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3 <title>MayaChemTools:Documentation:MolecularDescriptors::TPSADescriptors.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="./SLogPAndSMRDescriptors.html" title="SLogPAndSMRDescriptors.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./WeightAndMassDescriptors.html" title="WeightAndMassDescriptors.html">Next</a></td><td width="34%" align="middle"><strong>MolecularDescriptors::TPSADescriptors.pm</strong></td><td width="33%" align="right"><a href="././code/TPSADescriptors.html" title="View source code">Code</a> | <a href="./../pdf/TPSADescriptors.pdf" title="PDF US Letter Size">PDF</a> | <a href="./../pdfgreen/TPSADescriptors.pdf" title="PDF US Letter Size with narrow margins: www.changethemargins.com">PDFGreen</a> | <a href="./../pdfa4/TPSADescriptors.pdf" title="PDF A4 Size">PDFA4</a> | <a href="./../pdfa4green/TPSADescriptors.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>TPSADescriptors</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::TPSADescriptors;</p>
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26 <p>use MolecularDescriptors::TPSADescriptors 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>TPSADescriptors</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="#stringifytpsadescriptors">StringifyTPSADescriptors</a>
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32 </p><p><strong>TPSADescriptors</strong> is derived from <strong>MolecularDescriptors</strong> class which in turn
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33 is derived from <strong>ObjectProperty</strong> base class that provides methods not explicitly defined
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34 in <strong>TPSADescriptors</strong>, <strong>MolecularDescriptors</strong> or <strong>ObjectProperty</strong> classes using Perl's
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35 AUTOLOAD functionality. These methods are generated on-the-fly for a specified object property:</p>
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36 <div class="OptionsBox">
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37 Set<PropertyName>(<PropertyValue>);
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38 <br/> $PropertyValue = Get<PropertyName>();
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39 <br/> Delete<PropertyName>();</div>
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40 <p>After Topological Polar Surface Area (TPSA) atom types [ Ref 90-91 ] has been assigned
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41 to appropriate atoms in a molecule using AtomTypes::TPSAAtomTypes.pm module, TPSA value
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42 is calculated by adding up contributions of each appropriate atom type.</p>
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43 <p>By default, MayaChemTools only uses nitrogen and oxygen atoms during calculation
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44 of TPSA and ignores phosphorous and sulfur atoms. [ Ref 90 - 91 ]</p>
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45 <p>
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46 </p>
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47 <h2>METHODS</h2>
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48 <dl>
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49 <dt><strong><a name="new" class="item"><strong>new</strong></a></strong></dt>
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50 <dd>
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51 <div class="OptionsBox">
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52 $NewTPSADescriptors = new MolecularDescriptors::TPSADescriptors(
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53 %NamesAndValues);</div>
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54 <p>Using specified <em>TPSADescriptors</em> property names and values hash, <strong>new</strong>
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55 method creates a new object and returns a reference to newly created <strong>TPSADescriptors</strong>
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56 object. By default, the following properties are initialized:</p>
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57 <div class="OptionsBox">
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58 Molecule = ''
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59 <br/> Type = 'TPSA'
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60 <br/> IgnorePhosphorus = 1
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61 <br/> IgnoreSulfur = 1
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62 <br/> @DescriptorNames = ('TPSA')
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63 <br/> @DescriptorValues = ('None')</div>
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64 <p>Examples:</p>
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65 <div class="OptionsBox">
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66 $TPSADescriptors = new MolecularDescriptors::TPSADescriptors(
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67 'Molecule' => $Molecule);</div>
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68 <div class="OptionsBox">
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69 $TPSADescriptors = new MolecularDescriptors::TPSADescriptors();</div>
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70 <div class="OptionsBox">
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71 $TPSADescriptors = new MolecularDescriptors::TPSADescriptors(
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72 'IgnorePhosphorus' => 0,
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73 'IgnoreSulfur' => 0);</div>
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74 <div class="OptionsBox">
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75 $TPSADescriptors->SetMolecule($Molecule);
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76 <br/> $TPSADescriptors->GenerateDescriptors();
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77 <br/> print "TPSADescriptors: $TPSADescriptors\n";</div>
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78 </dd>
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79 <dt><strong><a name="generatedescriptors" class="item"><strong>GenerateDescriptors</strong></a></strong></dt>
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80 <dd>
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81 <div class="OptionsBox">
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82 $TPSADescriptors->GenerateDescriptors();</div>
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83 <p>Calculate TPSA value for a molecule and returns <em>TPSADescriptors</em>.</p>
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84 </dd>
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85 <dt><strong><a name="getdescriptornames" class="item"><strong>GetDescriptorNames</strong></a></strong></dt>
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86 <dd>
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87 <div class="OptionsBox">
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88 @DescriptorNames = $TPSADescriptors->GetDescriptorNames();
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89 <br/> @DescriptorNames = MolecularDescriptors::TPSADescriptors::
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90 GetDescriptorNames();</div>
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91 <p>Returns all available descriptor names as an array.</p>
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92 </dd>
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93 <dt><strong><a name="stringifytpsadescriptors" class="item"><strong>StringifyTPSADescriptors</strong></a></strong></dt>
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94 <dd>
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95 <div class="OptionsBox">
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96 $String = $TPSADescriptors->StringifyTPSADescriptors();</div>
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97 <p>Returns a string containing information about <em>TPSADescriptors</em> object.</p>
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98 </dd>
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99 </dl>
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100 <p>
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101 </p>
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102 <h2>AUTHOR</h2>
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103 <p><a href="mailto:msud@san.rr.com">Manish Sud</a></p>
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104 <p>
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105 </p>
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106 <h2>SEE ALSO</h2>
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107 <p><a href="./MolecularDescriptors.html">MolecularDescriptors.pm</a>, <a href="./MolecularDescriptorsGenerator.html">MolecularDescriptorsGenerator.pm</a>
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108 </p>
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109 <p>
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110 </p>
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111 <h2>COPYRIGHT</h2>
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112 <p>Copyright (C) 2015 Manish Sud. All rights reserved.</p>
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113 <p>This file is part of MayaChemTools.</p>
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114 <p>MayaChemTools is free software; you can redistribute it and/or modify it under
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115 the terms of the GNU Lesser General Public License as published by the Free
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116 Software Foundation; either version 3 of the License, or (at your option)
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117 any later version.</p>
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118 <p> </p><p> </p><div class="DocNav">
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119 <table width="100%" border=0 cellpadding=0 cellspacing=2>
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120 <tr align="left" valign="top"><td width="33%" align="left"><a href="./SLogPAndSMRDescriptors.html" title="SLogPAndSMRDescriptors.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./WeightAndMassDescriptors.html" title="WeightAndMassDescriptors.html">Next</a></td><td width="34%" align="middle"><strong>March 29, 2015</strong></td><td width="33%" align="right"><strong>MolecularDescriptors::TPSADescriptors.pm</strong></td></tr>
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121 </table>
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