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3 <title>MayaChemTools:Documentation:MolecularDescriptors::RotatableBondsDescriptors.pm</title>
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14 <table width="100%" border=0 cellpadding=0 cellspacing=2>
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15 <tr align="left" valign="top"><td width="33%" align="left"><a href="./RingsCountDescriptors.html" title="RingsCountDescriptors.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <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> | <a href="./../pdf/RotatableBondsDescriptors.pdf" title="PDF US Letter Size">PDF</a> | <a href="./../pdfgreen/RotatableBondsDescriptors.pdf" title="PDF US Letter Size with narrow margins: www.changethemargins.com">PDFGreen</a> | <a href="./../pdfa4/RotatableBondsDescriptors.pdf" title="PDF A4 Size">PDFA4</a> | <a href="./../pdfa4green/RotatableBondsDescriptors.pdf" title="PDF A4 Size with narrow margins: www.changethemargins.com">PDFA4Green</a></td></tr>
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16 </table>
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17 </div>
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18 <p>
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19 </p>
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20 <h2>NAME</h2>
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21 <p>RotatableBondsDescriptors</p>
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22 <p>
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23 </p>
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24 <h2>SYNOPSIS</h2>
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25 <p>use MolecularDescriptors::RotatableBondsDescriptors;</p>
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26 <p>use MolecularDescriptors::RotatableBondsDescriptors qw(:all);</p>
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27 <p>
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28 </p>
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29 <h2>DESCRIPTION</h2>
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30 <p><strong>RotatableBondsDescriptors</strong> class provides the following methods:</p>
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31 <p> <a href="#new">new</a>, <a href="#generatedescriptors">GenerateDescriptors</a>, <a href="#getdescriptornames">GetDescriptorNames</a>
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32 , <a href="#stringifyrotatablebondsdescriptors">StringifyRotatableBondsDescriptors</a>
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33 </p><p><strong>RotatableBondsDescriptors</strong> is derived from <strong>MolecularDescriptors</strong> class which in turn
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34 is derived from <strong>ObjectProperty</strong> base class that provides methods not explicitly defined
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35 in <strong>RotatableBondsDescriptors</strong>, <strong>MolecularDescriptors</strong> or <strong>ObjectProperty</strong> classes using Perl's
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36 AUTOLOAD functionality. These methods are generated on-the-fly for a specified object property:</p>
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37 <div class="OptionsBox">
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38 Set<PropertyName>(<PropertyValue>);
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39 <br/> $PropertyValue = Get<PropertyName>();
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40 <br/> Delete<PropertyName>();</div>
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41 <p>A rotatable bond [ Ref 92 ] is defined as any single bond which is not in a ring and involves only non-hydrogen
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42 atoms. By default, the following types of single bonds are not considered rotatable bonds:</p>
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43 <div class="OptionsBox">
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44 o Terminal bonds
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45 <br/> o Bonds attached to triple bonds
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46 <br/> o Amide C-N bonds
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47 <br/> o Thioamide C-N bond bonds
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48 <br/> o Sulfonamide S-N bonds</div>
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49 <p>
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50 </p>
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51 <h2>METHODS</h2>
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52 <dl>
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53 <dt><strong><a name="new" class="item"><strong>new</strong></a></strong></dt>
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54 <dd>
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55 <div class="OptionsBox">
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56 $RotatableBondsDescriptors = new MolecularDescriptors::
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57 RotatableBondsDescriptors(
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58 %NamesAndValues);</div>
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59 <p>Using specified <em>RotatableBondsDescriptors</em> property names and values hash, <strong>new</strong>
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60 method creates a new object and returns a reference to newly created <strong>RotatableBondsDescriptors</strong>
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61 object. By default, the following properties are initialized:</p>
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62 <div class="OptionsBox">
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63 Molecule = ''
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64 <br/> Type = 'RotatableBonds'
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65 <br/> IgnoreTerminalBonds = 1
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66 <br/> IgnoreBondsToTripleBonds = 1
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67 <br/> IgnoreAmideBonds = 1
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68 <br/> IgnoreThioamideBonds = 1
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69 <br/> IgnoreSulfonamideBonds = 1
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70 <br/> @DescriptorNames = ('RotatableBonds')
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71 <br/> @DescriptorValues = ('None')</div>
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72 <p>Examples:</p>
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73 <div class="OptionsBox">
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74 $RotatableBondsDescriptors = new MolecularDescriptors::
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75 RotatableBondsDescriptors();</div>
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76 <div class="OptionsBox">
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77 $RotatableBondsDescriptors = new MolecularDescriptors::
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78 RotatableBondsDescriptors(
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79 'IgnoreAmideBonds' => 0,
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80 'IgnoreThioamideBonds' => 0,
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81 'IgnoreSulfonamideBonds' => 0);</div>
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82 <div class="OptionsBox">
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83 $RotatableBondsDescriptors->SetMolecule($Molecule);
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84 <br/> $RotatableBondsDescriptors->GenerateDescriptors();
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85 <br/> print "RotatableBondsDescriptors: $RotatableBondsDescriptors\n";</div>
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86 </dd>
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87 <dt><strong><a name="generatedescriptors" class="item"><strong>GenerateDescriptors</strong></a></strong></dt>
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88 <dd>
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89 <div class="OptionsBox">
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90 $RotatableBondsDescriptors->GenerateDescriptors();</div>
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91 <p>Calculates number of rotatable bonds descriptors in a molecule and returns
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92 <em>RotatableBondsDescriptors</em>.</p>
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93 </dd>
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94 <dt><strong><a name="getdescriptornames" class="item"><strong>GetDescriptorNames</strong></a></strong></dt>
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95 <dd>
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96 <div class="OptionsBox">
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97 @DescriptorNames = $RotatableBondsDescriptors->GetDescriptorNames();
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98 <br/> @DescriptorNames = MolecularDescriptors::RotatableBondsDescriptors::
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99 GetDescriptorNames();</div>
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100 <p>Returns all available descriptor names as an array.</p>
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101 </dd>
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102 <dt><strong><a name="stringifyrotatablebondsdescriptors" class="item"><strong>StringifyRotatableBondsDescriptors</strong></a></strong></dt>
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103 <dd>
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104 <div class="OptionsBox">
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105 $String = $RotatableBondsDescriptors->StringifyRotatableBondsDescriptors();</div>
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106 <p>Returns a string containing information about <em>RotatableBondsDescriptors</em> object.</p>
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107 </dd>
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108 </dl>
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109 <p>
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110 </p>
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111 <h2>AUTHOR</h2>
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112 <p><a href="mailto:msud@san.rr.com">Manish Sud</a></p>
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113 <p>
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114 </p>
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115 <h2>SEE ALSO</h2>
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116 <p><a href="./MolecularDescriptors.html">MolecularDescriptors.pm</a>, <a href="./MolecularDescriptorsGenerator.html">MolecularDescriptorsGenerator.pm</a>
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117 </p>
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118 <p>
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119 </p>
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120 <h2>COPYRIGHT</h2>
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121 <p>Copyright (C) 2015 Manish Sud. All rights reserved.</p>
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122 <p>This file is part of MayaChemTools.</p>
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123 <p>MayaChemTools is free software; you can redistribute it and/or modify it under
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124 the terms of the GNU Lesser General Public License as published by the Free
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125 Software Foundation; either version 3 of the License, or (at your option)
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126 any later version.</p>
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127 <p> </p><p> </p><div class="DocNav">
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128 <table width="100%" border=0 cellpadding=0 cellspacing=2>
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129 <tr align="left" valign="top"><td width="33%" align="left"><a href="./RingsCountDescriptors.html" title="RingsCountDescriptors.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <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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130 </table>
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131 </div>
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132 <br />
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