chemaxon.marvin.alignment

Class AlignmentMolecule

java.lang.Object

chemaxon.marvin.alignment.AlignmentMolecule

@PublicAPI
public class AlignmentMolecule
extends java.lang.Object

Author:

Adrian Kalaszi

Field Summary

Fields

Modifier and Type	Field and Description
protected int	molID
chemaxon.marvin.alignment.NodeSum	nodes

Method Summary

Modifier and Type	Method and Description
void	clearAssigned()
AlignmentMolecule	cloneMolecule()
void	crdMolRefresh()
void	crdSafeRefresh()
static AlignmentMolecule	create(byte[] bytes) Deprecated.
chemaxon.marvin.alignment.DistanceRangeStore	distanceRangeStore()
int	getAtomCount()
AlignmentProperties.ColoringScheme	getColoringScheme()
chemaxon.marvin.alignment.NodeColor	getColors()
double[][]	getMolCrd()
Molecule	getMoleculeOrig() Gets back a clone of the unmodified input structure.
int	getMolID()
int	getNodeCount()
chemaxon.marvin.alignment.NodeSum	getNodes()
int	getRotBondCount()
chemaxon.marvin.alignment.Visualizable	getVisualizable()
double	getVolume()
void	initVariables(boolean enableTranslateAndRotate)
boolean	isEnableTranslateAndRotate()
double	ownOverlap(AlignmentAccuracyMode mode)
void	setAssigned(int i, boolean b)
void	setEnableTranslateAndRotate(boolean enableTranslateAndRotate)
void	setMolID(int molID)
Molecule	showSelectedNodes()
byte[]	toData() Deprecated.
java.lang.String	toString()

Methods inherited from class java.lang.Object

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

Field Detail

nodes

public chemaxon.marvin.alignment.NodeSum nodes

molID

protected int molID

Method Detail

setMolID

public void setMolID(int molID)

getNodes

public chemaxon.marvin.alignment.NodeSum getNodes()

initVariables

public void initVariables(boolean enableTranslateAndRotate)

Parameters:

enableTranslateAndRotate -

getColoringScheme

public AlignmentProperties.ColoringScheme getColoringScheme()

getColors

public chemaxon.marvin.alignment.NodeColor getColors()

getVisualizable

public chemaxon.marvin.alignment.Visualizable getVisualizable()

getRotBondCount

public int getRotBondCount()

create

@Deprecated
public static AlignmentMolecule create(byte[] bytes)

Deprecated.

cloneMolecule

public AlignmentMolecule cloneMolecule()

toData

@Deprecated
public byte[] toData()

Deprecated.

distanceRangeStore

public chemaxon.marvin.alignment.DistanceRangeStore distanceRangeStore()

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()

Gets back a clone of the unmodified input structure.

Returns:

clone of the unmodified input structure

setAssigned

public void setAssigned(int i,
                        boolean b)

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()

ownOverlap

public double ownOverlap(AlignmentAccuracyMode mode)