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3 <title>MayaChemTools:Code:Fingerprints::Fingerprints.pm</title>
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13 <pre>
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14 <a name="package-Fingerprints::Fingerprints-"></a> 1 <span class="k">package </span><span class="i">Fingerprints::Fingerprints</span><span class="sc">;</span>
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15 2 <span class="c">#</span>
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16 3 <span class="c"># $RCSfile: Fingerprints.pm,v $</span>
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17 4 <span class="c"># $Date: 2015/02/28 20:48:54 $</span>
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18 5 <span class="c"># $Revision: 1.33 $</span>
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19 6 <span class="c">#</span>
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20 7 <span class="c"># Author: Manish Sud <msud@san.rr.com></span>
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21 8 <span class="c">#</span>
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22 9 <span class="c"># Copyright (C) 2015 Manish Sud. All rights reserved.</span>
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23 10 <span class="c">#</span>
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24 11 <span class="c"># This file is part of MayaChemTools.</span>
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25 12 <span class="c">#</span>
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26 13 <span class="c"># MayaChemTools is free software; you can redistribute it and/or modify it under</span>
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27 14 <span class="c"># the terms of the GNU Lesser General Public License as published by the Free</span>
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28 15 <span class="c"># Software Foundation; either version 3 of the License, or (at your option) any</span>
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29 16 <span class="c"># later version.</span>
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30 17 <span class="c">#</span>
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31 18 <span class="c"># MayaChemTools is distributed in the hope that it will be useful, but without</span>
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32 19 <span class="c"># any warranty; without even the implied warranty of merchantability of fitness</span>
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33 20 <span class="c"># for a particular purpose. See the GNU Lesser General Public License for more</span>
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34 21 <span class="c"># details.</span>
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35 22 <span class="c">#</span>
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36 23 <span class="c"># You should have received a copy of the GNU Lesser General Public License</span>
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37 24 <span class="c"># along with MayaChemTools; if not, see <http://www.gnu.org/licenses/> or</span>
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38 25 <span class="c"># write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,</span>
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39 26 <span class="c"># Boston, MA, 02111-1307, USA.</span>
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40 27 <span class="c">#</span>
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41 28
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42 29 <span class="k">use</span> <span class="w">strict</span><span class="sc">;</span>
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43 30 <span class="k">use</span> <span class="w">Carp</span><span class="sc">;</span>
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44 31 <span class="k">use</span> <span class="w">Exporter</span><span class="sc">;</span>
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45 32 <span class="k">use</span> <span class="w">Scalar::Util</span> <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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46 33 <span class="k">use</span> <span class="w">ObjectProperty</span><span class="sc">;</span>
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47 34 <span class="k">use</span> <span class="w">MathUtil</span> <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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48 35 <span class="k">use</span> <span class="w">TextUtil</span> <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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49 36 <span class="k">use</span> <span class="w">Fingerprints::FingerprintsBitVector</span><span class="sc">;</span>
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50 37 <span class="k">use</span> <span class="w">Fingerprints::FingerprintsVector</span><span class="sc">;</span>
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51 38
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52 39 <span class="k">use</span> <span class="w">vars</span> <span class="q">qw(@ISA @EXPORT @EXPORT_OK %EXPORT_TAGS)</span><span class="sc">;</span>
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53 40
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54 41 <span class="i">@ISA</span> = <span class="q">qw(ObjectProperty Exporter)</span><span class="sc">;</span>
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55 42 <span class="i">@EXPORT</span> = <span class="q">qw()</span><span class="sc">;</span>
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56 43 <span class="i">@EXPORT_OK</span> = <span class="q">qw()</span><span class="sc">;</span>
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57 44
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58 45 <span class="i">%EXPORT_TAGS</span> = <span class="s">(</span><span class="w">all</span> <span class="cm">=></span> <span class="s">[</span><span class="i">@EXPORT</span><span class="cm">,</span> <span class="i">@EXPORT_OK</span><span class="s">]</span><span class="s">)</span><span class="sc">;</span>
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59 46
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60 47 <span class="c"># Setup class variables...</span>
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61 48 <span class="k">my</span><span class="s">(</span><span class="i">$ClassName</span><span class="s">)</span><span class="sc">;</span>
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62 49 <span class="i">_InitializeClass</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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63 50
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64 51 <span class="c"># Class constructor...</span>
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65 <a name="new-"></a> 52 <span class="k">sub </span><span class="m">new</span> <span class="s">{</span>
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66 53 <span class="k">my</span><span class="s">(</span><span class="i">$Class</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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67 54
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68 55 <span class="c"># Initialize object...</span>
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69 56 <span class="k">my</span> <span class="i">$This</span> = <span class="s">{</span><span class="s">}</span><span class="sc">;</span>
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70 57 <span class="k">bless</span> <span class="i">$This</span><span class="cm">,</span> <span class="k">ref</span><span class="s">(</span><span class="i">$Class</span><span class="s">)</span> || <span class="i">$Class</span><span class="sc">;</span>
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71 58 <span class="i">$This</span><span class="i">->_InitializeFingerprints</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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72 59
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73 60 <span class="i">$This</span><span class="i">->_InitializeFingerprintsProperties</span><span class="s">(</span><span class="i">%NamesAndValues</span><span class="s">)</span><span class="sc">;</span>
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74 61
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75 62 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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76 63 <span class="s">}</span>
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77 64
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78 65 <span class="c"># Initialize object data...</span>
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79 66 <span class="c">#</span>
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80 <a name="_InitializeFingerprints-"></a> 67 <span class="k">sub </span><span class="m">_InitializeFingerprints</span> <span class="s">{</span>
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81 68 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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82 69
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83 70 <span class="c"># Molecule object...</span>
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84 71 <span class="i">$This</span>->{<span class="w">Molecule</span>} = <span class="q">''</span><span class="sc">;</span>
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85 72
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86 73 <span class="c"># Type of fingerprints...</span>
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87 74 <span class="i">$This</span>->{<span class="w">Type</span>} = <span class="q">''</span><span class="sc">;</span>
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88 75
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89 76 <span class="c"># Type of fingerprints vector: FingerprintsBitVector or FingerprintsVector...</span>
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90 77 <span class="i">$This</span>->{<span class="w">VectorType</span>} = <span class="q">''</span><span class="sc">;</span>
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91 78
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92 79 <span class="c"># Marks successful generation of fingerprints...</span>
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93 80 <span class="i">$This</span>->{<span class="w">FingerprintsGenerated</span>} = <span class="n">0</span><span class="sc">;</span>
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94 81
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95 82 <span class="c"># Initialize values for FingerprintsBitVector...</span>
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96 83 <span class="i">_InitializeClassValuesForFingerprintsBitVector</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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97 84
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98 85 <span class="c"># Initialize values for FingerprintsVector...</span>
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99 86 <span class="i">_InitializeClassValuesForFingerprintsVector</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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100 87 <span class="s">}</span>
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101 88
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102 89 <span class="c"># Initialize class ...</span>
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103 <a name="_InitializeClass-"></a> 90 <span class="k">sub </span><span class="m">_InitializeClass</span> <span class="s">{</span>
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104 91 <span class="c">#Class name...</span>
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105 92 <span class="i">$ClassName</span> = <span class="w">__PACKAGE__</span><span class="sc">;</span>
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106 93 <span class="s">}</span>
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107 94
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108 95 <span class="c"># Initialize class values specific to FingerprintsBitVector...</span>
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109 96 <span class="c">#</span>
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110 <a name="_InitializeClassValuesForFingerprintsBitVector-"></a> 97 <span class="k">sub </span><span class="m">_InitializeClassValuesForFingerprintsBitVector</span> <span class="s">{</span>
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111 98 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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112 99
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113 100 <span class="c"># Size of FingerprintsBitVector...</span>
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114 101 <span class="i">$This</span>->{<span class="w">Size</span>} = <span class="q">''</span><span class="sc">;</span>
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115 102
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116 103 <span class="c"># Min/Max sizes used for folding FingerprintsBitVector...</span>
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117 104 <span class="i">$This</span>->{<span class="w">MinSize</span>} = <span class="q">''</span><span class="sc">;</span>
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118 105 <span class="i">$This</span>->{<span class="w">MaxSize</span>} = <span class="q">''</span><span class="sc">;</span>
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119 106
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120 107 <span class="c"># FingerprintsBitVector...</span>
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121 108 <span class="i">$This</span>->{<span class="w">FingerprintsBitVector</span>} = <span class="q">''</span><span class="sc">;</span>
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122 109 <span class="s">}</span>
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123 110
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124 111 <span class="c"># Initialize class values specific to FingerprintsVector...</span>
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125 112 <span class="c">#</span>
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126 <a name="_InitializeClassValuesForFingerprintsVector-"></a> 113 <span class="k">sub </span><span class="m">_InitializeClassValuesForFingerprintsVector</span> <span class="s">{</span>
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127 114 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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128 115
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129 116 <span class="c"># Types of FingerprintsVector values: OrderedNumericalValues, NumericalValues or AlphaNumericalValues.</span>
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130 117 <span class="i">$This</span>->{<span class="w">FingerprintsVectorType</span>} = <span class="q">''</span><span class="sc">;</span>
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131 118
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132 119 <span class="c"># Fingerprints vector...</span>
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133 120 <span class="i">$This</span>->{<span class="w">FingerprintsVector</span>} = <span class="q">''</span><span class="sc">;</span>
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134 121 <span class="s">}</span>
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135 122
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136 123 <span class="c"># Initialize object properties....</span>
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137 <a name="_InitializeFingerprintsProperties-"></a> 124 <span class="k">sub </span><span class="m">_InitializeFingerprintsProperties</span> <span class="s">{</span>
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138 125 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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139 126
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140 127 <span class="k">my</span><span class="s">(</span><span class="i">$Name</span><span class="cm">,</span> <span class="i">$Value</span><span class="cm">,</span> <span class="i">$MethodName</span><span class="s">)</span><span class="sc">;</span>
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141 128 <span class="k">while</span> <span class="s">(</span><span class="s">(</span><span class="i">$Name</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="k">each</span> <span class="i">%NamesAndValues</span><span class="s">)</span> <span class="s">{</span>
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142 129 <span class="i">$MethodName</span> = <span class="q">"Set${Name}"</span><span class="sc">;</span>
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143 130 <span class="i">$This</span><span class="i">->$MethodName</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="sc">;</span>
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144 131 <span class="s">}</span>
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145 132
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146 133 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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147 134 <span class="s">}</span>
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148 135
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149 136 <span class="c"># Set molecule object and make sure it's not already set...</span>
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150 137 <span class="c">#</span>
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151 <a name="SetMolecule-"></a> 138 <span class="k">sub </span><span class="m">SetMolecule</span> <span class="s">{</span>
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152 139 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Molecule</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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153 140
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154 141 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="s">)</span> <span class="s">{</span>
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155 142 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetMolecule: Can't change molecule object: It's already set..."</span><span class="sc">;</span>
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156 143 <span class="s">}</span>
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157 144 <span class="i">$This</span>->{<span class="w">Molecule</span>} = <span class="i">$Molecule</span><span class="sc">;</span>
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158 145
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159 146 <span class="c"># Weaken the reference to disable increment of reference count...</span>
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160 147 <span class="i">Scalar::Util::weaken</span><span class="s">(</span><span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="s">)</span><span class="sc">;</span>
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161 148
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162 149 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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163 150 <span class="s">}</span>
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164 151
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165 152 <span class="c"># Set type and make sure it's not already set...</span>
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166 153 <span class="c">#</span>
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167 <a name="SetType-"></a> 154 <span class="k">sub </span><span class="m">SetType</span> <span class="s">{</span>
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168 155 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Type</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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169 156
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170 157 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">Type</span>}<span class="s">)</span> <span class="s">{</span>
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171 158 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetType: Can't change fingerprint type: It's already set..."</span><span class="sc">;</span>
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172 159 <span class="s">}</span>
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173 160 <span class="i">$This</span>->{<span class="w">Type</span>} = <span class="i">$Type</span><span class="sc">;</span>
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174 161
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175 162 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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176 163 <span class="s">}</span>
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177 164
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178 165 <span class="c"># Is fingerprints generation successful?</span>
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179 166 <span class="c">#</span>
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180 167 <span class="c"># Notes:</span>
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181 168 <span class="c"># . The specific fingerprints generation class sets the value of FingerprinsGenerated</span>
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182 169 <span class="c"># to 1 after the successful generation of fingerprints; otherwise, it's set to 0.</span>
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183 170 <span class="c">#</span>
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184 <a name="IsFingerprintsGenerationSuccessful-"></a> 171 <span class="k">sub </span><span class="m">IsFingerprintsGenerationSuccessful</span> <span class="s">{</span>
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185 172 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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186 173
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187 174 <span class="k">return</span> <span class="i">$This</span>->{<span class="w">FingerprintsGenerated</span>} ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
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188 175 <span class="s">}</span>
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189 176
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190 177 <span class="c"># Set vector type and make sure it's not already set...</span>
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191 178 <span class="c">#</span>
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192 <a name="SetVectorType-"></a> 179 <span class="k">sub </span><span class="m">SetVectorType</span> <span class="s">{</span>
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193 180 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$VectorType</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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194 181
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195 182 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">VectorType</span>}<span class="s">)</span> <span class="s">{</span>
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196 183 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetVectorType: Can't change fingerprint vector type: It's already set..."</span><span class="sc">;</span>
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197 184 <span class="s">}</span>
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198 185 <span class="k">if</span> <span class="s">(</span><span class="i">$VectorType</span> !~ <span class="q">/^(FingerprintsBitVector|FingerprintsVector)$/i</span><span class="s">)</span> <span class="s">{</span>
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199 186 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetVectorType: Specified value, $VectorType, for Type is not vaild. Supported types in current release of MayaChemTools: FingerprintsBitVector and FingerprintsVector..."</span><span class="sc">;</span>
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200 187 <span class="s">}</span>
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201 188 <span class="i">$This</span>->{<span class="w">VectorType</span>} = <span class="i">$VectorType</span><span class="sc">;</span>
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202 189
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203 190 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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204 191 <span class="s">}</span>
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205 192
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206 193 <span class="c">#</span>
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207 194 <span class="c"># Methods/functions for FingerprintsBitVector...</span>
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208 195 <span class="c">#</span>
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209 196
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210 197 <span class="c"># Initialize fingerprint bit vector...</span>
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211 <a name="_InitializeFingerprintsBitVector-"></a> 198 <span class="k">sub </span><span class="m">_InitializeFingerprintsBitVector</span> <span class="s">{</span>
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212 199 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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213 200
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214 201 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">VectorType</span>} !~ <span class="q">/^FingerprintsBitVector$/i</span><span class="s">)</span> <span class="s">{</span>
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|
|
215 202 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->_InitializeFingerprintsBitVector: Can't initialize fingerprints bit vector: VectorType must be FingerprintsBitVector..."</span><span class="sc">;</span>
|
|
|
216 203 <span class="s">}</span>
|
|
|
217 204
|
|
|
218 205 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">Size</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
219 206 <span class="i">$This</span>->{<span class="w">FingerprintsBitVector</span>} = <span class="i">new</span> <span class="i">Fingerprints::FingerprintsBitVector</span><span class="s">(</span><span class="i">$This</span>->{<span class="w">Size</span>}<span class="s">)</span><span class="sc">;</span>
|
|
|
220 207 <span class="s">}</span>
|
|
|
221 208 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
222 209 <span class="s">}</span>
|
|
|
223 210
|
|
|
224 211 <span class="c"># Set size...</span>
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|
|
225 212 <span class="c">#</span>
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|
|
226 <a name="SetSize-"></a> 213 <span class="k">sub </span><span class="m">SetSize</span> <span class="s">{</span>
|
|
|
227 214 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Size</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
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228 215
|
|
|
229 216 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MinSize</span>} && <span class="i">$Size</span> < <span class="i">$This</span>->{<span class="w">MinSize</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
230 217 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetSize: Fingerprint size value, $Size, is not valid : It must be >= $This->{MinSize}..."</span><span class="sc">;</span>
|
|
|
231 218 <span class="s">}</span>
|
|
|
232 219 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MaxSize</span>} && <span class="i">$Size</span> > <span class="i">$This</span>->{<span class="w">MaxSize</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
233 220 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetSize: Fingerprint size value, $Size, is not valid: It must be <= $This->{MaxSize}..."</span><span class="sc">;</span>
|
|
|
234 221 <span class="s">}</span>
|
|
|
235 222
|
|
|
236 223 <span class="i">$This</span>->{<span class="w">Size</span>} = <span class="i">$Size</span><span class="sc">;</span>
|
|
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237 224
|
|
|
238 225 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
239 226 <span class="s">}</span>
|
|
|
240 227
|
|
|
241 228 <span class="c"># Set FingerprintsBitVector object and make sure it's not already set...</span>
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|
|
242 229 <span class="c">#</span>
|
|
|
243 <a name="SetFingerprintsBitVector-"></a> 230 <span class="k">sub </span><span class="m">SetFingerprintsBitVector</span> <span class="s">{</span>
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|
244 231 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$FingerprintsBitVector</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
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245 232
|
|
|
246 233 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">FingerprintsBitVector</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
247 234 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetFingerprintsBitVector: Can't change FingerprintsBitVector object: It's already set..."</span><span class="sc">;</span>
|
|
|
248 235 <span class="s">}</span>
|
|
|
249 236 <span class="i">$This</span>->{<span class="w">FingerprintsBitVector</span>} = <span class="i">$FingerprintsBitVector</span><span class="sc">;</span>
|
|
|
250 237
|
|
|
251 238 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
252 239 <span class="s">}</span>
|
|
|
253 240
|
|
|
254 241 <span class="c"># Fold fingerprints by recursively reducing its size by half untill bit density is greater than or equal to</span>
|
|
|
255 242 <span class="c"># specified bit density...</span>
|
|
|
256 243 <span class="c">#</span>
|
|
|
257 <a name="FoldFingerprintsByBitDensity-"></a> 244 <span class="k">sub </span><span class="m">FoldFingerprintsByBitDensity</span> <span class="s">{</span>
|
|
|
258 245 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$BitDensity</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
259 246
|
|
|
260 247 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="i">$BitDensity</span> >= <span class="n">0</span> && <span class="i">$BitDensity</span> <= <span class="n">1</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
261 248 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->FoldFingerprintsByBitDensity: Specified bit density, $BitDensity, is not valid: It must be > 0 && <= 1 ..."</span><span class="sc">;</span>
|
|
|
262 249 <span class="s">}</span>
|
|
|
263 250
|
|
|
264 251 <span class="k">return</span> <span class="i">$This</span><span class="i">->_FoldFingerprintsBitVector</span><span class="s">(</span><span class="q">'ByDensity'</span><span class="cm">,</span> <span class="i">$BitDensity</span><span class="s">)</span><span class="sc">;</span>
|
|
|
265 252 <span class="s">}</span>
|
|
|
266 253
|
|
|
267 254 <span class="c"># Fold fingerprints by recursively reducing its size by half untill size is less than or equal to</span>
|
|
|
268 255 <span class="c"># specified size...</span>
|
|
|
269 256 <span class="c">#</span>
|
|
|
270 <a name="FoldFingerprintsBySize-"></a> 257 <span class="k">sub </span><span class="m">FoldFingerprintsBySize</span> <span class="s">{</span>
|
|
|
271 258 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Size</span><span class="cm">,</span> <span class="i">$CheckSizeValue</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
272 259
|
|
|
273 260 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$CheckSizeValue</span><span class="s">)</span> <span class="s">{</span>
|
|
|
274 261 <span class="i">$CheckSizeValue</span> = <span class="n">1</span><span class="sc">;</span>
|
|
|
275 262 <span class="s">}</span>
|
|
|
276 263
|
|
|
277 264 <span class="k">if</span> <span class="s">(</span><span class="i">$CheckSizeValue</span><span class="s">)</span> <span class="s">{</span>
|
|
|
278 265 <span class="k">if</span> <span class="s">(</span>!<span class="i">TextUtil::IsPositiveInteger</span><span class="s">(</span><span class="i">$Size</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
279 266 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->FoldFingerprintsBySize: Specified size, $Size, is not valid: It must be a positive integer"</span><span class="sc">;</span>
|
|
|
280 267 <span class="s">}</span>
|
|
|
281 268 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="i">$Size</span> >= <span class="i">$This</span>->{<span class="w">MinSize</span>} && <span class="i">$Size</span> < <span class="i">$This</span>->{<span class="w">Size</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
282 269 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->FoldFingerprintsBySize: Specified size, $Size, is not valid: It must be greater than or equal to minimum size of $This->{MinSize} and less than current size of $This->{Size}..."</span><span class="sc">;</span>
|
|
|
283 270 <span class="s">}</span>
|
|
|
284 271 <span class="k">if</span> <span class="s">(</span>!<span class="i">TextUtil::IsNumberPowerOfNumber</span><span class="s">(</span><span class="i">$Size</span><span class="cm">,</span> <span class="n">2</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
285 272 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->FoldFingerprintsBySize: Specified size value, $Size, must be power of 2..."</span><span class="sc">;</span>
|
|
|
286 273 <span class="s">}</span>
|
|
|
287 274 <span class="s">}</span>
|
|
|
288 275
|
|
|
289 276 <span class="k">return</span> <span class="i">$This</span><span class="i">->_FoldFingerprintsBitVector</span><span class="s">(</span><span class="q">'BySize'</span><span class="cm">,</span> <span class="i">$Size</span><span class="s">)</span><span class="sc">;</span>
|
|
|
290 277 <span class="s">}</span>
|
|
|
291 278
|
|
|
292 279 <span class="c"># Fold fingerprints bit vector using specified size of bit density...</span>
|
|
|
293 280 <span class="c">#</span>
|
|
|
294 <a name="_FoldFingerprintsBitVector-"></a> 281 <span class="k">sub </span><span class="m">_FoldFingerprintsBitVector</span> <span class="s">{</span>
|
|
|
295 282 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Mode</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
296 283
|
|
|
297 284 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span>->{<span class="w">FingerprintsBitVector</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
298 285 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
299 286 <span class="s">}</span>
|
|
|
300 287 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsBitVector</span><span class="cm">,</span> <span class="i">$FoldedFingerprintsBitVector</span><span class="s">)</span><span class="sc">;</span>
|
|
|
301 288
|
|
|
302 289 <span class="i">$FoldedFingerprintsBitVector</span> = <span class="q">''</span><span class="sc">;</span>
|
|
|
303 290 <span class="i">$FingerprintsBitVector</span> = <span class="i">$This</span>->{<span class="w">FingerprintsBitVector</span>}<span class="sc">;</span>
|
|
|
304 291 <span class="j">MODE:</span> <span class="s">{</span>
|
|
|
305 292 <span class="k">if</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^BySize$/i</span><span class="s">)</span> <span class="s">{</span> <span class="i">$FoldedFingerprintsBitVector</span> = <span class="i">$FingerprintsBitVector</span><span class="i">->FoldFingerprintsBitVectorBySize</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="sc">;</span> <span class="k">last</span> <span class="j">MODE</span><span class="sc">;</span> <span class="s">}</span>
|
|
|
306 293 <span class="k">if</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^ByDensity$/i</span><span class="s">)</span> <span class="s">{</span> <span class="i">$FoldedFingerprintsBitVector</span> = <span class="i">$FingerprintsBitVector</span><span class="i">->FoldFingerprintsBitVectorByDensity</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="sc">;</span> <span class="k">last</span> <span class="j">MODE</span><span class="sc">;</span> <span class="s">}</span>
|
|
|
307 294 <span class="i">$FoldedFingerprintsBitVector</span> = <span class="q">''</span><span class="sc">;</span>
|
|
|
308 295 <span class="s">}</span>
|
|
|
309 296 <span class="k">if</span> <span class="s">(</span><span class="i">$FoldedFingerprintsBitVector</span><span class="s">)</span> <span class="s">{</span>
|
|
|
310 297 <span class="i">$This</span>->{<span class="w">FingerprintsBitVector</span>} = <span class="i">$FoldedFingerprintsBitVector</span><span class="sc">;</span>
|
|
|
311 298 <span class="i">$This</span>->{<span class="w">Size</span>} = <span class="i">$FoldedFingerprintsBitVector</span><span class="i">->GetSize</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
312 299 <span class="s">}</span>
|
|
|
313 300 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
314 301 <span class="s">}</span>
|
|
|
315 302
|
|
|
316 303 <span class="c"># Get fingerprints as a binary ascii string containing 0s and 1s...</span>
|
|
|
317 304 <span class="c">#</span>
|
|
|
318 <a name="GetFingerprintBitsAsBinaryString-"></a> 305 <span class="k">sub </span><span class="m">GetFingerprintBitsAsBinaryString</span> <span class="s">{</span>
|
|
|
319 306 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$BitOrder</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
320 307
|
|
|
321 308 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetFingerprintBitsAsString</span><span class="s">(</span><span class="q">'Binary'</span><span class="cm">,</span> <span class="i">$BitOrder</span><span class="s">)</span><span class="sc">;</span>
|
|
|
322 309 <span class="s">}</span>
|
|
|
323 310
|
|
|
324 311 <span class="c"># Get fingerprints as a hexadecimal string...</span>
|
|
|
325 312 <span class="c">#</span>
|
|
|
326 <a name="GetFingerprintBitsAsHexadecimalString-"></a> 313 <span class="k">sub </span><span class="m">GetFingerprintBitsAsHexadecimalString</span> <span class="s">{</span>
|
|
|
327 314 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$BitOrder</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
328 315
|
|
|
329 316 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetFingerprintBitsAsString</span><span class="s">(</span><span class="q">'Hexadecimal'</span><span class="cm">,</span> <span class="i">$BitOrder</span><span class="s">)</span><span class="sc">;</span>
|
|
|
330 317 <span class="s">}</span>
|
|
|
331 318
|
|
|
332 319 <span class="c"># Get fingerprints as a raw binary string containing packed bit values for each</span>
|
|
|
333 320 <span class="c"># byte...</span>
|
|
|
334 321 <span class="c">#</span>
|
|
|
335 <a name="GetFingerprintBitsAsRawBinaryString-"></a> 322 <span class="k">sub </span><span class="m">GetFingerprintBitsAsRawBinaryString</span> <span class="s">{</span>
|
|
|
336 323 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$BitOrder</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
337 324
|
|
|
338 325 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetFingerprintBitsAsString</span><span class="s">(</span><span class="q">'RawBinary'</span><span class="cm">,</span> <span class="i">$BitOrder</span><span class="s">)</span><span class="sc">;</span>
|
|
|
339 326 <span class="s">}</span>
|
|
|
340 327
|
|
|
341 328 <span class="c"># Get fingerprint bits as a string...</span>
|
|
|
342 329 <span class="c">#</span>
|
|
|
343 <a name="_GetFingerprintBitsAsString-"></a> 330 <span class="k">sub </span><span class="m">_GetFingerprintBitsAsString</span> <span class="s">{</span>
|
|
|
344 331 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Format</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
345 332
|
|
|
346 333 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span>->{<span class="w">FingerprintsBitVector</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
347 334 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
|
|
|
348 335 <span class="s">}</span>
|
|
|
349 336 <span class="j">FORMAT :</span> <span class="s">{</span>
|
|
|
350 337 <span class="k">if</span> <span class="s">(</span><span class="i">$Format</span> =~ <span class="q">/^(Binary|Bin|BinaryString)$/i</span><span class="s">)</span> <span class="s">{</span> <span class="k">return</span> <span class="i">$This</span>->{<span class="w">FingerprintsBitVector</span>}<span class="i">->GetBitsAsBinaryString</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> <span class="k">last</span> <span class="j">FORMAT</span><span class="sc">;</span> <span class="s">}</span>
|
|
|
351 338 <span class="k">if</span> <span class="s">(</span><span class="i">$Format</span> =~ <span class="q">/^(Hexadecimal|Hex|HexadecimalString)$/i</span><span class="s">)</span> <span class="s">{</span> <span class="k">return</span> <span class="i">$This</span>->{<span class="w">FingerprintsBitVector</span>}<span class="i">->GetBitsAsHexadecimalString</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> <span class="k">last</span> <span class="j">FORMAT</span><span class="sc">;</span> <span class="s">}</span>
|
|
|
352 339 <span class="k">if</span> <span class="s">(</span><span class="i">$Format</span> =~ <span class="q">/^(RawBinary|RawBin|RawBinaryString)$/i</span><span class="s">)</span> <span class="s">{</span> <span class="k">return</span> <span class="i">$This</span>->{<span class="w">FingerprintsBitVector</span>}<span class="i">->GetBitsAsRawBinaryString</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> <span class="k">last</span> <span class="j">FORMAT</span><span class="sc">;</span> <span class="s">}</span>
|
|
|
353 340 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->_GetFingerprintBitsAsString: Specified bit vector string format, $Format, is not supported. Value values: Binary, Bin, BinaryString, Hexdecimal, Hex, HexadecimalString, RawBinary, RawBin, RawBinaryString..."</span><span class="sc">;</span>
|
|
|
354 341 <span class="s">}</span>
|
|
|
355 342 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
|
|
|
356 343 <span class="s">}</span>
|
|
|
357 344
|
|
|
358 345 <span class="c">#</span>
|
|
|
359 346 <span class="c"># Methods/functions for FingerprintsVector...</span>
|
|
|
360 347 <span class="c">#</span>
|
|
|
361 348
|
|
|
362 349 <span class="c"># Initialize fingerprint vector...</span>
|
|
|
363 <a name="_InitializeFingerprintsVector-"></a> 350 <span class="k">sub </span><span class="m">_InitializeFingerprintsVector</span> <span class="s">{</span>
|
|
|
364 351 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
365 352
|
|
|
366 353 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">VectorType</span>} !~ <span class="q">/^FingerprintsVector$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
367 354 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->_InitializeFingerprintsVector: Can't initialize fingerprints vector: VectorType must be FingerprintsVector..."</span><span class="sc">;</span>
|
|
|
368 355 <span class="s">}</span>
|
|
|
369 356
|
|
|
370 357 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">FingerprintsVectorType</span>}<span class="s">)</span> <span class="s">{</span>
|
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371 358 <span class="i">$This</span>->{<span class="w">FingerprintsVector</span>} = <span class="i">new</span> <span class="i">Fingerprints::FingerprintsVector</span><span class="s">(</span><span class="q">'Type'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">FingerprintsVectorType</span>}<span class="s">)</span><span class="sc">;</span>
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372 359 <span class="s">}</span>
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373 360 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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374 361 <span class="s">}</span>
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375 362
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376 363 <span class="c"># Set FingerprintsVector object and make sure it's not already set...</span>
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377 364 <span class="c">#</span>
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378 <a name="SetFingerprintsVector-"></a> 365 <span class="k">sub </span><span class="m">SetFingerprintsVector</span> <span class="s">{</span>
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379 366 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$FingerprintsVector</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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380 367
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381 368 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">FingerprintsVector</span>}<span class="s">)</span> <span class="s">{</span>
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382 369 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetFingerprintsVector: Can't change FingerprintsVector object: It's already set..."</span><span class="sc">;</span>
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383 370 <span class="s">}</span>
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384 371 <span class="i">$This</span>->{<span class="w">FingerprintsVector</span>} = <span class="i">$FingerprintsVector</span><span class="sc">;</span>
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385 372
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386 373 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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387 374 <span class="s">}</span>
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388 375
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389 376 <span class="c"># Types of FingerprintsVector values: OrderedNumericalValues, NumericalValues or AlphaNumericalValues.</span>
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390 377 <span class="c">#</span>
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391 <a name="SetFingerprintsVectorType-"></a> 378 <span class="k">sub </span><span class="m">SetFingerprintsVectorType</span> <span class="s">{</span>
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392 379 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$FingerprintsVectorType</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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393 380
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394 381 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">FingerprintsVectorType</span>}<span class="s">)</span> <span class="s">{</span>
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395 382 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetFingerprintsVector: Can't change FingerprintsVectorType: It's already set..."</span><span class="sc">;</span>
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396 383 <span class="s">}</span>
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397 384 <span class="k">if</span> <span class="s">(</span><span class="i">$FingerprintsVectorType</span> !~ <span class="q">/^(OrderedNumericalValues|NumericalValues|AlphaNumericalValues)$/i</span><span class="s">)</span> <span class="s">{</span>
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398 385 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetFingerprintsVectorType: Specified value, $FingerprintsVectorType, for Type is not vaild. Supported types in current release of MayaChemTools: OrderedNumericalValues, NumericalValues or AlphaNumericalValues"</span><span class="sc">;</span>
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399 386 <span class="s">}</span>
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400 387 <span class="i">$This</span>->{<span class="w">FingerprintsVectorType</span>} = <span class="i">$FingerprintsVectorType</span><span class="sc">;</span>
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401 388
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402 389 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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403 390 <span class="s">}</span>
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404 391
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405 392 <span class="c"># Get fingerprints vector values as an array or reference to an array...</span>
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406 393 <span class="c">#</span>
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407 <a name="GetFingerprintsVectorValues-"></a> 394 <span class="k">sub </span><span class="m">GetFingerprintsVectorValues</span> <span class="s">{</span>
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408 395 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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409 396
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410 397 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span>->{<span class="w">FingerprintsVector</span>}<span class="s">)</span> <span class="s">{</span>
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411 398 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
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412 399 <span class="s">}</span>
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413 400 <span class="k">return</span> <span class="i">$This</span>->{<span class="w">FingerprintsVector</span>}<span class="i">->GetValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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414 401 <span class="s">}</span>
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415 402
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416 403 <span class="c"># Get fingerprints vector value IDs as an array or reference to an array...</span>
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417 404 <span class="c">#</span>
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418 <a name="GetFingerprintsVectorValueIDs-"></a> 405 <span class="k">sub </span><span class="m">GetFingerprintsVectorValueIDs</span> <span class="s">{</span>
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419 406 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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420 407
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421 408 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span>->{<span class="w">FingerprintsVector</span>}<span class="s">)</span> <span class="s">{</span>
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422 409 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
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423 410 <span class="s">}</span>
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424 411 <span class="k">return</span> <span class="i">$This</span>->{<span class="w">FingerprintsVector</span>}<span class="i">->GetValueIDs</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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425 412 <span class="s">}</span>
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426 413
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427 <a name="EOF-"></a></pre>
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428 <p> </p>
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429 <br />
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430 <center>
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431 <img src="../../../images/h2o2.png">
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432 </center>
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433 </body>
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434 </html>
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