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3 <title>MayaChemTools:Documentation:MolecularDescriptors::MolecularVolumeDescriptors.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="./MolecularDescriptorsGenerator.html" title="MolecularDescriptorsGenerator.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <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> | <a href="./../pdf/MolecularVolumeDescriptors.pdf" title="PDF US Letter Size">PDF</a> | <a href="./../pdfgreen/MolecularVolumeDescriptors.pdf" title="PDF US Letter Size with narrow margins: www.changethemargins.com">PDFGreen</a> | <a href="./../pdfa4/MolecularVolumeDescriptors.pdf" title="PDF A4 Size">PDFA4</a> | <a href="./../pdfa4green/MolecularVolumeDescriptors.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>MolecularVolumeDescriptors</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::MolecularVolumeDescriptors;</p>
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26 <p>use MolecularDescriptors::MolecularVolumeDescriptors 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>MolecularVolumeDescriptors</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>
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32 , <a href="#getvdwatomradiiandvolumesdata">GetVDWAtomRadiiAndVolumesData</a>, <a href="#stringifymolecularvolumedescriptors">StringifyMolecularVolumeDescriptors</a>
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33 </p><p><strong>MolecularVolumeDescriptors</strong> is derived from <strong>MolecularDescriptors</strong> class which in turn
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34 is derived from <strong>ObjectProperty</strong> base class that provides methods not explicitly defined
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35 in <strong>MolecularVolumeDescriptors</strong>, <strong>MolecularDescriptors</strong> or <strong>ObjectProperty</strong> classes using Perl's
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36 AUTOLOAD functionality. These methods are generated on-the-fly for a specified object property:</p>
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37 <div class="OptionsBox">
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38 Set<PropertyName>(<PropertyValue>);
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39 <br/> $PropertyValue = Get<PropertyName>();
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40 <br/> Delete<PropertyName>();</div>
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41 <p>van der Waals molecular volume [ Ref 93 ] (A**3/molecule) of a molecule is
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42 calculated using atomic and bonds contributions along with adjustments for
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43 aromatic and non-aromatic rings using the following equation:</p>
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44 <div class="OptionsBox">
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45 vdwMolecularVolume = SumOfAtomicVDWVolumeContributions
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46 - 5.92 * NumOfBonds
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47 - 14.7 * NumOfAromaticRings
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48 - 3.8 * NumOfNonAromaticRings</div>
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49 <p>van der Waals atomic volume for atoms is taken from data file VDWAtomRadiiAndVolumes.csv
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50 distributed with MayaChemTools. It contains van der Waals atom radii and atom and volumes
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51 data for 38 elements; Table 2 [ Ref 93 ] contains data for only 15 elements. After converting
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52 valid van der Waals atom radius data from pm (picometer) to A (Angstrom) available under column
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53 name VanderWaalsRadius in PeriodicTableElementsData.csv data file, van der Waals atom volume
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54 is calculated using: 4/3 * PI * (Radius ** 3). For elements specified in Table 2 [ Ref 93 ] -
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55 H, B, C, N, O, F, Si, P, S, Cl, As, Se, Br, Te, I - the van der Waals atom radii and calculated
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56 atom volumes match the values in the table.</p>
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57 <p>
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58 </p>
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59 <h2>METHODS</h2>
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60 <dl>
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61 <dt><strong><a name="new" class="item"><strong>new</strong></a></strong></dt>
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62 <dd>
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63 <div class="OptionsBox">
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64 $NewMolecularVolumeDescriptors = new MolecularDescriptors::
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65 MolecularVolumeDescriptors(
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66 %NamesAndValues);</div>
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67 <p>Using specified <em>MolecularVolumeDescriptors</em> property names and values hash, <strong>new</strong>
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68 method creates a new object and returns a reference to newly created <strong>MolecularVolumeDescriptors</strong>
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69 object. By default, the following properties are initialized:</p>
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70 <div class="OptionsBox">
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71 Molecule = ''
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72 <br/> Type = 'MolecularVolume'
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73 <br/> @DescriptorNames = ('MolecularVolume')
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74 <br/> @DescriptorValues = ('None')</div>
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75 <p>Examples:</p>
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76 <div class="OptionsBox">
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77 $MolecularVolumeDescriptors = new MolecularDescriptors::
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78 MolecularVolumeDescriptors();</div>
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79 <div class="OptionsBox">
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80 $MolecularVolumeDescriptors->SetMolecule($Molecule);
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81 <br/> $MolecularVolumeDescriptors->GenerateDescriptors();
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82 <br/> print "MolecularVolumeDescriptors: $MolecularVolumeDescriptors\n";</div>
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83 </dd>
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84 <dt><strong><a name="generatedescriptors" class="item"><strong>GenerateDescriptors</strong></a></strong></dt>
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85 <dd>
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86 <div class="OptionsBox">
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87 $MolecularVolumeDescriptors->GenerateDescriptors();</div>
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88 <p>Calculate van der Waals molecular volume descriptor for a molecule and returns
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89 <em>MolecularVolumeDescriptors</em>.</p>
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90 </dd>
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91 <dt><strong><a name="getdescriptornames" class="item"><strong>GetDescriptorNames</strong></a></strong></dt>
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92 <dd>
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93 <div class="OptionsBox">
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94 @DescriptorNames = $MolecularVolumeDescriptors->GetDescriptorNames();
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95 <br/> @DescriptorNames = MolecularDescriptors::MolecularVolumeDescriptors::
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96 GetDescriptorNames();</div>
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97 <p>Returns all available descriptor names as an array.</p>
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98 </dd>
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99 <dt><strong><a name="getvdwatomradiiandvolumesdata" class="item"><strong>GetVDWAtomRadiiAndVolumesData</strong></a></strong></dt>
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100 <dd>
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101 <div class="OptionsBox">
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102 $VDWVolumeDataMapRef = $MolecularVolumeDescriptors->
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103 GetVDWAtomRadiiAndVolumesData();
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104 <br/> $VDWVolumeDataMapRef = MolecularDescriptors::MolecularVolumeDescriptors::
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105 GetVDWAtomRadiiAndVolumesData();</div>
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106 <p>Returns a hash reference to van der Waals atom symbols corresponding to atom types
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107 and associated data loaded from VDWAtomRadiiAndVolumes.csv data file as a reference
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108 to hash with the following hash data format:</p>
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109 <div class="OptionsBox">
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110 @{$VDWVolumeDataMap{AtomTypes}} - Array of all possible atom
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111 types for all atom symbols
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112 <br/> @{$VDWVolumeDataMap->{ColLabels}} - Array of column labels
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113 <br/> %{$VDWVolumeDataMap->{DataCol<Num>}} - Hash keys pair:
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114 DataCol<Num>, AtomType</div>
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115 </dd>
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116 <dt><strong><a name="stringifymolecularvolumedescriptors" class="item"><strong>StringifyMolecularVolumeDescriptors</strong></a></strong></dt>
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117 <dd>
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118 <div class="OptionsBox">
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119 $String = $MolecularVolumeDescriptors->
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120 StringifyMolecularVolumeDescriptors();</div>
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121 <p>Returns a string containing information about <em>MolecularVolumeDescriptors</em> object.</p>
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122 </dd>
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123 </dl>
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124 <p>
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125 </p>
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126 <h2>AUTHOR</h2>
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127 <p><a href="mailto:msud@san.rr.com">Manish Sud</a></p>
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128 <p>
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129 </p>
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130 <h2>SEE ALSO</h2>
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131 <p><a href="./MolecularDescriptors.html">MolecularDescriptors.pm</a>, <a href="./MolecularDescriptorsGenerator.html">MolecularDescriptorsGenerator.pm</a>
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132 </p>
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133 <p>
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134 </p>
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135 <h2>COPYRIGHT</h2>
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136 <p>Copyright (C) 2015 Manish Sud. All rights reserved.</p>
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137 <p>This file is part of MayaChemTools.</p>
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138 <p>MayaChemTools is free software; you can redistribute it and/or modify it under
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139 the terms of the GNU Lesser General Public License as published by the Free
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140 Software Foundation; either version 3 of the License, or (at your option)
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141 any later version.</p>
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142 <p> </p><p> </p><div class="DocNav">
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143 <table width="100%" border=0 cellpadding=0 cellspacing=2>
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144 <tr align="left" valign="top"><td width="33%" align="left"><a href="./MolecularDescriptorsGenerator.html" title="MolecularDescriptorsGenerator.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <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>
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145 </table>
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146 </div>
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147 <br />
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148 <center>
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