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+<title>MayaChemTools:Code:MolecularDescriptors::RotatableBondsDescriptors.pm</title>
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+<a name="package-MolecularDescriptors::RotatableBondsDescriptors-"></a>   1 <span class="k">package </span><span class="i">MolecularDescriptors::RotatableBondsDescriptors</span><span class="sc">;</span>
+   2 <span class="c">#</span>
+   3 <span class="c"># $RCSfile: RotatableBondsDescriptors.pm,v $</span>
+   4 <span class="c"># $Date: 2015/02/28 20:49:20 $</span>
+   5 <span class="c"># $Revision: 1.18 $</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">Atom</span><span class="sc">;</span>
+  35 <span class="k">use</span> <span class="w">Molecule</span><span class="sc">;</span>
+  36 <span class="k">use</span> <span class="w">MolecularDescriptors::MolecularDescriptors</span><span class="sc">;</span>
+  37 
+  38 <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>
+  39 
+  40 <span class="i">@ISA</span> = <span class="q">qw(MolecularDescriptors::MolecularDescriptors Exporter)</span><span class="sc">;</span>
+  41 <span class="i">@EXPORT</span> = <span class="q">qw()</span><span class="sc">;</span>
+  42 <span class="i">@EXPORT_OK</span> = <span class="q">qw(GetDescriptorNames)</span><span class="sc">;</span>
+  43 
+  44 <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>
+  45 
+  46 <span class="c"># Setup class variables...</span>
+  47 <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>
+  48 <span class="i">_InitializeClass</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+  49 
+  50 <span class="c"># Overload Perl functions...</span>
+  51 <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;StringifyRotatableBondsDescriptors&#39;</span><span class="sc">;</span>
+  52 
+  53 <span class="c"># Class constructor...</span>
+<a name="new-"></a>  54 <span class="k">sub </span><span class="m">new</span> <span class="s">{</span>
+  55   <span class="k">my</span><span class="s">(</span><span class="i">$Class</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+  56 
+  57   <span class="c"># Initialize object...</span>
+  58   <span class="k">my</span> <span class="i">$This</span> = <span class="i">$Class</span><span class="i">-&gt;SUPER::new</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+  59   <span class="k">bless</span> <span class="i">$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>
+  60   <span class="i">$This</span><span class="i">-&gt;_InitializeRotatableBondsDescriptors</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+  61 
+  62   <span class="i">$This</span><span class="i">-&gt;_InitializeRotatableBondsDescriptorsProperties</span><span class="s">(</span><span class="i">%NamesAndValues</span><span class="s">)</span><span class="sc">;</span>
+  63 
+  64   <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
+  65 <span class="s">}</span>
+  66 
+  67 <span class="c"># Initialize class ...</span>
+<a name="_InitializeClass-"></a>  68 <span class="k">sub </span><span class="m">_InitializeClass</span> <span class="s">{</span>
+  69   <span class="c">#Class name...</span>
+  70   <span class="i">$ClassName</span> = <span class="w">__PACKAGE__</span><span class="sc">;</span>
+  71 
+  72   <span class="c"># Descriptor names...</span>
+  73   <span class="i">@DescriptorNames</span> = <span class="s">(</span><span class="q">&#39;RotatableBonds&#39;</span><span class="s">)</span><span class="sc">;</span>
+  74 
+  75 <span class="s">}</span>
+  76 
+  77 <span class="c"># Get descriptor names as an array.</span>
+  78 <span class="c">#</span>
+  79 <span class="c"># This functionality can be either invoked as a class function or an</span>
+  80 <span class="c"># object method.</span>
+  81 <span class="c">#</span>
+<a name="GetDescriptorNames-"></a>  82 <span class="k">sub </span><span class="m">GetDescriptorNames</span> <span class="s">{</span>
+  83   <span class="k">return</span> <span class="i">@DescriptorNames</span><span class="sc">;</span>
+  84 <span class="s">}</span>
+  85 
+  86 <span class="c"># Initialize object data...</span>
+  87 <span class="c">#</span>
+<a name="_InitializeRotatableBondsDescriptors-"></a>  88 <span class="k">sub </span><span class="m">_InitializeRotatableBondsDescriptors</span> <span class="s">{</span>
+  89   <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+  90 
+  91   <span class="c"># Type of MolecularDescriptor...</span>
+  92   <span class="i">$This</span>-&gt;{<span class="w">Type</span>} = <span class="q">&#39;RotatableBonds&#39;</span><span class="sc">;</span>
+  93 
+  94   <span class="c"># MayaChemTools rotatable bonds default definition corresponds to modifed</span>
+  95   <span class="c"># version of rotatable bonds definition used by Veber et al. [ Ref 92 ]</span>
+  96   <span class="c">#</span>
+  97   <span class="i">$This</span>-&gt;{<span class="w">IgnoreTerminalBonds</span>} = <span class="n">1</span><span class="sc">;</span>
+  98   <span class="i">$This</span>-&gt;{<span class="w">IgnoreBondsToTripleBonds</span>} = <span class="n">1</span><span class="sc">;</span>
+  99   <span class="i">$This</span>-&gt;{<span class="w">IgnoreAmideBonds</span>} = <span class="n">1</span><span class="sc">;</span>
+ 100   <span class="i">$This</span>-&gt;{<span class="w">IgnoreThioamideBonds</span>} = <span class="n">1</span><span class="sc">;</span>
+ 101   <span class="i">$This</span>-&gt;{<span class="w">IgnoreSulfonamideBonds</span>} = <span class="n">1</span><span class="sc">;</span>
+ 102 
+ 103   <span class="c"># Intialize descriptor names and values...</span>
+ 104   <span class="i">$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>
+ 105 
+ 106   <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
+ 107 <span class="s">}</span>
+ 108 
+ 109 <span class="c"># Initialize object properties...</span>
+ 110 <span class="c">#</span>
+<a name="_InitializeRotatableBondsDescriptorsProperties-"></a> 111 <span class="k">sub </span><span class="m">_InitializeRotatableBondsDescriptorsProperties</span> <span class="s">{</span>
+ 112   <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+ 113 
+ 114   <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">$MethodName</span><span class="s">)</span><span class="sc">;</span>
+ 115   <span class="k">while</span> <span class="s">(</span><span class="s">(</span><span class="i">$Name</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="k">each</span>  <span class="i">%NamesAndValues</span><span class="s">)</span> <span class="s">{</span>
+ 116     <span class="i">$MethodName</span> = <span class="q">&quot;Set${Name}&quot;</span><span class="sc">;</span>
+ 117     <span class="i">$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>
+ 118   <span class="s">}</span>
+ 119 
+ 120   <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
+ 121 <span class="s">}</span>
+ 122 
+ 123 <span class="c"># Calculate number of rotatable bonds in a molecule...</span>
+ 124 <span class="c">#</span>
+ 125 <span class="c"># A rotatable bond is defined as any single bond which is not in a ring</span>
+ 126 <span class="c"># and involves only non-hydrogen atoms. By default, the following types</span>
+ 127 <span class="c"># of single bonds are not considered rotatable bonds:</span>
+ 128 <span class="c">#</span>
+ 129 <span class="c">#   . Terminal bonds</span>
+ 130 <span class="c">#   . Bonds attached to triple bonds</span>
+ 131 <span class="c">#   . Amide C-N bonds</span>
+ 132 <span class="c">#   . Thioamide C-N bond bonds</span>
+ 133 <span class="c">#   . Sulfonamide S-N bonds</span>
+ 134 <span class="c">#</span>
+ 135 <span class="c"># MayaChemTools rotatable bonds default definition corresponds to modifed</span>
+ 136 <span class="c"># version of rotatable bonds definition used by Veber et al. [ Ref 92 ]</span>
+ 137 <span class="c">#</span>
+<a name="GenerateDescriptors-"></a> 138 <span class="k">sub </span><span class="m">GenerateDescriptors</span> <span class="s">{</span>
+ 139   <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+ 140 
+ 141   <span class="c"># Initialize descriptor values...</span>
+ 142   <span class="i">$This</span><span class="i">-&gt;_InitializeDescriptorValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 143 
+ 144   <span class="c"># Check availability of molecule...</span>
+ 145   <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span>-&gt;{<span class="w">Molecule</span>}<span class="s">)</span> <span class="s">{</span>
+ 146     <span class="w">carp</span> <span class="q">&quot;Warning: ${ClassName}-&gt;GenerateDescriptors: $This-&gt;{Type} molecular descriptors generation didn&#39;t succeed: Molecule data is not available: Molecule object hasn&#39;t been set...&quot;</span><span class="sc">;</span>
+ 147     <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
+ 148   <span class="s">}</span>
+ 149 
+ 150   <span class="c"># Calculate descriptor values...</span>
+ 151   <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">-&gt;_CalculateDescriptorValues</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+ 152     <span class="w">carp</span> <span class="q">&quot;Warning: ${ClassName}-&gt;GenerateDescriptors: $This-&gt;{Type} molecular descriptors generation didn&#39;t succeed: Couldn&#39;t calculate RotatableBonds values...&quot;</span><span class="sc">;</span>
+ 153     <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
+ 154   <span class="s">}</span>
+ 155 
+ 156   <span class="c"># Set final descriptor values...</span>
+ 157   <span class="i">$This</span><span class="i">-&gt;_SetFinalDescriptorValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 158 
+ 159   <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
+ 160 <span class="s">}</span>
+ 161 
+ 162 <span class="c"># Calculate RotatableBonds value...</span>
+ 163 <span class="c">#</span>
+<a name="_CalculateDescriptorValues-"></a> 164 <span class="k">sub </span><span class="m">_CalculateDescriptorValues</span> <span class="s">{</span>
+ 165   <span class="k">my</span><span class="s">(</span><span class="i">$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">$Bond</span><span class="cm">,</span> <span class="i">$RotatableBonds</span><span class="cm">,</span> <span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">)</span><span class="sc">;</span>
+ 167 
+ 168   <span class="i">$RotatableBonds</span> = <span class="n">0</span><span class="sc">;</span>
+ 169 
+ 170   <span class="j">BOND:</span> <span class="k">for</span> <span class="i">$Bond</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">Molecule</span>}<span class="i">-&gt;GetBonds</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+ 171     <span class="c"># Is it a non-ring ring bond?</span>
+ 172     <span class="k">if</span> <span class="s">(</span>!<span class="i">$Bond</span><span class="i">-&gt;IsSingle</span><span class="s">(</span><span class="s">)</span> || <span class="i">$Bond</span><span class="i">-&gt;IsInRing</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+ 173       <span class="k">next</span> <span class="j">BOND</span><span class="sc">;</span>
+ 174     <span class="s">}</span>
+ 175 
+ 176     <span class="s">(</span><span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">)</span> = <span class="i">$Bond</span><span class="i">-&gt;GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 177 
+ 178     <span class="c"># Does bond contain any Hydrogen atoms?</span>
+ 179     <span class="k">if</span> <span class="s">(</span><span class="i">$Atom1</span><span class="i">-&gt;IsHydrogen</span><span class="s">(</span><span class="s">)</span> || <span class="i">$Atom2</span><span class="i">-&gt;IsHydrogen</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+ 180       <span class="k">next</span> <span class="j">BOND</span><span class="sc">;</span>
+ 181     <span class="s">}</span>
+ 182 
+ 183     <span class="c"># Check for terminal bonds...</span>
+ 184     <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">IgnoreTerminalBonds</span>} &amp;&amp; <span class="i">$This</span><span class="i">-&gt;_IsTerminalBond</span><span class="s">(</span><span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+ 185       <span class="k">next</span> <span class="j">BOND</span><span class="sc">;</span>
+ 186     <span class="s">}</span>
+ 187 
+ 188     <span class="c"># Check for bonds attached to triple bonds...</span>
+ 189     <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">IgnoreBondsToTripleBonds</span>} &amp;&amp; <span class="i">$This</span><span class="i">-&gt;_IsAttachedToTripleBond</span><span class="s">(</span><span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+ 190       <span class="k">next</span> <span class="j">BOND</span><span class="sc">;</span>
+ 191     <span class="s">}</span>
+ 192 
+ 193     <span class="c"># Check for amide bonds...</span>
+ 194     <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">IgnoreAmideBonds</span>} &amp;&amp; <span class="i">$This</span><span class="i">-&gt;_IsAmideBond</span><span class="s">(</span><span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+ 195       <span class="k">next</span> <span class="j">BOND</span><span class="sc">;</span>
+ 196     <span class="s">}</span>
+ 197 
+ 198     <span class="c"># Check for amide bonds...</span>
+ 199     <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">IgnoreThioamideBonds</span>} &amp;&amp; <span class="i">$This</span><span class="i">-&gt;_IsThioamideBond</span><span class="s">(</span><span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+ 200       <span class="k">next</span> <span class="j">BOND</span><span class="sc">;</span>
+ 201     <span class="s">}</span>
+ 202 
+ 203     <span class="c"># Check for sulfonamide bonds...</span>
+ 204     <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">IgnoreSulfonamideBonds</span>} &amp;&amp; <span class="i">$This</span><span class="i">-&gt;_IsSulfonamideBond</span><span class="s">(</span><span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+ 205       <span class="k">next</span> <span class="j">BOND</span><span class="sc">;</span>
+ 206     <span class="s">}</span>
+ 207 
+ 208     <span class="i">$RotatableBonds</span> += <span class="n">1</span><span class="sc">;</span>
+ 209   <span class="s">}</span>
+ 210 
+ 211   <span class="c"># Track the calculated values...</span>
+ 212   <span class="i">$This</span>-&gt;{<span class="w">RotatableBonds</span>} = <span class="i">$RotatableBonds</span><span class="sc">;</span>
+ 213 
+ 214   <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
+ 215 <span class="s">}</span>
+ 216 
+ 217 <span class="c"># Is it a terminal bond?</span>
+ 218 <span class="c">#</span>
+<a name="_IsTerminalBond-"></a> 219 <span class="k">sub </span><span class="m">_IsTerminalBond</span> <span class="s">{</span>
+ 220   <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+ 221 
+ 222   <span class="k">return</span> <span class="s">(</span><span class="i">$Atom1</span><span class="i">-&gt;GetAtomicInvariantValue</span><span class="s">(</span><span class="q">&#39;X&#39;</span><span class="s">)</span> &lt;= <span class="n">1</span> || <span class="i">$Atom2</span><span class="i">-&gt;GetAtomicInvariantValue</span><span class="s">(</span><span class="q">&#39;X&#39;</span><span class="s">)</span> &lt;= <span class="n">1</span> <span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
+ 223 <span class="s">}</span>
+ 224 
+ 225 <span class="c"># Is it attached to a terminal bond?</span>
+ 226 <span class="c">#</span>
+<a name="_IsAttachedToTripleBond-"></a> 227 <span class="k">sub </span><span class="m">_IsAttachedToTripleBond</span> <span class="s">{</span>
+ 228   <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+ 229 
+ 230   <span class="k">return</span> <span class="s">(</span><span class="i">$Atom1</span><span class="i">-&gt;GetAtomicInvariantValue</span><span class="s">(</span><span class="q">&#39;LBO&#39;</span><span class="s">)</span> == <span class="n">3</span> || <span class="i">$Atom2</span><span class="i">-&gt;GetAtomicInvariantValue</span><span class="s">(</span><span class="q">&#39;LBO&#39;</span><span class="s">)</span> == <span class="n">3</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
+ 231 <span class="s">}</span>
+ 232 
+ 233 <span class="c"># Is it an amide bond?</span>
+ 234 <span class="c">#</span>
+ 235 <span class="c"># Amide: R-C(=O)-N(-R)(-R&quot;)</span>
+ 236 <span class="c">#</span>
+<a name="_IsAmideBond-"></a> 237 <span class="k">sub </span><span class="m">_IsAmideBond</span> <span class="s">{</span>
+ 238   <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+ 239   <span class="k">my</span><span class="s">(</span><span class="i">$CarbonAtom</span><span class="cm">,</span> <span class="i">$NitrogenAtom</span><span class="s">)</span><span class="sc">;</span>
+ 240 
+ 241   <span class="s">(</span><span class="i">$CarbonAtom</span><span class="cm">,</span> <span class="i">$NitrogenAtom</span><span class="s">)</span> = <span class="s">(</span><span class="k">undef</span><span class="cm">,</span> <span class="k">undef</span><span class="s">)</span><span class="sc">;</span>
+ 242 
+ 243   <span class="k">if</span> <span class="s">(</span><span class="i">$Atom1</span><span class="i">-&gt;IsCarbon</span><span class="s">(</span><span class="s">)</span> &amp;&amp; <span class="i">$Atom2</span><span class="i">-&gt;IsNitrogen</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+ 244     <span class="s">(</span><span class="i">$CarbonAtom</span><span class="cm">,</span> <span class="i">$NitrogenAtom</span><span class="s">)</span> = <span class="s">(</span><span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">)</span><span class="sc">;</span>
+ 245   <span class="s">}</span>
+ 246   <span class="k">elsif</span> <span class="s">(</span><span class="i">$Atom2</span><span class="i">-&gt;IsCarbon</span><span class="s">(</span><span class="s">)</span> &amp;&amp; <span class="i">$Atom1</span><span class="i">-&gt;IsNitrogen</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+ 247     <span class="s">(</span><span class="i">$CarbonAtom</span><span class="cm">,</span> <span class="i">$NitrogenAtom</span><span class="s">)</span> = <span class="s">(</span><span class="i">$Atom2</span><span class="cm">,</span> <span class="i">$Atom1</span><span class="s">)</span><span class="sc">;</span>
+ 248   <span class="s">}</span>
+ 249 
+ 250   <span class="k">if</span> <span class="s">(</span>!<span class="i">$CarbonAtom</span><span class="s">)</span> <span class="s">{</span>
+ 251     <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
+ 252   <span class="s">}</span>
+ 253 
+ 254   <span class="k">return</span> <span class="i">$CarbonAtom</span><span class="i">-&gt;DoesAtomNeighborhoodMatch</span><span class="s">(</span><span class="q">&#39;C.T3.DB1&#39;</span><span class="cm">,</span> <span class="s">[</span><span class="q">&#39;O&#39;</span><span class="cm">,</span> <span class="q">&#39;N&#39;</span><span class="cm">,</span> <span class="q">&#39;C,H&#39;</span><span class="s">]</span><span class="cm">,</span> <span class="s">[</span><span class="q">&#39;=&#39;</span><span class="cm">,</span> <span class="q">&#39;-&#39;</span><span class="cm">,</span> <span class="q">&#39;-&#39;</span><span class="s">]</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
+ 255 <span class="s">}</span>
+ 256 
+ 257 <span class="c"># Is it a thioamide bond?</span>
+ 258 <span class="c">#</span>
+ 259 <span class="c"># Thioamide: R-C(=S)-N(-R)(-R&quot;)</span>
+ 260 <span class="c">#</span>
+<a name="_IsThioamideBond-"></a> 261 <span class="k">sub </span><span class="m">_IsThioamideBond</span> <span class="s">{</span>
+ 262   <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</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">$CarbonAtom</span><span class="cm">,</span> <span class="i">$NitrogenAtom</span><span class="s">)</span><span class="sc">;</span>
+ 264 
+ 265   <span class="s">(</span><span class="i">$CarbonAtom</span><span class="cm">,</span> <span class="i">$NitrogenAtom</span><span class="s">)</span> = <span class="s">(</span><span class="k">undef</span><span class="cm">,</span> <span class="k">undef</span><span class="s">)</span><span class="sc">;</span>
+ 266 
+ 267   <span class="k">if</span> <span class="s">(</span><span class="i">$Atom1</span><span class="i">-&gt;IsCarbon</span><span class="s">(</span><span class="s">)</span> &amp;&amp; <span class="i">$Atom2</span><span class="i">-&gt;IsNitrogen</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+ 268     <span class="s">(</span><span class="i">$CarbonAtom</span><span class="cm">,</span> <span class="i">$NitrogenAtom</span><span class="s">)</span> = <span class="s">(</span><span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">)</span><span class="sc">;</span>
+ 269   <span class="s">}</span>
+ 270   <span class="k">elsif</span> <span class="s">(</span><span class="i">$Atom2</span><span class="i">-&gt;IsCarbon</span><span class="s">(</span><span class="s">)</span> &amp;&amp; <span class="i">$Atom1</span><span class="i">-&gt;IsNitrogen</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+ 271     <span class="s">(</span><span class="i">$CarbonAtom</span><span class="cm">,</span> <span class="i">$NitrogenAtom</span><span class="s">)</span> = <span class="s">(</span><span class="i">$Atom2</span><span class="cm">,</span> <span class="i">$Atom1</span><span class="s">)</span><span class="sc">;</span>
+ 272   <span class="s">}</span>
+ 273 
+ 274   <span class="k">if</span> <span class="s">(</span>!<span class="i">$CarbonAtom</span><span class="s">)</span> <span class="s">{</span>
+ 275     <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
+ 276   <span class="s">}</span>
+ 277 
+ 278   <span class="k">return</span> <span class="i">$CarbonAtom</span><span class="i">-&gt;DoesAtomNeighborhoodMatch</span><span class="s">(</span><span class="q">&#39;C.T3.DB1&#39;</span><span class="cm">,</span> <span class="s">[</span><span class="q">&#39;S&#39;</span><span class="cm">,</span> <span class="q">&#39;N&#39;</span><span class="cm">,</span> <span class="q">&#39;C,H&#39;</span><span class="s">]</span><span class="cm">,</span> <span class="s">[</span><span class="q">&#39;=&#39;</span><span class="cm">,</span> <span class="q">&#39;-&#39;</span><span class="cm">,</span> <span class="q">&#39;-&#39;</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>
+ 279 <span class="s">}</span>
+ 280 
+ 281 <span class="c"># Is it a sulfonamide bond?</span>
+ 282 <span class="c">#</span>
+ 283 <span class="c"># Sulfonamide: R-S(=O)(=O)-N(-R)(-R&quot;)</span>
+ 284 <span class="c">#</span>
+<a name="_IsSulfonamideBond-"></a> 285 <span class="k">sub </span><span class="m">_IsSulfonamideBond</span> <span class="s">{</span>
+ 286   <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+ 287   <span class="k">my</span><span class="s">(</span><span class="i">$SulfurAtom</span><span class="cm">,</span> <span class="i">$NitrogenAtom</span><span class="s">)</span><span class="sc">;</span>
+ 288 
+ 289   <span class="s">(</span><span class="i">$SulfurAtom</span><span class="cm">,</span> <span class="i">$NitrogenAtom</span><span class="s">)</span> = <span class="s">(</span><span class="k">undef</span><span class="cm">,</span> <span class="k">undef</span><span class="s">)</span><span class="sc">;</span>
+ 290 
+ 291   <span class="k">if</span> <span class="s">(</span><span class="i">$Atom1</span><span class="i">-&gt;IsSulfur</span><span class="s">(</span><span class="s">)</span> &amp;&amp; <span class="i">$Atom2</span><span class="i">-&gt;IsNitrogen</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+ 292     <span class="s">(</span><span class="i">$SulfurAtom</span><span class="cm">,</span> <span class="i">$NitrogenAtom</span><span class="s">)</span> = <span class="s">(</span><span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">)</span><span class="sc">;</span>
+ 293   <span class="s">}</span>
+ 294   <span class="k">elsif</span> <span class="s">(</span><span class="i">$Atom2</span><span class="i">-&gt;IsSulfur</span><span class="s">(</span><span class="s">)</span> &amp;&amp; <span class="i">$Atom1</span><span class="i">-&gt;IsNitrogen</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+ 295     <span class="s">(</span><span class="i">$SulfurAtom</span><span class="cm">,</span> <span class="i">$NitrogenAtom</span><span class="s">)</span> = <span class="s">(</span><span class="i">$Atom2</span><span class="cm">,</span> <span class="i">$Atom1</span><span class="s">)</span><span class="sc">;</span>
+ 296   <span class="s">}</span>
+ 297 
+ 298   <span class="k">if</span> <span class="s">(</span>!<span class="i">$SulfurAtom</span><span class="s">)</span> <span class="s">{</span>
+ 299     <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
+ 300   <span class="s">}</span>
+ 301 
+ 302   <span class="k">return</span> <span class="i">$SulfurAtom</span><span class="i">-&gt;DoesAtomNeighborhoodMatch</span><span class="s">(</span><span class="q">&#39;S.T4.DB2&#39;</span><span class="cm">,</span> <span class="s">[</span><span class="q">&#39;O&#39;</span><span class="cm">,</span> <span class="q">&#39;O&#39;</span><span class="cm">,</span> <span class="q">&#39;N&#39;</span><span class="cm">,</span> <span class="q">&#39;!O&#39;</span><span class="s">]</span><span class="cm">,</span> <span class="s">[</span><span class="q">&#39;=&#39;</span><span class="cm">,</span> <span class="q">&#39;=&#39;</span><span class="cm">,</span> <span class="q">&#39;-&#39;</span><span class="cm">,</span> <span class="q">&#39;-&#39;</span><span class="s">]</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
+ 303 <span class="s">}</span>
+ 304 
+ 305 <span class="c"># Setup final descriptor values...</span>
+ 306 <span class="c">#</span>
+<a name="_SetFinalDescriptorValues-"></a> 307 <span class="k">sub </span><span class="m">_SetFinalDescriptorValues</span> <span class="s">{</span>
+ 308   <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+ 309 
+ 310   <span class="i">$This</span>-&gt;{<span class="w">DescriptorsGenerated</span>} = <span class="n">1</span><span class="sc">;</span>
+ 311 
+ 312   <span class="i">$This</span><span class="i">-&gt;SetDescriptorValues</span><span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">RotatableBonds</span>}<span class="s">)</span><span class="sc">;</span>
+ 313 
+ 314   <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
+ 315 <span class="s">}</span>
+ 316 
+ 317 <span class="c"># Return a string containg data for RotatableBondsDescriptors object...</span>
+ 318 <span class="c">#</span>
+<a name="StringifyRotatableBondsDescriptors-"></a> 319 <span class="k">sub </span><span class="m">StringifyRotatableBondsDescriptors</span> <span class="s">{</span>
+ 320   <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+ 321   <span class="k">my</span><span class="s">(</span><span class="i">$RotatableBondsDescriptorsString</span><span class="s">)</span><span class="sc">;</span>
+ 322 
+ 323   <span class="c"># Type of MolecularDescriptors...</span>
+ 324   <span class="i">$RotatableBondsDescriptorsString</span> = <span class="q">&quot;MolecularDescriptorType: $This-&gt;{Type}; IgnoreTerminalBonds: &quot;</span> . <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">IgnoreTerminalBonds</span>} ? <span class="q">&quot;Yes&quot;</span> <span class="co">:</span> <span class="q">&quot;No&quot;</span><span class="s">)</span> . <span class="q">&quot;; IgnoreBondsToTripleBonds: &quot;</span> .  <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">IgnoreBondsToTripleBonds</span>} ? <span class="q">&quot;Yes&quot;</span> <span class="co">:</span> <span class="q">&quot;No&quot;</span><span class="s">)</span> . <span class="q">&quot;; IgnoreAmideBonds: &quot;</span> .  <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">IgnoreAmideBonds</span>} ? <span class="q">&quot;Yes&quot;</span> <span class="co">:</span> <span class="q">&quot;No&quot;</span><span class="s">)</span> . <span class="q">&quot;; IgnoreThioamideBonds: &quot;</span> .  <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">IgnoreThioamideBonds</span>} ? <span class="q">&quot;Yes&quot;</span> <span class="co">:</span> <span class="q">&quot;No&quot;</span><span class="s">)</span> . <span class="q">&quot;; IgnoreSulfonamideBonds: &quot;</span> .  <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">IgnoreSulfonamideBonds</span>} ? <span class="q">&quot;Yes&quot;</span> <span class="co">:</span> <span class="q">&quot;No&quot;</span><span class="s">)</span><span class="sc">;</span>
+ 325 
+ 326   <span class="c"># Setup molecular descriptor information...</span>
+ 327   <span class="i">$RotatableBondsDescriptorsString</span> .= <span class="q">&quot;; &quot;</span> . <span class="i">$This</span><span class="i">-&gt;_StringifyDescriptorNamesAndValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 328 
+ 329   <span class="k">return</span> <span class="i">$RotatableBondsDescriptorsString</span><span class="sc">;</span>
+ 330 <span class="s">}</span>
+ 331 
+ 332 <span class="c"># Is it a RotatableBondsDescriptors object?</span>
+<a name="_IsRotatableBondsDescriptors-"></a> 333 <span class="k">sub </span><span class="m">_IsRotatableBondsDescriptors</span> <span class="s">{</span>
+ 334   <span class="k">my</span><span class="s">(</span><span class="i">$Object</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+ 335 
+ 336   <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>
+ 337 <span class="s">}</span>
+ 338 
+<a name="EOF-"></a></pre>
+<p>&nbsp;</p>
+<br />
+<center>
+<img src="../../../images/h2o2.png">
+</center>
+</body>
+</html>