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<html> <head> <title>MayaChemTools:Code:MolecularDescriptors::WeightAndMassDescriptors.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::WeightAndMassDescriptors-"></a> 1 <span class="k">package </span><span class="i">MolecularDescriptors::WeightAndMassDescriptors</span><span class="sc">;</span> 2 <span class="c">#</span> 3 <span class="c"># $RCSfile: WeightAndMassDescriptors.pm,v $</span> 4 <span class="c"># $Date: 2015/02/28 20:49:20 $</span> 5 <span class="c"># $Revision: 1.10 $</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">TextUtil</span> <span class="s">(</span><span class="s">)</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">Atom</span><span class="sc">;</span> 36 <span class="k">use</span> <span class="w">Molecule</span><span class="sc">;</span> 37 <span class="k">use</span> <span class="w">MolecularDescriptors::MolecularDescriptors</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(MolecularDescriptors::MolecularDescriptors 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(GetDescriptorNames)</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="cm">,</span> <span class="i">@DescriptorNames</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"># Overload Perl functions...</span> 52 <span class="k">use</span> <span class="w">overload</span> <span class="q">'""'</span> <span class="cm">=></span> <span class="q">'StringifyWeightAndMassDescriptors'</span><span class="sc">;</span> 53 54 <span class="c"># Class constructor...</span> <a name="new-"></a> 55 <span class="k">sub </span><span class="m">new</span> <span class="s">{</span> 56 <span class="k">my</span><span class="s">(</span><span class="i">$Class</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 57 58 <span class="c"># Initialize object...</span> 59 <span class="k">my</span> <span class="i">$This</span> = <span class="i">$Class</span><span class="i">->SUPER::new</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 60 <span class="k">bless</span> <span class="i">$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> 61 <span class="i">$This</span><span class="i">->_InitializeWeightAndMassDescriptors</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 62 63 <span class="i">$This</span><span class="i">->_InitializeWeightAndMassDescriptorsProperties</span><span class="s">(</span><span class="i">%NamesAndValues</span><span class="s">)</span><span class="sc">;</span> 64 65 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 66 <span class="s">}</span> 67 68 <span class="c"># Initialize class ...</span> <a name="_InitializeClass-"></a> 69 <span class="k">sub </span><span class="m">_InitializeClass</span> <span class="s">{</span> 70 <span class="c">#Class name...</span> 71 <span class="i">$ClassName</span> = <span class="w">__PACKAGE__</span><span class="sc">;</span> 72 73 <span class="c"># Descriptor names...</span> 74 <span class="i">@DescriptorNames</span> = <span class="s">(</span><span class="q">'MolecularWeight'</span><span class="cm">,</span> <span class="q">'ExactMass'</span><span class="s">)</span><span class="sc">;</span> 75 76 <span class="s">}</span> 77 78 <span class="c"># Get descriptor names as an array.</span> 79 <span class="c">#</span> 80 <span class="c"># This functionality can be either invoked as a class function or an</span> 81 <span class="c"># object method.</span> 82 <span class="c">#</span> <a name="GetDescriptorNames-"></a> 83 <span class="k">sub </span><span class="m">GetDescriptorNames</span> <span class="s">{</span> 84 <span class="k">return</span> <span class="i">@DescriptorNames</span><span class="sc">;</span> 85 <span class="s">}</span> 86 87 <span class="c"># Initialize object data...</span> 88 <span class="c">#</span> <a name="_InitializeWeightAndMassDescriptors-"></a> 89 <span class="k">sub </span><span class="m">_InitializeWeightAndMassDescriptors</span> <span class="s">{</span> 90 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 91 92 <span class="c"># Type of MolecularDescriptor...</span> 93 <span class="i">$This</span>->{<span class="w">Type</span>} = <span class="q">'WeightAndMass'</span><span class="sc">;</span> 94 95 <span class="c"># Precision for molecular weight and exact mass values...</span> 96 <span class="i">$This</span>->{<span class="w">WeightPrecision</span>} = <span class="n">2</span><span class="sc">;</span> 97 <span class="i">$This</span>->{<span class="w">MassPrecision</span>} = <span class="n">4</span><span class="sc">;</span> 98 99 <span class="c"># Intialize descriptor names and values...</span> 100 <span class="i">$This</span><span class="i">->_InitializeDescriptorNamesAndValues</span><span class="s">(</span><span class="i">@DescriptorNames</span><span class="s">)</span><span class="sc">;</span> 101 102 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 103 <span class="s">}</span> 104 105 <span class="c"># Initialize object properties...</span> 106 <span class="c">#</span> <a name="_InitializeWeightAndMassDescriptorsProperties-"></a> 107 <span class="k">sub </span><span class="m">_InitializeWeightAndMassDescriptorsProperties</span> <span class="s">{</span> 108 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 109 110 <span class="k">my</span><span class="s">(</span><span class="i">$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> 111 <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> 112 <span class="i">$MethodName</span> = <span class="q">"Set${Name}"</span><span class="sc">;</span> 113 <span class="i">$This</span><span class="i">->$MethodName</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="sc">;</span> 114 <span class="s">}</span> 115 116 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 117 <span class="s">}</span> 118 119 <span class="c"># Set weight precision for moelcular weight...</span> 120 <span class="c">#</span> <a name="SetWeightPrecision-"></a> 121 <span class="k">sub </span><span class="m">SetWeightPrecision</span> <span class="s">{</span> 122 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 123 124 <span class="k">if</span> <span class="s">(</span>!<span class="i">TextUtil::IsInteger</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 125 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetWeightPrecision: WeightPrecision value, $Value, is not valid: It must be a an integer..."</span><span class="sc">;</span> 126 <span class="s">}</span> 127 <span class="i">$This</span>->{<span class="w">WeightPrecision</span>} = <span class="i">$Value</span><span class="sc">;</span> 128 129 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 130 <span class="s">}</span> 131 132 <span class="c"># Set mass precision for exact weight...</span> 133 <span class="c">#</span> <a name="SetMassPrecision-"></a> 134 <span class="k">sub </span><span class="m">SetMassPrecision</span> <span class="s">{</span> 135 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 136 137 <span class="k">if</span> <span class="s">(</span>!<span class="i">TextUtil::IsInteger</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 138 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetMassPrecision: MassPrecision value, $Value, is not valid: It must be a an integer..."</span><span class="sc">;</span> 139 <span class="s">}</span> 140 <span class="i">$This</span>->{<span class="w">MassPrecision</span>} = <span class="i">$Value</span><span class="sc">;</span> 141 142 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 143 <span class="s">}</span> 144 145 <span class="c"># Generate molecular weight and exact mass values...</span> 146 <span class="c">#</span> <a name="GenerateDescriptors-"></a> 147 <span class="k">sub </span><span class="m">GenerateDescriptors</span> <span class="s">{</span> 148 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 149 150 <span class="c"># Initialize descriptor values...</span> 151 <span class="i">$This</span><span class="i">->_InitializeDescriptorValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 152 153 <span class="c"># Check availability of molecule...</span> 154 <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 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->GenerateDescriptors: $This->{Type} molecular descriptors generation didn't succeed: Molecule data is not available: Molecule object hasn't been set..."</span><span class="sc">;</span> 156 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> 157 <span class="s">}</span> 158 159 <span class="c"># Calculate descriptor values...</span> 160 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->_CalculateDescriptorValues</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 161 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->GenerateDescriptors: $This->{Type} molecular descriptors generation didn't succeed..."</span><span class="sc">;</span> 162 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> 163 <span class="s">}</span> 164 165 <span class="c"># Set final descriptor values...</span> 166 <span class="i">$This</span><span class="i">->_SetFinalDescriptorValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 167 168 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 169 <span class="s">}</span> 170 171 <span class="c"># Calculate molecular weight and exact mass values..</span> 172 <span class="c">#</span> <a name="_CalculateDescriptorValues-"></a> 173 <span class="k">sub </span><span class="m">_CalculateDescriptorValues</span> <span class="s">{</span> 174 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 175 <span class="k">my</span><span class="s">(</span><span class="i">$MolecularWeight</span><span class="cm">,</span> <span class="i">$ExactMass</span><span class="s">)</span><span class="sc">;</span> 176 177 <span class="i">$MolecularWeight</span> = <span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="i">->GetMolecularWeight</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 178 <span class="i">$ExactMass</span> = <span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="i">->GetExactMass</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 179 180 <span class="c"># Track values...</span> 181 <span class="i">$This</span>->{<span class="w">MolecularWeight</span>} = <span class="i">MathUtil::round</span><span class="s">(</span><span class="i">$MolecularWeight</span><span class="cm">,</span> <span class="i">$This</span>->{<span class="w">WeightPrecision</span>}<span class="s">)</span><span class="sc">;</span> 182 <span class="i">$This</span>->{<span class="w">ExactMass</span>} = <span class="i">MathUtil::round</span><span class="s">(</span><span class="i">$ExactMass</span><span class="cm">,</span> <span class="i">$This</span>->{<span class="w">MassPrecision</span>}<span class="s">)</span><span class="sc">;</span> 183 184 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 185 <span class="s">}</span> 186 187 <span class="c"># Setup final descriptor values...</span> 188 <span class="c">#</span> <a name="_SetFinalDescriptorValues-"></a> 189 <span class="k">sub </span><span class="m">_SetFinalDescriptorValues</span> <span class="s">{</span> 190 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 191 192 <span class="i">$This</span>->{<span class="w">DescriptorsGenerated</span>} = <span class="n">1</span><span class="sc">;</span> 193 194 <span class="i">$This</span><span class="i">->SetDescriptorValues</span><span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularWeight</span>}<span class="cm">,</span> <span class="i">$This</span>->{<span class="w">ExactMass</span>}<span class="s">)</span><span class="sc">;</span> 195 196 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 197 <span class="s">}</span> 198 199 <span class="c"># Return a string containg data for WeightAndMassDescriptors object...</span> 200 <span class="c">#</span> <a name="StringifyWeightAndMassDescriptors-"></a> 201 <span class="k">sub </span><span class="m">StringifyWeightAndMassDescriptors</span> <span class="s">{</span> 202 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 203 <span class="k">my</span><span class="s">(</span><span class="i">$TheString</span><span class="s">)</span><span class="sc">;</span> 204 205 <span class="i">$TheString</span> = <span class="q">"MolecularDescriptorType: $This->{Type}; "</span> . <span class="i">$This</span><span class="i">->_StringifyDescriptorNamesAndValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 206 207 <span class="k">return</span> <span class="i">$TheString</span><span class="sc">;</span> 208 <span class="s">}</span> 209 210 <span class="c"># Is it a WeightAndMassDescriptors object?</span> <a name="_IsWeightAndMassDescriptors-"></a> 211 <span class="k">sub </span><span class="m">_IsWeightAndMassDescriptors</span> <span class="s">{</span> 212 <span class="k">my</span><span class="s">(</span><span class="i">$Object</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 213 214 <span class="k">return</span> <span class="s">(</span><span class="i">Scalar::Util::blessed</span><span class="s">(</span><span class="i">$Object</span><span class="s">)</span> && <span class="i">$Object</span><span class="i">->isa</span><span class="s">(</span><span class="i">$ClassName</span><span class="s">)</span><span class="s">)</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 <a name="EOF-"></a></pre> <p> </p> <br /> <center> <img src="../../../images/h2o2.png"> </center> </body> </html>