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+<a name="package-AtomicDescriptors::AtomicDescriptors-"></a>   1 <span class="k">package </span><span class="i">AtomicDescriptors::AtomicDescriptors</span><span class="sc">;</span>
+   2 <span class="c">#</span>
+   3 <span class="c"># $RCSfile: AtomicDescriptors.pm,v $</span>
+   4 <span class="c"># $Date: 2015/02/28 20:47:48 $</span>
+   5 <span class="c"># $Revision: 1.17 $</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">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">=&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="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">$Class</span><span class="cm">,</span> <span class="i">%PropertyNamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+  51 
+  52   <span class="c"># Initialize object...</span>
+  53   <span class="k">my</span> <span class="i">$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">-&gt;_InitializeAtomicDescriptors</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+  56 
+  57   <span class="i">$This</span><span class="i">-&gt;_InitializeAtomicDescriptorsProperties</span><span class="s">(</span><span class="i">%PropertyNamesAndValues</span><span class="s">)</span><span class="sc">;</span>
+  58 
+  59   <span class="k">return</span> <span class="i">$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="_InitializeAtomicDescriptors-"></a>  64 <span class="k">sub </span><span class="m">_InitializeAtomicDescriptors</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>-&gt;{<span class="w">Molecule</span>} = <span class="q">&#39;&#39;</span><span class="sc">;</span>
+  69 
+  70   <span class="c"># Type of atomic descriptors...</span>
+  71   <span class="i">$This</span>-&gt;{<span class="w">Type</span>} = <span class="q">&#39;&#39;</span><span class="sc">;</span>
+  72 
+  73   <span class="c"># By default, atomic decriptor values are also calculated for hydrogens...</span>
+  74   <span class="i">$This</span>-&gt;{<span class="w">IgnoreHydrogens</span>} = <span class="n">0</span><span class="sc">;</span>
+  75 
+  76   <span class="c"># Calculated atomic descriptor values hash. Instead of assigning the calculated values to Atom</span>
+  77   <span class="c"># objects, these values are stored in the current object in a hash with atom ID and atomic descriptor</span>
+  78   <span class="c"># values as key/value pairs.</span>
+  79   <span class="c">#</span>
+  80   <span class="c"># Unlike molecular descriptors, no descriptor names are assigned to individual atomic descriptor</span>
+  81   <span class="c"># values.</span>
+  82   <span class="c">#</span>
+  83   <span class="i">%</span>{<span class="i">$This</span>-&gt;{<span class="w">DescriptorValues</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+  84 <span class="s">}</span>
+  85 
+  86 <span class="c"># Initialize class ...</span>
+<a name="_InitializeClass-"></a>  87 <span class="k">sub </span><span class="m">_InitializeClass</span> <span class="s">{</span>
+  88   <span class="c">#Class name...</span>
+  89   <span class="i">$ClassName</span> = <span class="w">__PACKAGE__</span><span class="sc">;</span>
+  90 <span class="s">}</span>
+  91 
+  92 <span class="c"># Initialize object properties....</span>
+<a name="_InitializeAtomicDescriptorsProperties-"></a>  93 <span class="k">sub </span><span class="m">_InitializeAtomicDescriptorsProperties</span> <span class="s">{</span>
+  94   <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">%PropertiesNamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+  95 
+  96   <span class="k">my</span><span class="s">(</span><span class="i">$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>
+  97   <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">%PropertiesNamesAndValues</span><span class="s">)</span> <span class="s">{</span>
+  98     <span class="i">$MethodName</span> = <span class="q">&quot;Set${Name}&quot;</span><span class="sc">;</span>
+  99     <span class="i">$This</span><span class="i">-&gt;$MethodName</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="sc">;</span>
+ 100   <span class="s">}</span>
+ 101 
+ 102   <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
+ 103 <span class="s">}</span>
+ 104 
+ 105 <span class="c"># Initialize descriptor values for all atoms in a molecule...</span>
+ 106 <span class="c">#</span>
+<a name="_InitializeDescriptorValues-"></a> 107 <span class="k">sub </span><span class="m">_InitializeDescriptorValues</span> <span class="s">{</span>
+ 108   <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+ 109 
+ 110   <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span>-&gt;{<span class="w">Molecule</span>}<span class="s">)</span> <span class="s">{</span>
+ 111     <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
+ 112   <span class="s">}</span>
+ 113 
+ 114   <span class="c"># Assign &#39;None&#39; to all atomic descriptor values...</span>
+ 115   <span class="c">#</span>
+ 116   <span class="k">my</span><span class="s">(</span><span class="i">$Atom</span><span class="cm">,</span> <span class="i">$AtomID</span><span class="s">)</span><span class="sc">;</span>
+ 117 
+ 118   <span class="j">ATOM:</span> <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">Molecule</span>}<span class="i">-&gt;GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+ 119     <span class="i">$AtomID</span> = <span class="i">$Atom</span><span class="i">-&gt;GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 120     <span class="i">$This</span>-&gt;{<span class="w">DescriptorValues</span>}{<span class="i">$AtomID</span>} = <span class="q">&#39;None&#39;</span><span class="sc">;</span>
+ 121   <span class="s">}</span>
+ 122 
+ 123   <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
+ 124 <span class="s">}</span>
+ 125 
+ 126 <span class="c"># Set molecule object and make sure it&#39;s not already set...</span>
+ 127 <span class="c">#</span>
+<a name="SetMolecule-"></a> 128 <span class="k">sub </span><span class="m">SetMolecule</span> <span class="s">{</span>
+ 129   <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>
+ 130 
+ 131   <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>
+ 132     <span class="w">croak</span> <span class="q">&quot;Error: ${ClassName}-&gt;SetMolecule: Can&#39;t change molecule object:  It&#39;s already set...&quot;</span><span class="sc">;</span>
+ 133   <span class="s">}</span>
+ 134   <span class="i">$This</span>-&gt;{<span class="w">Molecule</span>} = <span class="i">$Molecule</span><span class="sc">;</span>
+ 135 
+ 136   <span class="c"># Weaken the reference to disable increment of reference count...</span>
+ 137   <span class="i">Scalar::Util::weaken</span><span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">Molecule</span>}<span class="s">)</span><span class="sc">;</span>
+ 138 
+ 139   <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
+ 140 <span class="s">}</span>
+ 141 
+ 142 <span class="c"># Set type and make sure it&#39;s not already set...</span>
+ 143 <span class="c">#</span>
+<a name="SetType-"></a> 144 <span class="k">sub </span><span class="m">SetType</span> <span class="s">{</span>
+ 145   <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Type</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+ 146 
+ 147   <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">Type</span>}<span class="s">)</span> <span class="s">{</span>
+ 148     <span class="w">croak</span> <span class="q">&quot;Error: ${ClassName}-&gt;SetType: Can&#39;t change AtomicDescriptors type:  It&#39;s already set...&quot;</span><span class="sc">;</span>
+ 149   <span class="s">}</span>
+ 150   <span class="i">$This</span>-&gt;{<span class="w">Type</span>} = <span class="i">$Type</span><span class="sc">;</span>
+ 151 
+ 152   <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
+ 153 <span class="s">}</span>
+ 154 
+ 155 <span class="c"># Set specific atomic descriptor value...</span>
+ 156 <span class="c">#</span>
+<a name="SetDescriptorValue-"></a> 157 <span class="k">sub </span><span class="m">SetDescriptorValue</span> <span class="s">{</span>
+ 158   <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Atom</span><span class="cm">,</span> <span class="i">$AtomicDescriptor</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+ 159   <span class="k">my</span><span class="s">(</span><span class="i">$AtomID</span><span class="s">)</span><span class="sc">;</span>
+ 160 
+ 161   <span class="i">$AtomID</span> = <span class="i">$Atom</span><span class="i">-&gt;GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 162   <span class="i">$This</span>-&gt;{<span class="w">DescriptorValues</span>}{<span class="i">$AtomID</span>} = <span class="i">$AtomicDescriptor</span><span class="sc">;</span>
+ 163 
+ 164   <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
+ 165 <span class="s">}</span>
+ 166 
+ 167 <span class="c"># Get specific atomic descriptor value...</span>
+ 168 <span class="c">#</span>
+<a name="GetDescriptorValue-"></a> 169 <span class="k">sub </span><span class="m">GetDescriptorValue</span> <span class="s">{</span>
+ 170   <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Atom</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+ 171   <span class="k">my</span><span class="s">(</span><span class="i">$AtomID</span><span class="s">)</span><span class="sc">;</span>
+ 172 
+ 173   <span class="i">$AtomID</span> = <span class="i">$Atom</span><span class="i">-&gt;GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 174 
+ 175   <span class="k">return</span> <span class="k">exists</span> <span class="i">$This</span>-&gt;{<span class="w">DescriptorValues</span>}{<span class="i">$AtomID</span>} ? <span class="i">$This</span>-&gt;{<span class="w">DescriptorValues</span>}{<span class="i">$AtomID</span>} <span class="co">:</span> <span class="q">&#39;None&#39;</span><span class="sc">;</span>
+ 176 <span class="s">}</span>
+ 177 
+ 178 <span class="c"># Get calculated atomic descriptor values as a  hash with atom ID and atomic descriptor</span>
+ 179 <span class="c"># values as key/value pairs...</span>
+ 180 <span class="c">#</span>
+<a name="GetDescriptorValues-"></a> 181 <span class="k">sub </span><span class="m">GetDescriptorValues</span> <span class="s">{</span>
+ 182   <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+ 183 
+ 184   <span class="k">return</span> <span class="i">%</span>{<span class="i">$This</span>-&gt;{<span class="w">DescriptorValues</span>}}<span class="sc">;</span>
+ 185 <span class="s">}</span>
+ 186 
+ 187 <span class="c"># Are all atomic descriptor values successfully calculated?</span>
+ 188 <span class="c">#</span>
+ 189 <span class="c"># Notes:</span>
+ 190 <span class="c">#   . Dynamic checking of calculated descriptor values for atoms eliminates the need</span>
+ 191 <span class="c">#     to check and synchronize valid descriptor values during SetDescriptorValue.</span>
+ 192 <span class="c">#</span>
+<a name="IsDescriptorsGenerationSuccessful-"></a> 193 <span class="k">sub </span><span class="m">IsDescriptorsGenerationSuccessful</span> <span class="s">{</span>
+ 194   <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+ 195   <span class="k">my</span><span class="s">(</span><span class="i">$Atom</span><span class="cm">,</span> <span class="i">$DescriptorValue</span><span class="cm">,</span> <span class="i">@Atoms</span><span class="s">)</span><span class="sc">;</span>
+ 196 
+ 197   <span class="j">ATOM:</span> <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">Molecule</span>}<span class="i">-&gt;GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+ 198     <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">IgnoreHydrogens</span>} &amp;&amp; <span class="i">$Atom</span><span class="i">-&gt;IsHydrogen</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+ 199       <span class="k">next</span> <span class="j">ATOM</span><span class="sc">;</span>
+ 200     <span class="s">}</span>
+ 201     <span class="i">$DescriptorValue</span> = <span class="i">$This</span><span class="i">-&gt;GetDescriptorValue</span><span class="s">(</span><span class="i">$Atom</span><span class="s">)</span><span class="sc">;</span>
+ 202     <span class="k">if</span> <span class="s">(</span><span class="i">$DescriptorValue</span> =~ <span class="q">/^None$/i</span><span class="s">)</span> <span class="s">{</span>
+ 203       <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
+ 204     <span class="s">}</span>
+ 205   <span class="s">}</span>
+ 206 
+ 207   <span class="k">return</span> <span class="n">1</span><span class="sc">;</span>
+ 208 <span class="s">}</span>
+ 209 
+<a name="EOF-"></a></pre>
+<p>&nbsp;</p>
+<br />
+<center>
+<img src="../../../images/h2o2.png">
+</center>
+</body>
+</html>