|
1
|
1 <html>
|
|
|
2 <head>
|
|
|
3 <title>MayaChemTools:Documentation:Fingerprints::EStateIndiciesFingerprints.pm</title>
|
|
|
4 <meta http-equiv="content-type" content="text/html;charset=utf-8">
|
|
|
5 <link rel="stylesheet" type="text/css" href="../../css/MayaChemTools.css">
|
|
|
6 </head>
|
|
|
7 <body leftmargin="20" rightmargin="20" topmargin="10" bottommargin="10">
|
|
|
8 <br/>
|
|
|
9 <center>
|
|
|
10 <a href="http://www.mayachemtools.org" title="MayaChemTools Home"><img src="../../images/MayaChemToolsLogo.gif" border="0" alt="MayaChemTools"></a>
|
|
|
11 </center>
|
|
|
12 <br/>
|
|
|
13 <div class="DocNav">
|
|
|
14 <table width="100%" border=0 cellpadding=0 cellspacing=2>
|
|
|
15 <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>
|
|
|
16 </table>
|
|
|
17 </div>
|
|
|
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<PropertyName>(<PropertyValue>);
|
|
|
39 <br/> $PropertyValue = Get<PropertyName>();
|
|
|
40 <br/> Delete<PropertyName>();</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' => $Molecule,
|
|
|
108 'EStateAtomTypesSetToUse' =>
|
|
|
109 'ArbitrarySize');</div>
|
|
|
110 <div class="OptionsBox">
|
|
|
111 $EStateIndiciesFingerprints = new AtomTypesFingerprints(
|
|
|
112 'Molecule' => $Molecule,
|
|
|
113 'EStateAtomTypesSetToUse' =>
|
|
|
114 'FixedSize');</div>
|
|
|
115 <div class="OptionsBox">
|
|
|
116 $EStateIndiciesFingerprints->GenerateFingerprints();
|
|
|
117 <br/> print "$EStateIndiciesFingerprints\n";</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->
|
|
|
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->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 $EStateIndiciesFingerprints->SetEStateAtomTypesSetToUse($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 $EStateIndiciesFingerprints->SetValuesPrecision($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->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>, <a href="./FingerprintsStringUtil.html">FingerprintsStringUtil.pm</a>, <a href="./AtomNeighborhoodsFingerprints.html">AtomNeighborhoodsFingerprints.pm</a>, <a href="./AtomTypesFingerprints.html">AtomTypesFingerprints.pm</a>, 
|
|
|
162 <a href="./ExtendedConnectivityFingerprints.html">ExtendedConnectivityFingerprints.pm</a>, <a href="./MACCSKeys.html">MACCSKeys.pm</a>, <a href="./PathLengthFingerprints.html">PathLengthFingerprints.pm</a>, 
|
|
|
163 <a href="./TopologicalAtomPairsFingerprints.html">TopologicalAtomPairsFingerprints.pm</a>, <a href="./TopologicalAtomTripletsFingerprints.html">TopologicalAtomTripletsFingerprints.pm</a>, 
|
|
|
164 <a href="./TopologicalAtomTorsionsFingerprints.html">TopologicalAtomTorsionsFingerprints.pm</a>, <a href="./TopologicalPharmacophoreAtomPairsFingerprints.html">TopologicalPharmacophoreAtomPairsFingerprints.pm</a>, 
|
|
|
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> </p><p> </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> <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>
|
|
|
179 </table>
|
|
|
180 </div>
|
|
|
181 <br />
|
|
|
182 <center>
|
|
|
183 <img src="../../images/h2o2.png">
|
|
|
184 </center>
|
|
|
185 </body>
|
|
|
186 </html>
|
