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3 <title>MayaChemTools:Documentation:Fingerprints::Fingerprints.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="./ExtendedConnectivityFingerprints.html" title="ExtendedConnectivityFingerprints.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./FingerprintsBitVector.html" title="FingerprintsBitVector.html">Next</a></td><td width="34%" align="middle"><strong>Fingerprints::Fingerprints.pm</strong></td><td width="33%" align="right"><a href="././code/Fingerprints.html" title="View source code">Code</a> | <a href="./../pdf/Fingerprints.pdf" title="PDF US Letter Size">PDF</a> | <a href="./../pdfgreen/Fingerprints.pdf" title="PDF US Letter Size with narrow margins: www.changethemargins.com">PDFGreen</a> | <a href="./../pdfa4/Fingerprints.pdf" title="PDF A4 Size">PDFA4</a> | <a href="./../pdfa4green/Fingerprints.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>Fingerprints - Fingerprints class</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::Fingerprints;</p>
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26 <p>use Fingerprints::Fingerprints 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>Fingerprints</strong> class provides the following methods:</p>
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31 <p> <a href="#new">new</a>, <a href="#foldfingerprintsbybitdensity">FoldFingerprintsByBitDensity</a>, <a href="#foldfingerprintsbysize">FoldFingerprintsBySize</a>
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32 , <a href="#getfingerprintbitsasbinarystring">GetFingerprintBitsAsBinaryString</a>, <a href="#getfingerprintbitsashexadecimalstring">GetFingerprintBitsAsHexadecimalString</a>
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33 , <a href="#getfingerprintbitsasrawbinarystring">GetFingerprintBitsAsRawBinaryString</a>, <a href="#getfingerprintsvectorvalueids">GetFingerprintsVectorValueIDs</a>
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34 , <a href="#getfingerprintsvectorvalues">GetFingerprintsVectorValues</a>, <a href="#isfingerprintsgenerationsuccessful">IsFingerprintsGenerationSuccessful</a>
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35 , <a href="#setfingerprintsbitvector">SetFingerprintsBitVector</a>, <a href="#setfingerprintsvector">SetFingerprintsVector</a>, <a href="#setfingerprintsvectortype">SetFingerprintsVectorType</a>
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36 , <a href="#setmolecule">SetMolecule</a>, <a href="#setsize">SetSize</a>, <a href="#settype">SetType</a>, <a href="#setvectortype">SetVectorType</a>
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37 </p><p><strong>Fingerprints</strong> class is used as a base class for various specific fingerprint classes such as
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38 <strong>AtomNeighborhoodsFingerprints</strong>, <strong>AtomTypesFingerprints</strong>, <strong>EStateIndiciesFingerprints</strong>,
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39 <strong>PathLengthFingerprints</strong>, <strong>ExtendedConnectivityFingerprints</strong>, <strong>MACCSKeys</strong> and so on.
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40 It implements functionality common to fingerprint classes.</p>
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41 <p><strong>Fingerprints</strong> class is derived from <strong>ObjectProperty</strong> base class which provides methods not
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42 explicitly defined in <strong>Fingerprints</strong> or <strong>ObjectProperty</strong> classes using Perl's AUTOLOAD functionality.
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43 These methods are 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>Fingerprints</strong> class uses <strong>FingerprintsBitVector</strong> class to provide bits manipulation functionality.</p>
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49 <p>
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50 </p>
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51 <h2>METHODS</h2>
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52 <dl>
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53 <dt><strong><a name="new" class="item"><strong>new</strong></a></strong></dt>
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54 <dd>
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55 <div class="OptionsBox">
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56 $NewFingerprints = new Fingerprints(%NamesAndValues);</div>
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57 <p>Using specified <em>Fingerprints</em> property names and values hash, <strong>new</strong> method creates a new object
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58 and returns a reference to newly created <strong>Fingerprints</strong> object. By default, following properties are
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59 initialized:</p>
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60 <div class="OptionsBox">
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61 Molecule = '';
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62 <br/> Type = '';
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63 <br/> VectorType = '';
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64 <br/> Size = '';
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65 <br/> MinSize = '';
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66 <br/> MaxSize = '';
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67 <br/> FingerprintsBitVector = '';
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68 <br/> FingerprintsVectorType = '';
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69 <br/> FingerprintsVector = '';</div>
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70 </dd>
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71 <dt><strong><a name="foldfingerprintsbybitdensity" class="item"><strong>FoldFingerprintsByBitDensity</strong></a></strong></dt>
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72 <dd>
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73 <div class="OptionsBox">
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74 $Fingerprints->FoldFingerprintsByBitDensity($BitDensity);</div>
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75 <p>Folds fingerprints by recursively reducing its size by half until bit density is greater than or equal to
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76 specified <em>BitDensity</em> and returns <em>Fingerprints</em>.</p>
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77 </dd>
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78 <dt><strong><a name="foldfingerprintsbysize" class="item"><strong>FoldFingerprintsBySize</strong></a></strong></dt>
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79 <dd>
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80 <div class="OptionsBox">
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81 $Fingerprints->FoldFingerprintsBySize($Size, [$CheckSizeValue]);</div>
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82 <p>Fold fingerprints by recursively reducing its size by half until size is less than or equal to specified
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83 <em>Size</em> and returns <em>Fingerprints</em>. By default, value <em>Size</em> is checked to make sure it's:</p>
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84 <div class="OptionsBox">
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85 >= MinSize and < Size and IsPowerOfTwo</div>
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86 </dd>
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87 <dt><strong><a name="getfingerprintbitsasbinarystring" class="item"><strong>GetFingerprintBitsAsBinaryString</strong></a></strong></dt>
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88 <dd>
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89 <div class="OptionsBox">
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90 $BinaryASCIIString =
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91 $Fingerprints->GetFingerprintBitsAsBinaryString();</div>
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92 <p>Returns fingerprints as a binary ASCII string containing 0s and 1s.</p>
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93 </dd>
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94 <dt><strong><a name="getfingerprintbitsashexadecimalstring" class="item"><strong>GetFingerprintBitsAsHexadecimalString</strong></a></strong></dt>
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95 <dd>
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96 <div class="OptionsBox">
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97 $HexadecimalString =
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98 $Fingerprints->GetFingerprintBitsAsHexadecimalString();</div>
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99 <p>Returns fingerprints as a hexadecimal string</p>
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100 </dd>
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101 <dt><strong><a name="getfingerprintbitsasrawbinarystring" class="item"><strong>GetFingerprintBitsAsRawBinaryString</strong></a></strong></dt>
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102 <dd>
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103 <div class="OptionsBox">
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104 $RawBinaryString =
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105 $Fingerprints->GetFingerprintBitsAsRawBinaryString();</div>
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106 <p>Returns fingerprints as a raw binary string containing packed bit values for each byte.</p>
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107 </dd>
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108 <dt><strong><a name="getfingerprintsvectorvalueids" class="item"><strong>GetFingerprintsVectorValueIDs</strong></a></strong></dt>
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109 <dd>
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110 <div class="OptionsBox">
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111 $ValueIDsRef = $Fingerprints->GetFingerprintsVectorValueIDs();
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112 <br/> @ValueIDs = $Fingerprints->GetFingerprintsVectorValueIDs();</div>
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113 <p>Returns fingerprints vector value IDs as an array or reference to an array.</p>
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114 </dd>
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115 <dt><strong><a name="getfingerprintsvectorvalues" class="item"><strong>GetFingerprintsVectorValues</strong></a></strong></dt>
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116 <dd>
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117 <div class="OptionsBox">
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118 $ValuesRef = $Fingerprints->GetFingerprintsVectorValues();
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119 <br/> @Values = $Fingerprints->GetFingerprintsVectorValues();</div>
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120 <p>Returns fingerprints vector values as an array or reference to an array.</p>
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121 </dd>
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122 <dt><strong><a name="isfingerprintsgenerationsuccessful" class="item"><strong>IsFingerprintsGenerationSuccessful</strong></a></strong></dt>
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123 <dd>
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124 <div class="OptionsBox">
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125 $Return = $Fingerprints->IsFingerprintsGenerationSuccessful();</div>
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126 <p>Returns 1 or 0 based on whether fingerprints were successfully generated.</p>
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127 </dd>
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128 <dt><strong><a name="setfingerprintsbitvector" class="item"><strong>SetFingerprintsBitVector</strong></a></strong></dt>
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129 <dd>
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130 <div class="OptionsBox">
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131 $Fingerprints->SetFingerprintsBitVector($FingerprintsBitVector);</div>
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132 <p>Sets <em>FingerprintsBitVector</em> object for <em>Fingerprints</em> and returns <em>Fingerprints</em>.</p>
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133 </dd>
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134 <dt><strong><a name="setfingerprintsvector" class="item"><strong>SetFingerprintsVector</strong></a></strong></dt>
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135 <dd>
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136 <div class="OptionsBox">
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137 $Fingerprints->SetFingerprintsVector();</div>
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138 <p>Sets <em>FingerprintsVector</em> object for <em>Fingerprints</em> and returns <em>Fingerprints</em>.</p>
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139 </dd>
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140 <dt><strong><a name="setfingerprintsvectortype" class="item"><strong>SetFingerprintsVectorType</strong></a></strong></dt>
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141 <dd>
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142 <div class="OptionsBox">
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143 $Fingerprints->SetFingerprintsVectorType($VectorType);</div>
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144 <p>Sets <em>FingerprintsVector</em> type for <em>Fingerprints</em> and returns <em>Fingerprints</em>. Possible
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145 <em>VectorType</em> values: <em>OrderedNumericalValues, NumericalValues or AlphaNumericalValues</em>.</p>
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146 </dd>
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147 <dt><strong><a name="setmolecule" class="item"><strong>SetMolecule</strong></a></strong></dt>
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148 <dd>
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149 <div class="OptionsBox">
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150 $Fingerprints->SetMolecule($Molecule);</div>
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151 <p>Sets <em>Molecule</em> object for <em>Fingerprints</em> and returns <em>Fingerprints</em>.</p>
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152 </dd>
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153 <dt><strong><a name="setsize" class="item"><strong>SetSize</strong></a></strong></dt>
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154 <dd>
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155 <div class="OptionsBox">
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156 $Fingerprints->SetSize($Size);</div>
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157 <p>Sets <em>Size</em> of fingerprints and returns <em>Fingerprints</em>.</p>
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158 </dd>
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159 <dt><strong><a name="settype" class="item"><strong>SetType</strong></a></strong></dt>
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160 <dd>
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161 <div class="OptionsBox">
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162 $Fingerprints->SetType($Type);</div>
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163 <p>Sets <em>Type</em> of fingerprints and returns <em>Fingerprints</em>.</p>
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164 </dd>
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165 <dt><strong><a name="setvectortype" class="item"><strong>SetVectorType</strong></a></strong></dt>
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166 <dd>
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167 <div class="OptionsBox">
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168 $Fingerprints->SetVectorType($Type);</div>
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169 <p>Sets <em>Type</em> of fingerprints vector and returns <em>Fingerprints</em>. Possible <em>Type</em> values:
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170 <em>FingerprintsBitVector or FingerprintsVector</em>.</p>
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171 </dd>
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172 </dl>
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173 <p>
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174 </p>
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175 <h2>AUTHOR</h2>
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176 <p><a href="mailto:msud@san.rr.com">Manish Sud</a></p>
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177 <p>
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178 </p>
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179 <h2>SEE ALSO</h2>
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180 <p><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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181 <a href="./EStateIndiciesFingerprints.html">EStateIndiciesFingerprints.pm</a>, <a href="./ExtendedConnectivityFingerprints.html">ExtendedConnectivityFingerprints.pm</a>, <a href="./MACCSKeys.html">MACCSKeys.pm</a>, 
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182 <a href="./PathLengthFingerprints.html">PathLengthFingerprints.pm</a>, <a href="./TopologicalAtomPairsFingerprints.html">TopologicalAtomPairsFingerprints.pm</a>, <a href="./TopologicalAtomTripletsFingerprints.html">TopologicalAtomTripletsFingerprints.pm</a>, 
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183 <a href="./TopologicalAtomTorsionsFingerprints.html">TopologicalAtomTorsionsFingerprints.pm</a>, <a href="./TopologicalPharmacophoreAtomPairsFingerprints.html">TopologicalPharmacophoreAtomPairsFingerprints.pm</a>, 
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184 <a href="./TopologicalPharmacophoreAtomTripletsFingerprints.html">TopologicalPharmacophoreAtomTripletsFingerprints.pm</a>
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185 </p>
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186 <p>
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187 </p>
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188 <h2>COPYRIGHT</h2>
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189 <p>Copyright (C) 2015 Manish Sud. All rights reserved.</p>
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190 <p>This file is part of MayaChemTools.</p>
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191 <p>MayaChemTools is free software; you can redistribute it and/or modify it under
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192 the terms of the GNU Lesser General Public License as published by the Free
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193 Software Foundation; either version 3 of the License, or (at your option)
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194 any later version.</p>
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195 <p> </p><p> </p><div class="DocNav">
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196 <table width="100%" border=0 cellpadding=0 cellspacing=2>
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197 <tr align="left" valign="top"><td width="33%" align="left"><a href="./ExtendedConnectivityFingerprints.html" title="ExtendedConnectivityFingerprints.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./FingerprintsBitVector.html" title="FingerprintsBitVector.html">Next</a></td><td width="34%" align="middle"><strong>March 29, 2015</strong></td><td width="33%" align="right"><strong>Fingerprints::Fingerprints.pm</strong></td></tr>
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198 </table>
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199 </div>
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