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| date | Wed, 20 Jan 2016 11:55:01 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mayachemtools/docs/modules/html/FingerprintsBitVector.html Wed Jan 20 11:55:01 2016 -0500 @@ -0,0 +1,553 @@ +<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>