Package chemaxon.marvin.alignment

Class AlignmentMoleculeFactory

java.lang.Object

chemaxon.marvin.alignment.AlignmentMoleculeFactory

@PublicApi
public class AlignmentMoleculeFactory
extends Object

Creates an AlignmentMolecule form a Molecule based on the settings.

Since:

Marvin 5.4

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static interface	AlignmentMoleculeFactory.ProgressBarInterface

Constructor Summary

Constructors

Constructor	Description
AlignmentMoleculeFactory()

Method Summary

Modifier and Type	Method	Description
AlignmentMolecule	create(ShapeData shapeData, AlignmentProperties.DegreeOfFreedomType df)
AlignmentMolecule	create(Molecule m, AlignmentProperties.DegreeOfFreedomType df)
AlignmentMolecule	generate(int cdID, int molID, Molecule m, boolean enableTranslateAndRotate, boolean flexible)	Deprecated, for removal: This API element is subject to removal in a future version. Use create(Molecule, AlignmentProperties.DegreeOfFreedomType) instead.
AlignmentMolecule	generate(int molID, Molecule m, boolean enableTranslateAndRotate, boolean flexible)	Deprecated. Use create(Molecule, AlignmentProperties.DegreeOfFreedomType) instead.
byte[]	generateData(int molID, Molecule m, boolean enableTranslateAndRotate, boolean flexible)	Deprecated, for removal: This API element is subject to removal in a future version. use invalid reference ShapeData.toData instead.
int	getFlexibleRingRotatableBondCount()
int	getFlexibleRingSize()
AlignmentMoleculeFactory.ProgressBarInterface	getProgressBar()
Molecule	getResultMolecule()
boolean	isAromatize()	Deprecated, for removal: This API element is subject to removal in a future version.
boolean	isCreateRingCenters()
boolean	isDehidrogenize()	Deprecated, for removal: This API element is subject to removal in a future version. The explicit Hydrogens are not removed from the original input structure.
boolean	isGenerateDistanceRanges()
void	setAromatize(boolean aromatize)	Deprecated, for removal: This API element is subject to removal in a future version. The original input structure is not aromatized.
void	setColor(AlignmentProperties.ColoringScheme color)	sets which atomtypes to use.
void	setDehidrogenize(boolean dehidrogenize)	Deprecated, for removal: This API element is subject to removal in a future version. The explicit Hydrogens are not removed from the original input structure.
void	setFlexibleRingRotatableBondCount(int rotatableBondsInRings)
void	setFlexibleRingSize(int flexibleRingSize)
void	setForcedFlexible(boolean forcedFlexible)	Deprecated, for removal: This API element is subject to removal in a future version. use AlignmentProperties.DegreeOfFreedomType.TRANSLATE_ROTATE_FLEXIBLE_EXTRA to get the same behavior in the create(chemaxon.marvin.alignment.ShapeData, chemaxon.marvin.alignment.AlignmentProperties.DegreeOfFreedomType) methods.
void	setGenerateDistanceRanges(boolean generateDistanceRanges)	Generate intermolecular atomic distance ranges by tweaking conformation.
void	setNodeType(AlignmentProperties.NodeType nodeType)
void	setNotSpecCase(AlignmentProperties.ColorNotSpecifiedCase ncase)
void	setProgressBar(AlignmentMoleculeFactory.ProgressBarInterface progressBar)
void	setUseAllAtoms(boolean useAllAtoms)
void	setUseOriginal(boolean useOriginal)	Deprecated, for removal: This API element is subject to removal in a future version. always false: Molecule is always converted before alignment, but coordinates are written back to the original one.

Methods inherited from class java.lang.Object

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

Constructor Details

AlignmentMoleculeFactory

public AlignmentMoleculeFactory()

Method Details

generateData

@Deprecated(forRemoval=true)
@SubjectToRemoval(date=JUL_01_2025)
public byte[] generateData(int molID,
 Molecule m,
 boolean enableTranslateAndRotate,
 boolean flexible)
                    throws AlignmentException

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

use

invalid reference

ShapeData.toData

instead.

Creates an AlignmentMolecule form a Molecule based on the values of the setters.

Parameters:

molID - molID of the molecule to return.

m - input Molecule

enableTranslateAndRotate - Enables translation and rotation degrees of freedom for this molecule

flexible - Enables rotation around rotatable bonds.

Returns:

AlignmentMolecule or FlexibleMolecule serialized to byte[] ready for writing to DB.

Throws:

AlignmentException

getProgressBar

public AlignmentMoleculeFactory.ProgressBarInterface getProgressBar()

setProgressBar

public void setProgressBar(AlignmentMoleculeFactory.ProgressBarInterface progressBar)

setUseAllAtoms

public void setUseAllAtoms(boolean useAllAtoms)

Parameters:

useAllAtoms - the useAllAtoms to set

setForcedFlexible

@Deprecated(forRemoval=true)
@SubjectToRemoval(date=JUL_01_2025)
public void setForcedFlexible(boolean forcedFlexible)

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

use AlignmentProperties.DegreeOfFreedomType.TRANSLATE_ROTATE_FLEXIBLE_EXTRA to get the same behavior in the create(chemaxon.marvin.alignment.ShapeData, chemaxon.marvin.alignment.AlignmentProperties.DegreeOfFreedomType) methods.

setUseOriginal

@Deprecated(forRemoval=true)
@SubjectToRemoval(date=JUL_01_2025)
public void setUseOriginal(boolean useOriginal)

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

always false: Molecule is always converted before alignment, but coordinates are written back to the original one.

Use original input structure during the calculation. Normally modifications are performed on the structure prior alignment.

Parameters:

useOriginal - the useOriginal to set

create

public AlignmentMolecule create(ShapeData shapeData,
 AlignmentProperties.DegreeOfFreedomType df)

generate

@Deprecated
public AlignmentMolecule generate(int molID,
 Molecule m,
 boolean enableTranslateAndRotate,
 boolean flexible)
                           throws AlignmentException

Deprecated.

Use create(Molecule, AlignmentProperties.DegreeOfFreedomType) instead.

Creates an AlignmentMolecule form a Molecule based on the values of the setters.

Parameters:

molID - molID of the molecule to return.

m - input Molecule

enableTranslateAndRotate - Enables translation and rotation degrees of freedom for this molecule

flexible - Enables rotation around rotatable bonds.

Returns:

AlignmentMolecule or FlexibleMolecule .

Throws:

AlignmentException

generate

@Deprecated(forRemoval=true)
@SubjectToRemoval(date=JUL_01_2025)
public AlignmentMolecule generate(int cdID,
 int molID,
 Molecule m,
 boolean enableTranslateAndRotate,
 boolean flexible)
                           throws AlignmentException

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

Use create(Molecule, AlignmentProperties.DegreeOfFreedomType) instead.

Returns:

AlignmentMolecule or FlexibleMolecule .

Throws:

AlignmentException

create

public AlignmentMolecule create(Molecule m,
 AlignmentProperties.DegreeOfFreedomType df)

isCreateRingCenters

public boolean isCreateRingCenters()

setNotSpecCase

public void setNotSpecCase(AlignmentProperties.ColorNotSpecifiedCase ncase)

setDehidrogenize

@Deprecated(forRemoval=true)
@SubjectToRemoval(date=JUL_01_2025)
public void setDehidrogenize(boolean dehidrogenize)

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

The explicit Hydrogens are not removed from the original input structure. No need to use.

Parameters:

dehidrogenize - no effect.

setGenerateDistanceRanges

public void setGenerateDistanceRanges(boolean generateDistanceRanges)

Generate intermolecular atomic distance ranges by tweaking conformation. Finding min max. Can take long.

Parameters:

generateDistanceRanges - default is false.

setAromatize

@Deprecated(forRemoval=true)
@SubjectToRemoval(date=JUL_01_2025)
public void setAromatize(boolean aromatize)

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

The original input structure is not aromatized. No need to use.

Aromatize the molecule.

Parameters:

aromatize - has no effect.

setFlexibleRingRotatableBondCount

public void setFlexibleRingRotatableBondCount(int rotatableBondsInRings)

setFlexibleRingSize

public void setFlexibleRingSize(int flexibleRingSize)

setNodeType

public void setNodeType(AlignmentProperties.NodeType nodeType)

setColor

public void setColor(AlignmentProperties.ColoringScheme color)

sets which atomtypes to use.

isAromatize

@Deprecated(forRemoval=true)
@SubjectToRemoval(date=JUL_01_2025)
public boolean isAromatize()

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

Original input structure is not aromatized

Returns:

false

isDehidrogenize

@Deprecated(forRemoval=true)
@SubjectToRemoval(date=JUL_01_2025)
public boolean isDehidrogenize()

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

The explicit Hydrogens are not removed from the original input structure. No need to use.

Returns:

false

isGenerateDistanceRanges

public boolean isGenerateDistanceRanges()

getFlexibleRingRotatableBondCount

public int getFlexibleRingRotatableBondCount()

getFlexibleRingSize

public int getFlexibleRingSize()

getResultMolecule

public Molecule getResultMolecule()

Returns:

the resultMolecule