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3 <title>MayaChemTools:Documentation:Fingerprints::EStateIndiciesFingerprints.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="./AtomTypesFingerprints.html" title="AtomTypesFingerprints.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./ExtendedConnectivityFingerprints.html" title="ExtendedConnectivityFingerprints.html">Next</a></td><td width="34%" align="middle"><strong>Fingerprints::EStateIndiciesFingerprints.pm</strong></td><td width="33%" align="right"><a href="././code/EStateIndiciesFingerprints.html" title="View source code">Code</a> | <a href="./../pdf/EStateIndiciesFingerprints.pdf" title="PDF US Letter Size">PDF</a> | <a href="./../pdfgreen/EStateIndiciesFingerprints.pdf" title="PDF US Letter Size with narrow margins: www.changethemargins.com">PDFGreen</a> | <a href="./../pdfa4/EStateIndiciesFingerprints.pdf" title="PDF A4 Size">PDFA4</a> | <a href="./../pdfa4green/EStateIndiciesFingerprints.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>EStateIndiciesFingerprints</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 Fingerprints::EStateIndiciesFingerprints;</p>
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26 <p>use Fingerprints::EStateIndiciesFingerprints 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>EStateIndiciesFingerprints</strong> [ Ref 75-78 ] class provides the following methods:</p>
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31 <p> <a href="#new">new</a>, <a href="#generatefingerprints">GenerateFingerprints</a>, <a href="#getdescription">GetDescription</a>, <a href="#setestateatomtypessettouse">SetEStateAtomTypesSetToUse</a>
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32 , <a href="#setvaluesprecision">SetValuesPrecision</a>, <a href="#stringifyestateindiciesfingerprints">StringifyEStateIndiciesFingerprints</a>
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33 </p><p><strong>EStateIndiciesFingerprints</strong> is derived from <strong>Fingerprints</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>AtomNeighborhoodsFingerprints</strong>, <strong>Fingerprints</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>E-state atom types are assigned to all non-hydrogen atoms in a molecule using module
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42 AtomTypes::EStateAtomTypes.pm and E-state values are calculated using module
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43 AtomicDescriptors::EStateValues.pm. Using E-state atom types and E-state values,
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44 <strong>EStateIndiciesFingerprints</strong> constituting sum of E-state values for E-sate atom types
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45 are generated.</p>
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46 <p>Two types of E-state atom types set size are allowed:</p>
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47 <div class="OptionsBox">
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48 ArbitrarySize - Corresponds to only E-state atom types detected
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49 in molecule
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50 <br/> FixedSize - Corresponds to fixed number of E-state atom types previously
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51 defined</div>
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52 <p>Module AtomTypes::EStateAtomTypes.pm, used to assign E-state atom types to
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53 non-hydrogen atoms in the molecule, is able to assign atom types to any valid
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54 atom group. However, for <em>FixedSize</em> value of <strong>EStateAtomTypesSetToUse</strong>, only a
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55 fixed set of E-state atom types corresponding to specific atom groups [ Appendix III in
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56 Ref 77 ] are used for fingerprints.</p>
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57 <p>The fixed size E-state atom type set size used during generation of fingerprints contains
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58 87 E-state non-hydrogen atom types in EStateAtomTypes.csv data file distributed with
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59 MayaChemTools.</p>
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60 <p>Combination of Type and EStateAtomTypesSetToUse allow generation of 2 different types of
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61 E-state indicies fingerprints:</p>
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62 <div class="OptionsBox">
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63 Type EStateAtomTypesSetToUse</div>
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64 <div class="OptionsBox">
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65 EStateIndicies ArbitrarySize [ default fingerprints ]
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66 <br/> EStateIndicies FixedSize</div>
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67 <p>The current release of MayaChemTools generates the following types of E-state
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68 fingerprints vector strings:</p>
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69 <div class="OptionsBox">
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70 FingerprintsVector;EStateIndicies:ArbitrarySize;11;NumericalValues;IDs
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71 <br/> AndValuesString;SaaCH SaasC SaasN SdO SdssC SsCH3 SsF SsOH SssCH2 SssN
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72 <br/> H SsssCH;24.778 4.387 1.993 25.023 -1.435 3.975 14.006 29.759 -0.073 3
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73 <br/> .024 -2.270</div>
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74 <div class="OptionsBox">
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75 FingerprintsVector;EStateIndicies:FixedSize;87;OrderedNumericalValues;
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76 <br/> ValuesString;0 0 0 0 0 0 0 3.975 0 -0.073 0 0 24.778 -2.270 0 0 -1.435
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77 <br/> 4.387 0 0 0 0 0 0 3.024 0 0 0 0 0 0 0 1.993 0 29.759 25.023 0 0 0 0 1
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78 <br/> 4.006 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
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79 <br/> 0 0 0 0 0 0 0 0 0 0 0 0 0 0</div>
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80 <div class="OptionsBox">
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81 FingerprintsVector;EStateIndicies:FixedSize;87;OrderedNumericalValues;
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82 <br/> IDsAndValuesString;SsLi SssBe SssssBem SsBH2 SssBH SsssB SssssBm SsCH3
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83 <br/> SdCH2 SssCH2 StCH SdsCH SaaCH SsssCH SddC StsC SdssC SaasC SaaaC Sssss
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84 <br/> C SsNH3p SsNH2 SssNH2p SdNH SssNH SaaNH StN SsssNHp SdsN SaaN SsssN Sd
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85 <br/> 0 0 0 0 0 0 0 3.975 0 -0.073 0 0 24.778 -2.270 0 0 -1.435 4.387 0 0 0
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86 <br/> 0 0 0 3.024 0 0 0 0 0 0 0 1.993 0 29.759 25.023 0 0 0 0 14.006 0 0 0 0
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87 <br/> 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0...</div>
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88 <p>
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89 </p>
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90 <h2>METHODS</h2>
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91 <dl>
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92 <dt><strong><a name="new" class="item"><strong>new</strong></a></strong></dt>
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93 <dd>
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94 <div class="OptionsBox">
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95 $EStateIndiciesFingerprints = new EStateIndiciesFingerprints(%NamesAndValues);</div>
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96 <p>Using specified <em>EStateIndiciesFingerprints</em> property names and values hash, <strong>new</strong> method creates a new object
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97 and returns a reference to newly created <strong>PathLengthFingerprints</strong> object. By default, the
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98 following properties are initialized:</p>
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99 <div class="OptionsBox">
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100 Molecule = '';
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101 <br/> Type = 'EStateIndicies'
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102 <br/> EStateAtomTypesSetToUse = 'ArbitrarySize'
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103 <br/> ValuesPrecision = 3</div>
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104 <p>Examples:</p>
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105 <div class="OptionsBox">
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106 $EStateIndiciesFingerprints = new AtomTypesFingerprints(
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107 'Molecule' => $Molecule,
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108 'EStateAtomTypesSetToUse' =>
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109 'ArbitrarySize');</div>
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110 <div class="OptionsBox">
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111 $EStateIndiciesFingerprints = new AtomTypesFingerprints(
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112 'Molecule' => $Molecule,
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113 'EStateAtomTypesSetToUse' =>
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114 'FixedSize');</div>
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115 <div class="OptionsBox">
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116 $EStateIndiciesFingerprints->GenerateFingerprints();
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117 <br/> print "$EStateIndiciesFingerprints\n";</div>
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118 </dd>
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119 <dt><strong><a name="generatefingerprints" class="item"><strong>GenerateFingerprints</strong></a></strong></dt>
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120 <dd>
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121 <div class="OptionsBox">
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122 $EStateIndiciesFingerprints = $EStateIndiciesFingerprints->
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123 GenerateEStateIndiciesFingerprints();</div>
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124 <p>Generates EState keys fingerprints and returns <em>EStateIndiciesFingerprints</em>.</p>
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125 </dd>
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126 <dt><strong><a name="getdescription" class="item"><strong>GetDescription</strong></a></strong></dt>
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127 <dd>
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128 <div class="OptionsBox">
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129 $Description = $EStateIndiciesFingerprints->GetDescription();</div>
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130 <p>Returns a string containing description of EState keys fingerprints.</p>
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131 </dd>
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132 <dt><strong><a name="setestateatomtypessettouse" class="item"><strong>SetEStateAtomTypesSetToUse</strong></a></strong></dt>
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133 <dd>
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134 <div class="OptionsBox">
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135 $EStateIndiciesFingerprints->SetEStateAtomTypesSetToUse($Value);</div>
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136 <p>Sets <em>Value</em> of <em>EStateAtomTypesSetToUse</em> and returns <em>EStateIndiciesFingerprints</em>.
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137 Possible values: <em>ArbitrarySize or FixedSize</em>. Default value: <em>ArbitrarySize</em>.</p>
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138 </dd>
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139 <dt><strong><a name="setvaluesprecision" class="item"><strong>SetValuesPrecision</strong></a></strong></dt>
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140 <dd>
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141 <div class="OptionsBox">
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142 $EStateIndiciesFingerprints->SetValuesPrecision($Precision);</div>
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143 <p>Sets precesion of E-state values to use during generation of E-state indices fingerprints
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144 and returns <em>EStateIndiciesFingerprints</em>. Possible values: <em>Positive integers</em>.
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145 Default value: <em>3</em>.</p>
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146 </dd>
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147 <dt><strong><a name="stringifyestateindiciesfingerprints" class="item"><strong>StringifyEStateIndiciesFingerprints</strong></a></strong></dt>
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148 <dd>
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149 <div class="OptionsBox">
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150 $String = $EStateIndiciesFingerprints->StringifyEStateIndiciesFingerprints();</div>
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151 <p>Returns a string containing information about <em>EStateIndiciesFingerprints</em> object.</p>
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152 </dd>
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153 </dl>
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154 <p>
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155 </p>
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156 <h2>AUTHOR</h2>
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157 <p><a href="mailto:msud@san.rr.com">Manish Sud</a></p>
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158 <p>
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159 </p>
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160 <h2>SEE ALSO</h2>
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161 <p><a href="./Fingerprints.html">Fingerprints.pm</a>, <a href="./FingerprintsStringUtil.html">FingerprintsStringUtil.pm</a>, <a href="./AtomNeighborhoodsFingerprints.html">AtomNeighborhoodsFingerprints.pm</a>, <a href="./AtomTypesFingerprints.html">AtomTypesFingerprints.pm</a>, 
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162 <a href="./ExtendedConnectivityFingerprints.html">ExtendedConnectivityFingerprints.pm</a>, <a href="./MACCSKeys.html">MACCSKeys.pm</a>, <a href="./PathLengthFingerprints.html">PathLengthFingerprints.pm</a>, 
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163 <a href="./TopologicalAtomPairsFingerprints.html">TopologicalAtomPairsFingerprints.pm</a>, <a href="./TopologicalAtomTripletsFingerprints.html">TopologicalAtomTripletsFingerprints.pm</a>, 
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164 <a href="./TopologicalAtomTorsionsFingerprints.html">TopologicalAtomTorsionsFingerprints.pm</a>, <a href="./TopologicalPharmacophoreAtomPairsFingerprints.html">TopologicalPharmacophoreAtomPairsFingerprints.pm</a>, 
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165 <a href="./TopologicalPharmacophoreAtomTripletsFingerprints.html">TopologicalPharmacophoreAtomTripletsFingerprints.pm</a>
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166 </p>
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167 <p>
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168 </p>
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169 <h2>COPYRIGHT</h2>
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170 <p>Copyright (C) 2015 Manish Sud. All rights reserved.</p>
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171 <p>This file is part of MayaChemTools.</p>
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172 <p>MayaChemTools is free software; you can redistribute it and/or modify it under
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173 the terms of the GNU Lesser General Public License as published by the Free
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174 Software Foundation; either version 3 of the License, or (at your option)
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175 any later version.</p>
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176 <p> </p><p> </p><div class="DocNav">
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177 <table width="100%" border=0 cellpadding=0 cellspacing=2>
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178 <tr align="left" valign="top"><td width="33%" align="left"><a href="./AtomTypesFingerprints.html" title="AtomTypesFingerprints.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./ExtendedConnectivityFingerprints.html" title="ExtendedConnectivityFingerprints.html">Next</a></td><td width="34%" align="middle"><strong>March 29, 2015</strong></td><td width="33%" align="right"><strong>Fingerprints::EStateIndiciesFingerprints.pm</strong></td></tr>
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179 </table>
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180 </div>
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181 <br />
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