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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="./MolecularDescriptors.html" title="MolecularDescriptors.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./MolecularVolumeDescriptors.html" title="MolecularVolumeDescriptors.html">Next</a></td><td width="34%" align="middle"><strong>MolecularDescriptors::MolecularDescriptorsGenerator.pm</strong></td><td width="33%" align="right"><a href="././code/MolecularDescriptorsGenerator.html" title="View source code">Code</a> | <a href="./../pdf/MolecularDescriptorsGenerator.pdf" title="PDF US Letter Size">PDF</a> | <a href="./../pdfgreen/MolecularDescriptorsGenerator.pdf" title="PDF US Letter Size with narrow margins: www.changethemargins.com">PDFGreen</a> | <a href="./../pdfa4/MolecularDescriptorsGenerator.pdf" title="PDF A4 Size">PDFA4</a> | <a href="./../pdfa4green/MolecularDescriptorsGenerator.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>MolecularDescriptorsGenerator</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::MolecularDescriptorsGenerator;</p>
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26 <p>use MolecularDescriptors::MolecularDescriptorsGenerator 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>MolecularDescriptorsGenerator</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="#getavailableclassanddescriptornames">GetAvailableClassAndDescriptorNames</a>
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32 , <a href="#getavailableclassnamefordescriptorname">GetAvailableClassNameForDescriptorName</a>, <a href="#getavailabledescriptorclassnames">GetAvailableDescriptorClassNames</a>
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33 , <a href="#getavailabledescriptornames">GetAvailableDescriptorNames</a>, <a href="#getavailabledescriptornamesfordescriptorclass">GetAvailableDescriptorNamesForDescriptorClass</a>
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34 , <a href="#getdescriptorclassparameters">GetDescriptorClassParameters</a>, <a href="#getdescriptornames">GetDescriptorNames</a>, <a href="#getdescriptornamesandvalues">GetDescriptorNamesAndValues</a>
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35 , <a href="#getdescriptorvaluebyname">GetDescriptorValueByName</a>, <a href="#getdescriptorvalues">GetDescriptorValues</a>, <a href="#getruleof3descriptornames">GetRuleOf3DescriptorNames</a>
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36 , <a href="#getruleof5descriptornames">GetRuleOf5DescriptorNames</a>, <a href="#isdescriptorclassnameavailable">IsDescriptorClassNameAvailable</a>
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37 , <a href="#isdescriptornameavailable">IsDescriptorNameAvailable</a>, <a href="#isdescriptorsgenerationsuccessful">IsDescriptorsGenerationSuccessful</a>
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38 , <a href="#setdescriptorclassparameters">SetDescriptorClassParameters</a>, <a href="#setdescriptornames">SetDescriptorNames</a>, <a href="#setmode">SetMode</a>, <a href="#setmolecule">SetMolecule</a>
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39 , <a href="#stringifymoleculardescriptorsgenerator">StringifyMolecularDescriptorsGenerator</a>
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40 </p><p><strong>MolecularDescriptorsGenerator</strong> is derived from is derived from <strong>ObjectProperty</strong>
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41 base class that provides methods not explicitly defined in <strong>MolecularDescriptorsGenerator</strong>
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42 or <strong>ObjectProperty</strong> classes using Perl's AUTOLOAD functionality. These methods are
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43 generated on-the-fly for a specified object property:</p>
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44 <div class="OptionsBox">
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45 Set<PropertyName>(<PropertyValue>);
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46 <br/> $PropertyValue = Get<PropertyName>();
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47 <br/> Delete<PropertyName>();</div>
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48 <p><strong>MolecularDescriptorsGenerator</strong> is designed to provide a plug-in environment for
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49 molecular descriptors development. The molecular descriptor class modules available
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50 in <strong>MolecularDescriptors</strong> directory under <strong>MayaChemTools/lib</strong> directory are
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51 automatically detected and loaded into the system. The descriptor names provided
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52 by each descriptor class module through its <strong>GetDescriptorNames</strong> function are
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53 retrieved and are made available for calculations of their values for a specified
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54 molecule.</p>
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55 <p>Any combination of available descriptor names can be specified during calculation
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56 of descriptor values using <strong>GenerateDescriptors</strong> method. The current release of
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57 MayaChemTools supports generation of four sets of descriptors: All available
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58 descriptors, rule of 5 or 3 descriptors, or a specified set of descriptor names.</p>
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59 <p>RuleOf5 [ Ref 91 ] descriptor names are: MolecularWeight, HydrogenBondDonors,
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60 HydrogenBondAcceptors, SLogP. RuleOf5 states: MolecularWeight <= 500,
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61 HydrogenBondDonors <= 5, HydrogenBondAcceptors <= 10, and logP <= 5.</p>
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62 <p>RuleOf3 [ Ref 92 ] descriptor names are: MolecularWeight, RotatableBonds,
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63 HydrogenBondDonors, HydrogenBondAcceptors, SLogP, TPSA. RuleOf3 states:
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64 MolecularWeight <= 300, RotatableBonds <= 3, HydrogenBondDonors <= 3,
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65 HydrogenBondAcceptors <= 3, logP <= 3, and TPSA <= 60.</p>
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66 <p>Before calculation of a specified set of descriptors by <strong>GenerateDescriptors</strong>
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67 method, a set of descriptor calculation control parameters for a specific descriptor
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68 class name can be set using <strong>SetDescriptorClassParameters</strong> method. The specified
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69 control parameter names and values are simply passed on to specified descriptor
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70 class during instantiation of descriptor class object without performing any validation
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71 of parameter names and associated values. It's up to the appropriate descriptor class methods
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72 to validate these parameters and values. In addition to specified parameter names and
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73 values, the parameter hash must also contain descriptor class name as key and
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74 value pair with DescriptorClassName as key with class name as value.</p>
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75 <p>
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76 </p>
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77 <h2>METHODS</h2>
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78 <dl>
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79 <dt><strong><a name="new" class="item"><strong>new</strong></a></strong></dt>
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80 <dd>
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81 <div class="OptionsBox">
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82 $NewMolecularDescriptorsGenerator = new MolecularDescriptors::
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83 MolecularDescriptorsGenerator(
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84 %NamesAndValues);</div>
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85 <p>Using specified <em>MolecularDescriptorsGenerator</em> property names and values hash, <strong>new</strong>
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86 method creates a new object and returns a reference to newly created <strong>MolecularDescriptorsGenerator</strong>
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87 object. By default, the following properties are initialized:</p>
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88 <div class="OptionsBox">
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89 Mode = 'All'
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90 <br/> @{$This->{DescriptorNames}} = ()
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91 <br/> %{$This->{DescriptorClassParameters}} = ()
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92 <br/> @{$This->{DescriptorClassNames}} = ()
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93 <br/> %{$This->{DescriptorClassObjects}} = ()
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94 <br/> @{$This->{DescriptorValues}} = ()</div>
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95 <p>Examples:</p>
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96 <div class="OptionsBox">
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97 $MolecularDescriptorsGenerator = new MolecularDescriptors::
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98 MolecularDescriptorsGenerator(
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99 'Molecule' => $Molecule);</div>
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100 <div class="OptionsBox">
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101 @DescriptorNames = qw(MolecularWeight HydrogenBondDonors Fsp3Carbons)
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102 <br/> $MolecularDescriptorsGenerator = new MolecularDescriptors::
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103 MolecularDescriptorsGenerator(
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104 'Mode' => 'Specify',
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105 'DescriptorNames' => \@DescriptorNames);</div>
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106 <div class="OptionsBox">
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107 $MolecularDescriptorsGenerator->SetDescriptorClassParameters(
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108 'DescriptorClassName' => 'WeightAndMassDescriptors',
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109 'WeightPrecision' => 2,
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110 'MassPrecision' => 2);</div>
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111 <div class="OptionsBox">
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112 $MolecularDescriptorsGenerator->SetDescriptorClassParameters(
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113 'DescriptorClassName' => 'HydrogenBondsDescriptors',
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114 'HydrogenBondsType' => 'HBondsType1');</div>
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115 <div class="OptionsBox">
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116 $MolecularDescriptorsGenerator->SetMolecule($Molecule);
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117 <br/> $MolecularDescriptorsGenerator->GenerateDescriptors();
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118 <br/> print "MolecularDescriptorsGenerator: $MolecularDescriptorsGenerator\n";</div>
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119 </dd>
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120 <dt><strong><a name="generatedescriptors" class="item"><strong>GenerateDescriptors</strong></a></strong></dt>
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121 <dd>
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122 <div class="OptionsBox">
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123 $MolecularDescriptorsGenerator->GenerateDescriptors();</div>
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124 <p>Calculates descriptor values for specified descriptors and returns <em>MolecularDescriptorsGenerator</em>.</p>
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125 <p>Descriptor class objects are instantiated only once at first invocation. During
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126 subsequent calls to <strong>GenerateDescriptors</strong> method, descriptor values are
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127 initialized and <strong>GenerateDescriptors</strong> method provided by descriptor class is
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128 used to calculate descriptor values for specified descriptors.</p>
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129 </dd>
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130 <dt><strong><a name="getavailableclassanddescriptornames" class="item"><strong>GetAvailableClassAndDescriptorNames</strong></a></strong></dt>
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131 <dd>
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132 <div class="OptionsBox">
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133 %ClassAndDescriptorNames = $MolecularDescriptorsGenerator->
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134 GetAvailableClassAndDescriptorNames();
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135 <br/> %ClassAndDescriptorNames = MolecularDescriptors::
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136 MolecularDescriptorsGenerator::
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137 GetAvailableClassAndDescriptorNames();</div>
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138 <p>Returns available descriptors class and descriptors names as a hash containing key
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139 and value pairs corresponding to class name and an array of descriptor names
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140 available for the class.</p>
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141 </dd>
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142 <dt><strong><a name="getavailableclassnamefordescriptorname" class="item"><strong>GetAvailableClassNameForDescriptorName</strong></a></strong></dt>
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143 <dd>
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144 <div class="OptionsBox">
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145 $DescriptorClassName = $MolecularDescriptorsGenerator->
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146 GetAvailableClassNameForDescriptorName($DescriptorName);</div>
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147 <div class="OptionsBox">
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148 $DescriptorClassName = MolecularDescriptors::MolecularDescriptorsGenerator::
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149 GetAvailableClassNameForDescriptorName($DescriptorName);</div>
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150 <p>Returns available descriptor class name for a descriptor name.</p>
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151 </dd>
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152 <dt><strong><a name="getavailabledescriptorclassnames" class="item"><strong>GetAvailableDescriptorClassNames</strong></a></strong></dt>
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153 <dd>
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154 <div class="OptionsBox">
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155 $Return = $MolecularDescriptorsGenerator->GetAvailableDescriptorClassNames();</div>
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156 <div class="OptionsBox">
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157 @DescriptorClassNames = $MolecularDescriptorsGenerator->
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158 GetAvailableDescriptorClassNames();
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159 <br/> @DescriptorClassNames = MolecularDescriptors::
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160 MolecularDescriptorsGenerator::
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161 GetAvailableDescriptorClassNames();</div>
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162 <p>Returns available descriptor class names as an array or number of available descriptor
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163 class names in scalar context.</p>
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164 </dd>
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165 <dt><strong><a name="getavailabledescriptornames" class="item"><strong>GetAvailableDescriptorNames</strong></a></strong></dt>
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166 <dd>
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167 <div class="OptionsBox">
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168 @DescriptorNames = $MolecularDescriptorsGenerator->
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169 GetAvailableDescriptorNames();
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170 <br/> @DescriptorNames = MolecularDescriptors::
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171 MolecularDescriptorsGenerator::
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172 GetAvailableDescriptorNames();</div>
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173 <p>Returns available descriptor names as an array or number of available descriptor
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174 names in scalar context.</p>
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175 </dd>
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176 <dt><strong><a name="getavailabledescriptornamesfordescriptorclass" class="item"><strong>GetAvailableDescriptorNamesForDescriptorClass</strong></a></strong></dt>
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177 <dd>
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178 <div class="OptionsBox">
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179 @DescriptorNames = $MolecularDescriptorsGenerator->
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180 GetAvailableDescriptorNamesForDescriptorClass($DescriptorClassName);
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181 <br/> @DescriptorNames = MolecularDescriptors::
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182 MolecularDescriptorsGenerator::
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183 GetAvailableDescriptorNamesForDescriptorClass($DescriptorClassName);</div>
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184 <p>Returns available descriptors names for a descriptor class as an array or number
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185 of available descriptor names in scalar context.</p>
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186 </dd>
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187 <dt><strong><a name="getdescriptorclassparameters" class="item"><strong>GetDescriptorClassParameters</strong></a></strong></dt>
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188 <dd>
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189 <div class="OptionsBox">
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190 $DescriptorClassParametersRef = $MolecularDescriptorsGenerator->
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191 GetDescriptorClassParameters();
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192 <br/> $DescriptorClassParametersRef = MolecularDescriptors::
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193 MolecularDescriptorsGenerator::
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194 GetDescriptorClassParameters();</div>
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195 <p>Returns descriptor name parameters as a reference to hash of hashes with hash
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196 keys corresponding to class name and class parameter name with hash value
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197 as class parameter value.</p>
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198 </dd>
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199 <dt><strong><a name="getdescriptornames" class="item"><strong>GetDescriptorNames</strong></a></strong></dt>
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200 <dd>
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201 <div class="OptionsBox">
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202 @DescriptorNames = $MolecularDescriptorsGenerator->GetDescriptorNames();
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203 <br/> @DescriptorNames = MolecularDescriptors::MolecularDescriptorsGenerator::
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204 GetDescriptorNames();</div>
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205 <p>Returns all available descriptor names as an array or number of available descriptors
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206 in scalar context.</p>
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207 </dd>
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208 <dt><strong><a name="getdescriptornamesandvalues" class="item"><strong>GetDescriptorNamesAndValues</strong></a></strong></dt>
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209 <dd>
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210 <div class="OptionsBox">
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211 %NamesAndValues = $MolecularDescriptorsGenerator->
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212 GetDescriptorNamesAndValues();</div>
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213 <p>Returns calculated molecular descriptor names and values as a hash with descriptor
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214 names and values as hash key and value pairs.</p>
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215 </dd>
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216 <dt><strong><a name="getdescriptorvaluebyname" class="item"><strong>GetDescriptorValueByName</strong></a></strong></dt>
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217 <dd>
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218 <div class="OptionsBox">
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219 $Value = $MolecularDescriptorsGenerator->
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220 GetDescriptorValueByName($Name);</div>
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221 <p>Returns calculated descriptor values for a specified descriptor name.</p>
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222 </dd>
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223 <dt><strong><a name="getdescriptorvalues" class="item"><strong>GetDescriptorValues</strong></a></strong></dt>
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224 <dd>
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225 <div class="OptionsBox">
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226 @DescriptorValues = $MolecularDescriptorsGenerator->GetDescriptorValues();</div>
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227 <p>Returns all calculated descriptor values as an array corresponding to specified
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228 descriptor names.</p>
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229 </dd>
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230 <dt><strong><a name="getruleof3descriptornames" class="item"><strong>GetRuleOf3DescriptorNames</strong></a></strong></dt>
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231 <dd>
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232 <div class="OptionsBox">
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233 @DescriptorNames = $MolecularDescriptorsGenerator->
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234 GetRuleOf3DescriptorNames();
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235 <br/> @DescriptorNames = MolecularDescriptors::
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236 MolecularDescriptorsGenerator::
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237 GetRuleOf3DescriptorNames();</div>
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238 <p>Returns rule of 3 descriptor names as an array or number of rule of 3 descriptors in scalar
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239 context.</p>
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240 <p>RuleOf3 [ Ref 92 ] descriptor names are: MolecularWeight, RotatableBonds,
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241 HydrogenBondDonors, HydrogenBondAcceptors, SLogP, TPSA. RuleOf3 states:
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242 MolecularWeight <= 300, RotatableBonds <= 3, HydrogenBondDonors <= 3,
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243 HydrogenBondAcceptors <= 3, logP <= 3, and TPSA <= 60.</p>
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244 </dd>
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245 <dt><strong><a name="getruleof5descriptornames" class="item"><strong>GetRuleOf5DescriptorNames</strong></a></strong></dt>
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246 <dd>
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247 <div class="OptionsBox">
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248 @DescriptorNames = $MolecularDescriptorsGenerator->
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249 GetRuleOf5DescriptorNames();
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250 <br/> @DescriptorNames = $MolecularDescriptorsGenerator::
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251 GetRuleOf5DescriptorNames();</div>
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252 <p>Returns rule of 5 descriptor names as an array or number of rule of 4 descriptors in scalar
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253 context.</p>
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254 <p>RuleOf5 [ Ref 91 ] descriptor names are: MolecularWeight, HydrogenBondDonors,
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255 HydrogenBondAcceptors, SLogP. RuleOf5 states: MolecularWeight <= 500,
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256 HydrogenBondDonors <= 5, HydrogenBondAcceptors <= 10, and logP <= 5.</p>
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257 </dd>
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258 <dt><strong><a name="isdescriptorclassnameavailable" class="item"><strong>IsDescriptorClassNameAvailable</strong></a></strong></dt>
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259 <dd>
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260 <div class="OptionsBox">
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261 $Status = $MolecularDescriptorsGenerator->
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262 IsDescriptorClassNameAvailable($ClassName);
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263 <br/> $Status = MolecularDescriptors::
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264 MolecularDescriptorsGenerator::
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265 IsDescriptorClassNameAvailable($ClassName);</div>
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266 <p>Returns 1 or 0 based on whether specified descriptor class name is available.</p>
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267 </dd>
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268 <dt><strong><a name="isdescriptornameavailable" class="item"><strong>IsDescriptorNameAvailable</strong></a></strong></dt>
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269 <dd>
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270 <div class="OptionsBox">
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271 $Status = $MolecularDescriptorsGenerator->
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272 IsDescriptorNameAvailable($DescriptorName);
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273 <br/> $Status = MolecularDescriptors::
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274 MolecularDescriptorsGenerator::
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275 IsDescriptorNameAvailable($DescriptorName);</div>
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276 <p>Returns 1 or 0 based on whether specified descriptor name is available.</p>
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277 </dd>
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278 <dt><strong><a name="isdescriptorsgenerationsuccessful" class="item"><strong>IsDescriptorsGenerationSuccessful</strong></a></strong></dt>
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279 <dd>
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280 <div class="OptionsBox">
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281 $Status = $MolecularDescriptorsGenerator->
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282 IsDescriptorsGenerationSuccessful();</div>
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283 <p>Returns 1 or 0 based on whether descriptors generation is successful.</p>
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284 </dd>
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285 <dt><strong><a name="setdescriptorclassparameters" class="item"><strong>SetDescriptorClassParameters</strong></a></strong></dt>
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286 <dd>
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287 <div class="OptionsBox">
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288 $MolecularDescriptorsGenerator->SetDescriptorClassParameters(
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289 %NamesAndValues);</div>
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290 <p>Sets descriptor calculation control parameters for a specified descriptor class name
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291 and returns <em>MolecularDescriptorsGenerator</em>.</p>
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292 <p>The specified parameter names and values are simply passed on to specified descriptor
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293 class during instantiation of descriptor class object without any performing any validation
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294 of parameter names and associated values. It's up to the appropriate descriptor class methods
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295 to validate these parameters and values.</p>
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296 <p>In addition to specified parameter names and values, the parameter hash must also contain
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297 descriptor class name as key and value pair with DescriptorClassName as key with class
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298 name as value.</p>
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299 </dd>
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300 <dt><strong><a name="setdescriptornames" class="item"><strong>SetDescriptorNames</strong></a></strong></dt>
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301 <dd>
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302 <div class="OptionsBox">
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303 $MolecularDescriptorsGenerator->SetDescriptorNames(@Names);
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304 <br/> $MolecularDescriptorsGenerator->SetDescriptorNames(\@Names);</div>
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305 <p>Sets descriptor names to use for generating descriptor values using an array
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306 or reference to an array and returns <em>MolecularDescriptorsGenerator</em>.</p>
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307 </dd>
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308 <dt><strong><a name="setmode" class="item"><strong>SetMode</strong></a></strong></dt>
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309 <dd>
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310 <div class="OptionsBox">
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311 $MolecularDescriptorsGenerator->SetMode($Mode);</div>
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312 <p>Sets descriptors generation mode and returns <em>MolecularDescriptorsGenerator</em>.
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313 Possible <em>Mode</em> values: <em>All, RuleOf5, RuleOf3, Specify</em>.</p>
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314 </dd>
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315 <dt><strong><a name="setmolecule" class="item"><strong>SetMolecule</strong></a></strong></dt>
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316 <dd>
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317 <div class="OptionsBox">
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318 $MolecularDescriptorsGenerator->SetMolecule($Molecule);</div>
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319 <p>Sets molecule to use during calculation of molecular descriptors and returns
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320 <em>MolecularDescriptorsGenerator</em>.</p>
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321 </dd>
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322 <dt><strong><a name="stringifymoleculardescriptorsgenerator" class="item"><strong>StringifyMolecularDescriptorsGenerator</strong></a></strong></dt>
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323 <dd>
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324 <div class="OptionsBox">
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325 $String = $MolecularDescriptorsGenerator->StringifyMolecularDescriptorsGenerator();</div>
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326 <p>Returns a string containing information about <em>MolecularDescriptorsGenerator</em> object.</p>
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327 </dd>
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328 </dl>
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329 <p>
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330 </p>
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331 <h2>AUTHOR</h2>
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332 <p><a href="mailto:msud@san.rr.com">Manish Sud</a></p>
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333 <p>
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334 </p>
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335 <h2>SEE ALSO</h2>
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336 <p><a href="./MolecularDescriptors.html">MolecularDescriptors.pm</a>
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337 </p>
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338 <p>
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339 </p>
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340 <h2>COPYRIGHT</h2>
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341 <p>Copyright (C) 2015 Manish Sud. All rights reserved.</p>
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342 <p>This file is part of MayaChemTools.</p>
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343 <p>MayaChemTools is free software; you can redistribute it and/or modify it under
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344 the terms of the GNU Lesser General Public License as published by the Free
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345 Software Foundation; either version 3 of the License, or (at your option)
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346 any later version.</p>
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347 <p> </p><p> </p><div class="DocNav">
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348 <table width="100%" border=0 cellpadding=0 cellspacing=2>
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349 <tr align="left" valign="top"><td width="33%" align="left"><a href="./MolecularDescriptors.html" title="MolecularDescriptors.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./MolecularVolumeDescriptors.html" title="MolecularVolumeDescriptors.html">Next</a></td><td width="34%" align="middle"><strong>March 29, 2015</strong></td><td width="33%" align="right"><strong>MolecularDescriptors::MolecularDescriptorsGenerator.pm</strong></td></tr>
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350 </table>
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351 </div>
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352 <br />
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353 <center>
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354 <img src="../../images/h2o2.png">
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355 </center>
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356 </body>
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357 </html>
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