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1 <html> | |
2 <head> | |
3 <title>MayaChemTools:Documentation:Fingerprints::Fingerprints.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="./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> | |
16 </table> | |
17 </div> | |
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<PropertyName>(<PropertyValue>); | |
46 <br/> $PropertyValue = Get<PropertyName>(); | |
47 <br/> Delete<PropertyName>();</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 $Fingerprints->FoldFingerprintsByBitDensity($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 $Fingerprints->FoldFingerprintsBySize($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 >= MinSize and < 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->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->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->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->GetFingerprintsVectorValueIDs(); | |
112 <br/> @ValueIDs = $Fingerprints->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->GetFingerprintsVectorValues(); | |
119 <br/> @Values = $Fingerprints->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->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 $Fingerprints->SetFingerprintsBitVector($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->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 $Fingerprints->SetFingerprintsVectorType($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 $Fingerprints->SetMolecule($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 $Fingerprints->SetSize($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 $Fingerprints->SetType($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 $Fingerprints->SetVectorType($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>, <a href="./AtomNeighborhoodsFingerprints.html">AtomNeighborhoodsFingerprints.pm</a>, <a href="./AtomTypesFingerprints.html">AtomTypesFingerprints.pm</a>,  | |
181 <a href="./EStateIndiciesFingerprints.html">EStateIndiciesFingerprints.pm</a>, <a href="./ExtendedConnectivityFingerprints.html">ExtendedConnectivityFingerprints.pm</a>, <a href="./MACCSKeys.html">MACCSKeys.pm</a>,  | |
182 <a href="./PathLengthFingerprints.html">PathLengthFingerprints.pm</a>, <a href="./TopologicalAtomPairsFingerprints.html">TopologicalAtomPairsFingerprints.pm</a>, <a href="./TopologicalAtomTripletsFingerprints.html">TopologicalAtomTripletsFingerprints.pm</a>,  | |
183 <a href="./TopologicalAtomTorsionsFingerprints.html">TopologicalAtomTorsionsFingerprints.pm</a>, <a href="./TopologicalPharmacophoreAtomPairsFingerprints.html">TopologicalPharmacophoreAtomPairsFingerprints.pm</a>,  | |
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> </p><p> </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> <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> | |
198 </table> | |
199 </div> | |
200 <br /> | |
201 <center> | |
202 <img src="../../images/h2o2.png"> | |
203 </center> | |
204 </body> | |
205 </html> |