Package com.actelion.research.chem.descriptor

Class DescriptorHandlerBinarySkelSpheres

java.lang.Object

com.actelion.research.chem.descriptor.AbstractDescriptorHandlerFP<StereoMolecule>

com.actelion.research.chem.descriptor.DescriptorHandlerBinarySkelSpheres

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.

Field Summary

Fields

Modifier and Type	Field	Description
static java.lang.String	VERSION

Fields inherited from class com.actelion.research.chem.descriptor.AbstractDescriptorHandlerFP

FAILED_OBJECT

Fields inherited from interface com.actelion.research.chem.descriptor.DescriptorHandler

FAILED_BYTES, FAILED_STRING

Constructor Summary

Constructors

Constructor	Description
DescriptorHandlerBinarySkelSpheres()

Method Summary

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

Methods inherited from class java.lang.Object

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

Field Detail

VERSION

public static final java.lang.String VERSION

Constructor Detail

DescriptorHandlerBinarySkelSpheres

public DescriptorHandlerBinarySkelSpheres()

Method Detail

getInfo

public DescriptorInfo getInfo()

getVersion

public java.lang.String getVersion()

createDescriptor

public int[] createDescriptor(StereoMolecule mol)

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:

getThreadSafeCopy

public DescriptorHandler getThreadSafeCopy()

Returns:

a deep copy for parallel computing.

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 interface ISimilarityCalculator<int[]>

Overrides:

getSimilarity in class AbstractDescriptorHandlerFP<StereoMolecule>

Parameters:

a1 -

a2 -

Returns:

normalized similarity.

getDefaultInstance

public static DescriptorHandlerBinarySkelSpheres getDefaultInstance()

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:

correctionTS

public static double correctionTS(double s)