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1 <html>
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3 <title>MayaChemTools:Documentation:MolecularDescriptors::RotatableBondsDescriptors.pm</title>
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15 <tr align="left" valign="top"><td width="33%" align="left"><a href="./RingsCountDescriptors.html" title="RingsCountDescriptors.html">Previous</a>&nbsp;&nbsp;<a href="./index.html" title="Table of Contents">TOC</a>&nbsp;&nbsp;<a href="./SLogPAndSMRDescriptors.html" title="SLogPAndSMRDescriptors.html">Next</a></td><td width="34%" align="middle"><strong>MolecularDescriptors::RotatableBondsDescriptors.pm</strong></td><td width="33%" align="right"><a href="././code/RotatableBondsDescriptors.html" title="View source code">Code</a>&nbsp;|&nbsp;<a href="./../pdf/RotatableBondsDescriptors.pdf" title="PDF US Letter Size">PDF</a>&nbsp;|&nbsp;<a href="./../pdfgreen/RotatableBondsDescriptors.pdf" title="PDF US Letter Size with narrow margins: www.changethemargins.com">PDFGreen</a>&nbsp;|&nbsp;<a href="./../pdfa4/RotatableBondsDescriptors.pdf" title="PDF A4 Size">PDFA4</a>&nbsp;|&nbsp;<a href="./../pdfa4green/RotatableBondsDescriptors.pdf" title="PDF A4 Size with narrow margins: www.changethemargins.com">PDFA4Green</a></td></tr>
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17 </div>
18 <p>
19 </p>
20 <h2>NAME</h2>
21 <p>RotatableBondsDescriptors</p>
22 <p>
23 </p>
24 <h2>SYNOPSIS</h2>
25 <p>use MolecularDescriptors::RotatableBondsDescriptors;</p>
26 <p>use MolecularDescriptors::RotatableBondsDescriptors qw(:all);</p>
27 <p>
28 </p>
29 <h2>DESCRIPTION</h2>
30 <p><strong>RotatableBondsDescriptors</strong> class provides the following methods:</p>
31 <p> <a href="#new">new</a>, <a href="#generatedescriptors">GenerateDescriptors</a>, <a href="#getdescriptornames">GetDescriptorNames</a>
32 , <a href="#stringifyrotatablebondsdescriptors">StringifyRotatableBondsDescriptors</a>
33 </p><p><strong>RotatableBondsDescriptors</strong> is derived from <strong>MolecularDescriptors</strong> class which in turn
34 is derived from <strong>ObjectProperty</strong> base class that provides methods not explicitly defined
35 in <strong>RotatableBondsDescriptors</strong>, <strong>MolecularDescriptors</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>A rotatable bond [ Ref 92 ] is defined as any single bond which is not in a ring and involves only non-hydrogen
42 atoms. By default, the following types of single bonds are not considered rotatable bonds:</p>
43 <div class="OptionsBox">
44 o Terminal bonds
45 <br/> o Bonds attached to triple bonds
46 <br/> o Amide C-N bonds
47 <br/> o Thioamide C-N bond bonds
48 <br/> o Sulfonamide S-N bonds</div>
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 $RotatableBondsDescriptors = new MolecularDescriptors::
57 RotatableBondsDescriptors(
58 %NamesAndValues);</div>
59 <p>Using specified <em>RotatableBondsDescriptors</em> property names and values hash, <strong>new</strong>
60 method creates a new object and returns a reference to newly created <strong>RotatableBondsDescriptors</strong>
61 object. By default, the following properties are initialized:</p>
62 <div class="OptionsBox">
63 Molecule = ''
64 <br/> Type = 'RotatableBonds'
65 <br/> IgnoreTerminalBonds = 1
66 <br/> IgnoreBondsToTripleBonds = 1
67 <br/> IgnoreAmideBonds = 1
68 <br/> IgnoreThioamideBonds = 1
69 <br/> IgnoreSulfonamideBonds = 1
70 <br/> @DescriptorNames = ('RotatableBonds')
71 <br/> @DescriptorValues = ('None')</div>
72 <p>Examples:</p>
73 <div class="OptionsBox">
74 $RotatableBondsDescriptors = new MolecularDescriptors::
75 RotatableBondsDescriptors();</div>
76 <div class="OptionsBox">
77 $RotatableBondsDescriptors = new MolecularDescriptors::
78 RotatableBondsDescriptors(
79 'IgnoreAmideBonds' =&gt; 0,
80 'IgnoreThioamideBonds' =&gt; 0,
81 'IgnoreSulfonamideBonds' =&gt; 0);</div>
82 <div class="OptionsBox">
83 $RotatableBondsDescriptors-&gt;SetMolecule($Molecule);
84 <br/> $RotatableBondsDescriptors-&gt;GenerateDescriptors();
85 <br/> print &quot;RotatableBondsDescriptors: $RotatableBondsDescriptors\n&quot;;</div>
86 </dd>
87 <dt><strong><a name="generatedescriptors" class="item"><strong>GenerateDescriptors</strong></a></strong></dt>
88 <dd>
89 <div class="OptionsBox">
90 $RotatableBondsDescriptors-&gt;GenerateDescriptors();</div>
91 <p>Calculates number of rotatable bonds descriptors in a molecule and returns
92 <em>RotatableBondsDescriptors</em>.</p>
93 </dd>
94 <dt><strong><a name="getdescriptornames" class="item"><strong>GetDescriptorNames</strong></a></strong></dt>
95 <dd>
96 <div class="OptionsBox">
97 @DescriptorNames = $RotatableBondsDescriptors-&gt;GetDescriptorNames();
98 <br/> @DescriptorNames = MolecularDescriptors::RotatableBondsDescriptors::
99 GetDescriptorNames();</div>
100 <p>Returns all available descriptor names as an array.</p>
101 </dd>
102 <dt><strong><a name="stringifyrotatablebondsdescriptors" class="item"><strong>StringifyRotatableBondsDescriptors</strong></a></strong></dt>
103 <dd>
104 <div class="OptionsBox">
105 $String = $RotatableBondsDescriptors-&gt;StringifyRotatableBondsDescriptors();</div>
106 <p>Returns a string containing information about <em>RotatableBondsDescriptors</em> object.</p>
107 </dd>
108 </dl>
109 <p>
110 </p>
111 <h2>AUTHOR</h2>
112 <p><a href="mailto:msud@san.rr.com">Manish Sud</a></p>
113 <p>
114 </p>
115 <h2>SEE ALSO</h2>
116 <p><a href="./MolecularDescriptors.html">MolecularDescriptors.pm</a>,&nbsp<a href="./MolecularDescriptorsGenerator.html">MolecularDescriptorsGenerator.pm</a>
117 </p>
118 <p>
119 </p>
120 <h2>COPYRIGHT</h2>
121 <p>Copyright (C) 2015 Manish Sud. All rights reserved.</p>
122 <p>This file is part of MayaChemTools.</p>
123 <p>MayaChemTools is free software; you can redistribute it and/or modify it under
124 the terms of the GNU Lesser General Public License as published by the Free
125 Software Foundation; either version 3 of the License, or (at your option)
126 any later version.</p>
127 <p>&nbsp</p><p>&nbsp</p><div class="DocNav">
128 <table width="100%" border=0 cellpadding=0 cellspacing=2>
129 <tr align="left" valign="top"><td width="33%" align="left"><a href="./RingsCountDescriptors.html" title="RingsCountDescriptors.html">Previous</a>&nbsp;&nbsp;<a href="./index.html" title="Table of Contents">TOC</a>&nbsp;&nbsp;<a href="./SLogPAndSMRDescriptors.html" title="SLogPAndSMRDescriptors.html">Next</a></td><td width="34%" align="middle"><strong>March 29, 2015</strong></td><td width="33%" align="right"><strong>MolecularDescriptors::RotatableBondsDescriptors.pm</strong></td></tr>
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