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NAME

FingerprintsBitVector

SYNOPSIS

use FingerprintsBitVector;

use FingerprintsBitVector qw(:coefficients);

use FingerprintsBitVector qw(:all);

DESCRIPTION

FingerprintsBitVector class provides the following methods:

new, BaroniUrbaniSimilarityCoefficient, BuserSimilarityCoefficient , CosineSimilarityCoefficient, DennisSimilarityCoefficient , DiceSimilarityCoefficient, EuclidSimilarityCoefficient , FoldFingerprintsBitVectorByDensity, FoldFingerprintsBitVectorBySize , ForbesSimilarityCoefficient, FossumSimilarityCoefficient, GetBitsAsBinaryString , GetBitsAsHexadecimalString, GetBitsAsRawBinaryString, GetFingerprintsBitDensity , GetSupportedSimilarityCoefficients, HamannSimilarityCoefficient , IsFingerprintsBitVector, IsSubSet, JacardSimilarityCoefficient , Kulczynski1SimilarityCoefficient, Kulczynski2SimilarityCoefficient , ManhattanSimilarityCoefficient, MatchingSimilarityCoefficient , McConnaugheySimilarityCoefficient, NewFromBinaryString , NewFromHexadecimalString, NewFromRawBinaryString , OchiaiSimilarityCoefficient, PearsonSimilarityCoefficient , RogersTanimotoSimilarityCoefficient, RussellRaoSimilarityCoefficient , 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:

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)

Euclid: SQRT ( ( Nc + Nd ) / Nt )

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 )

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

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:

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

$NewFPBitVector = new FingerprintsBitVector($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 = FingerprintsBitVector::BaroniUrbaniSimilarityCoefficient( $FingerprintsBitVectorA, $FingerprintBitVectorB);

Returns value of BaroniUrbani similarity coefficient between two same size FingerprintsBitVectors

BuserSimilarityCoefficient

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

Returns value of Buser similarity coefficient between two same size FingerprintsBitVectors

CosineSimilarityCoefficient

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

Returns value of Cosine similarity coefficient between two same size FingerprintsBitVectors

DennisSimilarityCoefficient

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

Returns value of Dennis similarity coefficient between two same size FingerprintsBitVectors

DiceSimilarityCoefficient

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

Returns value of Dice similarity coefficient between two same size FingerprintsBitVectors

EuclidSimilarityCoefficient

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

Returns value of Euclid 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 = FingerprintsBitVector::ForbesSimilarityCoefficient( $FingerprintsBitVectorA, $FingerprintBitVectorB);

Returns value of Forbes similarity coefficient between two same size FingerprintsBitVectors

FossumSimilarityCoefficient

$Value = $FingerprintsBitVector->FossumSimilarityCoefficient( $OtherFingerprintBitVector);
$Value = 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

GetFingerprintsBitDensity

$BitDensity = $FingerprintsBitVector->GetFingerprintsBitDensity();

Returns BitDensity of FingerprintsBitVector corresponding to bits set to 1s

GetSupportedSimilarityCoefficients

@SimilarityCoefficient = FingerprintsBitVector::GetSupportedSimilarityCoefficients();

Returns an array containing names of supported similarity coefficients

HamannSimilarityCoefficient

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

Returns value of Hamann similarity coefficient between two same size FingerprintsBitVectors

IsFingerprintsBitVector

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

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

IsSubSet

$Status = $FingerprintsBitVector->IsSubSet($OtherFPBitVector);
$Status = FingerprintsBitVector::IsSubSet($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 = FingerprintsBitVector::JacardSimilarityCoefficient( $FingerprintsBitVectorA, $FingerprintBitVectorB);

Returns value of Jacard similarity coefficient between two same size FingerprintsBitVectors

Kulczynski1SimilarityCoefficient

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

Returns value of Kulczynski1 similarity coefficient between two same size FingerprintsBitVectors

Kulczynski2SimilarityCoefficient

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

Returns value of Kulczynski2 similarity coefficient between two same size FingerprintsBitVectors

ManhattanSimilarityCoefficient

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

Returns value of Manhattan similarity coefficient between two same size FingerprintsBitVectors

MatchingSimilarityCoefficient

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

Returns value of Matching similarity coefficient between two same size FingerprintsBitVectors

McConnaugheySimilarityCoefficient

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

Returns value of McConnaughey similarity coefficient between two same size FingerprintsBitVectors

NewFromBinaryString

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

Creates a new FingerprintsBitVector using BinaryString and returns new FingerprintsBitVector object

NewFromHexadecimalString

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

Creates a new FingerprintsBitVector using HexdecimalString and returns new FingerprintsBitVector object

NewFromRawBinaryString

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

Creates a new FingerprintsBitVector using RawBinaryString and returns new FingerprintsBitVector object

OchiaiSimilarityCoefficient

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

Returns value of Ochiai similarity coefficient between two same size FingerprintsBitVectors

PearsonSimilarityCoefficient

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

Returns value of Pearson similarity coefficient between two same size FingerprintsBitVectors

RogersTanimotoSimilarityCoefficient

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

Returns value of RogersTanimoto similarity coefficient between two same size FingerprintsBitVectors

RussellRaoSimilarityCoefficient

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

Returns value of RussellRao similarity coefficient between two same size FingerprintsBitVectors

SimpsonSimilarityCoefficient

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

Returns value of Simpson similarity coefficient between two same size FingerprintsBitVectors

SkoalSneath1SimilarityCoefficient

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

Returns value of SkoalSneath1 similarity coefficient between two same size FingerprintsBitVectors

SkoalSneath2SimilarityCoefficient

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

Returns value of SkoalSneath2 similarity coefficient between two same size FingerprintsBitVectors

SkoalSneath3SimilarityCoefficient

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

Returns value of Tanimoto similarity coefficient between two same size FingerprintsBitVectors

TverskySimilarityCoefficient

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

Returns value of Tversky similarity coefficient between two same size FingerprintsBitVectors

WeightedTanimotoSimilarityCoefficient

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

Returns value of WeightedTanimoto similarity coefficient between two same size FingerprintsBitVectors

WeightedTverskySimilarityCoefficient

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

Returns value of WeightedTversky similarity coefficient between two same size FingerprintsBitVectors

YuleSimilarityCoefficient

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

Returns value of Yule similarity coefficient between two same size FingerprintsBitVectors

AUTHOR

Manish Sud

SEE ALSO

BitVector.pm, Fingerprints.pm, PathLengthFingerprints.pm

COPYRIGHT

Copyright (C) 2004-2008 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.