolAtom a)

Replaces a contained atom with another one.

Overrides:

replaceAtom in class MObject

Parameters:

orig - the original atom

a - the new atom

Since:

Marvin 3.5, 07/04/2004

getLocation

public void getLocation(DPoint3 q,
               CTransform3D trot)

Gets the location. The atom set's location is the weighted average of the atom locations.

Overrides:

getLocation in class MPoint

Parameters:

q - the output point object

trot - the viewing transformation or null

Since:

Marvin 4.1, 04/28/2006

setLocation

public void setLocation(DPoint3 p,
               CTransform3D trot)

Sets the atom coordinates. The atom set's location is the weighted average of the atom locations.

Overrides:

setLocation in class MPoint

Parameters:

p - the new location

trot - the viewing transformation or null

getPoint

public MPoint getPoint(int i)

Gets the point.

Overrides:

getPoint in class MPoint

Parameters:

i - the point index (must be 0)

Returns:

the point's clone

getWeights

public double[] getWeights()

Gets the atom weights used in average location calculation.

Returns:

the weights or null

Since:

Marvin 4.1, 04/21/2006

setWeights

public void setWeights(double[] w)

Sets the atom weights for location calculation.

Parameters:

w - the atom weights or null

Since:

Marvin 4.1, 04/21/2006

transform

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

Does not perform any operation. An atom set point's location is fixed to the atoms.

Overrides:

transform in class MPoint

Parameters:

t - the transformation matrix

opts - transform options or 0

trot - the viewing transformation or null

See Also:

MObject.TRANSFORM_DISTORT

isTransformable

public boolean isTransformable()

Is it a transformable object?

Overrides:

isTransformable in class MObject

Returns:

true if the object can be transformed, false otherwise

Since:

Marvin 3.5, 07/06/2004

checkValidity

public boolean checkValidity(MDocument doc,
                    Collection<MolAtom> invec)

Is it a valid object in the document?

Overrides:

checkValidity in class MObject

Parameters:

doc - the document

invec - collection of invalid atoms or null

Returns:

true if the object is valid, false if it contains an unknown atom

Since:

Marvin 3.5, 07/06/2004

finishCloning

public void finishCloning(MDocument olddoc,
                 MDocument newdoc)

Finish cloning a document. Called by the copy constructor.

Overrides:

finishCloning in class MObject

Since:

Marvin 3.5, 07/02/2004

getAtomArray

protected MolAtom[] getAtomArray()

toString

public String toString()

Description copied from class: MObject

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.

Overrides:

toString in class MObject

Returns:

a string representation of the object