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+<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 &lt;msud@san.rr.com&gt;</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 &lt;http://www.gnu.org/licenses/&gt; 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">=&gt;</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">&#39;&quot;&quot;&#39;</span> <span class="cm">=&gt;</span> <span class="q">&#39;StringifyWeightAndMassDescriptors&#39;</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">$Class</span><span class="i">-&gt;SUPER::new</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+  60   <span class="k">bless</span> <span class="i">$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">$This</span><span class="i">-&gt;_InitializeWeightAndMassDescriptors</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+  62 
+  63   <span class="i">$This</span><span class="i">-&gt;_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">&#39;MolecularWeight&#39;</span><span class="cm">,</span> <span class="q">&#39;ExactMass&#39;</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>-&gt;{<span class="w">Type</span>} = <span class="q">&#39;WeightAndMass&#39;</span><span class="sc">;</span>
+  94 
+  95   <span class="c"># Precision for molecular weight and exact mass values...</span>
+  96   <span class="i">$This</span>-&gt;{<span class="w">WeightPrecision</span>} = <span class="n">2</span><span class="sc">;</span>
+  97   <span class="i">$This</span>-&gt;{<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">$This</span><span class="i">-&gt;_InitializeDescriptorNamesAndValues</span><span class="s">(</span><span class="i">@DescriptorNames</span><span class="s">)</span><span class="sc">;</span>
+ 101 
+ 102   <span class="k">return</span> <span class="i">$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">$MethodName</span> = <span class="q">&quot;Set${Name}&quot;</span><span class="sc">;</span>
+ 113     <span class="i">$This</span><span class="i">-&gt;$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">&quot;Error: ${ClassName}-&gt;SetWeightPrecision: WeightPrecision value, $Value, is not valid:  It must be a an integer...&quot;</span><span class="sc">;</span>
+ 126   <span class="s">}</span>
+ 127   <span class="i">$This</span>-&gt;{<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">&quot;Error: ${ClassName}-&gt;SetMassPrecision: MassPrecision value, $Value, is not valid:  It must be a an integer...&quot;</span><span class="sc">;</span>
+ 139   <span class="s">}</span>
+ 140   <span class="i">$This</span>-&gt;{<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">-&gt;_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>-&gt;{<span class="w">Molecule</span>}<span class="s">)</span> <span class="s">{</span>
+ 155     <span class="w">carp</span> <span class="q">&quot;Warning: ${ClassName}-&gt;GenerateDescriptors: $This-&gt;{Type} molecular descriptors generation didn&#39;t succeed: Molecule data is not available: Molecule object hasn&#39;t been set...&quot;</span><span class="sc">;</span>
+ 156     <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
+ 157   <span class="s">}</span>
+ 158 
+ 159   <span class="c"># Calculate descriptor values...</span>
+ 160   <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">-&gt;_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">&quot;Warning: ${ClassName}-&gt;GenerateDescriptors: $This-&gt;{Type} molecular descriptors generation didn&#39;t succeed...&quot;</span><span class="sc">;</span>
+ 162     <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
+ 163   <span class="s">}</span>
+ 164 
+ 165   <span class="c"># Set final descriptor values...</span>
+ 166   <span class="i">$This</span><span class="i">-&gt;_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>-&gt;{<span class="w">Molecule</span>}<span class="i">-&gt;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>-&gt;{<span class="w">Molecule</span>}<span class="i">-&gt;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">$This</span>-&gt;{<span class="w">MolecularWeight</span>} = <span class="i">MathUtil::round</span><span class="s">(</span><span class="i">$MolecularWeight</span><span class="cm">,</span> <span class="i">$This</span>-&gt;{<span class="w">WeightPrecision</span>}<span class="s">)</span><span class="sc">;</span>
+ 182   <span class="i">$This</span>-&gt;{<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>-&gt;{<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">$This</span>-&gt;{<span class="w">DescriptorsGenerated</span>} = <span class="n">1</span><span class="sc">;</span>
+ 193 
+ 194   <span class="i">$This</span><span class="i">-&gt;SetDescriptorValues</span><span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">MolecularWeight</span>}<span class="cm">,</span> <span class="i">$This</span>-&gt;{<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">&quot;MolecularDescriptorType: $This-&gt;{Type}; &quot;</span> . <span class="i">$This</span><span class="i">-&gt;_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">$Object</span><span class="s">)</span> &amp;&amp; <span class="i">$Object</span><span class="i">-&gt;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>&nbsp;</p>
+<br />
+<center>
+<img src="../../../images/h2o2.png">
+</center>
+</body>
+</html>