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3 <title>MayaChemTools:Documentation:MolecularDescriptors::HydrogenBondsDescriptors.pm</title>
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13 <div class="DocNav">
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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="./Fsp3CarbonsDescriptors.html" title="Fsp3CarbonsDescriptors.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./MolecularComplexityDescriptors.html" title="MolecularComplexityDescriptors.html">Next</a></td><td width="34%" align="middle"><strong>MolecularDescriptors::HydrogenBondsDescriptors.pm</strong></td><td width="33%" align="right"><a href="././code/HydrogenBondsDescriptors.html" title="View source code">Code</a> | <a href="./../pdf/HydrogenBondsDescriptors.pdf" title="PDF US Letter Size">PDF</a> | <a href="./../pdfgreen/HydrogenBondsDescriptors.pdf" title="PDF US Letter Size with narrow margins: www.changethemargins.com">PDFGreen</a> | <a href="./../pdfa4/HydrogenBondsDescriptors.pdf" title="PDF A4 Size">PDFA4</a> | <a href="./../pdfa4green/HydrogenBondsDescriptors.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>HydrogenBondsDescriptors</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::HydrogenBondsDescriptors;</p>
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26 <p>use MolecularDescriptors::HydrogenBondsDescriptors 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>HydrogenBondsDescriptors</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>, <a href="#sethydrogenbondstype">SetHydrogenBondsType</a>
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32 , <a href="#stringifyhydrogenbondsdescriptors">StringifyHydrogenBondsDescriptors</a>
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33 </p><p><strong>HydrogenBondsDescriptors</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>HydrogenBondsDescriptors</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>The current release of MayaChemTools supports identification of two types of hydrogen bond
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42 donor and acceptor atoms with these names:</p>
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43 <div class="OptionsBox">
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44 HBondsType1 or HydrogenBondsType1
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45 <br/> HBondsType2 or HydrogenBondsType2</div>
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46 <p>The names of these hydrogen bond types are rather arbitrary. However, their definitions have
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47 specific meaning and are as follows:</p>
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48 <div class="OptionsBox">
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49 HydrogenBondsType1 [ Ref 60-61, Ref 65-66 ]:</div>
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50 <div class="OptionsBox">
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51 Donor: NH, NH2, OH - Any N and O with available H
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52 Acceptor: N[!H], O - Any N without available H and any O</div>
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53 <div class="OptionsBox">
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54 HydrogenBondsType2 [ Ref 91 ]:</div>
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55 <div class="OptionsBox">
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56 Donor: NH, NH2, OH - N and O with available H
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57 Acceptor: N, O - And N and O</div>
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58 <p>By default, <em>HydrogenBondsType2</em> is used to calculate number hydrogen bond donor
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59 and acceptor atoms. This corresponds to <strong>RuleOf5</strong> definition of hydrogen bond donors
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60 and acceptors.</p>
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61 <p>
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62 </p>
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63 <h2>METHODS</h2>
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64 <dl>
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65 <dt><strong><a name="new" class="item"><strong>new</strong></a></strong></dt>
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66 <dd>
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67 <div class="OptionsBox">
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68 $HydrogenBondsDescriptors = new MolecularDescriptors::
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69 HydrogenBondsDescriptors(%NamesAndValues);</div>
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70 <p>Using specified <em>HydrogenBondsDescriptors</em> property names and values hash, <strong>new</strong>
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71 method creates a new object and returns a reference to newly created <strong>HydrogenBondsDescriptors</strong>
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72 object. By default, the following properties are initialized:</p>
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73 <div class="OptionsBox">
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74 Molecule = ''
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75 <br/> Type = 'HydrogenBonds'
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76 <br/> HydrogenBondsType = 'HBondsType2'
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77 <br/> @DescriptorNames = ('HydrogenBondDonors', 'HydrogenBondAcceptors')
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78 <br/> @DescriptorValues = ('None', 'None')</div>
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79 <p>Examples:</p>
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80 <div class="OptionsBox">
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81 $HydrogenBondsDescriptors = new MolecularDescriptors::
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82 HydrogenBondsDescriptors();</div>
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83 <div class="OptionsBox">
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84 $HydrogenBondsDescriptors = new MolecularDescriptors::
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85 HydrogenBondsDescriptors(
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86 'HydrogenBondsType' => 'HBondsType2');</div>
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87 <div class="OptionsBox">
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88 $HydrogenBondsDescriptors->SetMolecule($Molecule);
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89 <br/> $HydrogenBondsDescriptors->GenerateDescriptors();
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90 <br/> print "HydrogenBondsDescriptors: $HydrogenBondsDescriptors\n";</div>
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91 </dd>
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92 <dt><strong><a name="generatedescriptors" class="item"><strong>GenerateDescriptors</strong></a></strong></dt>
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93 <dd>
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94 <div class="OptionsBox">
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95 $HydrogenBondsDescriptors->GenerateDescriptors();</div>
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96 <p>Calculates number of hydrogen bond donors and acceptors a molecule and returns
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97 <em>HydrogenBondsDescriptors</em>.</p>
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98 </dd>
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99 <dt><strong><a name="getdescriptornames" class="item"><strong>GetDescriptorNames</strong></a></strong></dt>
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100 <dd>
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101 <div class="OptionsBox">
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102 @DescriptorNames = $HydrogenBondsDescriptors->GetDescriptorNames();
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103 <br/> @DescriptorNames = MolecularDescriptors::HydrogenBondsDescriptors::
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104 GetDescriptorNames();</div>
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105 <p>Returns all available descriptor names as an array.</p>
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106 </dd>
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107 <dt><strong><a name="sethydrogenbondstype" class="item"><strong>SetHydrogenBondsType</strong></a></strong></dt>
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108 <dd>
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109 <div class="OptionsBox">
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110 $HydrogenBondsDescriptors->SetHydrogenBondsType($HBondsType);</div>
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111 <p>Sets value of hydrogen bonds type to use during calculation of descriptors and returns
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112 <em>HydrogenBondsDescriptors</em>. Possible values: <em>HBondsType1, HydrogenBondsType1,
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113 HBondsType2, HydrogenBondsType2</em>.</p>
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114 </dd>
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115 <dt><strong><a name="stringifyhydrogenbondsdescriptors" class="item"><strong>StringifyHydrogenBondsDescriptors</strong></a></strong></dt>
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116 <dd>
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117 <div class="OptionsBox">
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118 $String = $HydrogenBondsDescriptors->
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119 StringifyHydrogenBondsDescriptors();</div>
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120 <p>Returns a string containing information about <em>HydrogenBondsDescriptors</em> object.</p>
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121 </dd>
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122 </dl>
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123 <p>
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124 </p>
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125 <h2>AUTHOR</h2>
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126 <p><a href="mailto:msud@san.rr.com">Manish Sud</a></p>
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127 <p>
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128 </p>
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129 <h2>SEE ALSO</h2>
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130 <p><a href="./MolecularDescriptors.html">MolecularDescriptors.pm</a>, <a href="./MolecularDescriptorsGenerator.html">MolecularDescriptorsGenerator.pm</a>
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131 </p>
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132 <p>
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133 </p>
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134 <h2>COPYRIGHT</h2>
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135 <p>Copyright (C) 2015 Manish Sud. All rights reserved.</p>
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136 <p>This file is part of MayaChemTools.</p>
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137 <p>MayaChemTools is free software; you can redistribute it and/or modify it under
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138 the terms of the GNU Lesser General Public License as published by the Free
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139 Software Foundation; either version 3 of the License, or (at your option)
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140 any later version.</p>
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141 <p> </p><p> </p><div class="DocNav">
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142 <table width="100%" border=0 cellpadding=0 cellspacing=2>
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143 <tr align="left" valign="top"><td width="33%" align="left"><a href="./Fsp3CarbonsDescriptors.html" title="Fsp3CarbonsDescriptors.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./MolecularComplexityDescriptors.html" title="MolecularComplexityDescriptors.html">Next</a></td><td width="34%" align="middle"><strong>March 29, 2015</strong></td><td width="33%" align="right"><strong>MolecularDescriptors::HydrogenBondsDescriptors.pm</strong></td></tr>
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144 </table>
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145 </div>
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146 <br />
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147 <center>
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148 <img src="../../images/h2o2.png">
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