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<html> <head> <title>MayaChemTools:Documentation:Fingerprints::FingerprintsBitVector.pm</title> <meta http-equiv="content-type" content="text/html;charset=utf-8"> <link rel="stylesheet" type="text/css" href="../../css/MayaChemTools.css"> </head> <body leftmargin="20" rightmargin="20" topmargin="10" bottommargin="10"> <br/> <center> <a href="http://www.mayachemtools.org" title="MayaChemTools Home"><img src="../../images/MayaChemToolsLogo.gif" border="0" alt="MayaChemTools"></a> </center> <br/> <div class="DocNav"> <table width="100%" border=0 cellpadding=0 cellspacing=2> <tr align="left" valign="top"><td width="33%" align="left"><a href="./Fingerprints.html" title="Fingerprints.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./FingerprintsFileUtil.html" title="FingerprintsFileUtil.html">Next</a></td><td width="34%" align="middle"><strong>Fingerprints::FingerprintsBitVector.pm</strong></td><td width="33%" align="right"><a href="././code/FingerprintsBitVector.html" title="View source code">Code</a> | <a href="./../pdf/FingerprintsBitVector.pdf" title="PDF US Letter Size">PDF</a> | <a href="./../pdfgreen/FingerprintsBitVector.pdf" title="PDF US Letter Size with narrow margins: www.changethemargins.com">PDFGreen</a> | <a href="./../pdfa4/FingerprintsBitVector.pdf" title="PDF A4 Size">PDFA4</a> | <a href="./../pdfa4green/FingerprintsBitVector.pdf" title="PDF A4 Size with narrow margins: www.changethemargins.com">PDFA4Green</a></td></tr> </table> </div> <p> </p> <h2>NAME</h2> <p>FingerprintsBitVector</p> <p> </p> <h2>SYNOPSIS</h2> <p>use Fingerprints::FingerprintsBitVector;</p> <p>use Fingerprints::FingerprintsBitVector qw(:coefficients);</p> <p>use Fingerprints::FingerprintsBitVector qw(:all);</p> <p> </p> <h2>DESCRIPTION</h2> <p><strong>FingerprintsBitVector</strong> class provides the following methods:</p> <p> <a href="#new">new</a>, <a href="#baroniurbanisimilaritycoefficient">BaroniUrbaniSimilarityCoefficient</a>, <a href="#busersimilaritycoefficient">BuserSimilarityCoefficient</a> , <a href="#cosinesimilaritycoefficient">CosineSimilarityCoefficient</a>, <a href="#dennissimilaritycoefficient">DennisSimilarityCoefficient</a> , <a href="#dicesimilaritycoefficient">DiceSimilarityCoefficient</a>, <a href="#foldfingerprintsbitvectorbydensity">FoldFingerprintsBitVectorByDensity</a> , <a href="#foldfingerprintsbitvectorbysize">FoldFingerprintsBitVectorBySize</a>, <a href="#forbessimilaritycoefficient">ForbesSimilarityCoefficient</a> , <a href="#fossumsimilaritycoefficient">FossumSimilarityCoefficient</a>, <a href="#getbitsasbinarystring">GetBitsAsBinaryString</a>, <a href="#getbitsasdecimalstring">GetBitsAsDecimalString</a> , <a href="#getbitsashexadecimalstring">GetBitsAsHexadecimalString</a>, <a href="#getbitsasoctalstring">GetBitsAsOctalString</a>, <a href="#getbitsasrawbinarystring">GetBitsAsRawBinaryString</a> , <a href="#getdescription">GetDescription</a>, <a href="#getfingerprintsbitdensity">GetFingerprintsBitDensity</a>, <a href="#getid">GetID</a>, <a href="#getspecifiedsize">GetSpecifiedSize</a> , <a href="#getsupportedsimilaritycoefficients">GetSupportedSimilarityCoefficients</a>, <a href="#getvectortype">GetVectorType</a>, <a href="#hamannsimilaritycoefficient">HamannSimilarityCoefficient</a> , <a href="#isfingerprintsbitvector">IsFingerprintsBitVector</a>, <a href="#issubset">IsSubSet</a>, <a href="#jacardsimilaritycoefficient">JacardSimilarityCoefficient</a> , <a href="#kulczynski1similaritycoefficient">Kulczynski1SimilarityCoefficient</a>, <a href="#kulczynski2similaritycoefficient">Kulczynski2SimilarityCoefficient</a> , <a href="#matchingsimilaritycoefficient">MatchingSimilarityCoefficient</a>, <a href="#mcconnaugheysimilaritycoefficient">McConnaugheySimilarityCoefficient</a> , <a href="#newfrombinarystring">NewFromBinaryString</a>, <a href="#newfromdecimalstring">NewFromDecimalString</a>, <a href="#newfromhexadecimalstring">NewFromHexadecimalString</a> , <a href="#newfromoctalstring">NewFromOctalString</a>, <a href="#newfromrawbinarystring">NewFromRawBinaryString</a>, <a href="#ochiaisimilaritycoefficient">OchiaiSimilarityCoefficient</a> , <a href="#pearsonsimilaritycoefficient">PearsonSimilarityCoefficient</a>, <a href="#rogerstanimotosimilaritycoefficient">RogersTanimotoSimilarityCoefficient</a> , <a href="#russellraosimilaritycoefficient">RussellRaoSimilarityCoefficient</a>, <a href="#setdescription">SetDescription</a>, <a href="#setid">SetID</a>, <a href="#setspecifiedsize">SetSpecifiedSize</a> , <a href="#setvectortype">SetVectorType</a>, <a href="#simpsonsimilaritycoefficient">SimpsonSimilarityCoefficient</a>, <a href="#skoalsneath1similaritycoefficient">SkoalSneath1SimilarityCoefficient</a> , <a href="#skoalsneath2similaritycoefficient">SkoalSneath2SimilarityCoefficient</a>, <a href="#skoalsneath3similaritycoefficient">SkoalSneath3SimilarityCoefficient</a> , <a href="#stringifyfingerprintsbitvector">StringifyFingerprintsBitVector</a>, <a href="#tanimotosimilaritycoefficient">TanimotoSimilarityCoefficient</a> , <a href="#tverskysimilaritycoefficient">TverskySimilarityCoefficient</a>, <a href="#weightedtanimotosimilaritycoefficient">WeightedTanimotoSimilarityCoefficient</a> , <a href="#weightedtverskysimilaritycoefficient">WeightedTverskySimilarityCoefficient</a>, <a href="#yulesimilaritycoefficient">YuleSimilarityCoefficient</a> </p><p>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.</p> <p><strong>FingerprintsBitVector</strong> class is derived from <strong>BitVector</strong> class which provides the functionality to manipulate bits.</p> <p>For two fingerprints bit vectors A and B of same size, let:</p> <div class="OptionsBox"> Na = Number of bits set to "1" in A <br/> Nb = Number of bits set to "1" in B <br/> Nc = Number of bits set to "1" in both A and B <br/> Nd = Number of bits set to "0" in both A and B</div> <div class="OptionsBox"> Nt = Number of bits set to "1" or "0" in A or B (Size of A or B) <br/> Nt = Na + Nb - Nc + Nd</div> <div class="OptionsBox"> Na - Nc = Number of bits set to "1" in A but not in B <br/> Nb - Nc = Number of bits set to "1" in B but not in A</div> <p>Then, various similarity coefficients [ Ref. 40 - 42 ] for a pair of bit vectors A and B are defined as follows:</p> <p>BaroniUrbani: ( SQRT( Nc * Nd ) + Nc ) / ( SQRT ( Nc * Nd ) + Nc + ( Na - Nc ) + ( Nb - Nc ) ) ( same as Buser )</p> <p>Buser: ( SQRT ( Nc * Nd ) + Nc ) / ( SQRT ( Nc * Nd ) + Nc + ( Na - Nc ) + ( Nb - Nc ) ) ( same as BaroniUrbani )</p> <p>Cosine: Nc / SQRT ( Na * Nb ) (same as Ochiai)</p> <p>Dice: (2 * Nc) / ( Na + Nb )</p> <p>Dennis: ( Nc * Nd - ( ( Na - Nc ) * ( Nb - Nc ) ) ) / SQRT ( Nt * Na * Nb)</p> <p>Forbes: ( Nt * Nc ) / ( Na * Nb )</p> <p>Fossum: ( Nt * ( ( Nc - 1/2 ) ** 2 ) / ( Na * Nb )</p> <p>Hamann: ( ( Nc + Nd ) - ( Na - Nc ) - ( Nb - Nc ) ) / Nt</p> <p>Jaccard: Nc / ( ( Na - Nc) + ( Nb - Nc ) + Nc ) = Nc / ( Na + Nb - Nc ) (same as Tanimoto)</p> <p>Kulczynski1: Nc / ( ( Na - Nc ) + ( Nb - Nc) ) = Nc / ( Na + Nb - 2Nc )</p> <p>Kulczynski2: ( ( Nc / 2 ) * ( 2 * Nc + ( Na - Nc ) + ( Nb - Nc) ) ) / ( ( Nc + ( Na - Nc ) ) * ( Nc + ( Nb - Nc ) ) ) = 0.5 * ( Nc / Na + Nc / Nb )</p> <p>Matching: ( Nc + Nd ) / Nt</p> <p>McConnaughey: ( Nc ** 2 - ( Na - Nc ) * ( Nb - Nc) ) / ( Na * Nb )</p> <p>Ochiai: Nc / SQRT ( Na * Nb ) (same as Cosine)</p> <p>Pearson: ( ( Nc * Nd ) - ( ( Na - Nc ) * ( Nb - Nc ) ) / SQRT ( Na * Nb * ( Na - Nc + Nd ) * ( Nb - Nc + Nd ) )</p> <p>RogersTanimoto: ( Nc + Nd ) / ( ( Na - Nc) + ( Nb - Nc) + Nt) = ( Nc + Nd ) / ( Na + Nb - 2Nc + Nt)</p> <p>RussellRao: Nc / Nt</p> <p>Simpson: Nc / MIN ( Na, Nb)</p> <p>SkoalSneath1: Nc / ( Nc + 2 * ( Na - Nc) + 2 * ( Nb - Nc) ) = Nc / ( 2 * Na + 2 * Nb - 3 * Nc )</p> <p>SkoalSneath2: ( 2 * Nc + 2 * Nd ) / ( Nc + Nd + Nt )</p> <p>SkoalSneath3: ( Nc + Nd ) / ( ( Na - Nc ) + ( Nb - Nc ) ) = ( Nc + Nd ) / ( Na + Nb - 2 * Nc )</p> <p>Tanimoto: Nc / ( ( Na - Nc) + ( Nb - Nc ) + Nc ) = Nc / ( Na + Nb - Nc ) (same as Jaccard)</p> <p>Tversky: Nc / ( alpha * ( Na - Nc ) + ( 1 - alpha) * ( Nb - Nc) + Nc ) = Nc / ( alpha * ( Na - Nb ) + Nb)</p> <p>Yule: ( ( Nc * Nd ) - ( ( Na - Nc ) * ( Nb - Nc ) ) ) / ( ( Nc * Nd ) + ( ( Na - Nc ) * ( Nb - Nc ) ) )</p> <p>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.</p> <p>Let:</p> <div class="OptionsBox"> Na' = Number of bits set to "0" in A <br/> Nb' = Number of bits set to "0" in B <br/> Nc' = Number of bits set to "0" in both A and B</div> <p>Tanimoto': Nc' / ( ( Na' - Nc') + ( Nb' - Nc' ) + Nc' ) = Nc' / ( Na' + Nb' - Nc' )</p> <p>Tversky': Nc' / ( alpha * ( Na' - Nc' ) + ( 1 - alpha) * ( Nb' - Nc' ) + Nc' ) = Nc' / ( alpha * ( Na' - Nb' ) + Nb')</p> <p>Then:</p> <p>WeightedTanimoto = beta * Tanimoto + (1 - beta) * Tanimoto'</p> <p>WeightedTversky = beta * Tversky + (1 - beta) * Tversky'</p> <p> </p> <h2>METHODS</h2> <dl> <dt><strong><a name="new" class="item"><strong>new</strong></a></strong></dt> <dd> <div class="OptionsBox"> $NewFPBitVector = new Fingerprints::FingerprintsBitVector($Size);</div> <p>Creates a new <em>FingerprintsBitVector</em> object of size <em>Size</em> and returns newly created <strong>FingerprintsBitVector</strong>. Bit numbers range from 0 to 1 less than <em>Size</em>.</p> </dd> <dt><strong><a name="baroniurbanisimilaritycoefficient" class="item"><strong>BaroniUrbaniSimilarityCoefficient</strong></a></strong></dt> <dd> <div class="OptionsBox"> $Value = $FingerprintsBitVector->BaroniUrbaniSimilarityCoefficient( $OtherFingerprintBitVector); <br/> $Value = Fingerprints::FingerprintsBitVector:: BaroniUrbaniSimilarityCoefficient( $FingerprintsBitVectorA, $FingerprintBitVectorB);</div> <p>Returns value of <em>BaroniUrbani</em> similarity coefficient between two same size <em>FingerprintsBitVectors</em>.</p> </dd> <dt><strong><a name="busersimilaritycoefficient" class="item"><strong>BuserSimilarityCoefficient</strong></a></strong></dt> <dd> <div class="OptionsBox"> $Value = $FingerprintsBitVector->BuserSimilarityCoefficient( $OtherFingerprintBitVector); <br/> $Value = Fingerprints::FingerprintsBitVector::BuserSimilarityCoefficient( $FingerprintsBitVectorA, $FingerprintBitVectorB);</div> <p>Returns value of <em>Buser</em> similarity coefficient between two same size <em>FingerprintsBitVectors</em>.</p> </dd> <dt><strong><a name="cosinesimilaritycoefficient" class="item"><strong>CosineSimilarityCoefficient</strong></a></strong></dt> <dd> <div class="OptionsBox"> $Value = $FingerprintsBitVector->CosineSimilarityCoefficient( $OtherFingerprintBitVector); <br/> $Value = Fingerprints::FingerprintsBitVector::CosineSimilarityCoefficient( $FingerprintsBitVectorA, $FingerprintBitVectorB);</div> <p>Returns value of <em>Cosine</em> similarity coefficient between two same size <em>FingerprintsBitVectors</em>.</p> </dd> <dt><strong><a name="dennissimilaritycoefficient" class="item"><strong>DennisSimilarityCoefficient</strong></a></strong></dt> <dd> <div class="OptionsBox"> $Value = $FingerprintsBitVector->DennisSimilarityCoefficient( $OtherFingerprintBitVector); <br/> $Value = Fingerprints::FingerprintsBitVector::DennisSimilarityCoefficient( $FingerprintsBitVectorA, $FingerprintBitVectorB);</div> <p>Returns value of <em>Dennis</em> similarity coefficient between two same size <em>FingerprintsBitVectors</em>.</p> </dd> <dt><strong><a name="dicesimilaritycoefficient" class="item"><strong>DiceSimilarityCoefficient</strong></a></strong></dt> <dd> <div class="OptionsBox"> $Value = $FingerprintsBitVector->DiceSimilarityCoefficient( $OtherFingerprintBitVector); <br/> $Value = Fingerprints::FingerprintsBitVector::DiceSimilarityCoefficient( $FingerprintsBitVectorA, $FingerprintBitVectorB);</div> <p>Returns value of <em>Dice</em> similarity coefficient between two same size <em>FingerprintsBitVectors</em>.</p> </dd> <dt><strong><a name="foldfingerprintsbitvectorbydensity" class="item"><strong>FoldFingerprintsBitVectorByDensity</strong></a></strong></dt> <dd> <div class="OptionsBox"> $FingerprintsBitVector->FoldFingerprintsBitVectorByDensity($Density);</div> <p>Folds <em>FingerprintsBitVector</em> by recursively reducing its size by half until bit density of set bits is greater than or equal to specified <em>Density</em> and returns folded <em>FingerprintsBitVector</em>.</p> </dd> <dt><strong><a name="foldfingerprintsbitvectorbysize" class="item"><strong>FoldFingerprintsBitVectorBySize</strong></a></strong></dt> <dd> <div class="OptionsBox"> $FingerprintsBitVector->FoldFingerprintsBitVectorBySize($Size);</div> <p>Folds <em>FingerprintsBitVector</em> by recursively reducing its size by half until size is less than or equal to specified <em>Size</em> and returns folded <em>FingerprintsBitVector</em>.</p> </dd> <dt><strong><a name="forbessimilaritycoefficient" class="item"><strong>ForbesSimilarityCoefficient</strong></a></strong></dt> <dd> <div class="OptionsBox"> $Value = $FingerprintsBitVector->ForbesSimilarityCoefficient( $OtherFingerprintBitVector); <br/> $Value = Fingerprints::FingerprintsBitVector::ForbesSimilarityCoefficient( $FingerprintsBitVectorA, $FingerprintBitVectorB);</div> <p>Returns value of <em>Forbes</em> similarity coefficient between two same size <em>FingerprintsBitVectors</em>.</p> </dd> <dt><strong><a name="fossumsimilaritycoefficient" class="item"><strong>FossumSimilarityCoefficient</strong></a></strong></dt> <dd> <div class="OptionsBox"> $Value = $FingerprintsBitVector->FossumSimilarityCoefficient( $OtherFingerprintBitVector); <br/> $Value = Fingerprints::FingerprintsBitVector::FossumSimilarityCoefficient( $FingerprintsBitVectorA, $FingerprintBitVectorB);</div> <p>Returns value of <em>Fossum</em> similarity coefficient between two same size <em>FingerprintsBitVectors</em>.</p> </dd> <dt><strong><a name="getbitsasbinarystring" class="item"><strong>GetBitsAsBinaryString</strong></a></strong></dt> <dd> <div class="OptionsBox"> $BinaryASCIIString = $FingerprintsBitVector->GetBitsAsBinaryString();</div> <p>Returns fingerprints as a binary ASCII string containing 0s and 1s.</p> </dd> <dt><strong><a name="getbitsashexadecimalstring" class="item"><strong>GetBitsAsHexadecimalString</strong></a></strong></dt> <dd> <div class="OptionsBox"> $HexadecimalString = $FingerprintsBitVector->GetBitsAsHexadecimalString();</div> <p>Returns fingerprints as a hexadecimal string.</p> </dd> <dt><strong><a name="getbitsasrawbinarystring" class="item"><strong>GetBitsAsRawBinaryString</strong></a></strong></dt> <dd> <div class="OptionsBox"> $RawBinaryString = $FingerprintsBitVector->GetBitsAsRawBinaryString();</div> <p>Returns fingerprints as a raw binary string containing packed bit values for each byte.</p> </dd> <dt><strong><a name="getdescription" class="item"><strong>GetDescription</strong></a></strong></dt> <dd> <div class="OptionsBox"> $Description = $FingerprintsBitVector->GetDescription();</div> <p>Returns a string containing description of fingerprints bit vector.</p> </dd> <dt><strong><a name="getfingerprintsbitdensity" class="item"><strong>GetFingerprintsBitDensity</strong></a></strong></dt> <dd> <div class="OptionsBox"> $BitDensity = $FingerprintsBitVector->GetFingerprintsBitDensity();</div> <p>Returns <em>BitDensity</em> of <em>FingerprintsBitVector</em> corresponding to bits set to 1s.</p> </dd> <dt><strong><a name="getid" class="item"><strong>GetID</strong></a></strong></dt> <dd> <div class="OptionsBox"> $ID = $FingerprintsBitVector->GetID();</div> <p>Returns <em>ID</em> of <em>FingerprintsBitVector</em>.</p> </dd> <dt><strong><a name="getvectortype" class="item"><strong>GetVectorType</strong></a></strong></dt> <dd> <div class="OptionsBox"> $VectorType = $FingerprintsBitVector->GetVectorType();</div> <p>Returns <em>VectorType</em> of <em>FingerprintsBitVector</em>.</p> </dd> <dt><strong><a name="getspecifiedsize" class="item"><strong>GetSpecifiedSize</strong></a></strong></dt> <dd> <div class="OptionsBox"> $Size = $FingerprintsBitVector->GetSpecifiedSize();</div> <p>Returns value of specified size for bit vector.</p> </dd> <dt><strong><a name="getsupportedsimilaritycoefficients" class="item"><strong>GetSupportedSimilarityCoefficients</strong></a></strong></dt> <dd> <div class="OptionsBox"> @SimilarityCoefficient = Fingerprints::FingerprintsBitVector::GetSupportedSimilarityCoefficients();</div> <p>Returns an array containing names of supported similarity coefficients.</p> </dd> <dt><strong><a name="hamannsimilaritycoefficient" class="item"><strong>HamannSimilarityCoefficient</strong></a></strong></dt> <dd> <div class="OptionsBox"> $Value = $FingerprintsBitVector->HamannSimilarityCoefficient( $OtherFingerprintBitVector); <br/> $Value = Fingerprints::FingerprintsBitVector::HamannSimilarityCoefficient( $FingerprintsBitVectorA, $FingerprintBitVectorB);</div> <p>Returns value of <em>Hamann</em> similarity coefficient between two same size <em>FingerprintsBitVectors</em>.</p> </dd> <dt><strong><a name="isfingerprintsbitvector" class="item"><strong>IsFingerprintsBitVector</strong></a></strong></dt> <dd> <div class="OptionsBox"> $Status = Fingerprints::FingerprintsBitVector:: IsFingerprintsBitVector($Object);</div> <p>Returns 1 or 0 based on whether <em>Object</em> is a <strong>FingerprintsBitVector</strong> object.</p> </dd> <dt><strong><a name="issubset" class="item"><strong>IsSubSet</strong></a></strong></dt> <dd> <div class="OptionsBox"> $Status = $FingerprintsBitVector->IsSubSet($OtherFPBitVector); <br/> $Status = Fingerprints::FingerprintsBitVector::IsSubSet( $FPBitVectorA, $FPBitVectorB);</div> <p>Returns 1 or 0 based on whether first firngerprints bit vector is a subset of second fingerprints bit vector.</p> <p>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.</p> </dd> <dt><strong><a name="jacardsimilaritycoefficient" class="item"><strong>JacardSimilarityCoefficient</strong></a></strong></dt> <dd> <div class="OptionsBox"> $Value = $FingerprintsBitVector->JacardSimilarityCoefficient( $OtherFingerprintBitVector); <br/> $Value = Fingerprints::FingerprintsBitVector::JacardSimilarityCoefficient( $FingerprintsBitVectorA, $FingerprintBitVectorB);</div> <p>Returns value of <em>Jacard</em> similarity coefficient between two same size <em>FingerprintsBitVectors</em>.</p> </dd> <dt><strong><a name="kulczynski1similaritycoefficient" class="item"><strong>Kulczynski1SimilarityCoefficient</strong></a></strong></dt> <dd> <div class="OptionsBox"> $Value = $FingerprintsBitVector->Kulczynski1SimilarityCoefficient( $OtherFingerprintBitVector); <br/> $Value = Fingerprints::FingerprintsBitVector:: Kulczynski1SimilarityCoefficient( $FingerprintsBitVectorA, $FingerprintBitVectorB);</div> <p>Returns value of <em>Kulczynski1</em> similarity coefficient between two same size <em>FingerprintsBitVectors</em>.</p> </dd> <dt><strong><a name="kulczynski2similaritycoefficient" class="item"><strong>Kulczynski2SimilarityCoefficient</strong></a></strong></dt> <dd> <div class="OptionsBox"> $Value = $FingerprintsBitVector->Kulczynski2SimilarityCoefficient( $OtherFingerprintBitVector); <br/> $Value = Fingerprints::FingerprintsBitVector:: Kulczynski2SimilarityCoefficient( $FingerprintsBitVectorA, $FingerprintBitVectorB);</div> <p>Returns value of <em>Kulczynski2</em> similarity coefficient between two same size <em>FingerprintsBitVectors</em>.</p> </dd> <dt><strong><a name="matchingsimilaritycoefficient" class="item"><strong>MatchingSimilarityCoefficient</strong></a></strong></dt> <dd> <div class="OptionsBox"> $Value = $FingerprintsBitVector->MatchingSimilarityCoefficient( $OtherFingerprintBitVector); <br/> $Value = Fingerprints::FingerprintsBitVector:: MatchingSimilarityCoefficient( $FingerprintsBitVectorA, $FingerprintBitVectorB);</div> <p>Returns value of <em>Matching</em> similarity coefficient between two same size <em>FingerprintsBitVectors</em>.</p> </dd> <dt><strong><a name="mcconnaugheysimilaritycoefficient" class="item"><strong>McConnaugheySimilarityCoefficient</strong></a></strong></dt> <dd> <div class="OptionsBox"> $Value = $FingerprintsBitVector->McConnaugheySimilarityCoefficient( $OtherFingerprintBitVector); <br/> $Value = Fingerprints::FingerprintsBitVector:: McConnaugheySimilarityCoefficient( $FingerprintsBitVectorA, $FingerprintBitVectorB);</div> <p>Returns value of <em>McConnaughey</em> similarity coefficient between two same size <em>FingerprintsBitVectors</em>.</p> </dd> <dt><strong><a name="newfrombinarystring" class="item"><strong>NewFromBinaryString</strong></a></strong></dt> <dd> <div class="OptionsBox"> $NewFPBitVector = $FingerprintsBitVector->NewFromBinaryString( $BinaryString); <br/> $NewFPBitVector = Fingerprints::FingerprintsBitVector::NewFromBinaryString( $BinaryString);</div> <p>Creates a new <em>FingerprintsBitVector</em> using <em>BinaryString</em> and returns new <strong>FingerprintsBitVector</strong> object.</p> </dd> <dt><strong><a name="newfromhexadecimalstring" class="item"><strong>NewFromHexadecimalString</strong></a></strong></dt> <dd> <div class="OptionsBox"> $NewFPBitVector = $FingerprintsBitVector->NewFromHexadecimalString( $HexdecimalString); <br/> $NewFPBitVector = Fingerprints::FingerprintsBitVector:: NewFromHexadecimalString( $HexdecimalString);</div> <p>Creates a new <em>FingerprintsBitVector</em> using <em>HexdecimalString</em> and returns new <strong>FingerprintsBitVector</strong> object.</p> </dd> <dt><strong><a name="newfromrawbinarystring" class="item"><strong>NewFromRawBinaryString</strong></a></strong></dt> <dd> <div class="OptionsBox"> $NewFPBitVector = $FingerprintsBitVector->NewFromRawBinaryString( $RawBinaryString); <br/> $NewFPBitVector = Fingerprints::FingerprintsBitVector:: NewFromRawBinaryString( $RawBinaryString);</div> <p>Creates a new <em>FingerprintsBitVector</em> using <em>RawBinaryString</em> and returns new <strong>FingerprintsBitVector</strong> object.</p> </dd> <dt><strong><a name="ochiaisimilaritycoefficient" class="item"><strong>OchiaiSimilarityCoefficient</strong></a></strong></dt> <dd> <div class="OptionsBox"> $Value = $FingerprintsBitVector->OchiaiSimilarityCoefficient( $OtherFingerprintBitVector); <br/> $Value = Fingerprints::FingerprintsBitVector::OchiaiSimilarityCoefficient( $FingerprintsBitVectorA, $FingerprintBitVectorB);</div> <p>Returns value of <em>Ochiai</em> similarity coefficient between two same size <em>FingerprintsBitVectors</em>.</p> </dd> <dt><strong><a name="pearsonsimilaritycoefficient" class="item"><strong>PearsonSimilarityCoefficient</strong></a></strong></dt> <dd> <div class="OptionsBox"> $Value = $FingerprintsBitVector->PearsonSimilarityCoefficient( $OtherFingerprintBitVector); <br/> $Value = Fingerprints::FingerprintsBitVector::PearsonSimilarityCoefficient( $FingerprintsBitVectorA, $FingerprintBitVectorB);</div> <p>Returns value of <em>Pearson</em> similarity coefficient between two same size <em>FingerprintsBitVectors</em>.</p> </dd> <dt><strong><a name="rogerstanimotosimilaritycoefficient" class="item"><strong>RogersTanimotoSimilarityCoefficient</strong></a></strong></dt> <dd> <div class="OptionsBox"> $Value = $FingerprintsBitVector->RogersTanimotoSimilarityCoefficient( $OtherFingerprintBitVector); <br/> $Value = Fingerprints::FingerprintsBitVector:: RogersTanimotoSimilarityCoefficient( $FingerprintsBitVectorA, $FingerprintBitVectorB);</div> <p>Returns value of <em>RogersTanimoto</em> similarity coefficient between two same size <em>FingerprintsBitVectors</em>.</p> </dd> <dt><strong><a name="russellraosimilaritycoefficient" class="item"><strong>RussellRaoSimilarityCoefficient</strong></a></strong></dt> <dd> <div class="OptionsBox"> $Value = $FingerprintsBitVector->RussellRaoSimilarityCoefficient( $OtherFingerprintBitVector); <br/> $Value = Fingerprints::FingerprintsBitVector:: RussellRaoSimilarityCoefficient( $FingerprintsBitVectorA, $FingerprintBitVectorB);</div> <p>Returns value of <em>RussellRao</em> similarity coefficient between two same size <em>FingerprintsBitVectors</em>.</p> </dd> <dt><strong><a name="setspecifiedsize" class="item"><strong>SetSpecifiedSize</strong></a></strong></dt> <dd> <div class="OptionsBox"> $FingerprintsBitVector->SetSpecifiedSize($Size);</div> <p>Sets specified size for fingerprints bit vector.</p> <p>Irrespective of specified size, Perl functions used to handle bit data in <strong>BitVector</strong> class automatically sets the size to the next nearest power of 2. <em>SpecifiedSize</em> is used by <strong>FingerprintsBitVector</strong> class to process any aribitray size during similarity coefficient calculations.</p> </dd> <dt><strong><a name="setdescription" class="item"><strong>SetDescription</strong></a></strong></dt> <dd> <div class="OptionsBox"> $FingerprintsBitVector->SetDescription($Description);</div> <p>Sets <em>Description</em> of fingerprints bit vector and returns <em>FingerprintsBitVector</em>.</p> </dd> <dt><strong><a name="setid" class="item"><strong>SetID</strong></a></strong></dt> <dd> <div class="OptionsBox"> $FingerprintsBitVector->SetID($ID);</div> <p>Sets <em>ID</em> of fingerprints bit vector and returns <em>FingerprintsBitVector</em>.</p> </dd> <dt><strong><a name="setvectortype" class="item"><strong>SetVectorType</strong></a></strong></dt> <dd> <div class="OptionsBox"> $FingerprintsBitVector->SetVectorType($VectorType);</div> <p>Sets <em>VectorType</em> of fingerprints bit vector and returns <em>FingerprintsBitVector</em>.</p> </dd> <dt><strong><a name="simpsonsimilaritycoefficient" class="item"><strong>SimpsonSimilarityCoefficient</strong></a></strong></dt> <dd> <div class="OptionsBox"> $Value = $FingerprintsBitVector->SimpsonSimilarityCoefficient( $OtherFingerprintBitVector); <br/> $Value = Fingerprints::FingerprintsBitVector::SimpsonSimilarityCoefficient( $FingerprintsBitVectorA, $FingerprintBitVectorB);</div> <p>Returns value of <em>Simpson</em> similarity coefficient between two same size <em>FingerprintsBitVectors</em>.</p> </dd> <dt><strong><a name="skoalsneath1similaritycoefficient" class="item"><strong>SkoalSneath1SimilarityCoefficient</strong></a></strong></dt> <dd> <div class="OptionsBox"> $Value = $FingerprintsBitVector->SkoalSneath1SimilarityCoefficient( $OtherFingerprintBitVector); <br/> $Value = Fingerprints::FingerprintsBitVector:: SkoalSneath1SimilarityCoefficient( $FingerprintsBitVectorA, $FingerprintBitVectorB);</div> <p>Returns value of <em>SkoalSneath1</em> similarity coefficient between two same size <em>FingerprintsBitVectors</em>.</p> </dd> <dt><strong><a name="skoalsneath2similaritycoefficient" class="item"><strong>SkoalSneath2SimilarityCoefficient</strong></a></strong></dt> <dd> <div class="OptionsBox"> $Value = $FingerprintsBitVector->SkoalSneath2SimilarityCoefficient( $OtherFingerprintBitVector); <br/> $Value = Fingerprints::FingerprintsBitVector:: SkoalSneath2SimilarityCoefficient( $FingerprintsBitVectorA, $FingerprintBitVectorB);</div> <p>Returns value of <em>SkoalSneath2</em> similarity coefficient between two same size <em>FingerprintsBitVectors</em>.</p> </dd> <dt><strong><a name="skoalsneath3similaritycoefficient" class="item"><strong>SkoalSneath3SimilarityCoefficient</strong></a></strong></dt> <dd> <div class="OptionsBox"> $Value = $FingerprintsBitVector->SkoalSneath3SimilarityCoefficient( $OtherFingerprintBitVector); <br/> $Value = Fingerprints::FingerprintsBitVector:: SkoalSneath3SimilarityCoefficient( $FingerprintsBitVectorA, $FingerprintBitVectorB);</div> <p>Returns value of <em>SkoalSneath3</em> similarity coefficient between two same size <em>FingerprintsBitVectors</em></p> </dd> <dt><strong><a name="stringifyfingerprintsbitvector" class="item"><strong>StringifyFingerprintsBitVector</strong></a></strong></dt> <dd> <div class="OptionsBox"> $String = $FingerprintsBitVector->StringifyFingerprintsBitVector();</div> <p>Returns a string containing information about <em>FingerprintsBitVector</em> object.</p> </dd> <dt><strong><a name="tanimotosimilaritycoefficient" class="item"><strong>TanimotoSimilarityCoefficient</strong></a></strong></dt> <dd> <div class="OptionsBox"> $Value = $FingerprintsBitVector->TanimotoSimilarityCoefficient( $OtherFingerprintBitVector); <br/> $Value = Fingerprints::FingerprintsBitVector:: TanimotoSimilarityCoefficient( $FingerprintsBitVectorA, $FingerprintBitVectorB);</div> <p>Returns value of <em>Tanimoto</em> similarity coefficient between two same size <em>FingerprintsBitVectors</em>.</p> </dd> <dt><strong><a name="tverskysimilaritycoefficient" class="item"><strong>TverskySimilarityCoefficient</strong></a></strong></dt> <dd> <div class="OptionsBox"> $Value = $FingerprintsBitVector->TverskySimilarityCoefficient( $OtherFingerprintBitVector, $Alpha); <br/> $Value = Fingerprints::FingerprintsBitVector:: TverskySimilarityCoefficient( $FingerprintsBitVectorA, $FingerprintBitVectorB, $Alpha);</div> <p>Returns value of <em>Tversky</em> similarity coefficient between two same size <em>FingerprintsBitVectors</em>.</p> </dd> <dt><strong><a name="weightedtanimotosimilaritycoefficient" class="item"><strong>WeightedTanimotoSimilarityCoefficient</strong></a></strong></dt> <dd> <div class="OptionsBox"> $Value = $FingerprintsBitVector->WeightedTanimotoSimilarityCoefficient( $OtherFingerprintBitVector, $Beta); <br/> $Value = Fingerprints::FingerprintsBitVector:: WeightedTanimotoSimilarityCoefficient( $FingerprintsBitVectorA, $FingerprintBitVectorB, $Beta);</div> <p>Returns value of <em>WeightedTanimoto</em> similarity coefficient between two same size <em>FingerprintsBitVectors</em>.</p> </dd> <dt><strong><a name="weightedtverskysimilaritycoefficient" class="item"><strong>WeightedTverskySimilarityCoefficient</strong></a></strong></dt> <dd> <div class="OptionsBox"> $Value = $FingerprintsBitVector->WeightedTverskySimilarityCoefficient( $OtherFingerprintBitVector, $Alpha, $Beta); <br/> $Value = Fingerprints::FingerprintsBitVector:: WeightedTverskySimilarityCoefficient( $FingerprintsBitVectorA, $FingerprintBitVectorB, $Alpha, $Beta);</div> <p>Returns value of <em>WeightedTversky</em> similarity coefficient between two same size <em>FingerprintsBitVectors</em>.</p> </dd> <dt><strong><a name="yulesimilaritycoefficient" class="item"><strong>YuleSimilarityCoefficient</strong></a></strong></dt> <dd> <div class="OptionsBox"> $Value = $FingerprintsBitVector->YuleSimilarityCoefficient( $OtherFingerprintBitVector); <br/> $Value = Fingerprints::FingerprintsBitVector::YuleSimilarityCoefficient( $FingerprintsBitVectorA, $FingerprintBitVectorB);</div> <p>Returns value of <em>Yule</em> similarity coefficient between two same size <em>FingerprintsBitVectors</em>.</p> </dd> </dl> <p> </p> <h2>AUTHOR</h2> <p><a href="mailto:msud@san.rr.com">Manish Sud</a></p> <p> </p> <h2>SEE ALSO</h2> <p><a href="./BitVector.html">BitVector.pm</a>, <a href="./FingerprintsStringUtil.html">FingerprintsStringUtil.pm</a>, <a href="./FingerprintsVector.html">FingerprintsVector.pm</a>, <a href="./Vector.html">Vector.pm</a> </p> <p> </p> <h2>COPYRIGHT</h2> <p>Copyright (C) 2015 Manish Sud. All rights reserved.</p> <p>This file is part of MayaChemTools.</p> <p>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.</p> <p> </p><p> </p><div class="DocNav"> <table width="100%" border=0 cellpadding=0 cellspacing=2> <tr align="left" valign="top"><td width="33%" align="left"><a href="./Fingerprints.html" title="Fingerprints.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./FingerprintsFileUtil.html" title="FingerprintsFileUtil.html">Next</a></td><td width="34%" align="middle"><strong>March 29, 2015</strong></td><td width="33%" align="right"><strong>Fingerprints::FingerprintsBitVector.pm</strong></td></tr> </table> </div> <br /> <center> <img src="../../images/h2o2.png"> </center> </body> </html>