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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/Fingerprints.html Wed Jan 20 11:55:01 2016 -0500 @@ -0,0 +1,205 @@ +<html> +<head> +<title>MayaChemTools:Documentation:Fingerprints::Fingerprints.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="./ExtendedConnectivityFingerprints.html" title="ExtendedConnectivityFingerprints.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./FingerprintsBitVector.html" title="FingerprintsBitVector.html">Next</a></td><td width="34%" align="middle"><strong>Fingerprints::Fingerprints.pm</strong></td><td width="33%" align="right"><a href="././code/Fingerprints.html" title="View source code">Code</a> | <a href="./../pdf/Fingerprints.pdf" title="PDF US Letter Size">PDF</a> | <a href="./../pdfgreen/Fingerprints.pdf" title="PDF US Letter Size with narrow margins: www.changethemargins.com">PDFGreen</a> | <a href="./../pdfa4/Fingerprints.pdf" title="PDF A4 Size">PDFA4</a> | <a href="./../pdfa4green/Fingerprints.pdf" title="PDF A4 Size with narrow margins: www.changethemargins.com">PDFA4Green</a></td></tr> +</table> +</div> +<p> +</p> +<h2>NAME</h2> +<p>Fingerprints - Fingerprints class</p> +<p> +</p> +<h2>SYNOPSIS</h2> +<p>use Fingerprints::Fingerprints;</p> +<p>use Fingerprints::Fingerprints qw(:all);</p> +<p> +</p> +<h2>DESCRIPTION</h2> +<p><strong>Fingerprints</strong> class provides the following methods:</p> +<p> <a href="#new">new</a>, <a href="#foldfingerprintsbybitdensity">FoldFingerprintsByBitDensity</a>, <a href="#foldfingerprintsbysize">FoldFingerprintsBySize</a> +, <a href="#getfingerprintbitsasbinarystring">GetFingerprintBitsAsBinaryString</a>, <a href="#getfingerprintbitsashexadecimalstring">GetFingerprintBitsAsHexadecimalString</a> +, <a href="#getfingerprintbitsasrawbinarystring">GetFingerprintBitsAsRawBinaryString</a>, <a href="#getfingerprintsvectorvalueids">GetFingerprintsVectorValueIDs</a> +, <a href="#getfingerprintsvectorvalues">GetFingerprintsVectorValues</a>, <a href="#isfingerprintsgenerationsuccessful">IsFingerprintsGenerationSuccessful</a> +, <a href="#setfingerprintsbitvector">SetFingerprintsBitVector</a>, <a href="#setfingerprintsvector">SetFingerprintsVector</a>, <a href="#setfingerprintsvectortype">SetFingerprintsVectorType</a> +, <a href="#setmolecule">SetMolecule</a>, <a href="#setsize">SetSize</a>, <a href="#settype">SetType</a>, <a href="#setvectortype">SetVectorType</a> +</p><p><strong>Fingerprints</strong> class is used as a base class for various specific fingerprint classes such as +<strong>AtomNeighborhoodsFingerprints</strong>, <strong>AtomTypesFingerprints</strong>, <strong>EStateIndiciesFingerprints</strong>, +<strong>PathLengthFingerprints</strong>, <strong>ExtendedConnectivityFingerprints</strong>, <strong>MACCSKeys</strong> and so on. +It implements functionality common to fingerprint classes.</p> +<p><strong>Fingerprints</strong> class is derived from <strong>ObjectProperty</strong> base class which provides methods not +explicitly defined in <strong>Fingerprints</strong> or <strong>ObjectProperty</strong> classes using Perl's AUTOLOAD functionality. +These methods are generated on-the-fly for a specified object property:</p> +<div class="OptionsBox"> + Set<PropertyName>(<PropertyValue>); +<br/> $PropertyValue = Get<PropertyName>(); +<br/> Delete<PropertyName>();</div> +<p><strong>Fingerprints</strong> class uses <strong>FingerprintsBitVector</strong> class to provide bits manipulation functionality.</p> +<p> +</p> +<h2>METHODS</h2> +<dl> +<dt><strong><a name="new" class="item"><strong>new</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $NewFingerprints = new Fingerprints(%NamesAndValues);</div> +<p>Using specified <em>Fingerprints</em> property names and values hash, <strong>new</strong> method creates a new object +and returns a reference to newly created <strong>Fingerprints</strong> object. By default, following properties are +initialized:</p> +<div class="OptionsBox"> + Molecule = ''; +<br/> Type = ''; +<br/> VectorType = ''; +<br/> Size = ''; +<br/> MinSize = ''; +<br/> MaxSize = ''; +<br/> FingerprintsBitVector = ''; +<br/> FingerprintsVectorType = ''; +<br/> FingerprintsVector = '';</div> +</dd> +<dt><strong><a name="foldfingerprintsbybitdensity" class="item"><strong>FoldFingerprintsByBitDensity</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $Fingerprints->FoldFingerprintsByBitDensity($BitDensity);</div> +<p>Folds fingerprints by recursively reducing its size by half until bit density is greater than or equal to +specified <em>BitDensity</em> and returns <em>Fingerprints</em>.</p> +</dd> +<dt><strong><a name="foldfingerprintsbysize" class="item"><strong>FoldFingerprintsBySize</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $Fingerprints->FoldFingerprintsBySize($Size, [$CheckSizeValue]);</div> +<p>Fold fingerprints by recursively reducing its size by half until size is less than or equal to specified +<em>Size</em> and returns <em>Fingerprints</em>. By default, value <em>Size</em> is checked to make sure it's:</p> +<div class="OptionsBox"> + >= MinSize and < Size and IsPowerOfTwo</div> +</dd> +<dt><strong><a name="getfingerprintbitsasbinarystring" class="item"><strong>GetFingerprintBitsAsBinaryString</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $BinaryASCIIString = + $Fingerprints->GetFingerprintBitsAsBinaryString();</div> +<p>Returns fingerprints as a binary ASCII string containing 0s and 1s.</p> +</dd> +<dt><strong><a name="getfingerprintbitsashexadecimalstring" class="item"><strong>GetFingerprintBitsAsHexadecimalString</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $HexadecimalString = + $Fingerprints->GetFingerprintBitsAsHexadecimalString();</div> +<p>Returns fingerprints as a hexadecimal string</p> +</dd> +<dt><strong><a name="getfingerprintbitsasrawbinarystring" class="item"><strong>GetFingerprintBitsAsRawBinaryString</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $RawBinaryString = + $Fingerprints->GetFingerprintBitsAsRawBinaryString();</div> +<p>Returns fingerprints as a raw binary string containing packed bit values for each byte.</p> +</dd> +<dt><strong><a name="getfingerprintsvectorvalueids" class="item"><strong>GetFingerprintsVectorValueIDs</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $ValueIDsRef = $Fingerprints->GetFingerprintsVectorValueIDs(); +<br/> @ValueIDs = $Fingerprints->GetFingerprintsVectorValueIDs();</div> +<p>Returns fingerprints vector value IDs as an array or reference to an array.</p> +</dd> +<dt><strong><a name="getfingerprintsvectorvalues" class="item"><strong>GetFingerprintsVectorValues</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $ValuesRef = $Fingerprints->GetFingerprintsVectorValues(); +<br/> @Values = $Fingerprints->GetFingerprintsVectorValues();</div> +<p>Returns fingerprints vector values as an array or reference to an array.</p> +</dd> +<dt><strong><a name="isfingerprintsgenerationsuccessful" class="item"><strong>IsFingerprintsGenerationSuccessful</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $Return = $Fingerprints->IsFingerprintsGenerationSuccessful();</div> +<p>Returns 1 or 0 based on whether fingerprints were successfully generated.</p> +</dd> +<dt><strong><a name="setfingerprintsbitvector" class="item"><strong>SetFingerprintsBitVector</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $Fingerprints->SetFingerprintsBitVector($FingerprintsBitVector);</div> +<p>Sets <em>FingerprintsBitVector</em> object for <em>Fingerprints</em> and returns <em>Fingerprints</em>.</p> +</dd> +<dt><strong><a name="setfingerprintsvector" class="item"><strong>SetFingerprintsVector</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $Fingerprints->SetFingerprintsVector();</div> +<p>Sets <em>FingerprintsVector</em> object for <em>Fingerprints</em> and returns <em>Fingerprints</em>.</p> +</dd> +<dt><strong><a name="setfingerprintsvectortype" class="item"><strong>SetFingerprintsVectorType</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $Fingerprints->SetFingerprintsVectorType($VectorType);</div> +<p>Sets <em>FingerprintsVector</em> type for <em>Fingerprints</em> and returns <em>Fingerprints</em>. Possible +<em>VectorType</em> values: <em>OrderedNumericalValues, NumericalValues or AlphaNumericalValues</em>.</p> +</dd> +<dt><strong><a name="setmolecule" class="item"><strong>SetMolecule</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $Fingerprints->SetMolecule($Molecule);</div> +<p>Sets <em>Molecule</em> object for <em>Fingerprints</em> and returns <em>Fingerprints</em>.</p> +</dd> +<dt><strong><a name="setsize" class="item"><strong>SetSize</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $Fingerprints->SetSize($Size);</div> +<p>Sets <em>Size</em> of fingerprints and returns <em>Fingerprints</em>.</p> +</dd> +<dt><strong><a name="settype" class="item"><strong>SetType</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $Fingerprints->SetType($Type);</div> +<p>Sets <em>Type</em> of fingerprints and returns <em>Fingerprints</em>.</p> +</dd> +<dt><strong><a name="setvectortype" class="item"><strong>SetVectorType</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $Fingerprints->SetVectorType($Type);</div> +<p>Sets <em>Type</em> of fingerprints vector and returns <em>Fingerprints</em>. Possible <em>Type</em> values: +<em>FingerprintsBitVector or FingerprintsVector</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="./FingerprintsStringUtil.html">FingerprintsStringUtil.pm</a>, <a href="./AtomNeighborhoodsFingerprints.html">AtomNeighborhoodsFingerprints.pm</a>, <a href="./AtomTypesFingerprints.html">AtomTypesFingerprints.pm</a>,  +<a href="./EStateIndiciesFingerprints.html">EStateIndiciesFingerprints.pm</a>, <a href="./ExtendedConnectivityFingerprints.html">ExtendedConnectivityFingerprints.pm</a>, <a href="./MACCSKeys.html">MACCSKeys.pm</a>,  +<a href="./PathLengthFingerprints.html">PathLengthFingerprints.pm</a>, <a href="./TopologicalAtomPairsFingerprints.html">TopologicalAtomPairsFingerprints.pm</a>, <a href="./TopologicalAtomTripletsFingerprints.html">TopologicalAtomTripletsFingerprints.pm</a>,  +<a href="./TopologicalAtomTorsionsFingerprints.html">TopologicalAtomTorsionsFingerprints.pm</a>, <a href="./TopologicalPharmacophoreAtomPairsFingerprints.html">TopologicalPharmacophoreAtomPairsFingerprints.pm</a>,  +<a href="./TopologicalPharmacophoreAtomTripletsFingerprints.html">TopologicalPharmacophoreAtomTripletsFingerprints.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="./ExtendedConnectivityFingerprints.html" title="ExtendedConnectivityFingerprints.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./FingerprintsBitVector.html" title="FingerprintsBitVector.html">Next</a></td><td width="34%" align="middle"><strong>March 29, 2015</strong></td><td width="33%" align="right"><strong>Fingerprints::Fingerprints.pm</strong></td></tr> +</table> +</div> +<br /> +<center> +<img src="../../images/h2o2.png"> +</center> +</body> +</html>