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comparison mayachemtools/docs/modules/html/code/Fingerprints.html @ 0:73ae111cf86f draft
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| author | deepakjadmin |
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| date | Wed, 20 Jan 2016 11:55:01 -0500 |
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| 1 <html> | |
| 2 <head> | |
| 3 <title>MayaChemTools:Code:Fingerprints::Fingerprints.pm</title> | |
| 4 <meta http-equiv="content-type" content="text/html;charset=utf-8"> | |
| 5 <link rel="stylesheet" type="text/css" href="../../../css/MayaChemToolsCode.css"> | |
| 6 </head> | |
| 7 <body leftmargin="20" rightmargin="20" topmargin="10" bottommargin="10"> | |
| 8 <br/> | |
| 9 <center> | |
| 10 <a href="http://www.mayachemtools.org" title="MayaChemTools Home"><img src="../../../images/MayaChemToolsLogo.gif" border="0" alt="MayaChemTools"></a> | |
| 11 </center> | |
| 12 <br/> | |
| 13 <pre> | |
| 14 <a name="package-Fingerprints::Fingerprints-"></a> 1 <span class="k">package </span><span class="i">Fingerprints::Fingerprints</span><span class="sc">;</span> | |
| 15 2 <span class="c">#</span> | |
| 16 3 <span class="c"># $RCSfile: Fingerprints.pm,v $</span> | |
| 17 4 <span class="c"># $Date: 2015/02/28 20:48:54 $</span> | |
| 18 5 <span class="c"># $Revision: 1.33 $</span> | |
| 19 6 <span class="c">#</span> | |
| 20 7 <span class="c"># Author: Manish Sud <msud@san.rr.com></span> | |
| 21 8 <span class="c">#</span> | |
| 22 9 <span class="c"># Copyright (C) 2015 Manish Sud. All rights reserved.</span> | |
| 23 10 <span class="c">#</span> | |
| 24 11 <span class="c"># This file is part of MayaChemTools.</span> | |
| 25 12 <span class="c">#</span> | |
| 26 13 <span class="c"># MayaChemTools is free software; you can redistribute it and/or modify it under</span> | |
| 27 14 <span class="c"># the terms of the GNU Lesser General Public License as published by the Free</span> | |
| 28 15 <span class="c"># Software Foundation; either version 3 of the License, or (at your option) any</span> | |
| 29 16 <span class="c"># later version.</span> | |
| 30 17 <span class="c">#</span> | |
| 31 18 <span class="c"># MayaChemTools is distributed in the hope that it will be useful, but without</span> | |
| 32 19 <span class="c"># any warranty; without even the implied warranty of merchantability of fitness</span> | |
| 33 20 <span class="c"># for a particular purpose. See the GNU Lesser General Public License for more</span> | |
| 34 21 <span class="c"># details.</span> | |
| 35 22 <span class="c">#</span> | |
| 36 23 <span class="c"># You should have received a copy of the GNU Lesser General Public License</span> | |
| 37 24 <span class="c"># along with MayaChemTools; if not, see <http://www.gnu.org/licenses/> or</span> | |
| 38 25 <span class="c"># write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,</span> | |
| 39 26 <span class="c"># Boston, MA, 02111-1307, USA.</span> | |
| 40 27 <span class="c">#</span> | |
| 41 28 | |
| 42 29 <span class="k">use</span> <span class="w">strict</span><span class="sc">;</span> | |
| 43 30 <span class="k">use</span> <span class="w">Carp</span><span class="sc">;</span> | |
| 44 31 <span class="k">use</span> <span class="w">Exporter</span><span class="sc">;</span> | |
| 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> | |
| 46 33 <span class="k">use</span> <span class="w">ObjectProperty</span><span class="sc">;</span> | |
| 47 34 <span class="k">use</span> <span class="w">MathUtil</span> <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 48 35 <span class="k">use</span> <span class="w">TextUtil</span> <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 49 36 <span class="k">use</span> <span class="w">Fingerprints::FingerprintsBitVector</span><span class="sc">;</span> | |
| 50 37 <span class="k">use</span> <span class="w">Fingerprints::FingerprintsVector</span><span class="sc">;</span> | |
| 51 38 | |
| 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> | |
| 53 40 | |
| 54 41 <span class="i">@ISA</span> = <span class="q">qw(ObjectProperty Exporter)</span><span class="sc">;</span> | |
| 55 42 <span class="i">@EXPORT</span> = <span class="q">qw()</span><span class="sc">;</span> | |
| 56 43 <span class="i">@EXPORT_OK</span> = <span class="q">qw()</span><span class="sc">;</span> | |
| 57 44 | |
| 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> | |
| 59 46 | |
| 60 47 <span class="c"># Setup class variables...</span> | |
| 61 48 <span class="k">my</span><span class="s">(</span><span class="i">$ClassName</span><span class="s">)</span><span class="sc">;</span> | |
| 62 49 <span class="i">_InitializeClass</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 63 50 | |
| 64 51 <span class="c"># Class constructor...</span> | |
| 65 <a name="new-"></a> 52 <span class="k">sub </span><span class="m">new</span> <span class="s">{</span> | |
| 66 53 <span class="k">my</span><span class="s">(</span><span class="i">$Class</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 67 54 | |
| 68 55 <span class="c"># Initialize object...</span> | |
| 69 56 <span class="k">my</span> <span class="i">$This</span> = <span class="s">{</span><span class="s">}</span><span class="sc">;</span> | |
| 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">$Class</span><span class="sc">;</span> | |
| 71 58 <span class="i">$This</span><span class="i">->_InitializeFingerprints</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 72 59 | |
| 73 60 <span class="i">$This</span><span class="i">->_InitializeFingerprintsProperties</span><span class="s">(</span><span class="i">%NamesAndValues</span><span class="s">)</span><span class="sc">;</span> | |
| 74 61 | |
| 75 62 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 76 63 <span class="s">}</span> | |
| 77 64 | |
| 78 65 <span class="c"># Initialize object data...</span> | |
| 79 66 <span class="c">#</span> | |
| 80 <a name="_InitializeFingerprints-"></a> 67 <span class="k">sub </span><span class="m">_InitializeFingerprints</span> <span class="s">{</span> | |
| 81 68 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 82 69 | |
| 83 70 <span class="c"># Molecule object...</span> | |
| 84 71 <span class="i">$This</span>->{<span class="w">Molecule</span>} = <span class="q">''</span><span class="sc">;</span> | |
| 85 72 | |
| 86 73 <span class="c"># Type of fingerprints...</span> | |
| 87 74 <span class="i">$This</span>->{<span class="w">Type</span>} = <span class="q">''</span><span class="sc">;</span> | |
| 88 75 | |
| 89 76 <span class="c"># Type of fingerprints vector: FingerprintsBitVector or FingerprintsVector...</span> | |
| 90 77 <span class="i">$This</span>->{<span class="w">VectorType</span>} = <span class="q">''</span><span class="sc">;</span> | |
| 91 78 | |
| 92 79 <span class="c"># Marks successful generation of fingerprints...</span> | |
| 93 80 <span class="i">$This</span>->{<span class="w">FingerprintsGenerated</span>} = <span class="n">0</span><span class="sc">;</span> | |
| 94 81 | |
| 95 82 <span class="c"># Initialize values for FingerprintsBitVector...</span> | |
| 96 83 <span class="i">_InitializeClassValuesForFingerprintsBitVector</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 97 84 | |
| 98 85 <span class="c"># Initialize values for FingerprintsVector...</span> | |
| 99 86 <span class="i">_InitializeClassValuesForFingerprintsVector</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 100 87 <span class="s">}</span> | |
| 101 88 | |
| 102 89 <span class="c"># Initialize class ...</span> | |
| 103 <a name="_InitializeClass-"></a> 90 <span class="k">sub </span><span class="m">_InitializeClass</span> <span class="s">{</span> | |
| 104 91 <span class="c">#Class name...</span> | |
| 105 92 <span class="i">$ClassName</span> = <span class="w">__PACKAGE__</span><span class="sc">;</span> | |
| 106 93 <span class="s">}</span> | |
| 107 94 | |
| 108 95 <span class="c"># Initialize class values specific to FingerprintsBitVector...</span> | |
| 109 96 <span class="c">#</span> | |
| 110 <a name="_InitializeClassValuesForFingerprintsBitVector-"></a> 97 <span class="k">sub </span><span class="m">_InitializeClassValuesForFingerprintsBitVector</span> <span class="s">{</span> | |
| 111 98 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 112 99 | |
| 113 100 <span class="c"># Size of FingerprintsBitVector...</span> | |
| 114 101 <span class="i">$This</span>->{<span class="w">Size</span>} = <span class="q">''</span><span class="sc">;</span> | |
| 115 102 | |
| 116 103 <span class="c"># Min/Max sizes used for folding FingerprintsBitVector...</span> | |
| 117 104 <span class="i">$This</span>->{<span class="w">MinSize</span>} = <span class="q">''</span><span class="sc">;</span> | |
| 118 105 <span class="i">$This</span>->{<span class="w">MaxSize</span>} = <span class="q">''</span><span class="sc">;</span> | |
| 119 106 | |
| 120 107 <span class="c"># FingerprintsBitVector...</span> | |
| 121 108 <span class="i">$This</span>->{<span class="w">FingerprintsBitVector</span>} = <span class="q">''</span><span class="sc">;</span> | |
| 122 109 <span class="s">}</span> | |
| 123 110 | |
| 124 111 <span class="c"># Initialize class values specific to FingerprintsVector...</span> | |
| 125 112 <span class="c">#</span> | |
| 126 <a name="_InitializeClassValuesForFingerprintsVector-"></a> 113 <span class="k">sub </span><span class="m">_InitializeClassValuesForFingerprintsVector</span> <span class="s">{</span> | |
| 127 114 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 128 115 | |
| 129 116 <span class="c"># Types of FingerprintsVector values: OrderedNumericalValues, NumericalValues or AlphaNumericalValues.</span> | |
| 130 117 <span class="i">$This</span>->{<span class="w">FingerprintsVectorType</span>} = <span class="q">''</span><span class="sc">;</span> | |
| 131 118 | |
| 132 119 <span class="c"># Fingerprints vector...</span> | |
| 133 120 <span class="i">$This</span>->{<span class="w">FingerprintsVector</span>} = <span class="q">''</span><span class="sc">;</span> | |
| 134 121 <span class="s">}</span> | |
| 135 122 | |
| 136 123 <span class="c"># Initialize object properties....</span> | |
| 137 <a name="_InitializeFingerprintsProperties-"></a> 124 <span class="k">sub </span><span class="m">_InitializeFingerprintsProperties</span> <span class="s">{</span> | |
| 138 125 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 139 126 | |
| 140 127 <span class="k">my</span><span class="s">(</span><span class="i">$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> | |
| 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> | |
| 142 129 <span class="i">$MethodName</span> = <span class="q">"Set${Name}"</span><span class="sc">;</span> | |
| 143 130 <span class="i">$This</span><span class="i">->$MethodName</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="sc">;</span> | |
| 144 131 <span class="s">}</span> | |
| 145 132 | |
| 146 133 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 147 134 <span class="s">}</span> | |
| 148 135 | |
| 149 136 <span class="c"># Set molecule object and make sure it's not already set...</span> | |
| 150 137 <span class="c">#</span> | |
| 151 <a name="SetMolecule-"></a> 138 <span class="k">sub </span><span class="m">SetMolecule</span> <span class="s">{</span> | |
| 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> | |
| 153 140 | |
| 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> | |
| 155 142 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetMolecule: Can't change molecule object: It's already set..."</span><span class="sc">;</span> | |
| 156 143 <span class="s">}</span> | |
| 157 144 <span class="i">$This</span>->{<span class="w">Molecule</span>} = <span class="i">$Molecule</span><span class="sc">;</span> | |
| 158 145 | |
| 159 146 <span class="c"># Weaken the reference to disable increment of reference count...</span> | |
| 160 147 <span class="i">Scalar::Util::weaken</span><span class="s">(</span><span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="s">)</span><span class="sc">;</span> | |
| 161 148 | |
| 162 149 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 163 150 <span class="s">}</span> | |
| 164 151 | |
| 165 152 <span class="c"># Set type and make sure it's not already set...</span> | |
| 166 153 <span class="c">#</span> | |
| 167 <a name="SetType-"></a> 154 <span class="k">sub </span><span class="m">SetType</span> <span class="s">{</span> | |
| 168 155 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Type</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 169 156 | |
| 170 157 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">Type</span>}<span class="s">)</span> <span class="s">{</span> | |
| 171 158 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetType: Can't change fingerprint type: It's already set..."</span><span class="sc">;</span> | |
| 172 159 <span class="s">}</span> | |
| 173 160 <span class="i">$This</span>->{<span class="w">Type</span>} = <span class="i">$Type</span><span class="sc">;</span> | |
| 174 161 | |
| 175 162 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 176 163 <span class="s">}</span> | |
| 177 164 | |
| 178 165 <span class="c"># Is fingerprints generation successful?</span> | |
| 179 166 <span class="c">#</span> | |
| 180 167 <span class="c"># Notes:</span> | |
| 181 168 <span class="c"># . The specific fingerprints generation class sets the value of FingerprinsGenerated</span> | |
| 182 169 <span class="c"># to 1 after the successful generation of fingerprints; otherwise, it's set to 0.</span> | |
| 183 170 <span class="c">#</span> | |
| 184 <a name="IsFingerprintsGenerationSuccessful-"></a> 171 <span class="k">sub </span><span class="m">IsFingerprintsGenerationSuccessful</span> <span class="s">{</span> | |
| 185 172 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 186 173 | |
| 187 174 <span class="k">return</span> <span class="i">$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> | |
| 188 175 <span class="s">}</span> | |
| 189 176 | |
| 190 177 <span class="c"># Set vector type and make sure it's not already set...</span> | |
| 191 178 <span class="c">#</span> | |
| 192 <a name="SetVectorType-"></a> 179 <span class="k">sub </span><span class="m">SetVectorType</span> <span class="s">{</span> | |
| 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> | |
| 194 181 | |
| 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> | |
| 196 183 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetVectorType: Can't change fingerprint vector type: It's already set..."</span><span class="sc">;</span> | |
| 197 184 <span class="s">}</span> | |
| 198 185 <span class="k">if</span> <span class="s">(</span><span class="i">$VectorType</span> !~ <span class="q">/^(FingerprintsBitVector|FingerprintsVector)$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 199 186 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetVectorType: Specified value, $VectorType, for Type is not vaild. Supported types in current release of MayaChemTools: FingerprintsBitVector and FingerprintsVector..."</span><span class="sc">;</span> | |
| 200 187 <span class="s">}</span> | |
| 201 188 <span class="i">$This</span>->{<span class="w">VectorType</span>} = <span class="i">$VectorType</span><span class="sc">;</span> | |
| 202 189 | |
| 203 190 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 204 191 <span class="s">}</span> | |
| 205 192 | |
| 206 193 <span class="c">#</span> | |
| 207 194 <span class="c"># Methods/functions for FingerprintsBitVector...</span> | |
| 208 195 <span class="c">#</span> | |
| 209 196 | |
| 210 197 <span class="c"># Initialize fingerprint bit vector...</span> | |
| 211 <a name="_InitializeFingerprintsBitVector-"></a> 198 <span class="k">sub </span><span class="m">_InitializeFingerprintsBitVector</span> <span class="s">{</span> | |
| 212 199 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 213 200 | |
| 214 201 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">VectorType</span>} !~ <span class="q">/^FingerprintsBitVector$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 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">$This</span><span class="sc">;</span> | |
| 222 209 <span class="s">}</span> | |
| 223 210 | |
| 224 211 <span class="c"># Set size...</span> | |
| 225 212 <span class="c">#</span> | |
| 226 <a name="SetSize-"></a> 213 <span class="k">sub </span><span class="m">SetSize</span> <span class="s">{</span> | |
| 227 214 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Size</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 228 215 | |
| 229 216 <span class="k">if</span> <span class="s">(</span><span class="i">$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">$Size</span><span class="sc">;</span> | |
| 237 224 | |
| 238 225 <span class="k">return</span> <span class="i">$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> | |
| 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> | |
| 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> | |
| 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> | |
| 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> | |
| 372 359 <span class="s">}</span> | |
| 373 360 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 374 361 <span class="s">}</span> | |
| 375 362 | |
| 376 363 <span class="c"># Set FingerprintsVector object and make sure it's not already set...</span> | |
| 377 364 <span class="c">#</span> | |
| 378 <a name="SetFingerprintsVector-"></a> 365 <span class="k">sub </span><span class="m">SetFingerprintsVector</span> <span class="s">{</span> | |
| 379 366 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$FingerprintsVector</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 380 367 | |
| 381 368 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">FingerprintsVector</span>}<span class="s">)</span> <span class="s">{</span> | |
| 382 369 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetFingerprintsVector: Can't change FingerprintsVector object: It's already set..."</span><span class="sc">;</span> | |
| 383 370 <span class="s">}</span> | |
| 384 371 <span class="i">$This</span>->{<span class="w">FingerprintsVector</span>} = <span class="i">$FingerprintsVector</span><span class="sc">;</span> | |
| 385 372 | |
| 386 373 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 387 374 <span class="s">}</span> | |
| 388 375 | |
| 389 376 <span class="c"># Types of FingerprintsVector values: OrderedNumericalValues, NumericalValues or AlphaNumericalValues.</span> | |
| 390 377 <span class="c">#</span> | |
| 391 <a name="SetFingerprintsVectorType-"></a> 378 <span class="k">sub </span><span class="m">SetFingerprintsVectorType</span> <span class="s">{</span> | |
| 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> | |
| 393 380 | |
| 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> | |
| 395 382 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetFingerprintsVector: Can't change FingerprintsVectorType: It's already set..."</span><span class="sc">;</span> | |
| 396 383 <span class="s">}</span> | |
| 397 384 <span class="k">if</span> <span class="s">(</span><span class="i">$FingerprintsVectorType</span> !~ <span class="q">/^(OrderedNumericalValues|NumericalValues|AlphaNumericalValues)$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 398 385 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetFingerprintsVectorType: Specified value, $FingerprintsVectorType, for Type is not vaild. Supported types in current release of MayaChemTools: OrderedNumericalValues, NumericalValues or AlphaNumericalValues"</span><span class="sc">;</span> | |
| 399 386 <span class="s">}</span> | |
| 400 387 <span class="i">$This</span>->{<span class="w">FingerprintsVectorType</span>} = <span class="i">$FingerprintsVectorType</span><span class="sc">;</span> | |
| 401 388 | |
| 402 389 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 403 390 <span class="s">}</span> | |
| 404 391 | |
| 405 392 <span class="c"># Get fingerprints vector values as an array or reference to an array...</span> | |
| 406 393 <span class="c">#</span> | |
| 407 <a name="GetFingerprintsVectorValues-"></a> 394 <span class="k">sub </span><span class="m">GetFingerprintsVectorValues</span> <span class="s">{</span> | |
| 408 395 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 409 396 | |
| 410 397 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span>->{<span class="w">FingerprintsVector</span>}<span class="s">)</span> <span class="s">{</span> | |
| 411 398 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
| 412 399 <span class="s">}</span> | |
| 413 400 <span class="k">return</span> <span class="i">$This</span>->{<span class="w">FingerprintsVector</span>}<span class="i">->GetValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 414 401 <span class="s">}</span> | |
| 415 402 | |
| 416 403 <span class="c"># Get fingerprints vector value IDs as an array or reference to an array...</span> | |
| 417 404 <span class="c">#</span> | |
| 418 <a name="GetFingerprintsVectorValueIDs-"></a> 405 <span class="k">sub </span><span class="m">GetFingerprintsVectorValueIDs</span> <span class="s">{</span> | |
| 419 406 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 420 407 | |
| 421 408 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span>->{<span class="w">FingerprintsVector</span>}<span class="s">)</span> <span class="s">{</span> | |
| 422 409 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
| 423 410 <span class="s">}</span> | |
| 424 411 <span class="k">return</span> <span class="i">$This</span>->{<span class="w">FingerprintsVector</span>}<span class="i">->GetValueIDs</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 425 412 <span class="s">}</span> | |
| 426 413 | |
| 427 <a name="EOF-"></a></pre> | |
| 428 <p> </p> | |
| 429 <br /> | |
| 430 <center> | |
| 431 <img src="../../../images/h2o2.png"> | |
| 432 </center> | |
| 433 </body> | |
| 434 </html> |