chemaxon.marvin.alignment

Class MMPAlignmentProperties

java.lang.Object

chemaxon.marvin.alignment.MMPAlignmentProperties

@PublicAPI
public final class MMPAlignmentProperties
extends java.lang.Object

Input property settings for MMPAlignment.

Author:

Adrian Kalaszi

Constructor Summary

Constructors

Constructor and Description
MMPAlignmentProperties() Constructs a MMPAlignmentProperties object with the options: FlexibilityMode.KEEP_FIRST_RIGID_SECOND_FLEXIBLE_EXTRA, AlignmentAccuracyMode.ACCURATE, and MCS similarity limit :0.3
MMPAlignmentProperties(AlignmentProperties.FlexibilityMode flex, AlignmentAccuracyMode mode) Deprecated.
MMPAlignmentProperties(AlignmentProperties.FlexibilityMode flex, AlignmentAccuracyMode mode, double mcsLimit) Constructs a MMPAlignmentProperties object.
MMPAlignmentProperties(AlignmentProperties.FlexibilityMode flex, AlignmentAccuracyMode mode, double mcsLimit, boolean fastMode) Constructs a MMPAlignmentProperties object.
MMPAlignmentProperties(AlignmentProperties.FlexibilityMode flex, AlignmentAccuracyMode mode, double mcsLimit, boolean fastMode, int confTryCountLimit) Constructs a MMPAlignmentProperties object.
MMPAlignmentProperties(AlignmentProperties.FlexibilityMode flex, AlignmentAccuracyMode mode, double mcsLimit, int confTryCountLimit) Constructs a MMPAlignmentProperties object.

Method Summary

Modifier and Type	Method and Description
AlignmentAccuracyMode	getAccuracyMode()
int	getConfTryCountLimit()
AlignmentProperties.FlexibilityMode	getFlexibilityMode()
double	getMcsSimilarityLimit()

Methods inherited from class java.lang.Object

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

Constructor Detail

MMPAlignmentProperties

public MMPAlignmentProperties()

Constructs a MMPAlignmentProperties object with the options: FlexibilityMode.KEEP_FIRST_RIGID_SECOND_FLEXIBLE_EXTRA, AlignmentAccuracyMode.ACCURATE, and MCS similarity limit :0.3

MMPAlignmentProperties

public MMPAlignmentProperties(AlignmentProperties.FlexibilityMode flex,
                              AlignmentAccuracyMode mode,
                              double mcsLimit)

Constructs a MMPAlignmentProperties object.

Parameters:

flex - Controls which molecule should be kept flexible or rigid during the 3D overlay.

mode - Determines the shape representation accuracy for molecules.

mcsLimit - Determines the minimum limit for the MCS Tanimoto similarity McsSearchResult.getSimilarity(). If the value in the calculation is smaller than this limit, the MCS based Alignment falls back to the shape based overlay.

MMPAlignmentProperties

public MMPAlignmentProperties(AlignmentProperties.FlexibilityMode flex,
                              AlignmentAccuracyMode mode,
                              double mcsLimit,
                              int confTryCountLimit)

Constructs a MMPAlignmentProperties object.

Parameters:

flex - Controls which molecule should be kept flexible or rigid during the 3D overlay.

mode - Determines the shape representation accuracy for molecules.

mcsLimit - Determines the minimum limit for the MCS Tanimoto similarity McsSearchResult.getSimilarity(). If the value in the calculation is smaller than this limit, the MCS based Alignment falls back to the shape based overlay.

confTryCountLimit - number of starting conformations for the non-MCS part to start the optimization for maximizing the shape overlay.

MMPAlignmentProperties

public MMPAlignmentProperties(AlignmentProperties.FlexibilityMode flex,
                              AlignmentAccuracyMode mode,
                              double mcsLimit,
                              boolean fastMode)

Constructs a MMPAlignmentProperties object.

Parameters:

flex - Controls which molecule should be kept flexible or rigid during the 3D overlay.

mode - Determines the shape representation accuracy for molecules.

mcsLimit - Determines the minimum limit for the MCS Tanimoto similarity McsSearchResult.getSimilarity(). If the value in the calculation is smaller than this limit, the MCS based Alignment falls back to the shape based overlay.

fastMode - do fast mode Alignment

MMPAlignmentProperties

public MMPAlignmentProperties(AlignmentProperties.FlexibilityMode flex,
                              AlignmentAccuracyMode mode,
                              double mcsLimit,
                              boolean fastMode,
                              int confTryCountLimit)

Constructs a MMPAlignmentProperties object.

Parameters:

flex - Controls which molecule should be kept flexible or rigid during the 3D overlay.

mode - Determines the shape representation accuracy for molecules.

mcsLimit - Determines the minimum limit for the MCS Tanimoto similarity McsSearchResult.getSimilarity(). If the value in the calculation is smaller than this limit, the MCS based Alignment falls back to the shape based overlay.

fastMode - do fast mode Alignment

confTryCountLimit - number of starting conformations for the non-MCS part to start the optimization for maximizing the shape overlay.

MMPAlignmentProperties

@Deprecated
public MMPAlignmentProperties(AlignmentProperties.FlexibilityMode flex,
                                          AlignmentAccuracyMode mode)

Deprecated.

Method Detail

getAccuracyMode

public AlignmentAccuracyMode getAccuracyMode()

getFlexibilityMode

public AlignmentProperties.FlexibilityMode getFlexibilityMode()

Returns:

the selected conformational flexibility treatment mode during the alignment.

getMcsSimilarityLimit

public double getMcsSimilarityLimit()

Returns:

the mcs Tanimoto similarity limit.

getConfTryCountLimit

public int getConfTryCountLimit()

Returns:

the confTryCountLimit