chemaxon.marvin.alignment
Class AlignmentMoleculeFactory

java.lang.Object
  chemaxon.marvin.alignment.AlignmentMoleculeFactory

public class AlignmentMoleculeFactory
extends java.lang.Object

Creates an AlignmentMolecule form a Molecule based on the settings.

Since:

Marvin 5.4

Author:

Adrian Kalaszi

Nested Class Summary

static interface

AlignmentMoleculeFactory.ProgressBarInterface

Constructor Summary

AlignmentMoleculeFactory()

Method Summary

AlignmentMolecule	generate(int molID, Molecule m, boolean enableTranslateAndRotate, boolean flexible) Creates an AlignmentMolecule form a Molecule based on the values of the setters.
byte[]	generateData(int molID, Molecule m, boolean enableTranslateAndRotate, boolean flexible) Creates an AlignmentMolecule form a Molecule based on the values of the setters.
chemaxon.marvin.alignment.NodeColor	getColor()
int	getFlexibleRingRotatableBondCount()
int	getFlexibleRingSize()
AlignmentMoleculeFactory.ProgressBarInterface	getProgressBar()
Molecule	getResultMolecule()
boolean	isAromatize()
boolean	isCreateRingCenters()
boolean	isDehidrogenize()
boolean	isGenerateDistanceRanges()
void	setAromatize(boolean aromatize) Aromatize the input molecule
void	setColor(AlignmentProperties.ColoringScheme color) sets which atomtypes to use.
void	setDehidrogenize(boolean dehidrogenize) Remove hydrogens from input molecule.
void	setFlexibleRingRotatableBondCount(int rotatableBondsInRings)
void	setFlexibleRingSize(int rotatableRingSize)
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)

Methods inherited from class java.lang.Object

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

Constructor Detail

AlignmentMoleculeFactory

public AlignmentMoleculeFactory()

Method Detail

generateData

public byte[] generateData(int molID,
                           Molecule m,
                           boolean enableTranslateAndRotate,
                           boolean flexible)
                    throws chemaxon.marvin.alignment.AlignmentException

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:

chemaxon.marvin.alignment.AlignmentException

getProgressBar

public AlignmentMoleculeFactory.ProgressBarInterface getProgressBar()

setProgressBar

public void setProgressBar(AlignmentMoleculeFactory.ProgressBarInterface progressBar)

generate

public AlignmentMolecule generate(int molID,
                                  Molecule m,
                                  boolean enableTranslateAndRotate,
                                  boolean flexible)
                           throws chemaxon.marvin.alignment.AlignmentException

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:

chemaxon.marvin.alignment.AlignmentException

isCreateRingCenters

public boolean isCreateRingCenters()

setNotSpecCase

public void setNotSpecCase(AlignmentProperties.ColorNotSpecifiedCase ncase)

setDehidrogenize

public void setDehidrogenize(boolean dehidrogenize)

Remove hydrogens from input molecule.

Parameters:

dehidrogenize - Default is true.

getResultMolecule

public Molecule getResultMolecule()

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

public void setAromatize(boolean aromatize)

Aromatize the input molecule

Parameters:

aromatize - default is true.

setFlexibleRingRotatableBondCount

public void setFlexibleRingRotatableBondCount(int rotatableBondsInRings)

setFlexibleRingSize

public void setFlexibleRingSize(int rotatableRingSize)

setNodeType

public void setNodeType(AlignmentProperties.NodeType nodeType)

setColor

public void setColor(AlignmentProperties.ColoringScheme color)

sets which atomtypes to use.

Parameters:

color -

getColor

public chemaxon.marvin.alignment.NodeColor getColor()

isAromatize

public boolean isAromatize()

isDehidrogenize

public boolean isDehidrogenize()

isGenerateDistanceRanges

public boolean isGenerateDistanceRanges()

getFlexibleRingRotatableBondCount

public int getFlexibleRingRotatableBondCount()

getFlexibleRingSize

public int getFlexibleRingSize()