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NAME

FingerprintsBitVector

SYNOPSIS

use Fingerprints::FingerprintsBitVector;

use Fingerprints::FingerprintsBitVector qw(:coefficients);

use Fingerprints::FingerprintsBitVector qw(:all);

DESCRIPTION

FingerprintsBitVector class provides the following methods:

new, BaroniUrbaniSimilarityCoefficient, BuserSimilarityCoefficient, CosineSimilarityCoefficient, DennisSimilarityCoefficient, DiceSimilarityCoefficient, FoldFingerprintsBitVectorByDensity, FoldFingerprintsBitVectorBySize, ForbesSimilarityCoefficient, FossumSimilarityCoefficient, GetBitsAsBinaryString, GetBitsAsDecimalString, GetBitsAsHexadecimalString, GetBitsAsOctalString, GetBitsAsRawBinaryString, GetDescription, GetFingerprintsBitDensity, GetID, GetSpecifiedSize, GetSupportedSimilarityCoefficients, GetVectorType, HamannSimilarityCoefficient, IsFingerprintsBitVector, IsSubSet, JacardSimilarityCoefficient, Kulczynski1SimilarityCoefficient, Kulczynski2SimilarityCoefficient, MatchingSimilarityCoefficient, McConnaugheySimilarityCoefficient, NewFromBinaryString, NewFromDecimalString, NewFromHexadecimalString, NewFromOctalString, NewFromRawBinaryString, OchiaiSimilarityCoefficient, PearsonSimilarityCoefficient, RogersTanimotoSimilarityCoefficient, RussellRaoSimilarityCoefficient, SetDescription, SetID, SetSpecifiedSize, SetVectorType, SimpsonSimilarityCoefficient, SkoalSneath1SimilarityCoefficient, SkoalSneath2SimilarityCoefficient, SkoalSneath3SimilarityCoefficient, StringifyFingerprintsBitVector, TanimotoSimilarityCoefficient, TverskySimilarityCoefficient, WeightedTanimotoSimilarityCoefficient, WeightedTverskySimilarityCoefficient, YuleSimilarityCoefficient

The methods available to create fingerprints bit vector from strings and to calculate similarity coefficient between two bit vectors can also be invoked as class functions.

FingerprintsBitVector class is derived from BitVector class which provides the functionality to manipulate bits.

For two fingerprints bit vectors A and B of same size, let:

Na = Number of bits set to "1" in A
Nb = Number of bits set to "1" in B
Nc = Number of bits set to "1" in both A and B
Nd = Number of bits set to "0" in both A and B

Nt = Number of bits set to "1" or "0" in A or B (Size of A or B)
Nt = Na + Nb - Nc + Nd

Na - Nc = Number of bits set to "1" in A but not in B
Nb - Nc = Number of bits set to "1" in B but not in A

Then, various similarity coefficients [ Ref. 40 - 42 ] for a pair of bit vectors A and B are defined as follows:

BaroniUrbani: ( SQRT( Nc * Nd ) + Nc ) / ( SQRT ( Nc * Nd ) + Nc + ( Na - Nc ) + ( Nb - Nc ) ) ( same as Buser )

Buser: ( SQRT ( Nc * Nd ) + Nc ) / ( SQRT ( Nc * Nd ) + Nc + ( Na - Nc ) + ( Nb - Nc ) ) ( same as BaroniUrbani )

Cosine: Nc / SQRT ( Na * Nb ) (same as Ochiai)

Dice: (2 * Nc) / ( Na + Nb )

Dennis: ( Nc * Nd - ( ( Na - Nc ) * ( Nb - Nc ) ) ) / SQRT ( Nt * Na * Nb)

Forbes: ( Nt * Nc ) / ( Na * Nb )

Fossum: ( Nt * ( ( Nc - 1/2 ) ** 2 ) / ( Na * Nb )

Hamann: ( ( Nc + Nd ) - ( Na - Nc ) - ( Nb - Nc ) ) / Nt

Jaccard: Nc / ( ( Na - Nc) + ( Nb - Nc ) + Nc ) = Nc / ( Na + Nb - Nc ) (same as Tanimoto)

Kulczynski1: Nc / ( ( Na - Nc ) + ( Nb - Nc) ) = Nc / ( Na + Nb - 2Nc )

Kulczynski2: ( ( Nc / 2 ) * ( 2 * Nc + ( Na - Nc ) + ( Nb - Nc) ) ) / ( ( Nc + ( Na - Nc ) ) * ( Nc + ( Nb - Nc ) ) ) = 0.5 * ( Nc / Na + Nc / Nb )

Matching: ( Nc + Nd ) / Nt

McConnaughey: ( Nc ** 2 - ( Na - Nc ) * ( Nb - Nc) ) / ( Na * Nb )

Ochiai: Nc / SQRT ( Na * Nb ) (same as Cosine)

Pearson: ( ( Nc * Nd ) - ( ( Na - Nc ) * ( Nb - Nc ) ) / SQRT ( Na * Nb * ( Na - Nc + Nd ) * ( Nb - Nc + Nd ) )

RogersTanimoto: ( Nc + Nd ) / ( ( Na - Nc) + ( Nb - Nc) + Nt) = ( Nc + Nd ) / ( Na + Nb - 2Nc + Nt)

RussellRao: Nc / Nt

Simpson: Nc / MIN ( Na, Nb)

SkoalSneath1: Nc / ( Nc + 2 * ( Na - Nc) + 2 * ( Nb - Nc) ) = Nc / ( 2 * Na + 2 * Nb - 3 * Nc )

SkoalSneath2: ( 2 * Nc + 2 * Nd ) / ( Nc + Nd + Nt )

SkoalSneath3: ( Nc + Nd ) / ( ( Na - Nc ) + ( Nb - Nc ) ) = ( Nc + Nd ) / ( Na + Nb - 2 * Nc )

Tanimoto: Nc / ( ( Na - Nc) + ( Nb - Nc ) + Nc ) = Nc / ( Na + Nb - Nc ) (same as Jaccard)

Tversky: Nc / ( alpha * ( Na - Nc ) + ( 1 - alpha) * ( Nb - Nc) + Nc ) = Nc / ( alpha * ( Na - Nb ) + Nb)

Yule: ( ( Nc * Nd ) - ( ( Na - Nc ) * ( Nb - Nc ) ) ) / ( ( Nc * Nd ) + ( ( Na - Nc ) * ( Nb - Nc ) ) )

The values of Tanimoto/Jaccard and Tversky coefficients are dependent on only those bit which are set to "1" in both A and B. In order to take into account all bit positions, modified versions of Tanimoto [ Ref. 42 ] and Tversky [ Ref. 43 ] have been developed.

Let:

Na' = Number of bits set to "0" in A
Nb' = Number of bits set to "0" in B
Nc' = Number of bits set to "0" in both A and B

Tanimoto': Nc' / ( ( Na' - Nc') + ( Nb' - Nc' ) + Nc' ) = Nc' / ( Na' + Nb' - Nc' )

Tversky': Nc' / ( alpha * ( Na' - Nc' ) + ( 1 - alpha) * ( Nb' - Nc' ) + Nc' ) = Nc' / ( alpha * ( Na' - Nb' ) + Nb')

Then:

WeightedTanimoto = beta * Tanimoto + (1 - beta) * Tanimoto'

WeightedTversky = beta * Tversky + (1 - beta) * Tversky'

METHODS

new
$NewFPBitVector = new Fingerprints::FingerprintsBitVector($Size);

Creates a new FingerprintsBitVector object of size Size and returns newly created FingerprintsBitVector. Bit numbers range from 0 to 1 less than Size.

BaroniUrbaniSimilarityCoefficient
$Value = $FingerprintsBitVector->BaroniUrbaniSimilarityCoefficient( $OtherFingerprintBitVector);
$Value = Fingerprints::FingerprintsBitVector:: BaroniUrbaniSimilarityCoefficient( $FingerprintsBitVectorA, $FingerprintBitVectorB);

Returns value of BaroniUrbani similarity coefficient between two same size FingerprintsBitVectors.

BuserSimilarityCoefficient
$Value = $FingerprintsBitVector->BuserSimilarityCoefficient( $OtherFingerprintBitVector);
$Value = Fingerprints::FingerprintsBitVector::BuserSimilarityCoefficient( $FingerprintsBitVectorA, $FingerprintBitVectorB);

Returns value of Buser similarity coefficient between two same size FingerprintsBitVectors.

CosineSimilarityCoefficient
$Value = $FingerprintsBitVector->CosineSimilarityCoefficient( $OtherFingerprintBitVector);
$Value = Fingerprints::FingerprintsBitVector::CosineSimilarityCoefficient( $FingerprintsBitVectorA, $FingerprintBitVectorB);

Returns value of Cosine similarity coefficient between two same size FingerprintsBitVectors.

DennisSimilarityCoefficient
$Value = $FingerprintsBitVector->DennisSimilarityCoefficient( $OtherFingerprintBitVector);
$Value = Fingerprints::FingerprintsBitVector::DennisSimilarityCoefficient( $FingerprintsBitVectorA, $FingerprintBitVectorB);

Returns value of Dennis similarity coefficient between two same size FingerprintsBitVectors.

DiceSimilarityCoefficient
$Value = $FingerprintsBitVector->DiceSimilarityCoefficient( $OtherFingerprintBitVector);
$Value = Fingerprints::FingerprintsBitVector::DiceSimilarityCoefficient( $FingerprintsBitVectorA, $FingerprintBitVectorB);

Returns value of Dice similarity coefficient between two same size FingerprintsBitVectors.

FoldFingerprintsBitVectorByDensity
$FingerprintsBitVector->FoldFingerprintsBitVectorByDensity($Density);

Folds FingerprintsBitVector by recursively reducing its size by half until bit density of set bits is greater than or equal to specified Density and returns folded FingerprintsBitVector.

FoldFingerprintsBitVectorBySize
$FingerprintsBitVector->FoldFingerprintsBitVectorBySize($Size);

Folds FingerprintsBitVector by recursively reducing its size by half until size is less than or equal to specified Size and returns folded FingerprintsBitVector.

ForbesSimilarityCoefficient
$Value = $FingerprintsBitVector->ForbesSimilarityCoefficient( $OtherFingerprintBitVector);
$Value = Fingerprints::FingerprintsBitVector::ForbesSimilarityCoefficient( $FingerprintsBitVectorA, $FingerprintBitVectorB);

Returns value of Forbes similarity coefficient between two same size FingerprintsBitVectors.

FossumSimilarityCoefficient
$Value = $FingerprintsBitVector->FossumSimilarityCoefficient( $OtherFingerprintBitVector);
$Value = Fingerprints::FingerprintsBitVector::FossumSimilarityCoefficient( $FingerprintsBitVectorA, $FingerprintBitVectorB);

Returns value of Fossum similarity coefficient between two same size FingerprintsBitVectors.

GetBitsAsBinaryString
$BinaryASCIIString = $FingerprintsBitVector->GetBitsAsBinaryString();

Returns fingerprints as a binary ASCII string containing 0s and 1s.

GetBitsAsHexadecimalString
$HexadecimalString = $FingerprintsBitVector->GetBitsAsHexadecimalString();

Returns fingerprints as a hexadecimal string.

GetBitsAsRawBinaryString
$RawBinaryString = $FingerprintsBitVector->GetBitsAsRawBinaryString();

Returns fingerprints as a raw binary string containing packed bit values for each byte.

GetDescription
$Description = $FingerprintsBitVector->GetDescription();

Returns a string containing description of fingerprints bit vector.

GetFingerprintsBitDensity
$BitDensity = $FingerprintsBitVector->GetFingerprintsBitDensity();

Returns BitDensity of FingerprintsBitVector corresponding to bits set to 1s.

GetID
$ID = $FingerprintsBitVector->GetID();

Returns ID of FingerprintsBitVector.

GetVectorType
$VectorType = $FingerprintsBitVector->GetVectorType();

Returns VectorType of FingerprintsBitVector.

GetSpecifiedSize
$Size = $FingerprintsBitVector->GetSpecifiedSize();

Returns value of specified size for bit vector.

GetSupportedSimilarityCoefficients
@SimilarityCoefficient = Fingerprints::FingerprintsBitVector::GetSupportedSimilarityCoefficients();

Returns an array containing names of supported similarity coefficients.

HamannSimilarityCoefficient
$Value = $FingerprintsBitVector->HamannSimilarityCoefficient( $OtherFingerprintBitVector);
$Value = Fingerprints::FingerprintsBitVector::HamannSimilarityCoefficient( $FingerprintsBitVectorA, $FingerprintBitVectorB);

Returns value of Hamann similarity coefficient between two same size FingerprintsBitVectors.

IsFingerprintsBitVector
$Status = Fingerprints::FingerprintsBitVector:: IsFingerprintsBitVector($Object);

Returns 1 or 0 based on whether Object is a FingerprintsBitVector object.

IsSubSet
$Status = $FingerprintsBitVector->IsSubSet($OtherFPBitVector);
$Status = Fingerprints::FingerprintsBitVector::IsSubSet( $FPBitVectorA, $FPBitVectorB);

Returns 1 or 0 based on whether first firngerprints bit vector is a subset of second fingerprints bit vector.

For a bit vector to be a subset of another bit vector, both vectors must be of the same size and the bit positions set in first vector must also be set in the second bit vector.

JacardSimilarityCoefficient
$Value = $FingerprintsBitVector->JacardSimilarityCoefficient( $OtherFingerprintBitVector);
$Value = Fingerprints::FingerprintsBitVector::JacardSimilarityCoefficient( $FingerprintsBitVectorA, $FingerprintBitVectorB);

Returns value of Jacard similarity coefficient between two same size FingerprintsBitVectors.

Kulczynski1SimilarityCoefficient
$Value = $FingerprintsBitVector->Kulczynski1SimilarityCoefficient( $OtherFingerprintBitVector);
$Value = Fingerprints::FingerprintsBitVector:: Kulczynski1SimilarityCoefficient( $FingerprintsBitVectorA, $FingerprintBitVectorB);

Returns value of Kulczynski1 similarity coefficient between two same size FingerprintsBitVectors.

Kulczynski2SimilarityCoefficient
$Value = $FingerprintsBitVector->Kulczynski2SimilarityCoefficient( $OtherFingerprintBitVector);
$Value = Fingerprints::FingerprintsBitVector:: Kulczynski2SimilarityCoefficient( $FingerprintsBitVectorA, $FingerprintBitVectorB);

Returns value of Kulczynski2 similarity coefficient between two same size FingerprintsBitVectors.

MatchingSimilarityCoefficient
$Value = $FingerprintsBitVector->MatchingSimilarityCoefficient( $OtherFingerprintBitVector);
$Value = Fingerprints::FingerprintsBitVector:: MatchingSimilarityCoefficient( $FingerprintsBitVectorA, $FingerprintBitVectorB);

Returns value of Matching similarity coefficient between two same size FingerprintsBitVectors.

McConnaugheySimilarityCoefficient
$Value = $FingerprintsBitVector->McConnaugheySimilarityCoefficient( $OtherFingerprintBitVector);
$Value = Fingerprints::FingerprintsBitVector:: McConnaugheySimilarityCoefficient( $FingerprintsBitVectorA, $FingerprintBitVectorB);

Returns value of McConnaughey similarity coefficient between two same size FingerprintsBitVectors.

NewFromBinaryString
$NewFPBitVector = $FingerprintsBitVector->NewFromBinaryString( $BinaryString);
$NewFPBitVector = Fingerprints::FingerprintsBitVector::NewFromBinaryString( $BinaryString);

Creates a new FingerprintsBitVector using BinaryString and returns new FingerprintsBitVector object.

NewFromHexadecimalString
$NewFPBitVector = $FingerprintsBitVector->NewFromHexadecimalString( $HexdecimalString);
$NewFPBitVector = Fingerprints::FingerprintsBitVector::
                 NewFromHexadecimalString( $HexdecimalString);

Creates a new FingerprintsBitVector using HexdecimalString and returns new FingerprintsBitVector object.

NewFromRawBinaryString
$NewFPBitVector = $FingerprintsBitVector->NewFromRawBinaryString( $RawBinaryString);
$NewFPBitVector = Fingerprints::FingerprintsBitVector:: NewFromRawBinaryString( $RawBinaryString);

Creates a new FingerprintsBitVector using RawBinaryString and returns new FingerprintsBitVector object.

OchiaiSimilarityCoefficient
$Value = $FingerprintsBitVector->OchiaiSimilarityCoefficient( $OtherFingerprintBitVector);
$Value = Fingerprints::FingerprintsBitVector::OchiaiSimilarityCoefficient( $FingerprintsBitVectorA, $FingerprintBitVectorB);

Returns value of Ochiai similarity coefficient between two same size FingerprintsBitVectors.

PearsonSimilarityCoefficient
$Value = $FingerprintsBitVector->PearsonSimilarityCoefficient( $OtherFingerprintBitVector);
$Value = Fingerprints::FingerprintsBitVector::PearsonSimilarityCoefficient( $FingerprintsBitVectorA, $FingerprintBitVectorB);

Returns value of Pearson similarity coefficient between two same size FingerprintsBitVectors.

RogersTanimotoSimilarityCoefficient
$Value = $FingerprintsBitVector->RogersTanimotoSimilarityCoefficient( $OtherFingerprintBitVector);
$Value = Fingerprints::FingerprintsBitVector:: RogersTanimotoSimilarityCoefficient( $FingerprintsBitVectorA, $FingerprintBitVectorB);

Returns value of RogersTanimoto similarity coefficient between two same size FingerprintsBitVectors.

RussellRaoSimilarityCoefficient
$Value = $FingerprintsBitVector->RussellRaoSimilarityCoefficient( $OtherFingerprintBitVector);
$Value = Fingerprints::FingerprintsBitVector:: RussellRaoSimilarityCoefficient( $FingerprintsBitVectorA, $FingerprintBitVectorB);

Returns value of RussellRao similarity coefficient between two same size FingerprintsBitVectors.

SetSpecifiedSize
$FingerprintsBitVector->SetSpecifiedSize($Size);

Sets specified size for fingerprints bit vector.

Irrespective of specified size, Perl functions used to handle bit data in BitVector class automatically sets the size to the next nearest power of 2. SpecifiedSize is used by FingerprintsBitVector class to process any aribitray size during similarity coefficient calculations.

SetDescription
$FingerprintsBitVector->SetDescription($Description);

Sets Description of fingerprints bit vector and returns FingerprintsBitVector.

SetID
$FingerprintsBitVector->SetID($ID);

Sets ID of fingerprints bit vector and returns FingerprintsBitVector.

SetVectorType
$FingerprintsBitVector->SetVectorType($VectorType);

Sets VectorType of fingerprints bit vector and returns FingerprintsBitVector.

SimpsonSimilarityCoefficient
$Value = $FingerprintsBitVector->SimpsonSimilarityCoefficient( $OtherFingerprintBitVector);
$Value = Fingerprints::FingerprintsBitVector::SimpsonSimilarityCoefficient( $FingerprintsBitVectorA, $FingerprintBitVectorB);

Returns value of Simpson similarity coefficient between two same size FingerprintsBitVectors.

SkoalSneath1SimilarityCoefficient
$Value = $FingerprintsBitVector->SkoalSneath1SimilarityCoefficient( $OtherFingerprintBitVector);
$Value = Fingerprints::FingerprintsBitVector:: SkoalSneath1SimilarityCoefficient( $FingerprintsBitVectorA, $FingerprintBitVectorB);

Returns value of SkoalSneath1 similarity coefficient between two same size FingerprintsBitVectors.

SkoalSneath2SimilarityCoefficient
$Value = $FingerprintsBitVector->SkoalSneath2SimilarityCoefficient( $OtherFingerprintBitVector);
$Value = Fingerprints::FingerprintsBitVector:: SkoalSneath2SimilarityCoefficient( $FingerprintsBitVectorA, $FingerprintBitVectorB);

Returns value of SkoalSneath2 similarity coefficient between two same size FingerprintsBitVectors.

SkoalSneath3SimilarityCoefficient
$Value = $FingerprintsBitVector->SkoalSneath3SimilarityCoefficient( $OtherFingerprintBitVector);
$Value = Fingerprints::FingerprintsBitVector:: SkoalSneath3SimilarityCoefficient( $FingerprintsBitVectorA, $FingerprintBitVectorB);

Returns value of SkoalSneath3 similarity coefficient between two same size FingerprintsBitVectors

StringifyFingerprintsBitVector
$String = $FingerprintsBitVector->StringifyFingerprintsBitVector();

Returns a string containing information about FingerprintsBitVector object.

TanimotoSimilarityCoefficient
$Value = $FingerprintsBitVector->TanimotoSimilarityCoefficient( $OtherFingerprintBitVector);
$Value = Fingerprints::FingerprintsBitVector:: TanimotoSimilarityCoefficient( $FingerprintsBitVectorA, $FingerprintBitVectorB);

Returns value of Tanimoto similarity coefficient between two same size FingerprintsBitVectors.

TverskySimilarityCoefficient
$Value = $FingerprintsBitVector->TverskySimilarityCoefficient( $OtherFingerprintBitVector, $Alpha);
$Value = Fingerprints::FingerprintsBitVector:: TverskySimilarityCoefficient( $FingerprintsBitVectorA, $FingerprintBitVectorB, $Alpha);

Returns value of Tversky similarity coefficient between two same size FingerprintsBitVectors.

WeightedTanimotoSimilarityCoefficient
$Value = $FingerprintsBitVector->WeightedTanimotoSimilarityCoefficient( $OtherFingerprintBitVector, $Beta);
$Value = Fingerprints::FingerprintsBitVector:: WeightedTanimotoSimilarityCoefficient( $FingerprintsBitVectorA, $FingerprintBitVectorB, $Beta);

Returns value of WeightedTanimoto similarity coefficient between two same size FingerprintsBitVectors.

WeightedTverskySimilarityCoefficient
$Value = $FingerprintsBitVector->WeightedTverskySimilarityCoefficient( $OtherFingerprintBitVector, $Alpha, $Beta);
$Value = Fingerprints::FingerprintsBitVector::
     WeightedTverskySimilarityCoefficient(
     $FingerprintsBitVectorA, $FingerprintBitVectorB, $Alpha, $Beta);

Returns value of WeightedTversky similarity coefficient between two same size FingerprintsBitVectors.

YuleSimilarityCoefficient
$Value = $FingerprintsBitVector->YuleSimilarityCoefficient( $OtherFingerprintBitVector);
$Value = Fingerprints::FingerprintsBitVector::YuleSimilarityCoefficient( $FingerprintsBitVectorA, $FingerprintBitVectorB);

Returns value of Yule similarity coefficient between two same size FingerprintsBitVectors.

AUTHOR

Manish Sud

SEE ALSO

BitVector.pm, FingerprintsStringUtil.pm, FingerprintsVector.pm, Vector.pm

COPYRIGHT

Copyright (C) 2019 Manish Sud. All rights reserved.

This file is part of MayaChemTools.

MayaChemTools is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 3 of the License, or (at your option) any later version.

 

 

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