Class DescriptorHandlerBinarySkelSpheres
- java.lang.Object
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- com.actelion.research.chem.descriptor.AbstractDescriptorHandlerFP<StereoMolecule>
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- com.actelion.research.chem.descriptor.DescriptorHandlerBinarySkelSpheres
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- All Implemented Interfaces:
DescriptorHandler<int[],StereoMolecule>
,ISimilarityCalculator<int[]>
public class DescriptorHandlerBinarySkelSpheres extends AbstractDescriptorHandlerFP<StereoMolecule>
DescriptorHandlerBinarySkelSpheres This descriptor is a binary representation of the Skeleton Spheres descriptor. The correlation with the SkeletonSpheres descriptor was calculated with R²=0.9891. Basis for the correlation were one million similartiy values calculated from 1000 RND samples from /home/korffmo1/Projects/Software/Development/VirtualScreening/data/CalibrationDataset/gpcr_ligandsAllDescriptors.dwar the fraction of 0.25 of the highest similarity values was used to calculate the Pearson correlation coefficient. Created by korffmo1 on 09.05.17.
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Field Summary
Fields Modifier and Type Field Description static java.lang.String
VERSION
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Fields inherited from class com.actelion.research.chem.descriptor.AbstractDescriptorHandlerFP
FAILED_OBJECT
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Fields inherited from interface com.actelion.research.chem.descriptor.DescriptorHandler
FAILED_BYTES, FAILED_STRING
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Constructor Summary
Constructors Constructor Description DescriptorHandlerBinarySkelSpheres()
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description static double
correctionTS(double s)
int[]
createDescriptor(StereoMolecule mol)
static int[]
createDescriptorFromSkelSpheresArrayCompressed(byte[] arrSkelSpheres)
Calculates a binary vector with half number of bits as fields in the original SkeletonSpheres descriptor.static DescriptorHandlerBinarySkelSpheres
getDefaultInstance()
DescriptorInfo
getInfo()
float
getSimilarity(int[] a1, int[] a2)
Calculates the similarity by the number of common bits devided by the total number of bts.DescriptorHandler
getThreadSafeCopy()
java.lang.String
getVersion()
static double
standardize(double s)
The parameter were derived from one million similarity scores with com.actelion.research.chem.descriptor.util.SimilarityCalibration and com.actelion.research.chem.descriptor.util.CalculateStandardsationFactorFromSimilarityMatrix-
Methods inherited from class com.actelion.research.chem.descriptor.AbstractDescriptorHandlerFP
calculationFailed, decode, decode, encode
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Method Detail
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getInfo
public DescriptorInfo getInfo()
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getVersion
public java.lang.String getVersion()
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createDescriptor
public int[] createDescriptor(StereoMolecule mol)
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createDescriptorFromSkelSpheresArrayCompressed
public static int[] createDescriptorFromSkelSpheresArrayCompressed(byte[] arrSkelSpheres)
Calculates a binary vector with half number of bits as fields in the original SkeletonSpheres descriptor. Th length is 512 bits. Two fields of the original SkeletonSpheres descriptor are summarized.- Parameters:
arrSkelSpheres
-- Returns:
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getThreadSafeCopy
public DescriptorHandler getThreadSafeCopy()
- Returns:
- a deep copy for parallel computing.
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getSimilarity
public float getSimilarity(int[] a1, int[] a2)
Calculates the similarity by the number of common bits devided by the total number of bts.- Specified by:
getSimilarity
in interfaceISimilarityCalculator<int[]>
- Overrides:
getSimilarity
in classAbstractDescriptorHandlerFP<StereoMolecule>
- Parameters:
a1
-a2
-- Returns:
- normalized similarity.
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getDefaultInstance
public static DescriptorHandlerBinarySkelSpheres getDefaultInstance()
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standardize
public static double standardize(double s)
The parameter were derived from one million similarity scores with com.actelion.research.chem.descriptor.util.SimilarityCalibration and com.actelion.research.chem.descriptor.util.CalculateStandardsationFactorFromSimilarityMatrix- Parameters:
s
-- Returns:
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correctionTS
public static double correctionTS(double s)
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