@PublicAPI public final class MMPAlignmentProperties extends java.lang.Object
Constructor and Description |
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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(AlignmentProperties.FlexibilityMode flex,
AlignmentAccuracyMode mode)
Deprecated.
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MMPAlignmentProperties(AlignmentProperties.FlexibilityMode flex,
AlignmentAccuracyMode mode,
double mcsLimit)
Constructs a MMPAlignmentProperties object.
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MMPAlignmentProperties(AlignmentProperties.FlexibilityMode flex,
AlignmentAccuracyMode mode,
double mcsLimit,
boolean fastMode)
Constructs a MMPAlignmentProperties object.
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MMPAlignmentProperties(AlignmentProperties.FlexibilityMode flex,
AlignmentAccuracyMode mode,
double mcsLimit,
boolean fastMode,
int confTryCountLimit)
Constructs a MMPAlignmentProperties object.
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MMPAlignmentProperties(AlignmentProperties.FlexibilityMode flex,
AlignmentAccuracyMode mode,
double mcsLimit,
int confTryCountLimit)
Constructs a MMPAlignmentProperties object.
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Modifier and Type | Method and Description |
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AlignmentAccuracyMode |
getAccuracyMode() |
int |
getConfTryCountLimit() |
AlignmentProperties.FlexibilityMode |
getFlexibilityMode() |
double |
getMcsSimilarityLimit() |
public MMPAlignmentProperties()
public MMPAlignmentProperties(AlignmentProperties.FlexibilityMode flex, AlignmentAccuracyMode mode, double mcsLimit)
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.public MMPAlignmentProperties(AlignmentProperties.FlexibilityMode flex, AlignmentAccuracyMode mode, double mcsLimit, int confTryCountLimit)
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.public MMPAlignmentProperties(AlignmentProperties.FlexibilityMode flex, AlignmentAccuracyMode mode, double mcsLimit, boolean fastMode)
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 Alignmentpublic MMPAlignmentProperties(AlignmentProperties.FlexibilityMode flex, AlignmentAccuracyMode mode, double mcsLimit, boolean fastMode, int confTryCountLimit)
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 AlignmentconfTryCountLimit
- number of starting conformations for the non-MCS part to start the optimization for
maximizing the shape overlay.@Deprecated public MMPAlignmentProperties(AlignmentProperties.FlexibilityMode flex, AlignmentAccuracyMode mode)
public AlignmentAccuracyMode getAccuracyMode()
public AlignmentProperties.FlexibilityMode getFlexibilityMode()
public double getMcsSimilarityLimit()
public int getConfTryCountLimit()