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3 <title>MayaChemTools:Documentation:Fingerprints::EStateIndiciesFingerprints.pm</title>
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15 <tr align="left" valign="top"><td width="33%" align="left"><a href="./AtomTypesFingerprints.html" title="AtomTypesFingerprints.html">Previous</a>&nbsp;&nbsp;<a href="./index.html" title="Table of Contents">TOC</a>&nbsp;&nbsp;<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>&nbsp;|&nbsp;<a href="./../pdf/EStateIndiciesFingerprints.pdf" title="PDF US Letter Size">PDF</a>&nbsp;|&nbsp;<a href="./../pdfgreen/EStateIndiciesFingerprints.pdf" title="PDF US Letter Size with narrow margins: www.changethemargins.com">PDFGreen</a>&nbsp;|&nbsp;<a href="./../pdfa4/EStateIndiciesFingerprints.pdf" title="PDF A4 Size">PDFA4</a>&nbsp;|&nbsp;<a href="./../pdfa4green/EStateIndiciesFingerprints.pdf" title="PDF A4 Size with narrow margins: www.changethemargins.com">PDFA4Green</a></td></tr>
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18 <p>
19 </p>
20 <h2>NAME</h2>
21 <p>EStateIndiciesFingerprints</p>
22 <p>
23 </p>
24 <h2>SYNOPSIS</h2>
25 <p>use Fingerprints::EStateIndiciesFingerprints;</p>
26 <p>use Fingerprints::EStateIndiciesFingerprints qw(:all);</p>
27 <p>
28 </p>
29 <h2>DESCRIPTION</h2>
30 <p><strong>EStateIndiciesFingerprints</strong> [ Ref 75-78 ] class provides the following methods:</p>
31 <p> <a href="#new">new</a>, <a href="#generatefingerprints">GenerateFingerprints</a>, <a href="#getdescription">GetDescription</a>, <a href="#setestateatomtypessettouse">SetEStateAtomTypesSetToUse</a>
32 , <a href="#setvaluesprecision">SetValuesPrecision</a>, <a href="#stringifyestateindiciesfingerprints">StringifyEStateIndiciesFingerprints</a>
33 </p><p><strong>EStateIndiciesFingerprints</strong> is derived from <strong>Fingerprints</strong> class which in turn
34 is derived from <strong>ObjectProperty</strong> base class that provides methods not explicitly defined
35 in <strong>AtomNeighborhoodsFingerprints</strong>, <strong>Fingerprints</strong> or <strong>ObjectProperty</strong> classes using Perl's
36 AUTOLOAD functionality. These methods are generated on-the-fly for a specified object property:</p>
37 <div class="OptionsBox">
38 Set&lt;PropertyName&gt;(&lt;PropertyValue&gt;);
39 <br/> $PropertyValue = Get&lt;PropertyName&gt;();
40 <br/> Delete&lt;PropertyName&gt;();</div>
41 <p>E-state atom types are assigned to all non-hydrogen atoms in a molecule using module
42 AtomTypes::EStateAtomTypes.pm and E-state values are calculated using module
43 AtomicDescriptors::EStateValues.pm. Using E-state atom types and E-state values,
44 <strong>EStateIndiciesFingerprints</strong> constituting sum of E-state values for E-sate atom types
45 are generated.</p>
46 <p>Two types of E-state atom types set size are allowed:</p>
47 <div class="OptionsBox">
48 ArbitrarySize - Corresponds to only E-state atom types detected
49 in molecule
50 <br/> FixedSize - Corresponds to fixed number of E-state atom types previously
51 defined</div>
52 <p>Module AtomTypes::EStateAtomTypes.pm, used to assign E-state atom types to
53 non-hydrogen atoms in the molecule, is able to assign atom types to any valid
54 atom group. However, for <em>FixedSize</em> value of <strong>EStateAtomTypesSetToUse</strong>, only a
55 fixed set of E-state atom types corresponding to specific atom groups [ Appendix III in
56 Ref 77 ] are used for fingerprints.</p>
57 <p>The fixed size E-state atom type set size used during generation of fingerprints contains
58 87 E-state non-hydrogen atom types in EStateAtomTypes.csv data file distributed with
59 MayaChemTools.</p>
60 <p>Combination of Type and EStateAtomTypesSetToUse allow generation of 2 different types of
61 E-state indicies fingerprints:</p>
62 <div class="OptionsBox">
63 Type EStateAtomTypesSetToUse</div>
64 <div class="OptionsBox">
65 EStateIndicies ArbitrarySize [ default fingerprints ]
66 <br/> EStateIndicies FixedSize</div>
67 <p>The current release of MayaChemTools generates the following types of E-state
68 fingerprints vector strings:</p>
69 <div class="OptionsBox">
70 FingerprintsVector;EStateIndicies:ArbitrarySize;11;NumericalValues;IDs
71 <br/> AndValuesString;SaaCH SaasC SaasN SdO SdssC SsCH3 SsF SsOH SssCH2 SssN
72 <br/> H SsssCH;24.778 4.387 1.993 25.023 -1.435 3.975 14.006 29.759 -0.073 3
73 <br/> .024 -2.270</div>
74 <div class="OptionsBox">
75 FingerprintsVector;EStateIndicies:FixedSize;87;OrderedNumericalValues;
76 <br/> ValuesString;0 0 0 0 0 0 0 3.975 0 -0.073 0 0 24.778 -2.270 0 0 -1.435
77 <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
78 <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
79 <br/> 0 0 0 0 0 0 0 0 0 0 0 0 0 0</div>
80 <div class="OptionsBox">
81 FingerprintsVector;EStateIndicies:FixedSize;87;OrderedNumericalValues;
82 <br/> IDsAndValuesString;SsLi SssBe SssssBem SsBH2 SssBH SsssB SssssBm SsCH3
83 <br/> SdCH2 SssCH2 StCH SdsCH SaaCH SsssCH SddC StsC SdssC SaasC SaaaC Sssss
84 <br/> C SsNH3p SsNH2 SssNH2p SdNH SssNH SaaNH StN SsssNHp SdsN SaaN SsssN Sd
85 <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
86 <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
87 <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>
88 <p>
89 </p>
90 <h2>METHODS</h2>
91 <dl>
92 <dt><strong><a name="new" class="item"><strong>new</strong></a></strong></dt>
93 <dd>
94 <div class="OptionsBox">
95 $EStateIndiciesFingerprints = new EStateIndiciesFingerprints(%NamesAndValues);</div>
96 <p>Using specified <em>EStateIndiciesFingerprints</em> property names and values hash, <strong>new</strong> method creates a new object
97 and returns a reference to newly created <strong>PathLengthFingerprints</strong> object. By default, the
98 following properties are initialized:</p>
99 <div class="OptionsBox">
100 Molecule = '';
101 <br/> Type = 'EStateIndicies'
102 <br/> EStateAtomTypesSetToUse = 'ArbitrarySize'
103 <br/> ValuesPrecision = 3</div>
104 <p>Examples:</p>
105 <div class="OptionsBox">
106 $EStateIndiciesFingerprints = new AtomTypesFingerprints(
107 'Molecule' =&gt; $Molecule,
108 'EStateAtomTypesSetToUse' =&gt;
109 'ArbitrarySize');</div>
110 <div class="OptionsBox">
111 $EStateIndiciesFingerprints = new AtomTypesFingerprints(
112 'Molecule' =&gt; $Molecule,
113 'EStateAtomTypesSetToUse' =&gt;
114 'FixedSize');</div>
115 <div class="OptionsBox">
116 $EStateIndiciesFingerprints-&gt;GenerateFingerprints();
117 <br/> print &quot;$EStateIndiciesFingerprints\n&quot;;</div>
118 </dd>
119 <dt><strong><a name="generatefingerprints" class="item"><strong>GenerateFingerprints</strong></a></strong></dt>
120 <dd>
121 <div class="OptionsBox">
122 $EStateIndiciesFingerprints = $EStateIndiciesFingerprints-&gt;
123 GenerateEStateIndiciesFingerprints();</div>
124 <p>Generates EState keys fingerprints and returns <em>EStateIndiciesFingerprints</em>.</p>
125 </dd>
126 <dt><strong><a name="getdescription" class="item"><strong>GetDescription</strong></a></strong></dt>
127 <dd>
128 <div class="OptionsBox">
129 $Description = $EStateIndiciesFingerprints-&gt;GetDescription();</div>
130 <p>Returns a string containing description of EState keys fingerprints.</p>
131 </dd>
132 <dt><strong><a name="setestateatomtypessettouse" class="item"><strong>SetEStateAtomTypesSetToUse</strong></a></strong></dt>
133 <dd>
134 <div class="OptionsBox">
135 $EStateIndiciesFingerprints-&gt;SetEStateAtomTypesSetToUse($Value);</div>
136 <p>Sets <em>Value</em> of <em>EStateAtomTypesSetToUse</em> and returns <em>EStateIndiciesFingerprints</em>.
137 Possible values: <em>ArbitrarySize or FixedSize</em>. Default value: <em>ArbitrarySize</em>.</p>
138 </dd>
139 <dt><strong><a name="setvaluesprecision" class="item"><strong>SetValuesPrecision</strong></a></strong></dt>
140 <dd>
141 <div class="OptionsBox">
142 $EStateIndiciesFingerprints-&gt;SetValuesPrecision($Precision);</div>
143 <p>Sets precesion of E-state values to use during generation of E-state indices fingerprints
144 and returns <em>EStateIndiciesFingerprints</em>. Possible values: <em>Positive integers</em>.
145 Default value: <em>3</em>.</p>
146 </dd>
147 <dt><strong><a name="stringifyestateindiciesfingerprints" class="item"><strong>StringifyEStateIndiciesFingerprints</strong></a></strong></dt>
148 <dd>
149 <div class="OptionsBox">
150 $String = $EStateIndiciesFingerprints-&gt;StringifyEStateIndiciesFingerprints();</div>
151 <p>Returns a string containing information about <em>EStateIndiciesFingerprints</em> object.</p>
152 </dd>
153 </dl>
154 <p>
155 </p>
156 <h2>AUTHOR</h2>
157 <p><a href="mailto:msud@san.rr.com">Manish Sud</a></p>
158 <p>
159 </p>
160 <h2>SEE ALSO</h2>
161 <p><a href="./Fingerprints.html">Fingerprints.pm</a>,&nbsp<a href="./FingerprintsStringUtil.html">FingerprintsStringUtil.pm</a>,&nbsp<a href="./AtomNeighborhoodsFingerprints.html">AtomNeighborhoodsFingerprints.pm</a>,&nbsp<a href="./AtomTypesFingerprints.html">AtomTypesFingerprints.pm</a>,&nbsp
162 <a href="./ExtendedConnectivityFingerprints.html">ExtendedConnectivityFingerprints.pm</a>,&nbsp<a href="./MACCSKeys.html">MACCSKeys.pm</a>,&nbsp<a href="./PathLengthFingerprints.html">PathLengthFingerprints.pm</a>,&nbsp
163 <a href="./TopologicalAtomPairsFingerprints.html">TopologicalAtomPairsFingerprints.pm</a>,&nbsp<a href="./TopologicalAtomTripletsFingerprints.html">TopologicalAtomTripletsFingerprints.pm</a>,&nbsp
164 <a href="./TopologicalAtomTorsionsFingerprints.html">TopologicalAtomTorsionsFingerprints.pm</a>,&nbsp<a href="./TopologicalPharmacophoreAtomPairsFingerprints.html">TopologicalPharmacophoreAtomPairsFingerprints.pm</a>,&nbsp
165 <a href="./TopologicalPharmacophoreAtomTripletsFingerprints.html">TopologicalPharmacophoreAtomTripletsFingerprints.pm</a>
166 </p>
167 <p>
168 </p>
169 <h2>COPYRIGHT</h2>
170 <p>Copyright (C) 2015 Manish Sud. All rights reserved.</p>
171 <p>This file is part of MayaChemTools.</p>
172 <p>MayaChemTools is free software; you can redistribute it and/or modify it under
173 the terms of the GNU Lesser General Public License as published by the Free
174 Software Foundation; either version 3 of the License, or (at your option)
175 any later version.</p>
176 <p>&nbsp</p><p>&nbsp</p><div class="DocNav">
177 <table width="100%" border=0 cellpadding=0 cellspacing=2>
178 <tr align="left" valign="top"><td width="33%" align="left"><a href="./AtomTypesFingerprints.html" title="AtomTypesFingerprints.html">Previous</a>&nbsp;&nbsp;<a href="./index.html" title="Table of Contents">TOC</a>&nbsp;&nbsp;<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>
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