chemaxon.marvin.alignment
Class AlignmentMolecule

java.lang.Object
  chemaxon.marvin.alignment.AlignmentMolecule

All Implemented Interfaces:

java.io.Serializable

public class AlignmentMolecule
extends java.lang.Object
implements java.io.Serializable

Author:

Adrian Kalaszi

See Also:

Serialized Form

Method Summary

void	clearAssigned()
AlignmentMolecule	clone()
void	crdMolRefresh()
void	crdSafeRefresh()
static AlignmentMolecule	create(byte[] bytes)
int	getAtomCount()
AlignmentProperties.ColoringScheme	getColoringScheme()
chemaxon.marvin.alignment.NodeColor	getColors()
double[][]	getMolCrd()
Molecule	getMoleculeOrig()
int	getMolID()
int	getNodeCount()
chemaxon.marvin.alignment.NodeList<? extends chemaxon.marvin.alignment.Node>	getNodes()
int	getRotBondCount()
chemaxon.marvin.alignment.Visualizable	getVisualizable()
double	getVolume()
void	initVariables(boolean enableTranslateAndRotate) After reading from byte[] with create(byte[] bytes) initialize variables.
boolean	isAssigned(int i)
boolean	isEnableTranslateAndRotate()
void	setAssigned(int i, boolean b)
void	setEnableTranslateAndRotate(boolean enableTranslateAndRotate)
Molecule	showSelectedNodes()
byte[]	toData() Serializes the current object to a byte array
java.lang.String	toString()

Methods inherited from class java.lang.Object

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

Method Detail

getNodes

public chemaxon.marvin.alignment.NodeList<? extends chemaxon.marvin.alignment.Node> getNodes()

initVariables

public void initVariables(boolean enableTranslateAndRotate)

After reading from byte[] with create(byte[] bytes) initialize variables.

Parameters:

enableTranslateAndRotate - enable translation and rotation degrees of freedom.

getColoringScheme

public AlignmentProperties.ColoringScheme getColoringScheme()

getColors

public chemaxon.marvin.alignment.NodeColor getColors()

getVisualizable

public chemaxon.marvin.alignment.Visualizable getVisualizable()

getRotBondCount

public int getRotBondCount()

create

public static AlignmentMolecule create(byte[] bytes)

clone

public AlignmentMolecule clone()

Overrides:

clone in class java.lang.Object

toData

public byte[] toData()

Serializes the current object to a byte array

Returns:

the serialized array

getVolume

public double getVolume()

Returns:

the volume of the molecule in A^3

getAtomCount

public int getAtomCount()

crdSafeRefresh

public void crdSafeRefresh()

crdMolRefresh

public void crdMolRefresh()

getMolID

public int getMolID()

getNodeCount

public int getNodeCount()

getMolCrd

public double[][] getMolCrd()

getMoleculeOrig

public Molecule getMoleculeOrig()

setAssigned

public void setAssigned(int i,
                        boolean b)

isAssigned

public boolean isAssigned(int i)

clearAssigned

public void clearAssigned()

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object

isEnableTranslateAndRotate

public boolean isEnableTranslateAndRotate()

setEnableTranslateAndRotate

public void setEnableTranslateAndRotate(boolean enableTranslateAndRotate)
                                 throws chemaxon.marvin.alignment.AlignmentException

Throws:

chemaxon.marvin.alignment.AlignmentException

showSelectedNodes

public Molecule showSelectedNodes()