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<html> <head> <title>MayaChemTools:Code:MolecularDescriptors::MolecularDescriptors.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-MolecularDescriptors::MolecularDescriptors-"></a> 1 <span class="k">package </span><span class="i">MolecularDescriptors::MolecularDescriptors</span><span class="sc">;</span> 2 <span class="c">#</span> 3 <span class="c"># $RCSfile: MolecularDescriptors.pm,v $</span> 4 <span class="c"># $Date: 2015/02/28 20:49:20 $</span> 5 <span class="c"># $Revision: 1.14 $</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">TextUtil</span> <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 35 36 <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> 37 38 <span class="i">@ISA</span> = <span class="q">qw(ObjectProperty Exporter)</span><span class="sc">;</span> 39 <span class="i">@EXPORT</span> = <span class="q">qw()</span><span class="sc">;</span> 40 <span class="i">@EXPORT_OK</span> = <span class="q">qw()</span><span class="sc">;</span> 41 42 <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> 43 44 <span class="c"># Setup class variables...</span> 45 <span class="k">my</span><span class="s">(</span><span class="i">$ClassName</span><span class="s">)</span><span class="sc">;</span> 46 <span class="i">_InitializeClass</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 47 48 <span class="c"># Class constructor...</span> <a name="new-"></a> 49 <span class="k">sub </span><span class="m">new</span> <span class="s">{</span> 50 <span class="k">my</span><span class="s">(</span><span class="i">$Class</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 51 52 <span class="c"># Initialize object...</span> 53 <span class="k">my</span> <span class="i">$This</span> = <span class="s">{</span><span class="s">}</span><span class="sc">;</span> 54 <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">$Class</span><span class="sc">;</span> 55 <span class="i">$This</span><span class="i">->_InitializeMolecularDescriptors</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 56 57 <span class="i">$This</span><span class="i">->_InitializeMolecularDescriptorsProperties</span><span class="s">(</span><span class="i">%NamesAndValues</span><span class="s">)</span><span class="sc">;</span> 58 59 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 60 <span class="s">}</span> 61 62 <span class="c"># Initialize object data...</span> 63 <span class="c">#</span> <a name="_InitializeMolecularDescriptors-"></a> 64 <span class="k">sub </span><span class="m">_InitializeMolecularDescriptors</span> <span class="s">{</span> 65 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 66 67 <span class="c"># Molecule object...</span> 68 <span class="i">$This</span>->{<span class="w">Molecule</span>} = <span class="q">''</span><span class="sc">;</span> 69 70 <span class="c"># Type of molecular descriptors...</span> 71 <span class="i">$This</span>->{<span class="w">Type</span>} = <span class="q">''</span><span class="sc">;</span> 72 73 <span class="c"># Names and calculated value of molecular descriptors...</span> 74 <span class="c">#</span> 75 <span class="c"># The specific descriptor class, derived from this base class, populate descriptor names and values</span> 76 <span class="c"># arrays...</span> 77 <span class="c">#</span> 78 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DescriptorNames</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 79 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DescriptorValues</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 80 81 <span class="c"># Marks successful generation of descriptors...</span> 82 <span class="i">$This</span>->{<span class="w">DescriptorsGenerated</span>} = <span class="n">0</span><span class="sc">;</span> 83 84 <span class="s">}</span> 85 86 <span class="c"># Initialize class ...</span> <a name="_InitializeClass-"></a> 87 <span class="k">sub </span><span class="m">_InitializeClass</span> <span class="s">{</span> 88 <span class="c">#Class name...</span> 89 <span class="i">$ClassName</span> = <span class="w">__PACKAGE__</span><span class="sc">;</span> 90 <span class="s">}</span> 91 92 93 <span class="c"># Initialize object properties....</span> <a name="_InitializeMolecularDescriptorsProperties-"></a> 94 <span class="k">sub </span><span class="m">_InitializeMolecularDescriptorsProperties</span> <span class="s">{</span> 95 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 96 97 <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">$MethodName</span><span class="s">)</span><span class="sc">;</span> 98 <span class="k">while</span> <span class="s">(</span><span class="s">(</span><span class="i">$Name</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="k">each</span> <span class="i">%NamesAndValues</span><span class="s">)</span> <span class="s">{</span> 99 <span class="i">$MethodName</span> = <span class="q">"Set${Name}"</span><span class="sc">;</span> 100 <span class="i">$This</span><span class="i">->$MethodName</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="sc">;</span> 101 <span class="s">}</span> 102 103 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 104 <span class="s">}</span> 105 106 <span class="c"># Initialize descriptor names and values...</span> 107 <span class="c">#</span> <a name="_InitializeDescriptorNamesAndValues-"></a> 108 <span class="k">sub </span><span class="m">_InitializeDescriptorNamesAndValues</span> <span class="s">{</span> 109 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">@Names</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 110 111 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DescriptorNames</span>}} = <span class="i">@Names</span><span class="sc">;</span> 112 113 <span class="i">$This</span><span class="i">->_InitializeDescriptorValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 114 115 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 116 <span class="s">}</span> 117 118 <span class="c"># Initialize descriptor values...</span> 119 <span class="c">#</span> <a name="_InitializeDescriptorValues-"></a> 120 <span class="k">sub </span><span class="m">_InitializeDescriptorValues</span> <span class="s">{</span> 121 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 122 123 <span class="i">$This</span>->{<span class="w">DescriptorsGenerated</span>} = <span class="n">0</span><span class="sc">;</span> 124 125 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DescriptorValues</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 126 127 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 128 <span class="s">}</span> 129 130 <span class="c"># Set molecule object...</span> 131 <span class="c">#</span> <a name="SetMolecule-"></a> 132 <span class="k">sub </span><span class="m">SetMolecule</span> <span class="s">{</span> 133 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Molecule</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 134 135 <span class="i">$This</span>->{<span class="w">Molecule</span>} = <span class="i">$Molecule</span><span class="sc">;</span> 136 137 <span class="c"># Weaken the reference to disable increment of reference count...</span> 138 <span class="i">Scalar::Util::weaken</span><span class="s">(</span><span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="s">)</span><span class="sc">;</span> 139 140 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 141 <span class="s">}</span> 142 143 <span class="c"># Set type and make sure it's not already set...</span> 144 <span class="c">#</span> <a name="SetType-"></a> 145 <span class="k">sub </span><span class="m">SetType</span> <span class="s">{</span> 146 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Type</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 147 148 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">Type</span>}<span class="s">)</span> <span class="s">{</span> 149 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetType: Can't change MolecularDescriptors type: It's already set..."</span><span class="sc">;</span> 150 <span class="s">}</span> 151 <span class="i">$This</span>->{<span class="w">Type</span>} = <span class="i">$Type</span><span class="sc">;</span> 152 153 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 154 <span class="s">}</span> 155 156 <span class="c"># Get molecular descriptor names as an array...</span> 157 <span class="c">#</span> <a name="GetDescriptorNames-"></a> 158 <span class="k">sub </span><span class="m">GetDescriptorNames</span> <span class="s">{</span> 159 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 160 161 <span class="k">return</span> <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DescriptorNames</span>}}<span class="sc">;</span> 162 <span class="s">}</span> 163 164 <span class="c"># Set descriptor names...</span> 165 <span class="c">#</span> <a name="SetDescriptorNames-"></a> 166 <span class="k">sub </span><span class="m">SetDescriptorNames</span> <span class="s">{</span> 167 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">@Names</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 168 169 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DescriptorNames</span>}} = <span class="i">@Names</span><span class="sc">;</span> 170 171 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 172 <span class="s">}</span> 173 174 <span class="c"># Add descriptor names...</span> 175 <span class="c">#</span> <a name="AddDescriptorNames-"></a> 176 <span class="k">sub </span><span class="m">AddDescriptorNames</span> <span class="s">{</span> 177 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">@Names</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 178 179 <span class="k">push</span> <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DescriptorNames</span>}}<span class="cm">,</span> <span class="i">@Names</span><span class="sc">;</span> 180 181 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 182 <span class="s">}</span> 183 184 <span class="c"># Set descriptor values...</span> 185 <span class="c">#</span> <a name="SetDescriptorValues-"></a> 186 <span class="k">sub </span><span class="m">SetDescriptorValues</span> <span class="s">{</span> 187 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">@Values</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 188 189 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DescriptorValues</span>}} = <span class="i">@Values</span><span class="sc">;</span> 190 191 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 192 <span class="s">}</span> 193 194 <span class="c"># Add descriptor values...</span> 195 <span class="c">#</span> <a name="AddDescriptorValues-"></a> 196 <span class="k">sub </span><span class="m">AddDescriptorValues</span> <span class="s">{</span> 197 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">@Values</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 198 199 <span class="k">push</span> <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DescriptorValues</span>}}<span class="cm">,</span> <span class="i">@Values</span><span class="sc">;</span> 200 201 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 202 <span class="s">}</span> 203 204 <span class="c"># Is descriptors generation successful?</span> 205 <span class="c">#</span> 206 <span class="c"># Notes:</span> 207 <span class="c"># . The specific molecular descriptor class generation class sets the value of</span> 208 <span class="c"># DescriptorsCalculated to 1 after the successful generation of descriptors;</span> 209 <span class="c"># otherwise, it's set to 0.</span> 210 <span class="c">#</span> <a name="IsDescriptorsGenerationSuccessful-"></a> 211 <span class="k">sub </span><span class="m">IsDescriptorsGenerationSuccessful</span> <span class="s">{</span> 212 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 213 214 <span class="k">return</span> <span class="i">$This</span>->{<span class="w">DescriptorsGenerated</span>} ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> 215 <span class="s">}</span> 216 217 <span class="c"># Get all descriptor values as an array...</span> 218 <span class="c">#</span> <a name="GetDescriptorValues-"></a> 219 <span class="k">sub </span><span class="m">GetDescriptorValues</span> <span class="s">{</span> 220 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 221 222 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">DescriptorsGenerated</span>}<span class="s">)</span> <span class="s">{</span> 223 <span class="k">return</span> <span class="k">wantarray</span> ? <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DescriptorValues</span>}} <span class="co">:</span> <span class="k">scalar</span> <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DescriptorValues</span>}}<span class="sc">;</span> 224 <span class="s">}</span> 225 <span class="k">else</span> <span class="s">{</span> 226 <span class="k">my</span><span class="s">(</span><span class="i">@DescriptorValues</span><span class="s">)</span><span class="sc">;</span> 227 228 <span class="i">@DescriptorValues</span> = <span class="s">(</span><span class="q">'None'</span><span class="s">)</span> x <span class="k">scalar</span> <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DescriptorNames</span>}}<span class="sc">;</span> 229 230 <span class="k">return</span> <span class="k">wantarray</span> ? <span class="i">@DescriptorValues</span> <span class="co">:</span> <span class="k">scalar</span> <span class="i">@DescriptorValues</span><span class="sc">;</span> 231 <span class="s">}</span> 232 <span class="s">}</span> 233 234 <span class="c"># Get descriptor value for a specified descriptor name...</span> 235 <span class="c">#</span> <a name="GetDescriptorValueByName-"></a> 236 <span class="k">sub </span><span class="m">GetDescriptorValueByName</span> <span class="s">{</span> 237 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Name</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 238 <span class="k">my</span><span class="s">(</span><span class="i">%NamesAndValues</span><span class="s">)</span><span class="sc">;</span> 239 240 <span class="i">%NamesAndValues</span> = <span class="i">$This</span><span class="i">->GetDescriptorNamesAndValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 241 242 <span class="k">return</span> <span class="k">exists</span> <span class="i">$NamesAndValues</span>{<span class="i">$Name</span>} ? <span class="i">$NamesAndValues</span>{<span class="i">$Name</span>} <span class="co">:</span> <span class="q">'None'</span><span class="sc">;</span> 243 244 <span class="s">}</span> 245 246 <span class="c"># Get calculated molecular descriptor names sand values as a to a hash with names</span> 247 <span class="c"># and values as key/value pairs...</span> 248 <span class="c">#</span> <a name="GetDescriptorNamesAndValues-"></a> 249 <span class="k">sub </span><span class="m">GetDescriptorNamesAndValues</span> <span class="s">{</span> 250 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 251 <span class="k">my</span><span class="s">(</span><span class="i">%NamesAndValues</span><span class="s">)</span><span class="sc">;</span> 252 253 <span class="i">%NamesAndValues</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 254 <span class="i">@NamesAndValues</span>{ <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DescriptorNames</span>}} } = <span class="i">$This</span><span class="i">->GetDescriptorValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 255 256 <span class="k">return</span> <span class="i">%NamesAndValues</span><span class="sc">;</span> 257 <span class="s">}</span> 258 259 <span class="c"># Return a string containing descriptor names and values...</span> 260 <span class="c">#</span> <a name="_StringifyDescriptorNamesAndValues-"></a> 261 <span class="k">sub </span><span class="m">_StringifyDescriptorNamesAndValues</span> <span class="s">{</span> 262 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 263 <span class="k">my</span><span class="s">(</span><span class="i">$NamesAndValuesString</span><span class="cm">,</span> <span class="i">$Name</span><span class="cm">,</span> <span class="i">$Value</span><span class="cm">,</span> <span class="i">@NamesAndValuesInfo</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span><span class="sc">;</span> 264 265 <span class="i">@NamesAndValuesInfo</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 266 <span class="i">%NamesAndValues</span> = <span class="i">$This</span><span class="i">->GetDescriptorNamesAndValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 267 268 <span class="k">for</span> <span class="i">$Name</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DescriptorNames</span>}}<span class="s">)</span> <span class="s">{</span> 269 <span class="i">$Value</span> = <span class="i">$NamesAndValues</span>{<span class="i">$Name</span>}<span class="sc">;</span> 270 <span class="i">$Value</span> = <span class="s">(</span><span class="i">TextUtil::IsEmpty</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span> || <span class="i">$Value</span> =~ <span class="q">/^None$/i</span><span class="s">)</span> ? <span class="q">'None'</span> <span class="co">:</span> <span class="i">$Value</span><span class="sc">;</span> 271 <span class="k">push</span> <span class="i">@NamesAndValuesInfo</span><span class="cm">,</span> <span class="q">"$Name - $Value"</span><span class="sc">;</span> 272 <span class="s">}</span> 273 <span class="k">if</span> <span class="s">(</span><span class="i">@NamesAndValuesInfo</span><span class="s">)</span> <span class="s">{</span> 274 <span class="i">$NamesAndValuesString</span> = <span class="q">"Names - Values: <"</span> . <span class="i">TextUtil::JoinWords</span><span class="s">(</span>\<span class="i">@NamesAndValuesInfo</span><span class="cm">,</span> <span class="q">", "</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span> . <span class="q">">"</span><span class="sc">;</span> 275 <span class="s">}</span> 276 <span class="k">else</span> <span class="s">{</span> 277 <span class="i">$NamesAndValuesString</span> = <span class="q">"Names - Values: < None>"</span><span class="sc">;</span> 278 <span class="s">}</span> 279 <span class="k">return</span> <span class="i">$NamesAndValuesString</span><span class="sc">;</span> 280 <span class="s">}</span> 281 <a name="EOF-"></a></pre> <p> </p> <br /> <center> <img src="../../../images/h2o2.png"> </center> </body> </html>