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3 <title>MayaChemTools:Documentation:Fingerprints::Fingerprints.pm</title>
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15 <tr align="left" valign="top"><td width="33%" align="left"><a href="./ExtendedConnectivityFingerprints.html" title="ExtendedConnectivityFingerprints.html">Previous</a>&nbsp;&nbsp;<a href="./index.html" title="Table of Contents">TOC</a>&nbsp;&nbsp;<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>&nbsp;|&nbsp;<a href="./../pdf/Fingerprints.pdf" title="PDF US Letter Size">PDF</a>&nbsp;|&nbsp;<a href="./../pdfgreen/Fingerprints.pdf" title="PDF US Letter Size with narrow margins: www.changethemargins.com">PDFGreen</a>&nbsp;|&nbsp;<a href="./../pdfa4/Fingerprints.pdf" title="PDF A4 Size">PDFA4</a>&nbsp;|&nbsp;<a href="./../pdfa4green/Fingerprints.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>Fingerprints - Fingerprints class</p>
22 <p>
23 </p>
24 <h2>SYNOPSIS</h2>
25 <p>use Fingerprints::Fingerprints;</p>
26 <p>use Fingerprints::Fingerprints qw(:all);</p>
27 <p>
28 </p>
29 <h2>DESCRIPTION</h2>
30 <p><strong>Fingerprints</strong> class provides the following methods:</p>
31 <p> <a href="#new">new</a>, <a href="#foldfingerprintsbybitdensity">FoldFingerprintsByBitDensity</a>, <a href="#foldfingerprintsbysize">FoldFingerprintsBySize</a>
32 , <a href="#getfingerprintbitsasbinarystring">GetFingerprintBitsAsBinaryString</a>, <a href="#getfingerprintbitsashexadecimalstring">GetFingerprintBitsAsHexadecimalString</a>
33 , <a href="#getfingerprintbitsasrawbinarystring">GetFingerprintBitsAsRawBinaryString</a>, <a href="#getfingerprintsvectorvalueids">GetFingerprintsVectorValueIDs</a>
34 , <a href="#getfingerprintsvectorvalues">GetFingerprintsVectorValues</a>, <a href="#isfingerprintsgenerationsuccessful">IsFingerprintsGenerationSuccessful</a>
35 , <a href="#setfingerprintsbitvector">SetFingerprintsBitVector</a>, <a href="#setfingerprintsvector">SetFingerprintsVector</a>, <a href="#setfingerprintsvectortype">SetFingerprintsVectorType</a>
36 , <a href="#setmolecule">SetMolecule</a>, <a href="#setsize">SetSize</a>, <a href="#settype">SetType</a>, <a href="#setvectortype">SetVectorType</a>
37 </p><p><strong>Fingerprints</strong> class is used as a base class for various specific fingerprint classes such as
38 <strong>AtomNeighborhoodsFingerprints</strong>, <strong>AtomTypesFingerprints</strong>, <strong>EStateIndiciesFingerprints</strong>,
39 <strong>PathLengthFingerprints</strong>, <strong>ExtendedConnectivityFingerprints</strong>, <strong>MACCSKeys</strong> and so on.
40 It implements functionality common to fingerprint classes.</p>
41 <p><strong>Fingerprints</strong> class is derived from <strong>ObjectProperty</strong> base class which provides methods not
42 explicitly defined in <strong>Fingerprints</strong> or <strong>ObjectProperty</strong> classes using Perl's AUTOLOAD functionality.
43 These methods are generated on-the-fly for a specified object property:</p>
44 <div class="OptionsBox">
45 Set&lt;PropertyName&gt;(&lt;PropertyValue&gt;);
46 <br/> $PropertyValue = Get&lt;PropertyName&gt;();
47 <br/> Delete&lt;PropertyName&gt;();</div>
48 <p><strong>Fingerprints</strong> class uses <strong>FingerprintsBitVector</strong> class to provide bits manipulation functionality.</p>
49 <p>
50 </p>
51 <h2>METHODS</h2>
52 <dl>
53 <dt><strong><a name="new" class="item"><strong>new</strong></a></strong></dt>
54 <dd>
55 <div class="OptionsBox">
56 $NewFingerprints = new Fingerprints(%NamesAndValues);</div>
57 <p>Using specified <em>Fingerprints</em> property names and values hash, <strong>new</strong> method creates a new object
58 and returns a reference to newly created <strong>Fingerprints</strong> object. By default, following properties are
59 initialized:</p>
60 <div class="OptionsBox">
61 Molecule = '';
62 <br/> Type = '';
63 <br/> VectorType = '';
64 <br/> Size = '';
65 <br/> MinSize = '';
66 <br/> MaxSize = '';
67 <br/> FingerprintsBitVector = '';
68 <br/> FingerprintsVectorType = '';
69 <br/> FingerprintsVector = '';</div>
70 </dd>
71 <dt><strong><a name="foldfingerprintsbybitdensity" class="item"><strong>FoldFingerprintsByBitDensity</strong></a></strong></dt>
72 <dd>
73 <div class="OptionsBox">
74 $Fingerprints-&gt;FoldFingerprintsByBitDensity($BitDensity);</div>
75 <p>Folds fingerprints by recursively reducing its size by half until bit density is greater than or equal to
76 specified <em>BitDensity</em> and returns <em>Fingerprints</em>.</p>
77 </dd>
78 <dt><strong><a name="foldfingerprintsbysize" class="item"><strong>FoldFingerprintsBySize</strong></a></strong></dt>
79 <dd>
80 <div class="OptionsBox">
81 $Fingerprints-&gt;FoldFingerprintsBySize($Size, [$CheckSizeValue]);</div>
82 <p>Fold fingerprints by recursively reducing its size by half until size is less than or equal to specified
83 <em>Size</em> and returns <em>Fingerprints</em>. By default, value <em>Size</em> is checked to make sure it's:</p>
84 <div class="OptionsBox">
85 &gt;= MinSize and &lt; Size and IsPowerOfTwo</div>
86 </dd>
87 <dt><strong><a name="getfingerprintbitsasbinarystring" class="item"><strong>GetFingerprintBitsAsBinaryString</strong></a></strong></dt>
88 <dd>
89 <div class="OptionsBox">
90 $BinaryASCIIString =
91 $Fingerprints-&gt;GetFingerprintBitsAsBinaryString();</div>
92 <p>Returns fingerprints as a binary ASCII string containing 0s and 1s.</p>
93 </dd>
94 <dt><strong><a name="getfingerprintbitsashexadecimalstring" class="item"><strong>GetFingerprintBitsAsHexadecimalString</strong></a></strong></dt>
95 <dd>
96 <div class="OptionsBox">
97 $HexadecimalString =
98 $Fingerprints-&gt;GetFingerprintBitsAsHexadecimalString();</div>
99 <p>Returns fingerprints as a hexadecimal string</p>
100 </dd>
101 <dt><strong><a name="getfingerprintbitsasrawbinarystring" class="item"><strong>GetFingerprintBitsAsRawBinaryString</strong></a></strong></dt>
102 <dd>
103 <div class="OptionsBox">
104 $RawBinaryString =
105 $Fingerprints-&gt;GetFingerprintBitsAsRawBinaryString();</div>
106 <p>Returns fingerprints as a raw binary string containing packed bit values for each byte.</p>
107 </dd>
108 <dt><strong><a name="getfingerprintsvectorvalueids" class="item"><strong>GetFingerprintsVectorValueIDs</strong></a></strong></dt>
109 <dd>
110 <div class="OptionsBox">
111 $ValueIDsRef = $Fingerprints-&gt;GetFingerprintsVectorValueIDs();
112 <br/> @ValueIDs = $Fingerprints-&gt;GetFingerprintsVectorValueIDs();</div>
113 <p>Returns fingerprints vector value IDs as an array or reference to an array.</p>
114 </dd>
115 <dt><strong><a name="getfingerprintsvectorvalues" class="item"><strong>GetFingerprintsVectorValues</strong></a></strong></dt>
116 <dd>
117 <div class="OptionsBox">
118 $ValuesRef = $Fingerprints-&gt;GetFingerprintsVectorValues();
119 <br/> @Values = $Fingerprints-&gt;GetFingerprintsVectorValues();</div>
120 <p>Returns fingerprints vector values as an array or reference to an array.</p>
121 </dd>
122 <dt><strong><a name="isfingerprintsgenerationsuccessful" class="item"><strong>IsFingerprintsGenerationSuccessful</strong></a></strong></dt>
123 <dd>
124 <div class="OptionsBox">
125 $Return = $Fingerprints-&gt;IsFingerprintsGenerationSuccessful();</div>
126 <p>Returns 1 or 0 based on whether fingerprints were successfully generated.</p>
127 </dd>
128 <dt><strong><a name="setfingerprintsbitvector" class="item"><strong>SetFingerprintsBitVector</strong></a></strong></dt>
129 <dd>
130 <div class="OptionsBox">
131 $Fingerprints-&gt;SetFingerprintsBitVector($FingerprintsBitVector);</div>
132 <p>Sets <em>FingerprintsBitVector</em> object for <em>Fingerprints</em> and returns <em>Fingerprints</em>.</p>
133 </dd>
134 <dt><strong><a name="setfingerprintsvector" class="item"><strong>SetFingerprintsVector</strong></a></strong></dt>
135 <dd>
136 <div class="OptionsBox">
137 $Fingerprints-&gt;SetFingerprintsVector();</div>
138 <p>Sets <em>FingerprintsVector</em> object for <em>Fingerprints</em> and returns <em>Fingerprints</em>.</p>
139 </dd>
140 <dt><strong><a name="setfingerprintsvectortype" class="item"><strong>SetFingerprintsVectorType</strong></a></strong></dt>
141 <dd>
142 <div class="OptionsBox">
143 $Fingerprints-&gt;SetFingerprintsVectorType($VectorType);</div>
144 <p>Sets <em>FingerprintsVector</em> type for <em>Fingerprints</em> and returns <em>Fingerprints</em>. Possible
145 <em>VectorType</em> values: <em>OrderedNumericalValues, NumericalValues or AlphaNumericalValues</em>.</p>
146 </dd>
147 <dt><strong><a name="setmolecule" class="item"><strong>SetMolecule</strong></a></strong></dt>
148 <dd>
149 <div class="OptionsBox">
150 $Fingerprints-&gt;SetMolecule($Molecule);</div>
151 <p>Sets <em>Molecule</em> object for <em>Fingerprints</em> and returns <em>Fingerprints</em>.</p>
152 </dd>
153 <dt><strong><a name="setsize" class="item"><strong>SetSize</strong></a></strong></dt>
154 <dd>
155 <div class="OptionsBox">
156 $Fingerprints-&gt;SetSize($Size);</div>
157 <p>Sets <em>Size</em> of fingerprints and returns <em>Fingerprints</em>.</p>
158 </dd>
159 <dt><strong><a name="settype" class="item"><strong>SetType</strong></a></strong></dt>
160 <dd>
161 <div class="OptionsBox">
162 $Fingerprints-&gt;SetType($Type);</div>
163 <p>Sets <em>Type</em> of fingerprints and returns <em>Fingerprints</em>.</p>
164 </dd>
165 <dt><strong><a name="setvectortype" class="item"><strong>SetVectorType</strong></a></strong></dt>
166 <dd>
167 <div class="OptionsBox">
168 $Fingerprints-&gt;SetVectorType($Type);</div>
169 <p>Sets <em>Type</em> of fingerprints vector and returns <em>Fingerprints</em>. Possible <em>Type</em> values:
170 <em>FingerprintsBitVector or FingerprintsVector</em>.</p>
171 </dd>
172 </dl>
173 <p>
174 </p>
175 <h2>AUTHOR</h2>
176 <p><a href="mailto:msud@san.rr.com">Manish Sud</a></p>
177 <p>
178 </p>
179 <h2>SEE ALSO</h2>
180 <p><a href="./FingerprintsStringUtil.html">FingerprintsStringUtil.pm</a>,&nbsp<a href="./AtomNeighborhoodsFingerprints.html">AtomNeighborhoodsFingerprints.pm</a>,&nbsp<a href="./AtomTypesFingerprints.html">AtomTypesFingerprints.pm</a>,&nbsp
181 <a href="./EStateIndiciesFingerprints.html">EStateIndiciesFingerprints.pm</a>,&nbsp<a href="./ExtendedConnectivityFingerprints.html">ExtendedConnectivityFingerprints.pm</a>,&nbsp<a href="./MACCSKeys.html">MACCSKeys.pm</a>,&nbsp
182 <a href="./PathLengthFingerprints.html">PathLengthFingerprints.pm</a>,&nbsp<a href="./TopologicalAtomPairsFingerprints.html">TopologicalAtomPairsFingerprints.pm</a>,&nbsp<a href="./TopologicalAtomTripletsFingerprints.html">TopologicalAtomTripletsFingerprints.pm</a>,&nbsp
183 <a href="./TopologicalAtomTorsionsFingerprints.html">TopologicalAtomTorsionsFingerprints.pm</a>,&nbsp<a href="./TopologicalPharmacophoreAtomPairsFingerprints.html">TopologicalPharmacophoreAtomPairsFingerprints.pm</a>,&nbsp
184 <a href="./TopologicalPharmacophoreAtomTripletsFingerprints.html">TopologicalPharmacophoreAtomTripletsFingerprints.pm</a>
185 </p>
186 <p>
187 </p>
188 <h2>COPYRIGHT</h2>
189 <p>Copyright (C) 2015 Manish Sud. All rights reserved.</p>
190 <p>This file is part of MayaChemTools.</p>
191 <p>MayaChemTools is free software; you can redistribute it and/or modify it under
192 the terms of the GNU Lesser General Public License as published by the Free
193 Software Foundation; either version 3 of the License, or (at your option)
194 any later version.</p>
195 <p>&nbsp</p><p>&nbsp</p><div class="DocNav">
196 <table width="100%" border=0 cellpadding=0 cellspacing=2>
197 <tr align="left" valign="top"><td width="33%" align="left"><a href="./ExtendedConnectivityFingerprints.html" title="ExtendedConnectivityFingerprints.html">Previous</a>&nbsp;&nbsp;<a href="./index.html" title="Table of Contents">TOC</a>&nbsp;&nbsp;<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>
198 </table>
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