Package chemaxon.marvin.alignment
Class MMPAlignmentProperties
- java.lang.Object
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- chemaxon.marvin.alignment.MMPAlignmentProperties
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@PublicAPI public final class MMPAlignmentProperties extends Object
Input property settings for MMPAlignment.
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Constructor Summary
Constructors Constructor Description MMPAlignmentProperties()
Constructs a MMPAlignmentProperties object with the options: FlexibilityMode.KEEP_FIRST_RIGID_SECOND_FLEXIBLE_EXTRA, AlignmentAccuracyMode.ACCURATE, and MCS similarity limit :0.3MMPAlignmentProperties(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.
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description AlignmentAccuracyMode
getAccuracyMode()
int
getConfTryCountLimit()
AlignmentProperties.FlexibilityMode
getFlexibilityMode()
double
getMcsSimilarityLimit()
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Constructor Detail
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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
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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 similarityMcsSearchResult.getSimilarity()
. If the value in the calculation is smaller than this limit, the MCS based Alignment falls back to the shape based overlay.
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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 similarityMcsSearchResult.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.
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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 similarityMcsSearchResult.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
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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 similarityMcsSearchResult.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 AlignmentconfTryCountLimit
- number of starting conformations for the non-MCS part to start the optimization for maximizing the shape overlay.
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MMPAlignmentProperties
@Deprecated public MMPAlignmentProperties(AlignmentProperties.FlexibilityMode flex, AlignmentAccuracyMode mode)
Deprecated.
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Method Detail
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getAccuracyMode
public AlignmentAccuracyMode getAccuracyMode()
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getFlexibilityMode
public AlignmentProperties.FlexibilityMode getFlexibilityMode()
- Returns:
- the selected conformational flexibility treatment mode during the alignment.
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getMcsSimilarityLimit
public double getMcsSimilarityLimit()
- Returns:
- the mcs Tanimoto similarity limit.
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getConfTryCountLimit
public int getConfTryCountLimit()
- Returns:
- the confTryCountLimit
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