Mercurial > repos > deepakjadmin > mayatool3_test3
view mayachemtools/docs/modules/html/code/Fingerprints.html @ 0:73ae111cf86f draft
Uploaded
| author | deepakjadmin |
|---|---|
| date | Wed, 20 Jan 2016 11:55:01 -0500 |
| parents | |
| children |
line wrap: on
line source
<html> <head> <title>MayaChemTools:Code:Fingerprints::Fingerprints.pm</title> <meta http-equiv="content-type" content="text/html;charset=utf-8"> <link rel="stylesheet" type="text/css" href="../../../css/MayaChemToolsCode.css"> </head> <body leftmargin="20" rightmargin="20" topmargin="10" bottommargin="10"> <br/> <center> <a href="http://www.mayachemtools.org" title="MayaChemTools Home"><img src="../../../images/MayaChemToolsLogo.gif" border="0" alt="MayaChemTools"></a> </center> <br/> <pre> <a name="package-Fingerprints::Fingerprints-"></a> 1 <span class="k">package </span><span class="i">Fingerprints::Fingerprints</span><span class="sc">;</span> 2 <span class="c">#</span> 3 <span class="c"># $RCSfile: Fingerprints.pm,v $</span> 4 <span class="c"># $Date: 2015/02/28 20:48:54 $</span> 5 <span class="c"># $Revision: 1.33 $</span> 6 <span class="c">#</span> 7 <span class="c"># Author: Manish Sud <msud@san.rr.com></span> 8 <span class="c">#</span> 9 <span class="c"># Copyright (C) 2015 Manish Sud. All rights reserved.</span> 10 <span class="c">#</span> 11 <span class="c"># This file is part of MayaChemTools.</span> 12 <span class="c">#</span> 13 <span class="c"># MayaChemTools is free software; you can redistribute it and/or modify it under</span> 14 <span class="c"># the terms of the GNU Lesser General Public License as published by the Free</span> 15 <span class="c"># Software Foundation; either version 3 of the License, or (at your option) any</span> 16 <span class="c"># later version.</span> 17 <span class="c">#</span> 18 <span class="c"># MayaChemTools is distributed in the hope that it will be useful, but without</span> 19 <span class="c"># any warranty; without even the implied warranty of merchantability of fitness</span> 20 <span class="c"># for a particular purpose. See the GNU Lesser General Public License for more</span> 21 <span class="c"># details.</span> 22 <span class="c">#</span> 23 <span class="c"># You should have received a copy of the GNU Lesser General Public License</span> 24 <span class="c"># along with MayaChemTools; if not, see <http://www.gnu.org/licenses/> or</span> 25 <span class="c"># write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,</span> 26 <span class="c"># Boston, MA, 02111-1307, USA.</span> 27 <span class="c">#</span> 28 29 <span class="k">use</span> <span class="w">strict</span><span class="sc">;</span> 30 <span class="k">use</span> <span class="w">Carp</span><span class="sc">;</span> 31 <span class="k">use</span> <span class="w">Exporter</span><span class="sc">;</span> 32 <span class="k">use</span> <span class="w">Scalar::Util</span> <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 33 <span class="k">use</span> <span class="w">ObjectProperty</span><span class="sc">;</span> 34 <span class="k">use</span> <span class="w">MathUtil</span> <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 35 <span class="k">use</span> <span class="w">TextUtil</span> <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 36 <span class="k">use</span> <span class="w">Fingerprints::FingerprintsBitVector</span><span class="sc">;</span> 37 <span class="k">use</span> <span class="w">Fingerprints::FingerprintsVector</span><span class="sc">;</span> 38 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> 40 41 <span class="i">@ISA</span> = <span class="q">qw(ObjectProperty Exporter)</span><span class="sc">;</span> 42 <span class="i">@EXPORT</span> = <span class="q">qw()</span><span class="sc">;</span> 43 <span class="i">@EXPORT_OK</span> = <span class="q">qw()</span><span class="sc">;</span> 44 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> 46 47 <span class="c"># Setup class variables...</span> 48 <span class="k">my</span><span class="s">(</span><span class="i">$ClassName</span><span class="s">)</span><span class="sc">;</span> 49 <span class="i">_InitializeClass</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 50 51 <span class="c"># Class constructor...</span> <a name="new-"></a> 52 <span class="k">sub </span><span class="m">new</span> <span class="s">{</span> 53 <span class="k">my</span><span class="s">(</span><span class="i">$Class</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 54 55 <span class="c"># Initialize object...</span> 56 <span class="k">my</span> <span class="i">$This</span> = <span class="s">{</span><span class="s">}</span><span class="sc">;</span> 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">$Class</span><span class="sc">;</span> 58 <span class="i">$This</span><span class="i">->_InitializeFingerprints</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 59 60 <span class="i">$This</span><span class="i">->_InitializeFingerprintsProperties</span><span class="s">(</span><span class="i">%NamesAndValues</span><span class="s">)</span><span class="sc">;</span> 61 62 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 63 <span class="s">}</span> 64 65 <span class="c"># Initialize object data...</span> 66 <span class="c">#</span> <a name="_InitializeFingerprints-"></a> 67 <span class="k">sub </span><span class="m">_InitializeFingerprints</span> <span class="s">{</span> 68 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 69 70 <span class="c"># Molecule object...</span> 71 <span class="i">$This</span>->{<span class="w">Molecule</span>} = <span class="q">''</span><span class="sc">;</span> 72 73 <span class="c"># Type of fingerprints...</span> 74 <span class="i">$This</span>->{<span class="w">Type</span>} = <span class="q">''</span><span class="sc">;</span> 75 76 <span class="c"># Type of fingerprints vector: FingerprintsBitVector or FingerprintsVector...</span> 77 <span class="i">$This</span>->{<span class="w">VectorType</span>} = <span class="q">''</span><span class="sc">;</span> 78 79 <span class="c"># Marks successful generation of fingerprints...</span> 80 <span class="i">$This</span>->{<span class="w">FingerprintsGenerated</span>} = <span class="n">0</span><span class="sc">;</span> 81 82 <span class="c"># Initialize values for FingerprintsBitVector...</span> 83 <span class="i">_InitializeClassValuesForFingerprintsBitVector</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 84 85 <span class="c"># Initialize values for FingerprintsVector...</span> 86 <span class="i">_InitializeClassValuesForFingerprintsVector</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 87 <span class="s">}</span> 88 89 <span class="c"># Initialize class ...</span> <a name="_InitializeClass-"></a> 90 <span class="k">sub </span><span class="m">_InitializeClass</span> <span class="s">{</span> 91 <span class="c">#Class name...</span> 92 <span class="i">$ClassName</span> = <span class="w">__PACKAGE__</span><span class="sc">;</span> 93 <span class="s">}</span> 94 95 <span class="c"># Initialize class values specific to FingerprintsBitVector...</span> 96 <span class="c">#</span> <a name="_InitializeClassValuesForFingerprintsBitVector-"></a> 97 <span class="k">sub </span><span class="m">_InitializeClassValuesForFingerprintsBitVector</span> <span class="s">{</span> 98 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 99 100 <span class="c"># Size of FingerprintsBitVector...</span> 101 <span class="i">$This</span>->{<span class="w">Size</span>} = <span class="q">''</span><span class="sc">;</span> 102 103 <span class="c"># Min/Max sizes used for folding FingerprintsBitVector...</span> 104 <span class="i">$This</span>->{<span class="w">MinSize</span>} = <span class="q">''</span><span class="sc">;</span> 105 <span class="i">$This</span>->{<span class="w">MaxSize</span>} = <span class="q">''</span><span class="sc">;</span> 106 107 <span class="c"># FingerprintsBitVector...</span> 108 <span class="i">$This</span>->{<span class="w">FingerprintsBitVector</span>} = <span class="q">''</span><span class="sc">;</span> 109 <span class="s">}</span> 110 111 <span class="c"># Initialize class values specific to FingerprintsVector...</span> 112 <span class="c">#</span> <a name="_InitializeClassValuesForFingerprintsVector-"></a> 113 <span class="k">sub </span><span class="m">_InitializeClassValuesForFingerprintsVector</span> <span class="s">{</span> 114 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 115 116 <span class="c"># Types of FingerprintsVector values: OrderedNumericalValues, NumericalValues or AlphaNumericalValues.</span> 117 <span class="i">$This</span>->{<span class="w">FingerprintsVectorType</span>} = <span class="q">''</span><span class="sc">;</span> 118 119 <span class="c"># Fingerprints vector...</span> 120 <span class="i">$This</span>->{<span class="w">FingerprintsVector</span>} = <span class="q">''</span><span class="sc">;</span> 121 <span class="s">}</span> 122 123 <span class="c"># Initialize object properties....</span> <a name="_InitializeFingerprintsProperties-"></a> 124 <span class="k">sub </span><span class="m">_InitializeFingerprintsProperties</span> <span class="s">{</span> 125 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 126 127 <span class="k">my</span><span class="s">(</span><span class="i">$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> 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> 129 <span class="i">$MethodName</span> = <span class="q">"Set${Name}"</span><span class="sc">;</span> 130 <span class="i">$This</span><span class="i">->$MethodName</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="sc">;</span> 131 <span class="s">}</span> 132 133 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 134 <span class="s">}</span> 135 136 <span class="c"># Set molecule object and make sure it's not already set...</span> 137 <span class="c">#</span> <a name="SetMolecule-"></a> 138 <span class="k">sub </span><span class="m">SetMolecule</span> <span class="s">{</span> 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> 140 141 <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> 142 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetMolecule: Can't change molecule object: It's already set..."</span><span class="sc">;</span> 143 <span class="s">}</span> 144 <span class="i">$This</span>->{<span class="w">Molecule</span>} = <span class="i">$Molecule</span><span class="sc">;</span> 145 146 <span class="c"># Weaken the reference to disable increment of reference count...</span> 147 <span class="i">Scalar::Util::weaken</span><span class="s">(</span><span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="s">)</span><span class="sc">;</span> 148 149 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 150 <span class="s">}</span> 151 152 <span class="c"># Set type and make sure it's not already set...</span> 153 <span class="c">#</span> <a name="SetType-"></a> 154 <span class="k">sub </span><span class="m">SetType</span> <span class="s">{</span> 155 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Type</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 156 157 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">Type</span>}<span class="s">)</span> <span class="s">{</span> 158 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetType: Can't change fingerprint type: It's already set..."</span><span class="sc">;</span> 159 <span class="s">}</span> 160 <span class="i">$This</span>->{<span class="w">Type</span>} = <span class="i">$Type</span><span class="sc">;</span> 161 162 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 163 <span class="s">}</span> 164 165 <span class="c"># Is fingerprints generation successful?</span> 166 <span class="c">#</span> 167 <span class="c"># Notes:</span> 168 <span class="c"># . The specific fingerprints generation class sets the value of FingerprinsGenerated</span> 169 <span class="c"># to 1 after the successful generation of fingerprints; otherwise, it's set to 0.</span> 170 <span class="c">#</span> <a name="IsFingerprintsGenerationSuccessful-"></a> 171 <span class="k">sub </span><span class="m">IsFingerprintsGenerationSuccessful</span> <span class="s">{</span> 172 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 173 174 <span class="k">return</span> <span class="i">$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> 175 <span class="s">}</span> 176 177 <span class="c"># Set vector type and make sure it's not already set...</span> 178 <span class="c">#</span> <a name="SetVectorType-"></a> 179 <span class="k">sub </span><span class="m">SetVectorType</span> <span class="s">{</span> 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> 181 182 <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> 183 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetVectorType: Can't change fingerprint vector type: It's already set..."</span><span class="sc">;</span> 184 <span class="s">}</span> 185 <span class="k">if</span> <span class="s">(</span><span class="i">$VectorType</span> !~ <span class="q">/^(FingerprintsBitVector|FingerprintsVector)$/i</span><span class="s">)</span> <span class="s">{</span> 186 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetVectorType: Specified value, $VectorType, for Type is not vaild. Supported types in current release of MayaChemTools: FingerprintsBitVector and FingerprintsVector..."</span><span class="sc">;</span> 187 <span class="s">}</span> 188 <span class="i">$This</span>->{<span class="w">VectorType</span>} = <span class="i">$VectorType</span><span class="sc">;</span> 189 190 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 191 <span class="s">}</span> 192 193 <span class="c">#</span> 194 <span class="c"># Methods/functions for FingerprintsBitVector...</span> 195 <span class="c">#</span> 196 197 <span class="c"># Initialize fingerprint bit vector...</span> <a name="_InitializeFingerprintsBitVector-"></a> 198 <span class="k">sub </span><span class="m">_InitializeFingerprintsBitVector</span> <span class="s">{</span> 199 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 200 201 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">VectorType</span>} !~ <span class="q">/^FingerprintsBitVector$/i</span><span class="s">)</span> <span class="s">{</span> 202 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->_InitializeFingerprintsBitVector: Can't initialize fingerprints bit vector: VectorType must be FingerprintsBitVector..."</span><span class="sc">;</span> 203 <span class="s">}</span> 204 205 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">Size</span>}<span class="s">)</span> <span class="s">{</span> 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> 207 <span class="s">}</span> 208 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 209 <span class="s">}</span> 210 211 <span class="c"># Set size...</span> 212 <span class="c">#</span> <a name="SetSize-"></a> 213 <span class="k">sub </span><span class="m">SetSize</span> <span class="s">{</span> 214 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Size</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 215 216 <span class="k">if</span> <span class="s">(</span><span class="i">$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> 217 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetSize: Fingerprint size value, $Size, is not valid : It must be >= $This->{MinSize}..."</span><span class="sc">;</span> 218 <span class="s">}</span> 219 <span class="k">if</span> <span class="s">(</span><span class="i">$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> 220 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetSize: Fingerprint size value, $Size, is not valid: It must be <= $This->{MaxSize}..."</span><span class="sc">;</span> 221 <span class="s">}</span> 222 223 <span class="i">$This</span>->{<span class="w">Size</span>} = <span class="i">$Size</span><span class="sc">;</span> 224 225 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 226 <span class="s">}</span> 227 228 <span class="c"># Set FingerprintsBitVector object and make sure it's not already set...</span> 229 <span class="c">#</span> <a name="SetFingerprintsBitVector-"></a> 230 <span class="k">sub </span><span class="m">SetFingerprintsBitVector</span> <span class="s">{</span> 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> 232 233 <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> 234 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetFingerprintsBitVector: Can't change FingerprintsBitVector object: It's already set..."</span><span class="sc">;</span> 235 <span class="s">}</span> 236 <span class="i">$This</span>->{<span class="w">FingerprintsBitVector</span>} = <span class="i">$FingerprintsBitVector</span><span class="sc">;</span> 237 238 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 239 <span class="s">}</span> 240 241 <span class="c"># Fold fingerprints by recursively reducing its size by half untill bit density is greater than or equal to</span> 242 <span class="c"># specified bit density...</span> 243 <span class="c">#</span> <a name="FoldFingerprintsByBitDensity-"></a> 244 <span class="k">sub </span><span class="m">FoldFingerprintsByBitDensity</span> <span class="s">{</span> 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> 246 247 <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> 248 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->FoldFingerprintsByBitDensity: Specified bit density, $BitDensity, is not valid: It must be > 0 && <= 1 ..."</span><span class="sc">;</span> 249 <span class="s">}</span> 250 251 <span class="k">return</span> <span class="i">$This</span><span class="i">->_FoldFingerprintsBitVector</span><span class="s">(</span><span class="q">'ByDensity'</span><span class="cm">,</span> <span class="i">$BitDensity</span><span class="s">)</span><span class="sc">;</span> 252 <span class="s">}</span> 253 254 <span class="c"># Fold fingerprints by recursively reducing its size by half untill size is less than or equal to</span> 255 <span class="c"># specified size...</span> 256 <span class="c">#</span> <a name="FoldFingerprintsBySize-"></a> 257 <span class="k">sub </span><span class="m">FoldFingerprintsBySize</span> <span class="s">{</span> 258 <span class="k">my</span><span class="s">(</span><span class="i">$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> 259 260 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$CheckSizeValue</span><span class="s">)</span> <span class="s">{</span> 261 <span class="i">$CheckSizeValue</span> = <span class="n">1</span><span class="sc">;</span> 262 <span class="s">}</span> 263 264 <span class="k">if</span> <span class="s">(</span><span class="i">$CheckSizeValue</span><span class="s">)</span> <span class="s">{</span> 265 <span class="k">if</span> <span class="s">(</span>!<span class="i">TextUtil::IsPositiveInteger</span><span class="s">(</span><span class="i">$Size</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 266 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->FoldFingerprintsBySize: Specified size, $Size, is not valid: It must be a positive integer"</span><span class="sc">;</span> 267 <span class="s">}</span> 268 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="i">$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> 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 $This->{Size}..."</span><span class="sc">;</span> 270 <span class="s">}</span> 271 <span class="k">if</span> <span class="s">(</span>!<span class="i">TextUtil::IsNumberPowerOfNumber</span><span class="s">(</span><span class="i">$Size</span><span class="cm">,</span> <span class="n">2</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 272 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->FoldFingerprintsBySize: Specified size value, $Size, must be power of 2..."</span><span class="sc">;</span> 273 <span class="s">}</span> 274 <span class="s">}</span> 275 276 <span class="k">return</span> <span class="i">$This</span><span class="i">->_FoldFingerprintsBitVector</span><span class="s">(</span><span class="q">'BySize'</span><span class="cm">,</span> <span class="i">$Size</span><span class="s">)</span><span class="sc">;</span> 277 <span class="s">}</span> 278 279 <span class="c"># Fold fingerprints bit vector using specified size of bit density...</span> 280 <span class="c">#</span> <a name="_FoldFingerprintsBitVector-"></a> 281 <span class="k">sub </span><span class="m">_FoldFingerprintsBitVector</span> <span class="s">{</span> 282 <span class="k">my</span><span class="s">(</span><span class="i">$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> 283 284 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span>->{<span class="w">FingerprintsBitVector</span>}<span class="s">)</span> <span class="s">{</span> 285 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 286 <span class="s">}</span> 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> 288 289 <span class="i">$FoldedFingerprintsBitVector</span> = <span class="q">''</span><span class="sc">;</span> 290 <span class="i">$FingerprintsBitVector</span> = <span class="i">$This</span>->{<span class="w">FingerprintsBitVector</span>}<span class="sc">;</span> 291 <span class="j">MODE:</span> <span class="s">{</span> 292 <span class="k">if</span> <span class="s">(</span><span class="i">$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> 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">$Value</span><span class="s">)</span><span class="sc">;</span> <span class="k">last</span> <span class="j">MODE</span><span class="sc">;</span> <span class="s">}</span> 294 <span class="i">$FoldedFingerprintsBitVector</span> = <span class="q">''</span><span class="sc">;</span> 295 <span class="s">}</span> 296 <span class="k">if</span> <span class="s">(</span><span class="i">$FoldedFingerprintsBitVector</span><span class="s">)</span> <span class="s">{</span> 297 <span class="i">$This</span>->{<span class="w">FingerprintsBitVector</span>} = <span class="i">$FoldedFingerprintsBitVector</span><span class="sc">;</span> 298 <span class="i">$This</span>->{<span class="w">Size</span>} = <span class="i">$FoldedFingerprintsBitVector</span><span class="i">->GetSize</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 299 <span class="s">}</span> 300 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 301 <span class="s">}</span> 302 303 <span class="c"># Get fingerprints as a binary ascii string containing 0s and 1s...</span> 304 <span class="c">#</span> <a name="GetFingerprintBitsAsBinaryString-"></a> 305 <span class="k">sub </span><span class="m">GetFingerprintBitsAsBinaryString</span> <span class="s">{</span> 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> 307 308 <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> 309 <span class="s">}</span> 310 311 <span class="c"># Get fingerprints as a hexadecimal string...</span> 312 <span class="c">#</span> <a name="GetFingerprintBitsAsHexadecimalString-"></a> 313 <span class="k">sub </span><span class="m">GetFingerprintBitsAsHexadecimalString</span> <span class="s">{</span> 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> 315 316 <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> 317 <span class="s">}</span> 318 319 <span class="c"># Get fingerprints as a raw binary string containing packed bit values for each</span> 320 <span class="c"># byte...</span> 321 <span class="c">#</span> <a name="GetFingerprintBitsAsRawBinaryString-"></a> 322 <span class="k">sub </span><span class="m">GetFingerprintBitsAsRawBinaryString</span> <span class="s">{</span> 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> 324 325 <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> 326 <span class="s">}</span> 327 328 <span class="c"># Get fingerprint bits as a string...</span> 329 <span class="c">#</span> <a name="_GetFingerprintBitsAsString-"></a> 330 <span class="k">sub </span><span class="m">_GetFingerprintBitsAsString</span> <span class="s">{</span> 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> 332 333 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span>->{<span class="w">FingerprintsBitVector</span>}<span class="s">)</span> <span class="s">{</span> 334 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> 335 <span class="s">}</span> 336 <span class="j">FORMAT :</span> <span class="s">{</span> 337 <span class="k">if</span> <span class="s">(</span><span class="i">$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> 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">$This</span>->{<span class="w">FingerprintsBitVector</span>}<span class="i">->GetBitsAsHexadecimalString</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> <span class="k">last</span> <span class="j">FORMAT</span><span class="sc">;</span> <span class="s">}</span> 339 <span class="k">if</span> <span class="s">(</span><span class="i">$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> 340 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->_GetFingerprintBitsAsString: Specified bit vector string format, $Format, is not supported. Value values: Binary, Bin, BinaryString, Hexdecimal, Hex, HexadecimalString, RawBinary, RawBin, RawBinaryString..."</span><span class="sc">;</span> 341 <span class="s">}</span> 342 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> 343 <span class="s">}</span> 344 345 <span class="c">#</span> 346 <span class="c"># Methods/functions for FingerprintsVector...</span> 347 <span class="c">#</span> 348 349 <span class="c"># Initialize fingerprint vector...</span> <a name="_InitializeFingerprintsVector-"></a> 350 <span class="k">sub </span><span class="m">_InitializeFingerprintsVector</span> <span class="s">{</span> 351 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 352 353 <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> 354 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->_InitializeFingerprintsVector: Can't initialize fingerprints vector: VectorType must be FingerprintsVector..."</span><span class="sc">;</span> 355 <span class="s">}</span> 356 357 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">FingerprintsVectorType</span>}<span class="s">)</span> <span class="s">{</span> 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> 359 <span class="s">}</span> 360 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 361 <span class="s">}</span> 362 363 <span class="c"># Set FingerprintsVector object and make sure it's not already set...</span> 364 <span class="c">#</span> <a name="SetFingerprintsVector-"></a> 365 <span class="k">sub </span><span class="m">SetFingerprintsVector</span> <span class="s">{</span> 366 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$FingerprintsVector</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 367 368 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">FingerprintsVector</span>}<span class="s">)</span> <span class="s">{</span> 369 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetFingerprintsVector: Can't change FingerprintsVector object: It's already set..."</span><span class="sc">;</span> 370 <span class="s">}</span> 371 <span class="i">$This</span>->{<span class="w">FingerprintsVector</span>} = <span class="i">$FingerprintsVector</span><span class="sc">;</span> 372 373 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 374 <span class="s">}</span> 375 376 <span class="c"># Types of FingerprintsVector values: OrderedNumericalValues, NumericalValues or AlphaNumericalValues.</span> 377 <span class="c">#</span> <a name="SetFingerprintsVectorType-"></a> 378 <span class="k">sub </span><span class="m">SetFingerprintsVectorType</span> <span class="s">{</span> 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> 380 381 <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> 382 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetFingerprintsVector: Can't change FingerprintsVectorType: It's already set..."</span><span class="sc">;</span> 383 <span class="s">}</span> 384 <span class="k">if</span> <span class="s">(</span><span class="i">$FingerprintsVectorType</span> !~ <span class="q">/^(OrderedNumericalValues|NumericalValues|AlphaNumericalValues)$/i</span><span class="s">)</span> <span class="s">{</span> 385 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetFingerprintsVectorType: Specified value, $FingerprintsVectorType, for Type is not vaild. Supported types in current release of MayaChemTools: OrderedNumericalValues, NumericalValues or AlphaNumericalValues"</span><span class="sc">;</span> 386 <span class="s">}</span> 387 <span class="i">$This</span>->{<span class="w">FingerprintsVectorType</span>} = <span class="i">$FingerprintsVectorType</span><span class="sc">;</span> 388 389 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 390 <span class="s">}</span> 391 392 <span class="c"># Get fingerprints vector values as an array or reference to an array...</span> 393 <span class="c">#</span> <a name="GetFingerprintsVectorValues-"></a> 394 <span class="k">sub </span><span class="m">GetFingerprintsVectorValues</span> <span class="s">{</span> 395 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 396 397 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span>->{<span class="w">FingerprintsVector</span>}<span class="s">)</span> <span class="s">{</span> 398 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> 399 <span class="s">}</span> 400 <span class="k">return</span> <span class="i">$This</span>->{<span class="w">FingerprintsVector</span>}<span class="i">->GetValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 401 <span class="s">}</span> 402 403 <span class="c"># Get fingerprints vector value IDs as an array or reference to an array...</span> 404 <span class="c">#</span> <a name="GetFingerprintsVectorValueIDs-"></a> 405 <span class="k">sub </span><span class="m">GetFingerprintsVectorValueIDs</span> <span class="s">{</span> 406 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 407 408 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span>->{<span class="w">FingerprintsVector</span>}<span class="s">)</span> <span class="s">{</span> 409 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> 410 <span class="s">}</span> 411 <span class="k">return</span> <span class="i">$This</span>->{<span class="w">FingerprintsVector</span>}<span class="i">->GetValueIDs</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 412 <span class="s">}</span> 413 <a name="EOF-"></a></pre> <p> </p> <br /> <center> <img src="../../../images/h2o2.png"> </center> </body> </html>