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