diff mayachemtools/docs/modules/html/code/RingsCountDescriptors.html @ 0:73ae111cf86f draft

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+<a name="package-MolecularDescriptors::RingsCountDescriptors-"></a>   1 <span class="k">package </span><span class="i">MolecularDescriptors::RingsCountDescriptors</span><span class="sc">;</span>
+   2 <span class="c">#</span>
+   3 <span class="c"># $RCSfile: RingsCountDescriptors.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">Molecule</span><span class="sc">;</span>
+  34 <span class="k">use</span> <span class="w">MolecularDescriptors::MolecularDescriptors</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(MolecularDescriptors::MolecularDescriptors 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(GetDescriptorNames)</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">=&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>
+  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="cm">,</span> <span class="i">@DescriptorNames</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"># Overload Perl functions...</span>
+  49 <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;StringifyRingsCountDescriptors&#39;</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="i">$Class</span><span class="i">-&gt;SUPER::new</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+  57   <span class="k">bless</span> <span class="i">$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">$This</span><span class="i">-&gt;_InitializeRingsCountDescriptors</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+  59 
+  60   <span class="i">$This</span><span class="i">-&gt;_InitializeRingsCountDescriptorsProperties</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">$This</span><span class="sc">;</span>
+  63 <span class="s">}</span>
+  64 
+  65 <span class="c"># Initialize class ...</span>
+<a name="_InitializeClass-"></a>  66 <span class="k">sub </span><span class="m">_InitializeClass</span> <span class="s">{</span>
+  67   <span class="c">#Class name...</span>
+  68   <span class="i">$ClassName</span> = <span class="w">__PACKAGE__</span><span class="sc">;</span>
+  69 
+  70   <span class="c"># Descriptor names...</span>
+  71   <span class="i">@DescriptorNames</span> = <span class="s">(</span><span class="q">&#39;Rings&#39;</span><span class="cm">,</span> <span class="q">&#39;AromaticRings&#39;</span><span class="s">)</span><span class="sc">;</span>
+  72 
+  73 <span class="s">}</span>
+  74 
+  75 <span class="c"># Get descriptor names as an array.</span>
+  76 <span class="c">#</span>
+  77 <span class="c"># This functionality can be either invoked as a class function or an</span>
+  78 <span class="c"># object method.</span>
+  79 <span class="c">#</span>
+<a name="GetDescriptorNames-"></a>  80 <span class="k">sub </span><span class="m">GetDescriptorNames</span> <span class="s">{</span>
+  81   <span class="k">return</span> <span class="i">@DescriptorNames</span><span class="sc">;</span>
+  82 <span class="s">}</span>
+  83 
+  84 <span class="c"># Initialize object data...</span>
+  85 <span class="c">#</span>
+<a name="_InitializeRingsCountDescriptors-"></a>  86 <span class="k">sub </span><span class="m">_InitializeRingsCountDescriptors</span> <span class="s">{</span>
+  87   <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+  88 
+  89   <span class="c"># Type of MolecularDescriptor...</span>
+  90   <span class="i">$This</span>-&gt;{<span class="w">Type</span>} = <span class="q">&#39;RingsCount&#39;</span><span class="sc">;</span>
+  91 
+  92   <span class="c"># Intialize descriptor names and values...</span>
+  93   <span class="i">$This</span><span class="i">-&gt;_InitializeDescriptorNamesAndValues</span><span class="s">(</span><span class="i">@DescriptorNames</span><span class="s">)</span><span class="sc">;</span>
+  94 
+  95   <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
+  96 <span class="s">}</span>
+  97 
+  98 <span class="c"># Initialize object properties...</span>
+  99 <span class="c">#</span>
+<a name="_InitializeRingsCountDescriptorsProperties-"></a> 100 <span class="k">sub </span><span class="m">_InitializeRingsCountDescriptorsProperties</span> <span class="s">{</span>
+ 101   <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+ 102 
+ 103   <span class="k">my</span><span class="s">(</span><span class="i">$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>
+ 104   <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>
+ 105     <span class="i">$MethodName</span> = <span class="q">&quot;Set${Name}&quot;</span><span class="sc">;</span>
+ 106     <span class="i">$This</span><span class="i">-&gt;$MethodName</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="sc">;</span>
+ 107   <span class="s">}</span>
+ 108 
+ 109   <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
+ 110 <span class="s">}</span>
+ 111 
+ 112 <span class="c"># Generate molecular weight and exact mass values...</span>
+ 113 <span class="c">#</span>
+<a name="GenerateDescriptors-"></a> 114 <span class="k">sub </span><span class="m">GenerateDescriptors</span> <span class="s">{</span>
+ 115   <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+ 116 
+ 117   <span class="c"># Initialize descriptor values...</span>
+ 118   <span class="i">$This</span><span class="i">-&gt;_InitializeDescriptorValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 119 
+ 120   <span class="c"># Check availability of molecule...</span>
+ 121   <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>
+ 122     <span class="w">carp</span> <span class="q">&quot;Warning: ${ClassName}-&gt;GenerateDescriptors: $This-&gt;{Type} molecular descriptors generation didn&#39;t succeed: Molecule data is not available: Molecule object hasn&#39;t been set...&quot;</span><span class="sc">;</span>
+ 123     <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
+ 124   <span class="s">}</span>
+ 125 
+ 126   <span class="c"># Calculate descriptor values...</span>
+ 127   <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">-&gt;_CalculateDescriptorValues</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+ 128     <span class="w">carp</span> <span class="q">&quot;Warning: ${ClassName}-&gt;GenerateDescriptors: $This-&gt;{Type} molecular descriptors generation didn&#39;t succeed...&quot;</span><span class="sc">;</span>
+ 129     <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
+ 130   <span class="s">}</span>
+ 131 
+ 132   <span class="c"># Set final descriptor values...</span>
+ 133   <span class="i">$This</span><span class="i">-&gt;_SetFinalDescriptorValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 134 
+ 135   <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
+ 136 <span class="s">}</span>
+ 137 
+ 138 <span class="c"># Calculate molecular weight and exact mass values..</span>
+ 139 <span class="c">#</span>
+<a name="_CalculateDescriptorValues-"></a> 140 <span class="k">sub </span><span class="m">_CalculateDescriptorValues</span> <span class="s">{</span>
+ 141   <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+ 142   <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>
+ 143 
+ 144   <span class="i">$This</span>-&gt;{<span class="w">Rings</span>} = <span class="i">$This</span>-&gt;{<span class="w">Molecule</span>}<span class="i">-&gt;GetNumOfRings</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 145   <span class="i">$This</span>-&gt;{<span class="w">AromaticRings</span>} = <span class="i">$This</span>-&gt;{<span class="w">Molecule</span>}<span class="i">-&gt;GetNumOfAromaticRings</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 146 
+ 147   <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
+ 148 <span class="s">}</span>
+ 149 
+ 150 <span class="c"># Setup final descriptor values...</span>
+ 151 <span class="c">#</span>
+<a name="_SetFinalDescriptorValues-"></a> 152 <span class="k">sub </span><span class="m">_SetFinalDescriptorValues</span> <span class="s">{</span>
+ 153   <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+ 154 
+ 155   <span class="i">$This</span>-&gt;{<span class="w">DescriptorsGenerated</span>} = <span class="n">1</span><span class="sc">;</span>
+ 156 
+ 157   <span class="i">$This</span><span class="i">-&gt;SetDescriptorValues</span><span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">Rings</span>}<span class="cm">,</span> <span class="i">$This</span>-&gt;{<span class="w">AromaticRings</span>}<span class="s">)</span><span class="sc">;</span>
+ 158 
+ 159   <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
+ 160 <span class="s">}</span>
+ 161 
+ 162 <span class="c"># Return a string containg data for RingsCountDescriptors object...</span>
+ 163 <span class="c">#</span>
+<a name="StringifyRingsCountDescriptors-"></a> 164 <span class="k">sub </span><span class="m">StringifyRingsCountDescriptors</span> <span class="s">{</span>
+ 165   <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+ 166   <span class="k">my</span><span class="s">(</span><span class="i">$TheString</span><span class="s">)</span><span class="sc">;</span>
+ 167 
+ 168   <span class="i">$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>
+ 169 
+ 170   <span class="k">return</span> <span class="i">$TheString</span><span class="sc">;</span>
+ 171 <span class="s">}</span>
+ 172 
+ 173 <span class="c"># Is it a RingsCountDescriptors object?</span>
+<a name="_IsRingsCountDescriptors-"></a> 174 <span class="k">sub </span><span class="m">_IsRingsCountDescriptors</span> <span class="s">{</span>
+ 175   <span class="k">my</span><span class="s">(</span><span class="i">$Object</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+ 176 
+ 177   <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>
+ 178 <span class="s">}</span>
+ 179 
+<a name="EOF-"></a></pre>
+<p>&nbsp;</p>
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