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<html> <head> <title>MayaChemTools:Documentation:Fingerprints::EStateIndiciesFingerprints.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="./AtomTypesFingerprints.html" title="AtomTypesFingerprints.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./ExtendedConnectivityFingerprints.html" title="ExtendedConnectivityFingerprints.html">Next</a></td><td width="34%" align="middle"><strong>Fingerprints::EStateIndiciesFingerprints.pm</strong></td><td width="33%" align="right"><a href="././code/EStateIndiciesFingerprints.html" title="View source code">Code</a> | <a href="./../pdf/EStateIndiciesFingerprints.pdf" title="PDF US Letter Size">PDF</a> | <a href="./../pdfgreen/EStateIndiciesFingerprints.pdf" title="PDF US Letter Size with narrow margins: www.changethemargins.com">PDFGreen</a> | <a href="./../pdfa4/EStateIndiciesFingerprints.pdf" title="PDF A4 Size">PDFA4</a> | <a href="./../pdfa4green/EStateIndiciesFingerprints.pdf" title="PDF A4 Size with narrow margins: www.changethemargins.com">PDFA4Green</a></td></tr> </table> </div> <p> </p> <h2>NAME</h2> <p>EStateIndiciesFingerprints</p> <p> </p> <h2>SYNOPSIS</h2> <p>use Fingerprints::EStateIndiciesFingerprints;</p> <p>use Fingerprints::EStateIndiciesFingerprints qw(:all);</p> <p> </p> <h2>DESCRIPTION</h2> <p><strong>EStateIndiciesFingerprints</strong> [ Ref 75-78 ] class provides the following methods:</p> <p> <a href="#new">new</a>, <a href="#generatefingerprints">GenerateFingerprints</a>, <a href="#getdescription">GetDescription</a>, <a href="#setestateatomtypessettouse">SetEStateAtomTypesSetToUse</a> , <a href="#setvaluesprecision">SetValuesPrecision</a>, <a href="#stringifyestateindiciesfingerprints">StringifyEStateIndiciesFingerprints</a> </p><p><strong>EStateIndiciesFingerprints</strong> is derived from <strong>Fingerprints</strong> class which in turn is derived from <strong>ObjectProperty</strong> base class that provides methods not explicitly defined in <strong>AtomNeighborhoodsFingerprints</strong>, <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>E-state atom types are assigned to all non-hydrogen atoms in a molecule using module AtomTypes::EStateAtomTypes.pm and E-state values are calculated using module AtomicDescriptors::EStateValues.pm. Using E-state atom types and E-state values, <strong>EStateIndiciesFingerprints</strong> constituting sum of E-state values for E-sate atom types are generated.</p> <p>Two types of E-state atom types set size are allowed:</p> <div class="OptionsBox"> ArbitrarySize - Corresponds to only E-state atom types detected in molecule <br/> FixedSize - Corresponds to fixed number of E-state atom types previously defined</div> <p>Module AtomTypes::EStateAtomTypes.pm, used to assign E-state atom types to non-hydrogen atoms in the molecule, is able to assign atom types to any valid atom group. However, for <em>FixedSize</em> value of <strong>EStateAtomTypesSetToUse</strong>, only a fixed set of E-state atom types corresponding to specific atom groups [ Appendix III in Ref 77 ] are used for fingerprints.</p> <p>The fixed size E-state atom type set size used during generation of fingerprints contains 87 E-state non-hydrogen atom types in EStateAtomTypes.csv data file distributed with MayaChemTools.</p> <p>Combination of Type and EStateAtomTypesSetToUse allow generation of 2 different types of E-state indicies fingerprints:</p> <div class="OptionsBox"> Type EStateAtomTypesSetToUse</div> <div class="OptionsBox"> EStateIndicies ArbitrarySize [ default fingerprints ] <br/> EStateIndicies FixedSize</div> <p>The current release of MayaChemTools generates the following types of E-state fingerprints vector strings:</p> <div class="OptionsBox"> FingerprintsVector;EStateIndicies:ArbitrarySize;11;NumericalValues;IDs <br/> AndValuesString;SaaCH SaasC SaasN SdO SdssC SsCH3 SsF SsOH SssCH2 SssN <br/> H SsssCH;24.778 4.387 1.993 25.023 -1.435 3.975 14.006 29.759 -0.073 3 <br/> .024 -2.270</div> <div class="OptionsBox"> FingerprintsVector;EStateIndicies:FixedSize;87;OrderedNumericalValues; <br/> ValuesString;0 0 0 0 0 0 0 3.975 0 -0.073 0 0 24.778 -2.270 0 0 -1.435 <br/> 4.387 0 0 0 0 0 0 3.024 0 0 0 0 0 0 0 1.993 0 29.759 25.023 0 0 0 0 1 <br/> 4.006 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 <br/> 0 0 0 0 0 0 0 0 0 0 0 0 0 0</div> <div class="OptionsBox"> FingerprintsVector;EStateIndicies:FixedSize;87;OrderedNumericalValues; <br/> IDsAndValuesString;SsLi SssBe SssssBem SsBH2 SssBH SsssB SssssBm SsCH3 <br/> SdCH2 SssCH2 StCH SdsCH SaaCH SsssCH SddC StsC SdssC SaasC SaaaC Sssss <br/> C SsNH3p SsNH2 SssNH2p SdNH SssNH SaaNH StN SsssNHp SdsN SaaN SsssN Sd <br/> 0 0 0 0 0 0 0 3.975 0 -0.073 0 0 24.778 -2.270 0 0 -1.435 4.387 0 0 0 <br/> 0 0 0 3.024 0 0 0 0 0 0 0 1.993 0 29.759 25.023 0 0 0 0 14.006 0 0 0 0 <br/> 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0...</div> <p> </p> <h2>METHODS</h2> <dl> <dt><strong><a name="new" class="item"><strong>new</strong></a></strong></dt> <dd> <div class="OptionsBox"> $EStateIndiciesFingerprints = new EStateIndiciesFingerprints(%NamesAndValues);</div> <p>Using specified <em>EStateIndiciesFingerprints</em> property names and values hash, <strong>new</strong> method creates a new object and returns a reference to newly created <strong>PathLengthFingerprints</strong> object. By default, the following properties are initialized:</p> <div class="OptionsBox"> Molecule = ''; <br/> Type = 'EStateIndicies' <br/> EStateAtomTypesSetToUse = 'ArbitrarySize' <br/> ValuesPrecision = 3</div> <p>Examples:</p> <div class="OptionsBox"> $EStateIndiciesFingerprints = new AtomTypesFingerprints( 'Molecule' => $Molecule, 'EStateAtomTypesSetToUse' => 'ArbitrarySize');</div> <div class="OptionsBox"> $EStateIndiciesFingerprints = new AtomTypesFingerprints( 'Molecule' => $Molecule, 'EStateAtomTypesSetToUse' => 'FixedSize');</div> <div class="OptionsBox"> $EStateIndiciesFingerprints->GenerateFingerprints(); <br/> print "$EStateIndiciesFingerprints\n";</div> </dd> <dt><strong><a name="generatefingerprints" class="item"><strong>GenerateFingerprints</strong></a></strong></dt> <dd> <div class="OptionsBox"> $EStateIndiciesFingerprints = $EStateIndiciesFingerprints-> GenerateEStateIndiciesFingerprints();</div> <p>Generates EState keys fingerprints and returns <em>EStateIndiciesFingerprints</em>.</p> </dd> <dt><strong><a name="getdescription" class="item"><strong>GetDescription</strong></a></strong></dt> <dd> <div class="OptionsBox"> $Description = $EStateIndiciesFingerprints->GetDescription();</div> <p>Returns a string containing description of EState keys fingerprints.</p> </dd> <dt><strong><a name="setestateatomtypessettouse" class="item"><strong>SetEStateAtomTypesSetToUse</strong></a></strong></dt> <dd> <div class="OptionsBox"> $EStateIndiciesFingerprints->SetEStateAtomTypesSetToUse($Value);</div> <p>Sets <em>Value</em> of <em>EStateAtomTypesSetToUse</em> and returns <em>EStateIndiciesFingerprints</em>. Possible values: <em>ArbitrarySize or FixedSize</em>. Default value: <em>ArbitrarySize</em>.</p> </dd> <dt><strong><a name="setvaluesprecision" class="item"><strong>SetValuesPrecision</strong></a></strong></dt> <dd> <div class="OptionsBox"> $EStateIndiciesFingerprints->SetValuesPrecision($Precision);</div> <p>Sets precesion of E-state values to use during generation of E-state indices fingerprints and returns <em>EStateIndiciesFingerprints</em>. Possible values: <em>Positive integers</em>. Default value: <em>3</em>.</p> </dd> <dt><strong><a name="stringifyestateindiciesfingerprints" class="item"><strong>StringifyEStateIndiciesFingerprints</strong></a></strong></dt> <dd> <div class="OptionsBox"> $String = $EStateIndiciesFingerprints->StringifyEStateIndiciesFingerprints();</div> <p>Returns a string containing information about <em>EStateIndiciesFingerprints</em> object.</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="./Fingerprints.html">Fingerprints.pm</a>, <a href="./FingerprintsStringUtil.html">FingerprintsStringUtil.pm</a>, <a href="./AtomNeighborhoodsFingerprints.html">AtomNeighborhoodsFingerprints.pm</a>, <a href="./AtomTypesFingerprints.html">AtomTypesFingerprints.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="./AtomTypesFingerprints.html" title="AtomTypesFingerprints.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./ExtendedConnectivityFingerprints.html" title="ExtendedConnectivityFingerprints.html">Next</a></td><td width="34%" align="middle"><strong>March 29, 2015</strong></td><td width="33%" align="right"><strong>Fingerprints::EStateIndiciesFingerprints.pm</strong></td></tr> </table> </div> <br /> <center> <img src="../../images/h2o2.png"> </center> </body> </html>