Package chemaxon.alignment

Class AlignmentMoleculeFactory

java.lang.Object

chemaxon.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	Interface for providing progress feedback during alignment operations.

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 molID, Molecule m, boolean enableTranslateAndRotate, boolean flexible)	Deprecated. Use create(Molecule, AlignmentProperties.DegreeOfFreedomType) instead.
int	getFlexibleRingRotatableBondCount()
int	getFlexibleRingSize()
AlignmentMoleculeFactory.ProgressBarInterface	getProgressBar()
Molecule	getResultMolecule()
boolean	isCreateRingCenters()
boolean	isGenerateDistanceRanges()
void	setColor(AlignmentProperties.ColoringScheme color)	sets which atomtypes to use.
void	setFlexibleRingRotatableBondCount(int rotatableBondsInRings)
void	setFlexibleRingSize(int flexibleRingSize)
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)

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

getProgressBar

public AlignmentMoleculeFactory.ProgressBarInterface getProgressBar()

setProgressBar

public void setProgressBar(AlignmentMoleculeFactory.ProgressBarInterface progressBar)

setUseAllAtoms

public void setUseAllAtoms(boolean useAllAtoms)

Parameters:

useAllAtoms - the useAllAtoms 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

create

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

isCreateRingCenters

public boolean isCreateRingCenters()

setNotSpecCase

public void setNotSpecCase(AlignmentProperties.ColorNotSpecifiedCase ncase)

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.

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.

isGenerateDistanceRanges

public boolean isGenerateDistanceRanges()

getFlexibleRingRotatableBondCount

public int getFlexibleRingRotatableBondCount()

getFlexibleRingSize

public int getFlexibleRingSize()

getResultMolecule

public Molecule getResultMolecule()

Returns:

the resultMolecule