Package chemaxon.marvin.alignment

Class AlignmentMolecule

java.lang.Object

chemaxon.marvin.alignment.AlignmentMolecule

@PublicApi
public class AlignmentMolecule
extends Object

Field Summary

Fields

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

Method Summary

Modifier and Type	Method	Description
void	clearAssigned()
AlignmentMolecule	cloneMolecule()
void	crdMolRefresh()
void	crdSafeRefresh()
static AlignmentMolecule	create(byte[] bytes)	Deprecated, for removal: This API element is subject to removal in a future version. Call create(byte[], DegreeOfFreedomType) with AlignmentProperties.DegreeOfFreedomType.TRANSLATE_ROTATE_FLEXIBLE.
static AlignmentMolecule	create(byte[] bytes, AlignmentProperties.DegreeOfFreedomType df)	Deserializes an AlignmentMolecule from a byte array.
int	getAtomCount()
double[][]	getMolCrd()
Molecule	getMoleculeOrig()	Gets back a clone of the unmodified input structure.
int	getMolID()
int	getNodeCount()
int	getRotBondCount()
chemaxon.marvin.alignment.Visualizable	getVisualizable()	For internal use only.
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. use ShapeData.toData() instead.
String	toString()

Methods inherited from class java.lang.Object

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

Field Details

nodes

public chemaxon.marvin.alignment.NodeSum nodes

molID

protected int molID

Method Details

setMolID

public void setMolID(int molID)

initVariables

public void initVariables(boolean enableTranslateAndRotate)

getVisualizable

public chemaxon.marvin.alignment.Visualizable getVisualizable()

For internal use only.

getRotBondCount

public int getRotBondCount()

create

@Deprecated(forRemoval=true)
@SubjectToRemoval(date=JUL_01_2025)
public static AlignmentMolecule create(byte[] bytes)

Deprecated, for removal: This API element is subject to removal in a future version.

Call create(byte[], DegreeOfFreedomType) with AlignmentProperties.DegreeOfFreedomType.TRANSLATE_ROTATE_FLEXIBLE.

Deserializes an AlignmentMolecule from a byte array.

Parameters:

bytes - ShapeData object in a serialized form created by ShapeData.toData() method.

Returns:

the AlignmentMolecule created with AlignmentMoleculeFactory.create(chemaxon.marvin.alignment.ShapeData, chemaxon.marvin.alignment.AlignmentProperties.DegreeOfFreedomType) with AlignmentProperties.DegreeOfFreedomType.TRANSLATE_ROTATE_FLEXIBLE

create

public static AlignmentMolecule create(byte[] bytes,
 AlignmentProperties.DegreeOfFreedomType df)

Deserializes an AlignmentMolecule from a byte array.

Parameters:

bytes - ShapeData object in a serialized form created by ShapeData.toData() method.

Returns:

the AlignmentMolecule created with AlignmentMoleculeFactory.create(chemaxon.marvin.alignment.ShapeData, chemaxon.marvin.alignment.AlignmentProperties.DegreeOfFreedomType)

cloneMolecule

public AlignmentMolecule cloneMolecule()

toData

@Deprecated
public byte[] toData()

Deprecated.

use ShapeData.toData() instead.

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()

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 String toString()

Overrides:

toString in class Object

isEnableTranslateAndRotate

public boolean isEnableTranslateAndRotate()

setEnableTranslateAndRotate

public void setEnableTranslateAndRotate(boolean enableTranslateAndRotate)
                                 throws AlignmentException

Throws:

AlignmentException

showSelectedNodes

public Molecule showSelectedNodes()

ownOverlap

public double ownOverlap(AlignmentAccuracyMode mode)