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15 <tr align="left" valign="top"><td width="33%" align="left"><a href="./Fsp3CarbonsDescriptors.html" title="Fsp3CarbonsDescriptors.html">Previous</a>&nbsp;&nbsp;<a href="./index.html" title="Table of Contents">TOC</a>&nbsp;&nbsp;<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>&nbsp;|&nbsp;<a href="./../pdf/HydrogenBondsDescriptors.pdf" title="PDF US Letter Size">PDF</a>&nbsp;|&nbsp;<a href="./../pdfgreen/HydrogenBondsDescriptors.pdf" title="PDF US Letter Size with narrow margins: www.changethemargins.com">PDFGreen</a>&nbsp;|&nbsp;<a href="./../pdfa4/HydrogenBondsDescriptors.pdf" title="PDF A4 Size">PDFA4</a>&nbsp;|&nbsp;<a href="./../pdfa4green/HydrogenBondsDescriptors.pdf" title="PDF A4 Size with narrow margins: www.changethemargins.com">PDFA4Green</a></td></tr>
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18 <p>
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20 <h2>NAME</h2>
21 <p>HydrogenBondsDescriptors</p>
22 <p>
23 </p>
24 <h2>SYNOPSIS</h2>
25 <p>use MolecularDescriptors::HydrogenBondsDescriptors;</p>
26 <p>use MolecularDescriptors::HydrogenBondsDescriptors qw(:all);</p>
27 <p>
28 </p>
29 <h2>DESCRIPTION</h2>
30 <p><strong>HydrogenBondsDescriptors</strong> class provides the following methods:</p>
31 <p> <a href="#new">new</a>, <a href="#generatedescriptors">GenerateDescriptors</a>, <a href="#getdescriptornames">GetDescriptorNames</a>, <a href="#sethydrogenbondstype">SetHydrogenBondsType</a>
32 , <a href="#stringifyhydrogenbondsdescriptors">StringifyHydrogenBondsDescriptors</a>
33 </p><p><strong>HydrogenBondsDescriptors</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>HydrogenBondsDescriptors</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>The current release of MayaChemTools supports identification of two types of hydrogen bond
42 donor and acceptor atoms with these names:</p>
43 <div class="OptionsBox">
44 HBondsType1 or HydrogenBondsType1
45 <br/> HBondsType2 or HydrogenBondsType2</div>
46 <p>The names of these hydrogen bond types are rather arbitrary. However, their definitions have
47 specific meaning and are as follows:</p>
48 <div class="OptionsBox">
49 HydrogenBondsType1 [ Ref 60-61, Ref 65-66 ]:</div>
50 <div class="OptionsBox">
51 &nbsp;&nbsp;&nbsp;&nbsp; Donor: NH, NH2, OH - Any N and O with available H
52 Acceptor: N[!H], O - Any N without available H and any O</div>
53 <div class="OptionsBox">
54 HydrogenBondsType2 [ Ref 91 ]:</div>
55 <div class="OptionsBox">
56 &nbsp;&nbsp;&nbsp;&nbsp; Donor: NH, NH2, OH - N and O with available H
57 Acceptor: N, O - And N and O</div>
58 <p>By default, <em>HydrogenBondsType2</em> is used to calculate number hydrogen bond donor
59 and acceptor atoms. This corresponds to <strong>RuleOf5</strong> definition of hydrogen bond donors
60 and acceptors.</p>
61 <p>
62 </p>
63 <h2>METHODS</h2>
64 <dl>
65 <dt><strong><a name="new" class="item"><strong>new</strong></a></strong></dt>
66 <dd>
67 <div class="OptionsBox">
68 $HydrogenBondsDescriptors = new MolecularDescriptors::
69 HydrogenBondsDescriptors(%NamesAndValues);</div>
70 <p>Using specified <em>HydrogenBondsDescriptors</em> property names and values hash, <strong>new</strong>
71 method creates a new object and returns a reference to newly created <strong>HydrogenBondsDescriptors</strong>
72 object. By default, the following properties are initialized:</p>
73 <div class="OptionsBox">
74 Molecule = ''
75 <br/> Type = 'HydrogenBonds'
76 <br/> HydrogenBondsType = 'HBondsType2'
77 <br/> @DescriptorNames = ('HydrogenBondDonors', 'HydrogenBondAcceptors')
78 <br/> @DescriptorValues = ('None', 'None')</div>
79 <p>Examples:</p>
80 <div class="OptionsBox">
81 $HydrogenBondsDescriptors = new MolecularDescriptors::
82 HydrogenBondsDescriptors();</div>
83 <div class="OptionsBox">
84 $HydrogenBondsDescriptors = new MolecularDescriptors::
85 HydrogenBondsDescriptors(
86 'HydrogenBondsType' =&gt; 'HBondsType2');</div>
87 <div class="OptionsBox">
88 $HydrogenBondsDescriptors-&gt;SetMolecule($Molecule);
89 <br/> $HydrogenBondsDescriptors-&gt;GenerateDescriptors();
90 <br/> print &quot;HydrogenBondsDescriptors: $HydrogenBondsDescriptors\n&quot;;</div>
91 </dd>
92 <dt><strong><a name="generatedescriptors" class="item"><strong>GenerateDescriptors</strong></a></strong></dt>
93 <dd>
94 <div class="OptionsBox">
95 $HydrogenBondsDescriptors-&gt;GenerateDescriptors();</div>
96 <p>Calculates number of hydrogen bond donors and acceptors a molecule and returns
97 <em>HydrogenBondsDescriptors</em>.</p>
98 </dd>
99 <dt><strong><a name="getdescriptornames" class="item"><strong>GetDescriptorNames</strong></a></strong></dt>
100 <dd>
101 <div class="OptionsBox">
102 @DescriptorNames = $HydrogenBondsDescriptors-&gt;GetDescriptorNames();
103 <br/> @DescriptorNames = MolecularDescriptors::HydrogenBondsDescriptors::
104 GetDescriptorNames();</div>
105 <p>Returns all available descriptor names as an array.</p>
106 </dd>
107 <dt><strong><a name="sethydrogenbondstype" class="item"><strong>SetHydrogenBondsType</strong></a></strong></dt>
108 <dd>
109 <div class="OptionsBox">
110 $HydrogenBondsDescriptors-&gt;SetHydrogenBondsType($HBondsType);</div>
111 <p>Sets value of hydrogen bonds type to use during calculation of descriptors and returns
112 <em>HydrogenBondsDescriptors</em>. Possible values: <em>HBondsType1, HydrogenBondsType1,
113 HBondsType2, HydrogenBondsType2</em>.</p>
114 </dd>
115 <dt><strong><a name="stringifyhydrogenbondsdescriptors" class="item"><strong>StringifyHydrogenBondsDescriptors</strong></a></strong></dt>
116 <dd>
117 <div class="OptionsBox">
118 $String = $HydrogenBondsDescriptors-&gt;
119 StringifyHydrogenBondsDescriptors();</div>
120 <p>Returns a string containing information about <em>HydrogenBondsDescriptors</em> object.</p>
121 </dd>
122 </dl>
123 <p>
124 </p>
125 <h2>AUTHOR</h2>
126 <p><a href="mailto:msud@san.rr.com">Manish Sud</a></p>
127 <p>
128 </p>
129 <h2>SEE ALSO</h2>
130 <p><a href="./MolecularDescriptors.html">MolecularDescriptors.pm</a>,&nbsp<a href="./MolecularDescriptorsGenerator.html">MolecularDescriptorsGenerator.pm</a>
131 </p>
132 <p>
133 </p>
134 <h2>COPYRIGHT</h2>
135 <p>Copyright (C) 2015 Manish Sud. All rights reserved.</p>
136 <p>This file is part of MayaChemTools.</p>
137 <p>MayaChemTools is free software; you can redistribute it and/or modify it under
138 the terms of the GNU Lesser General Public License as published by the Free
139 Software Foundation; either version 3 of the License, or (at your option)
140 any later version.</p>
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143 <tr align="left" valign="top"><td width="33%" align="left"><a href="./Fsp3CarbonsDescriptors.html" title="Fsp3CarbonsDescriptors.html">Previous</a>&nbsp;&nbsp;<a href="./index.html" title="Table of Contents">TOC</a>&nbsp;&nbsp;<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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