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3 <title>MayaChemTools:Documentation:AtomicDescriptors::EStateValuesDescriptors.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="./AtomicDescriptors.html" title="AtomicDescriptors.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./AtomicInvariantsAtomTypes.html" title="AtomicInvariantsAtomTypes.html">Next</a></td><td width="34%" align="middle"><strong>AtomicDescriptors::EStateValuesDescriptors.pm</strong></td><td width="33%" align="right"><a href="././code/EStateValuesDescriptors.html" title="View source code">Code</a> | <a href="./../pdf/EStateValuesDescriptors.pdf" title="PDF US Letter Size">PDF</a> | <a href="./../pdfgreen/EStateValuesDescriptors.pdf" title="PDF US Letter Size with narrow margins: www.changethemargins.com">PDFGreen</a> | <a href="./../pdfa4/EStateValuesDescriptors.pdf" title="PDF A4 Size">PDFA4</a> | <a href="./../pdfa4green/EStateValuesDescriptors.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>EStateValuesDescriptors</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 AtomicDescriptors::EStateValuesDescriptors;</p>
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26 <p>use AtomicDescriptors::EStateValuesDescriptors 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>EStateValuesDescriptors</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="#stringifyestatevaluesdescriptors">StringifyEStateValuesDescriptors</a>
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32 </p><p><strong>EStateValuesDescriptors</strong> is derived from <strong>AtomicValues</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>EStateValuesDescriptors</strong>, <strong>AtomicValues</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>For calculation of electrotopological state (E-state) values for non-hydrogen atoms:</p>
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41 <p>Let:</p>
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42 <div class="OptionsBox">
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43 N = Principal quantum number or period number corresponding to
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44 <br/> element symbol</div>
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45 <div class="OptionsBox">
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46 Sigma = Number of sigma electrons involves in bonds to hydrogen and
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47 non-hydrogen atoms attached to atom
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48 = Number of sigma bonds to hydrogen and non-hydrogen atoms
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49 attached to atom
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50 <br/> PI = Number of PI electrons involved in bonds to non-hydrogen atoms
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51 attached to atom
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52 = Number of PI bonds to non-hydrogen atoms attached to atom</div>
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53 <div class="OptionsBox">
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54 LP = Number of lone pair electrons on atom</div>
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55 <div class="OptionsBox">
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56 Zv = Number of electrons in valence shell of atom</div>
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57 <div class="OptionsBox">
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58 X = Number of non-hydrogen atom neighbors or heavy atoms attached
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59 <br/> to atom
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60 <br/> H = Number of implicit and explicit hydrogens for atom</div>
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61 <div class="OptionsBox">
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62 Delta = Number of sigma electrons involved to bonds to non-hydrogen
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63 atoms
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64 <br/> DeltaV = ValenceDelta = Number of valence shell electrons not involved
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65 in bonding to hydrogen atoms</div>
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66 <div class="OptionsBox">
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67 Ii = Intrinsic state value for atom i</div>
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68 <div class="OptionsBox">
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69 DeltaIi = Sum of perturbations to intrinsic state value Ii of atom i
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70 by all other atoms besides atom i</div>
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71 <div class="OptionsBox">
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72 DeltaIij = Perturbation to intrinsic state value Ii of atom i by atom j</div>
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73 <div class="OptionsBox">
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74 Dij = Graph/bond distance between atom i and j
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75 <br/> Rij = Dij + 1</div>
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76 <div class="OptionsBox">
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77 Si = E-state value for atom i</div>
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78 <p>Then:</p>
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79 <div class="OptionsBox">
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80 Delta = Sigma - H = X</div>
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81 <div class="OptionsBox">
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82 DeltaV = Zv - H
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83 = Sigma + PI + LP - H</div>
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84 <div class="OptionsBox">
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85 Ii = ( ( ( 2 / N ) ** 2 ) * DeltaV + 1 ) / Delta</div>
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86 <div class="OptionsBox">
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87 DeltaIi = SUM ( (Ii - Ij) / (Rij ** 2) ) for j = 1 to num of atoms skipping atom i</div>
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88 <div class="OptionsBox">
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89 Si = Ii + DeltaIi</div>
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90 <p>The current release of MayaChemTools doesn't support calculation of E-state
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91 values [ Ref 75-78 ] for hydrogens.</p>
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92 <p>
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93 </p>
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94 <h2>METHODS</h2>
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95 <dl>
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96 <dt><strong><a name="new" class="item"><strong>new</strong></a></strong></dt>
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97 <dd>
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98 <div class="OptionsBox">
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99 $NewEStateValuesDescriptors = new AtomicDescriptors::
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100 EStateValuesDescriptors(%NamesAndValues);</div>
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101 <p>Using specified <em>EStateValuesDescriptors</em> property names and values hash, <strong>new</strong>
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102 method creates a new object and returns a reference to newly created <strong>EStateValuesDescriptors</strong>
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103 object. By default, the following properties are initialized:</p>
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104 <div class="OptionsBox">
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105 Molecule = ''
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106 <br/> Type = 'EState'
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107 <br/> IgnoreHydrogens = 1</div>
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108 <p>Examples:</p>
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109 <div class="OptionsBox">
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110 $EStateValuesDescriptors = new AtomicDescriptors::EStateValuesDescriptors(
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111 'Molecule' => $Molecule,
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112 'IgnoreHydrogens' => 1);</div>
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113 </dd>
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114 <dt><strong><a name="generatedescriptors" class="item"><strong>GenerateDescriptors</strong></a></strong></dt>
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115 <dd>
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116 <div class="OptionsBox">
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117 $EStateValuesDescriptors->GenerateDescriptors();</div>
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118 <p>Calculates E-state atomic descriptors for all the atoms in a molecule and returns
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119 <em>EStateValuesDescriptors</em>.</p>
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120 </dd>
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121 <dt><strong><a name="stringifyestatevaluesdescriptors" class="item"><strong>StringifyEStateValuesDescriptors</strong></a></strong></dt>
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122 <dd>
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123 <div class="OptionsBox">
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124 $String = $EStateValuesDescriptors->StringifyEStateValuesDescriptors();</div>
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125 <p>Returns a string containing information about <em>EStateValuesDescriptors</em> object.</p>
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126 </dd>
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127 </dl>
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128 <p>
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129 </p>
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130 <h2>AUTHOR</h2>
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131 <p><a href="mailto:msud@san.rr.com">Manish Sud</a></p>
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132 <p>
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133 </p>
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134 <h2>SEE ALSO</h2>
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135 <p><a href="./AtomicDescriptors.html">AtomicDescriptors.pm</a>
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136 </p>
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137 <p>
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138 </p>
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139 <h2>COPYRIGHT</h2>
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140 <p>Copyright (C) 2015 Manish Sud. All rights reserved.</p>
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141 <p>This file is part of MayaChemTools.</p>
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142 <p>MayaChemTools is free software; you can redistribute it and/or modify it under
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143 the terms of the GNU Lesser General Public License as published by the Free
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144 Software Foundation; either version 3 of the License, or (at your option)
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145 any later version.</p>
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146 <p> </p><p> </p><div class="DocNav">
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147 <table width="100%" border=0 cellpadding=0 cellspacing=2>
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148 <tr align="left" valign="top"><td width="33%" align="left"><a href="./AtomicDescriptors.html" title="AtomicDescriptors.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./AtomicInvariantsAtomTypes.html" title="AtomicInvariantsAtomTypes.html">Next</a></td><td width="34%" align="middle"><strong>March 29, 2015</strong></td><td width="33%" align="right"><strong>AtomicDescriptors::EStateValuesDescriptors.pm</strong></td></tr>
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149 </table>
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150 </div>
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