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<p>
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<h2>NAME</h2>
<p>HydrogenBondsDescriptors</p>
<p>
</p>
<h2>SYNOPSIS</h2>
<p>use MolecularDescriptors::HydrogenBondsDescriptors;</p>
<p>use MolecularDescriptors::HydrogenBondsDescriptors qw(:all);</p>
<p>
</p>
<h2>DESCRIPTION</h2>
<p><strong>HydrogenBondsDescriptors</strong> class provides the following methods:</p>
<p> <a href="#new">new</a>, <a href="#generatedescriptors">GenerateDescriptors</a>, <a href="#getdescriptornames">GetDescriptorNames</a>, <a href="#sethydrogenbondstype">SetHydrogenBondsType</a>
, <a href="#stringifyhydrogenbondsdescriptors">StringifyHydrogenBondsDescriptors</a>
</p><p><strong>HydrogenBondsDescriptors</strong> is derived from <strong>MolecularDescriptors</strong> class which in turn
is  derived from <strong>ObjectProperty</strong> base class that provides methods not explicitly defined
in <strong>HydrogenBondsDescriptors</strong>, <strong>MolecularDescriptors</strong> or <strong>ObjectProperty</strong> classes using Perl's
AUTOLOAD functionality. These methods are generated on-the-fly for a specified object property:</p>
<div class="OptionsBox">
    Set&lt;PropertyName&gt;(&lt;PropertyValue&gt;);
<br/>    $PropertyValue = Get&lt;PropertyName&gt;();
<br/>    Delete&lt;PropertyName&gt;();</div>
<p>The current release of MayaChemTools supports identification of two types of hydrogen bond
donor and acceptor atoms with these names:</p>
<div class="OptionsBox">
    HBondsType1 or HydrogenBondsType1
<br/>    HBondsType2 or HydrogenBondsType2</div>
<p>The names of these hydrogen bond types are rather arbitrary. However, their definitions have
specific meaning and are as follows:</p>
<div class="OptionsBox">
    HydrogenBondsType1 [ Ref 60-61, Ref 65-66 ]:</div>
<div class="OptionsBox">
&nbsp;&nbsp;&nbsp;&nbsp;        Donor: NH, NH2, OH - Any N and O with available H
        Acceptor: N[!H], O - Any N without available H and any O</div>
<div class="OptionsBox">
    HydrogenBondsType2 [ Ref 91 ]:</div>
<div class="OptionsBox">
&nbsp;&nbsp;&nbsp;&nbsp;        Donor: NH, NH2, OH - N and O with available H
        Acceptor: N, O - And N and O</div>
<p>By default, <em>HydrogenBondsType2</em> is used to calculate number hydrogen bond donor
and acceptor atoms. This corresponds to <strong>RuleOf5</strong> definition of hydrogen bond donors
and acceptors.</p>
<p>
</p>
<h2>METHODS</h2>
<dl>
<dt><strong><a name="new" class="item"><strong>new</strong></a></strong></dt>
<dd>
<div class="OptionsBox">
    $HydrogenBondsDescriptors = new MolecularDescriptors::
                                HydrogenBondsDescriptors(%NamesAndValues);</div>
<p>Using specified <em>HydrogenBondsDescriptors</em> property names and values hash, <strong>new</strong>
method creates a new object and returns a reference to newly created <strong>HydrogenBondsDescriptors</strong>
object. By default, the following properties are initialized:</p>
<div class="OptionsBox">
    Molecule = ''
<br/>    Type = 'HydrogenBonds'
<br/>    HydrogenBondsType = 'HBondsType2'
<br/>    @DescriptorNames = ('HydrogenBondDonors', 'HydrogenBondAcceptors')
<br/>    @DescriptorValues = ('None', 'None')</div>
<p>Examples:</p>
<div class="OptionsBox">
    $HydrogenBondsDescriptors = new MolecularDescriptors::
                                HydrogenBondsDescriptors();</div>
<div class="OptionsBox">
    $HydrogenBondsDescriptors = new MolecularDescriptors::
                                HydrogenBondsDescriptors(
                                'HydrogenBondsType' =&gt; 'HBondsType2');</div>
<div class="OptionsBox">
    $HydrogenBondsDescriptors-&gt;SetMolecule($Molecule);
<br/>    $HydrogenBondsDescriptors-&gt;GenerateDescriptors();
<br/>    print &quot;HydrogenBondsDescriptors: $HydrogenBondsDescriptors\n&quot;;</div>
</dd>
<dt><strong><a name="generatedescriptors" class="item"><strong>GenerateDescriptors</strong></a></strong></dt>
<dd>
<div class="OptionsBox">
    $HydrogenBondsDescriptors-&gt;GenerateDescriptors();</div>
<p>Calculates number of hydrogen bond donors and acceptors a molecule and returns
<em>HydrogenBondsDescriptors</em>.</p>
</dd>
<dt><strong><a name="getdescriptornames" class="item"><strong>GetDescriptorNames</strong></a></strong></dt>
<dd>
<div class="OptionsBox">
    @DescriptorNames = $HydrogenBondsDescriptors-&gt;GetDescriptorNames();
<br/>    @DescriptorNames = MolecularDescriptors::HydrogenBondsDescriptors::
                       GetDescriptorNames();</div>
<p>Returns all available descriptor names as an array.</p>
</dd>
<dt><strong><a name="sethydrogenbondstype" class="item"><strong>SetHydrogenBondsType</strong></a></strong></dt>
<dd>
<div class="OptionsBox">
    $HydrogenBondsDescriptors-&gt;SetHydrogenBondsType($HBondsType);</div>
<p>Sets value of hydrogen bonds type to use during calculation of descriptors and returns
<em>HydrogenBondsDescriptors</em>. Possible values: <em>HBondsType1, HydrogenBondsType1,
HBondsType2, HydrogenBondsType2</em>.</p>
</dd>
<dt><strong><a name="stringifyhydrogenbondsdescriptors" class="item"><strong>StringifyHydrogenBondsDescriptors</strong></a></strong></dt>
<dd>
<div class="OptionsBox">
    $String = $HydrogenBondsDescriptors-&gt;
                              StringifyHydrogenBondsDescriptors();</div>
<p>Returns a string containing information about <em>HydrogenBondsDescriptors</em> object.</p>
</dd>
</dl>
<p>
</p>
<h2>AUTHOR</h2>
<p><a href="mailto:msud@san.rr.com">Manish Sud</a></p>
<p>
</p>
<h2>SEE ALSO</h2>
<p><a href="./MolecularDescriptors.html">MolecularDescriptors.pm</a>,&nbsp<a href="./MolecularDescriptorsGenerator.html">MolecularDescriptorsGenerator.pm</a>
</p>
<p>
</p>
<h2>COPYRIGHT</h2>
<p>Copyright (C) 2015 Manish Sud. All rights reserved.</p>
<p>This file is part of MayaChemTools.</p>
<p>MayaChemTools is free software; you can redistribute it and/or modify it under
the terms of the GNU Lesser General Public License as published by the Free
Software Foundation; either version 3 of the License, or (at your option)
any later version.</p>
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