comparison mayachemtools/docs/modules/html/MolecularVolumeDescriptors.html @ 0:73ae111cf86f draft

Uploaded
author deepakjadmin
date Wed, 20 Jan 2016 11:55:01 -0500
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:73ae111cf86f
1 <html>
2 <head>
3 <title>MayaChemTools:Documentation:MolecularDescriptors::MolecularVolumeDescriptors.pm</title>
4 <meta http-equiv="content-type" content="text/html;charset=utf-8">
5 <link rel="stylesheet" type="text/css" href="../../css/MayaChemTools.css">
6 </head>
7 <body leftmargin="20" rightmargin="20" topmargin="10" bottommargin="10">
8 <br/>
9 <center>
10 <a href="http://www.mayachemtools.org" title="MayaChemTools Home"><img src="../../images/MayaChemToolsLogo.gif" border="0" alt="MayaChemTools"></a>
11 </center>
12 <br/>
13 <div class="DocNav">
14 <table width="100%" border=0 cellpadding=0 cellspacing=2>
15 <tr align="left" valign="top"><td width="33%" align="left"><a href="./MolecularDescriptorsGenerator.html" title="MolecularDescriptorsGenerator.html">Previous</a>&nbsp;&nbsp;<a href="./index.html" title="Table of Contents">TOC</a>&nbsp;&nbsp;<a href="./RingsCountDescriptors.html" title="RingsCountDescriptors.html">Next</a></td><td width="34%" align="middle"><strong>MolecularDescriptors::MolecularVolumeDescriptors.pm</strong></td><td width="33%" align="right"><a href="././code/MolecularVolumeDescriptors.html" title="View source code">Code</a>&nbsp;|&nbsp;<a href="./../pdf/MolecularVolumeDescriptors.pdf" title="PDF US Letter Size">PDF</a>&nbsp;|&nbsp;<a href="./../pdfgreen/MolecularVolumeDescriptors.pdf" title="PDF US Letter Size with narrow margins: www.changethemargins.com">PDFGreen</a>&nbsp;|&nbsp;<a href="./../pdfa4/MolecularVolumeDescriptors.pdf" title="PDF A4 Size">PDFA4</a>&nbsp;|&nbsp;<a href="./../pdfa4green/MolecularVolumeDescriptors.pdf" title="PDF A4 Size with narrow margins: www.changethemargins.com">PDFA4Green</a></td></tr>
16 </table>
17 </div>
18 <p>
19 </p>
20 <h2>NAME</h2>
21 <p>MolecularVolumeDescriptors</p>
22 <p>
23 </p>
24 <h2>SYNOPSIS</h2>
25 <p>use MolecularDescriptors::MolecularVolumeDescriptors;</p>
26 <p>use MolecularDescriptors::MolecularVolumeDescriptors qw(:all);</p>
27 <p>
28 </p>
29 <h2>DESCRIPTION</h2>
30 <p><strong>MolecularVolumeDescriptors</strong> class provides the following methods:</p>
31 <p> <a href="#new">new</a>, <a href="#generatedescriptors">GenerateDescriptors</a>, <a href="#getdescriptornames">GetDescriptorNames</a>
32 , <a href="#getvdwatomradiiandvolumesdata">GetVDWAtomRadiiAndVolumesData</a>, <a href="#stringifymolecularvolumedescriptors">StringifyMolecularVolumeDescriptors</a>
33 </p><p><strong>MolecularVolumeDescriptors</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>MolecularVolumeDescriptors</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>van der Waals molecular volume [ Ref 93 ] (A**3/molecule) of a molecule is
42 calculated using atomic and bonds contributions along with adjustments for
43 aromatic and non-aromatic rings using the following equation:</p>
44 <div class="OptionsBox">
45 vdwMolecularVolume = SumOfAtomicVDWVolumeContributions
46 - 5.92 * NumOfBonds
47 - 14.7 * NumOfAromaticRings
48 - 3.8 * NumOfNonAromaticRings</div>
49 <p>van der Waals atomic volume for atoms is taken from data file VDWAtomRadiiAndVolumes.csv
50 distributed with MayaChemTools. It contains van der Waals atom radii and atom and volumes
51 data for 38 elements; Table 2 [ Ref 93 ] contains data for only 15 elements. After converting
52 valid van der Waals atom radius data from pm (picometer) to A (Angstrom) available under column
53 name VanderWaalsRadius in PeriodicTableElementsData.csv data file, van der Waals atom volume
54 is calculated using: 4/3 * PI * (Radius ** 3). For elements specified in Table 2 [ Ref 93 ] -
55 H, B, C, N, O, F, Si, P, S, Cl, As, Se, Br, Te, I - the van der Waals atom radii and calculated
56 atom volumes match the values in the table.</p>
57 <p>
58 </p>
59 <h2>METHODS</h2>
60 <dl>
61 <dt><strong><a name="new" class="item"><strong>new</strong></a></strong></dt>
62 <dd>
63 <div class="OptionsBox">
64 $NewMolecularVolumeDescriptors = new MolecularDescriptors::
65 MolecularVolumeDescriptors(
66 %NamesAndValues);</div>
67 <p>Using specified <em>MolecularVolumeDescriptors</em> property names and values hash, <strong>new</strong>
68 method creates a new object and returns a reference to newly created <strong>MolecularVolumeDescriptors</strong>
69 object. By default, the following properties are initialized:</p>
70 <div class="OptionsBox">
71 Molecule = ''
72 <br/> Type = 'MolecularVolume'
73 <br/> @DescriptorNames = ('MolecularVolume')
74 <br/> @DescriptorValues = ('None')</div>
75 <p>Examples:</p>
76 <div class="OptionsBox">
77 $MolecularVolumeDescriptors = new MolecularDescriptors::
78 MolecularVolumeDescriptors();</div>
79 <div class="OptionsBox">
80 $MolecularVolumeDescriptors-&gt;SetMolecule($Molecule);
81 <br/> $MolecularVolumeDescriptors-&gt;GenerateDescriptors();
82 <br/> print &quot;MolecularVolumeDescriptors: $MolecularVolumeDescriptors\n&quot;;</div>
83 </dd>
84 <dt><strong><a name="generatedescriptors" class="item"><strong>GenerateDescriptors</strong></a></strong></dt>
85 <dd>
86 <div class="OptionsBox">
87 $MolecularVolumeDescriptors-&gt;GenerateDescriptors();</div>
88 <p>Calculate van der Waals molecular volume descriptor for a molecule and returns
89 <em>MolecularVolumeDescriptors</em>.</p>
90 </dd>
91 <dt><strong><a name="getdescriptornames" class="item"><strong>GetDescriptorNames</strong></a></strong></dt>
92 <dd>
93 <div class="OptionsBox">
94 @DescriptorNames = $MolecularVolumeDescriptors-&gt;GetDescriptorNames();
95 <br/> @DescriptorNames = MolecularDescriptors::MolecularVolumeDescriptors::
96 GetDescriptorNames();</div>
97 <p>Returns all available descriptor names as an array.</p>
98 </dd>
99 <dt><strong><a name="getvdwatomradiiandvolumesdata" class="item"><strong>GetVDWAtomRadiiAndVolumesData</strong></a></strong></dt>
100 <dd>
101 <div class="OptionsBox">
102 $VDWVolumeDataMapRef = $MolecularVolumeDescriptors-&gt;
103 GetVDWAtomRadiiAndVolumesData();
104 <br/> $VDWVolumeDataMapRef = MolecularDescriptors::MolecularVolumeDescriptors::
105 GetVDWAtomRadiiAndVolumesData();</div>
106 <p>Returns a hash reference to van der Waals atom symbols corresponding to atom types
107 and associated data loaded from VDWAtomRadiiAndVolumes.csv data file as a reference
108 to hash with the following hash data format:</p>
109 <div class="OptionsBox">
110 @{$VDWVolumeDataMap{AtomTypes}} - Array of all possible atom
111 types for all atom symbols
112 <br/> @{$VDWVolumeDataMap-&gt;{ColLabels}} - Array of column labels
113 <br/> %{$VDWVolumeDataMap-&gt;{DataCol&lt;Num&gt;}} - Hash keys pair:
114 DataCol&lt;Num&gt;, AtomType</div>
115 </dd>
116 <dt><strong><a name="stringifymolecularvolumedescriptors" class="item"><strong>StringifyMolecularVolumeDescriptors</strong></a></strong></dt>
117 <dd>
118 <div class="OptionsBox">
119 $String = $MolecularVolumeDescriptors-&gt;
120 StringifyMolecularVolumeDescriptors();</div>
121 <p>Returns a string containing information about <em>MolecularVolumeDescriptors</em> object.</p>
122 </dd>
123 </dl>
124 <p>
125 </p>
126 <h2>AUTHOR</h2>
127 <p><a href="mailto:msud@san.rr.com">Manish Sud</a></p>
128 <p>
129 </p>
130 <h2>SEE ALSO</h2>
131 <p><a href="./MolecularDescriptors.html">MolecularDescriptors.pm</a>,&nbsp<a href="./MolecularDescriptorsGenerator.html">MolecularDescriptorsGenerator.pm</a>
132 </p>
133 <p>
134 </p>
135 <h2>COPYRIGHT</h2>
136 <p>Copyright (C) 2015 Manish Sud. All rights reserved.</p>
137 <p>This file is part of MayaChemTools.</p>
138 <p>MayaChemTools is free software; you can redistribute it and/or modify it under
139 the terms of the GNU Lesser General Public License as published by the Free
140 Software Foundation; either version 3 of the License, or (at your option)
141 any later version.</p>
142 <p>&nbsp</p><p>&nbsp</p><div class="DocNav">
143 <table width="100%" border=0 cellpadding=0 cellspacing=2>
144 <tr align="left" valign="top"><td width="33%" align="left"><a href="./MolecularDescriptorsGenerator.html" title="MolecularDescriptorsGenerator.html">Previous</a>&nbsp;&nbsp;<a href="./index.html" title="Table of Contents">TOC</a>&nbsp;&nbsp;<a href="./RingsCountDescriptors.html" title="RingsCountDescriptors.html">Next</a></td><td width="34%" align="middle"><strong>March 29, 2015</strong></td><td width="33%" align="right"><strong>MolecularDescriptors::MolecularVolumeDescriptors.pm</strong></td></tr>
145 </table>
146 </div>
147 <br />
148 <center>
149 <img src="../../images/h2o2.png">
150 </center>
151 </body>
152 </html>