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+<a name="package-Fingerprints::EStateIndiciesFingerprints-"></a>   1 <span class="k">package </span><span class="i">Fingerprints::EStateIndiciesFingerprints</span><span class="sc">;</span>
+   2 <span class="c">#</span>
+   3 <span class="c"># $RCSfile: EStateIndiciesFingerprints.pm,v $</span>
+   4 <span class="c"># $Date: 2015/02/28 20:48:54 $</span>
+   5 <span class="c"># $Revision: 1.19 $</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">Text::ParseWords</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">FileUtil</span> <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+  35 <span class="k">use</span> <span class="w">MathUtil</span> <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+  36 <span class="k">use</span> <span class="w">Fingerprints::Fingerprints</span><span class="sc">;</span>
+  37 <span class="k">use</span> <span class="w">Molecule</span><span class="sc">;</span>
+  38 <span class="k">use</span> <span class="w">AtomTypes::EStateAtomTypes</span><span class="sc">;</span>
+  39 <span class="k">use</span> <span class="w">AtomicDescriptors::EStateValuesDescriptors</span><span class="sc">;</span>
+  40 
+  41 <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>
+  42 
+  43 <span class="i">@ISA</span> = <span class="q">qw(Fingerprints::Fingerprints Exporter)</span><span class="sc">;</span>
+  44 <span class="i">@EXPORT</span> = <span class="q">qw()</span><span class="sc">;</span>
+  45 <span class="i">@EXPORT_OK</span> = <span class="q">qw()</span><span class="sc">;</span>
+  46 
+  47 <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>
+  48 
+  49 <span class="c"># Setup class variables...</span>
+  50 <span class="k">my</span><span class="s">(</span><span class="i">$ClassName</span><span class="s">)</span><span class="sc">;</span>
+  51 <span class="i">_InitializeClass</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+  52 
+  53 <span class="c"># Overload Perl functions...</span>
+  54 <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;StringifyEStateIndiciesFingerprints&#39;</span><span class="sc">;</span>
+  55 
+  56 <span class="c"># Class constructor...</span>
+<a name="new-"></a>  57 <span class="k">sub </span><span class="m">new</span> <span class="s">{</span>
+  58   <span class="k">my</span><span class="s">(</span><span class="i">$Class</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+  59 
+  60   <span class="c"># Initialize object...</span>
+  61   <span class="k">my</span> <span class="i">$This</span> = <span class="i">$Class</span><span class="i">-&gt;SUPER::new</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+  62   <span class="k">bless</span> <span class="i">$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>
+  63   <span class="i">$This</span><span class="i">-&gt;_InitializeEStateIndiciesFingerprints</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+  64 
+  65   <span class="i">$This</span><span class="i">-&gt;_InitializeEStateIndiciesFingerprintsProperties</span><span class="s">(</span><span class="i">%NamesAndValues</span><span class="s">)</span><span class="sc">;</span>
+  66 
+  67   <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
+  68 <span class="s">}</span>
+  69 
+  70 <span class="c"># Initialize object data...</span>
+  71 <span class="c">#</span>
+<a name="_InitializeEStateIndiciesFingerprints-"></a>  72 <span class="k">sub </span><span class="m">_InitializeEStateIndiciesFingerprints</span> <span class="s">{</span>
+  73   <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+  74 
+  75   <span class="c"># EStateIndicies is a vector containing sum of E-state values for E-state atom types</span>
+  76   <span class="c">#</span>
+  77   <span class="i">$This</span>-&gt;{<span class="w">Type</span>} = <span class="q">&#39;EStateIndicies&#39;</span><span class="sc">;</span>
+  78 
+  79   <span class="c"># EStateAtomTypesSetToUse for EStateIndicies:</span>
+  80   <span class="c">#</span>
+  81   <span class="c"># ArbitrarySize - Corrresponds to only E-state atom types detected in molecule</span>
+  82   <span class="c"># FixedSize - Corresponds to fixed number of E-state atom types previously defined [ Ref 77 ]</span>
+  83   <span class="c">#</span>
+  84   <span class="c"># The default EStateAtomTypesSetToUse value for EStateIndicies fingerprints type: ArbitrarySize.</span>
+  85   <span class="c"># Possible values: ArbitrarySize or FixedSize.</span>
+  86   <span class="c">#</span>
+  87   <span class="i">$This</span>-&gt;{<span class="w">EStateAtomTypesSetToUse</span>} = <span class="q">&#39;&#39;</span><span class="sc">;</span>
+  88 
+  89   <span class="c"># Assigned E-state atom types...</span>
+  90   <span class="i">%</span>{<span class="i">$This</span>-&gt;{<span class="w">EStateAtomTypes</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+  91 
+  92   <span class="c"># Vector values precision for real values during E-state indicies...</span>
+  93   <span class="i">$This</span>-&gt;{<span class="w">ValuesPrecision</span>} = <span class="n">3</span><span class="sc">;</span>
+  94 
+  95   <span class="c"># Calculated E-state values and indicies for generating E-state indicies fingerprints...</span>
+  96   <span class="i">%</span>{<span class="i">$This</span>-&gt;{<span class="w">EStateValues</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+  97   <span class="i">%</span>{<span class="i">$This</span>-&gt;{<span class="w">EStateIndicies</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+  98 <span class="s">}</span>
+  99 
+ 100 <span class="c"># Initialize class ...</span>
+<a name="_InitializeClass-"></a> 101 <span class="k">sub </span><span class="m">_InitializeClass</span> <span class="s">{</span>
+ 102   <span class="c">#Class name...</span>
+ 103   <span class="i">$ClassName</span> = <span class="w">__PACKAGE__</span><span class="sc">;</span>
+ 104 
+ 105 <span class="s">}</span>
+ 106 
+ 107 <span class="c"># Initialize object properties....</span>
+<a name="_InitializeEStateIndiciesFingerprintsProperties-"></a> 108 <span class="k">sub </span><span class="m">_InitializeEStateIndiciesFingerprintsProperties</span> <span class="s">{</span>
+ 109   <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+ 110 
+ 111   <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">$MethodName</span><span class="s">)</span><span class="sc">;</span>
+ 112   <span class="k">while</span> <span class="s">(</span><span class="s">(</span><span class="i">$Name</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="k">each</span>  <span class="i">%NamesAndValues</span><span class="s">)</span> <span class="s">{</span>
+ 113     <span class="i">$MethodName</span> = <span class="q">&quot;Set${Name}&quot;</span><span class="sc">;</span>
+ 114     <span class="i">$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>
+ 115   <span class="s">}</span>
+ 116 
+ 117   <span class="c"># Make sure molecule object was specified...</span>
+ 118   <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$NamesAndValues</span>{<span class="w">Molecule</span>}<span class="s">)</span> <span class="s">{</span>
+ 119     <span class="w">croak</span> <span class="q">&quot;Error: ${ClassName}-&gt;New: Object can&#39;t be instantiated without specifying molecule...&quot;</span><span class="sc">;</span>
+ 120   <span class="s">}</span>
+ 121 
+ 122   <span class="i">$This</span><span class="i">-&gt;_InitializeEstateIndicies</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 123 
+ 124   <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
+ 125 <span class="s">}</span>
+ 126 
+ 127 <span class="c"># Initialize E-state indicies...</span>
+ 128 <span class="c">#</span>
+<a name="_InitializeEstateIndicies-"></a> 129 <span class="k">sub </span><span class="m">_InitializeEstateIndicies</span> <span class="s">{</span>
+ 130   <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+ 131 
+ 132   <span class="c"># Set default EStateAtomTypesSetToUse...</span>
+ 133   <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span>-&gt;{<span class="w">EStateAtomTypesSetToUse</span>}<span class="s">)</span> <span class="s">{</span>
+ 134     <span class="i">$This</span>-&gt;{<span class="w">EStateAtomTypesSetToUse</span>} = <span class="q">&#39;ArbitrarySize&#39;</span><span class="sc">;</span>
+ 135   <span class="s">}</span>
+ 136 
+ 137   <span class="c"># Vector type...</span>
+ 138   <span class="i">$This</span>-&gt;{<span class="w">VectorType</span>} = <span class="q">&#39;FingerprintsVector&#39;</span><span class="sc">;</span>
+ 139 
+ 140   <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">EStateAtomTypesSetToUse</span>} =~ <span class="q">/^FixedSize$/i</span><span class="s">)</span> <span class="s">{</span>
+ 141     <span class="i">$This</span>-&gt;{<span class="w">FingerprintsVectorType</span>} = <span class="q">&#39;OrderedNumericalValues&#39;</span><span class="sc">;</span>
+ 142   <span class="s">}</span>
+ 143   <span class="k">else</span> <span class="s">{</span>
+ 144     <span class="i">$This</span>-&gt;{<span class="w">FingerprintsVectorType</span>} = <span class="q">&#39;NumericalValues&#39;</span><span class="sc">;</span>
+ 145   <span class="s">}</span>
+ 146 
+ 147   <span class="i">$This</span><span class="i">-&gt;_InitializeFingerprintsVector</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 148 
+ 149   <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
+ 150 <span class="s">}</span>
+ 151 
+ 152 <span class="c"># Disable set size method...</span>
+ 153 <span class="c">#</span>
+<a name="SetSize-"></a> 154 <span class="k">sub </span><span class="m">SetSize</span> <span class="s">{</span>
+ 155   <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Type</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+ 156 
+ 157   <span class="w">croak</span> <span class="q">&quot;Error: ${ClassName}-&gt;SetSize: Can&#39;t change size:  It&#39;s not allowed...&quot;</span><span class="sc">;</span>
+ 158 <span class="s">}</span>
+ 159 
+ 160 <span class="c"># Set E-state atom types set to use...</span>
+ 161 <span class="c">#</span>
+<a name="SetEStateAtomTypesSetToUse-"></a> 162 <span class="k">sub </span><span class="m">SetEStateAtomTypesSetToUse</span> <span class="s">{</span>
+ 163   <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+ 164 
+ 165   <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">EStateAtomTypesSetToUse</span>}<span class="s">)</span> <span class="s">{</span>
+ 166     <span class="w">croak</span> <span class="q">&quot;Error: ${ClassName}-&gt;SetEStateAtomTypesSetToUse: Can&#39;t change size:  It&#39;s already set...&quot;</span><span class="sc">;</span>
+ 167   <span class="s">}</span>
+ 168 
+ 169   <span class="k">if</span> <span class="s">(</span><span class="i">$Value</span> !~ <span class="q">/^(ArbitrarySize|FixedSize)/i</span><span class="s">)</span> <span class="s">{</span>
+ 170     <span class="w">croak</span> <span class="q">&quot;Error: ${ClassName}-&gt;SetEStateAtomTypesSetToUse: Unknown EStateAtomTypesSetToUse value: $Value; Supported values: ArbitrarySize or FixedSize&quot;</span><span class="sc">;</span>
+ 171   <span class="s">}</span>
+ 172 
+ 173   <span class="i">$This</span>-&gt;{<span class="w">EStateAtomTypesSetToUse</span>} = <span class="i">$Value</span><span class="sc">;</span>
+ 174 
+ 175   <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
+ 176 <span class="s">}</span>
+ 177 
+ 178 <span class="c"># Set vector values precision for real values for E-state indicies...</span>
+ 179 <span class="c">#</span>
+<a name="SetValuesPrecision-"></a> 180 <span class="k">sub </span><span class="m">SetValuesPrecision</span> <span class="s">{</span>
+ 181   <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>
+ 182 
+ 183   <span class="k">if</span> <span class="s">(</span>!<span class="i">TextUtil::IsPositiveInteger</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+ 184     <span class="w">croak</span> <span class="q">&quot;Error: ${ClassName}-&gt;SetValuesPrecision: ValuesPrecision value, $Value, is not valid:  It must be a positive integer...&quot;</span><span class="sc">;</span>
+ 185   <span class="s">}</span>
+ 186   <span class="i">$This</span>-&gt;{<span class="w">ValuesPrecision</span>} = <span class="i">$Value</span><span class="sc">;</span>
+ 187 
+ 188   <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
+ 189 <span class="s">}</span>
+ 190 
+ 191 <span class="c"># Generate fingerprints description...</span>
+ 192 <span class="c">#</span>
+<a name="GetDescription-"></a> 193 <span class="k">sub </span><span class="m">GetDescription</span> <span class="s">{</span>
+ 194   <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+ 195 
+ 196   <span class="c"># Is description explicity set?</span>
+ 197   <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$This</span>-&gt;{<span class="w">Description</span>}<span class="s">)</span> <span class="s">{</span>
+ 198     <span class="k">return</span> <span class="i">$This</span>-&gt;{<span class="w">Description</span>}<span class="sc">;</span>
+ 199   <span class="s">}</span>
+ 200 
+ 201   <span class="c"># Generate fingerprints description...</span>
+ 202 
+ 203   <span class="k">return</span> <span class="q">&quot;$This-&gt;{Type}:$This-&gt;{EStateAtomTypesSetToUse}&quot;</span><span class="sc">;</span>
+ 204 <span class="s">}</span>
+ 205 
+ 206 <span class="c"># Generate electrotopological state indicies (E-state) [ Ref 75-78 ] fingerprints for</span>
+ 207 <span class="c"># non-hydrogen atoms in a molecule...</span>
+ 208 <span class="c">#</span>
+ 209 <span class="c"># EStateIndicies fingerprints constitute a vector containing sum of E-state values</span>
+ 210 <span class="c"># for E-state atom types. Two types of E-state atom types set size are allowed:</span>
+ 211 <span class="c">#</span>
+ 212 <span class="c"># ArbitrarySize - Corrresponds to only E-state atom types detected in molecule</span>
+ 213 <span class="c"># FixedSize - Corresponds to fixed number of E-state atom types previously defined</span>
+ 214 <span class="c">#</span>
+ 215 <span class="c"># Module AtomTypes::EStateAtomTypes.pm is used to assign E-state atom types to</span>
+ 216 <span class="c"># non-hydrogen atoms in the molecule which is able to assign atom types to any valid</span>
+ 217 <span class="c"># atom group. However, for FixedSize value of EStateAtomTypesSetToUse, only a fixed</span>
+ 218 <span class="c"># set of E-state atom types corresponding to specific atom groups [ Appendix III in</span>
+ 219 <span class="c"># Ref 77 ] are used for fingerprints.</span>
+ 220 <span class="c">#</span>
+ 221 <span class="c"># The fixed size E-state atom type set size used during generation of fingerprints corresponding</span>
+ 222 <span class="c"># FixedSize value of EStateAtomTypesSetToUse contains 87 E-state non-hydrogen atom types</span>
+ 223 <span class="c"># in EStateAtomTypes.csv data file distributed with MayaChemTools.</span>
+ 224 <span class="c">#</span>
+ 225 <span class="c"># Combination of Type and EStateAtomTypesSetToUse allow generation of 2 different types of</span>
+ 226 <span class="c"># E-state indicies fingerprints:</span>
+ 227 <span class="c">#</span>
+ 228 <span class="c"># Type                        EStateAtomTypesSetToUse</span>
+ 229 <span class="c">#</span>
+ 230 <span class="c"># EStateIndicies               ArbitrarySize      [ default fingerprints ]</span>
+ 231 <span class="c"># EStateIndicies               FixedSize</span>
+ 232 <span class="c">#</span>
+ 233 <span class="c"># The default is generate EStateIndicies type fingeprints corresponding to ArbitrarySize as</span>
+ 234 <span class="c"># EStateAtomTypesSetToUse value.</span>
+ 235 <span class="c">#</span>
+ 236 <span class="c">#</span>
+<a name="GenerateFingerprints-"></a> 237 <span class="k">sub </span><span class="m">GenerateFingerprints</span> <span class="s">{</span>
+ 238   <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>
+ 239 
+ 240   <span class="c"># Cache appropriate molecule data...</span>
+ 241   <span class="i">$This</span><span class="i">-&gt;_SetupMoleculeDataCache</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 242 
+ 243   <span class="c"># Assign E-state atom types...</span>
+ 244   <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">-&gt;_AssignEStateAtomTypes</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+ 245     <span class="w">carp</span> <span class="q">&quot;Warning: ${ClassName}-&gt;GenerateFingerprints: $This-&gt;{Type} fingerprints generation didn&#39;t succeed: Couldn&#39;t assign valid E-state atom types to all atoms...&quot;</span><span class="sc">;</span>
+ 246     <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
+ 247   <span class="s">}</span>
+ 248 
+ 249   <span class="c"># Calculate E-state indicies...</span>
+ 250   <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">-&gt;_CalculateEStateIndicies</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+ 251     <span class="w">carp</span> <span class="q">&quot;Warning: ${ClassName}-&gt;GenerateFingerprints: $This-&gt;{Type} fingerprints generation didn&#39;t succeed: Couldn&#39;t calculate E-state values for all atoms...&quot;</span><span class="sc">;</span>
+ 252     <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
+ 253   <span class="s">}</span>
+ 254 
+ 255   <span class="c"># Set final fingerprints...</span>
+ 256   <span class="i">$This</span><span class="i">-&gt;_SetFinalFingerprints</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 257 
+ 258   <span class="c"># Clear cached molecule data...</span>
+ 259   <span class="i">$This</span><span class="i">-&gt;_ClearMoleculeDataCache</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 260 
+ 261   <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
+ 262 <span class="s">}</span>
+ 263 
+ 264 <span class="c"># Assign E-state atom types...</span>
+ 265 <span class="c">#</span>
+<a name="_AssignEStateAtomTypes-"></a> 266 <span class="k">sub </span><span class="m">_AssignEStateAtomTypes</span> <span class="s">{</span>
+ 267   <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+ 268   <span class="k">my</span><span class="s">(</span><span class="i">$EStateAtomTypes</span><span class="cm">,</span> <span class="i">$Atom</span><span class="cm">,</span> <span class="i">$AtomID</span><span class="cm">,</span> <span class="i">$AtomType</span><span class="s">)</span><span class="sc">;</span>
+ 269 
+ 270   <span class="i">%</span>{<span class="i">$This</span>-&gt;{<span class="w">EStateAtomTypes</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 271 
+ 272   <span class="c"># Assign E-state atom types...</span>
+ 273   <span class="i">$EStateAtomTypes</span> = <span class="i">new</span> <span class="i">AtomTypes::EStateAtomTypes</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span> <span class="cm">=&gt;</span> <span class="i">$This</span>-&gt;{<span class="w">Molecule</span>}<span class="cm">,</span> <span class="q">&#39;IgnoreHydrogens&#39;</span> <span class="cm">=&gt;</span> <span class="n">1</span><span class="s">)</span><span class="sc">;</span>
+ 274   <span class="i">$EStateAtomTypes</span><span class="i">-&gt;AssignAtomTypes</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 275 
+ 276   <span class="c"># Make sure atom types assignment is successful...</span>
+ 277   <span class="k">if</span> <span class="s">(</span>!<span class="i">$EStateAtomTypes</span><span class="i">-&gt;IsAtomTypesAssignmentSuccessful</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+ 278     <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
+ 279   <span class="s">}</span>
+ 280 
+ 281   <span class="c"># Collect assigned atom types...</span>
+ 282   <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$This</span>-&gt;{<span class="w">Atoms</span>}}<span class="s">)</span> <span class="s">{</span>
+ 283     <span class="i">$AtomID</span> = <span class="i">$Atom</span><span class="i">-&gt;GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 284 
+ 285     <span class="i">$AtomType</span> = <span class="i">$EStateAtomTypes</span><span class="i">-&gt;GetAtomType</span><span class="s">(</span><span class="i">$Atom</span><span class="s">)</span><span class="sc">;</span>
+ 286     <span class="i">$This</span>-&gt;{<span class="w">EStateAtomTypes</span>}{<span class="i">$AtomID</span>} = <span class="i">$AtomType</span><span class="sc">;</span>
+ 287   <span class="s">}</span>
+ 288   <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
+ 289 <span class="s">}</span>
+ 290 
+ 291 <span class="c"># Calculate E-state indicies by summing up E-state values for specific</span>
+ 292 <span class="c"># E-state atom types...</span>
+ 293 <span class="c">#</span>
+<a name="_CalculateEStateIndicies-"></a> 294 <span class="k">sub </span><span class="m">_CalculateEStateIndicies</span> <span class="s">{</span>
+ 295   <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+ 296   <span class="k">my</span><span class="s">(</span><span class="i">$Atom</span><span class="cm">,</span> <span class="i">$AtomID</span><span class="cm">,</span> <span class="i">$AtomType</span><span class="cm">,</span> <span class="i">$EStateValue</span><span class="s">)</span><span class="sc">;</span>
+ 297 
+ 298   <span class="c"># Calculate E-state values to generate E-state indicies...</span>
+ 299   <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">-&gt;_CalculateEStateValuesDescriptors</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+ 300     <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
+ 301   <span class="s">}</span>
+ 302 
+ 303   <span class="c"># Calculate E-state indicies...</span>
+ 304   <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$This</span>-&gt;{<span class="w">Atoms</span>}}<span class="s">)</span> <span class="s">{</span>
+ 305     <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>
+ 306 
+ 307     <span class="i">$AtomType</span> = <span class="i">$This</span>-&gt;{<span class="w">EStateAtomTypes</span>}{<span class="i">$AtomID</span>}<span class="sc">;</span>
+ 308     <span class="i">$EStateValue</span> = <span class="i">$This</span>-&gt;{<span class="w">EStateValues</span>}{<span class="i">$AtomID</span>}<span class="sc">;</span>
+ 309 
+ 310     <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$This</span>-&gt;{<span class="w">EStateIndicies</span>}{<span class="i">$AtomType</span>}<span class="s">)</span> <span class="s">{</span>
+ 311       <span class="i">$This</span>-&gt;{<span class="w">EStateIndicies</span>}{<span class="i">$AtomType</span>} = <span class="n">0</span><span class="sc">;</span>
+ 312     <span class="s">}</span>
+ 313 
+ 314     <span class="i">$This</span>-&gt;{<span class="w">EStateIndicies</span>}{<span class="i">$AtomType</span>} += <span class="i">$EStateValue</span><span class="sc">;</span>
+ 315   <span class="s">}</span>
+ 316   <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
+ 317 <span class="s">}</span>
+ 318 
+ 319 <span class="c"># Calculate E-state values for E-state indicies...</span>
+ 320 <span class="c">#</span>
+<a name="_CalculateEStateValuesDescriptors-"></a> 321 <span class="k">sub </span><span class="m">_CalculateEStateValuesDescriptors</span> <span class="s">{</span>
+ 322   <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+ 323   <span class="k">my</span><span class="s">(</span><span class="i">$EStateValuesDescriptors</span><span class="cm">,</span> <span class="i">$Atom</span><span class="cm">,</span> <span class="i">$AtomID</span><span class="cm">,</span> <span class="i">$EStateValue</span><span class="s">)</span><span class="sc">;</span>
+ 324 
+ 325   <span class="i">%</span>{<span class="i">$This</span>-&gt;{<span class="w">EStateValues</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 326 
+ 327   <span class="c"># Calculate and assign E-state values...</span>
+ 328   <span class="i">$EStateValuesDescriptors</span> = <span class="i">new</span> <span class="i">AtomicDescriptors::EStateValuesDescriptors</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span> <span class="cm">=&gt;</span> <span class="i">$This</span>-&gt;{<span class="w">Molecule</span>}<span class="s">)</span><span class="sc">;</span>
+ 329   <span class="i">$EStateValuesDescriptors</span><span class="i">-&gt;GenerateDescriptors</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 330 
+ 331   <span class="c"># Make sure E-state values calculation is successful...</span>
+ 332   <span class="k">if</span> <span class="s">(</span>!<span class="i">$EStateValuesDescriptors</span><span class="i">-&gt;IsDescriptorsGenerationSuccessful</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+ 333     <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
+ 334   <span class="s">}</span>
+ 335 
+ 336   <span class="c"># Collect assigned E-state values...</span>
+ 337   <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$This</span>-&gt;{<span class="w">Atoms</span>}}<span class="s">)</span> <span class="s">{</span>
+ 338     <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>
+ 339     <span class="i">$EStateValue</span> = <span class="i">$EStateValuesDescriptors</span><span class="i">-&gt;GetDescriptorValue</span><span class="s">(</span><span class="i">$Atom</span><span class="s">)</span><span class="sc">;</span>
+ 340     <span class="i">$This</span>-&gt;{<span class="w">EStateValues</span>}{<span class="i">$AtomID</span>} = <span class="i">$EStateValue</span><span class="sc">;</span>
+ 341   <span class="s">}</span>
+ 342   <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
+ 343 <span class="s">}</span>
+ 344 
+ 345 <span class="c"># Set final final fingerpritns for E-state indicies...</span>
+ 346 <span class="c">#</span>
+<a name="_SetFinalFingerprints-"></a> 347 <span class="k">sub </span><span class="m">_SetFinalFingerprints</span> <span class="s">{</span>
+ 348   <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+ 349   <span class="k">my</span><span class="s">(</span><span class="i">$AtomType</span><span class="cm">,</span> <span class="i">$ValuesPrecision</span><span class="cm">,</span> <span class="i">$EStateAtomTypesDataRef</span><span class="cm">,</span> <span class="i">@Values</span><span class="cm">,</span> <span class="i">@IDs</span><span class="s">)</span><span class="sc">;</span>
+ 350 
+ 351   <span class="c"># Mark successful generation of fingerprints...</span>
+ 352   <span class="i">$This</span>-&gt;{<span class="w">FingerprintsGenerated</span>} = <span class="n">1</span><span class="sc">;</span>
+ 353 
+ 354   <span class="i">@Values</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 355   <span class="i">@IDs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 356 
+ 357   <span class="i">$ValuesPrecision</span> = <span class="i">$This</span>-&gt;{<span class="w">ValuesPrecision</span>}<span class="sc">;</span>
+ 358 
+ 359   <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">EStateAtomTypesSetToUse</span>} =~ <span class="q">/^FixedSize$/i</span><span class="s">)</span> <span class="s">{</span>
+ 360     <span class="c"># Use fixed size E-state atom types set for non-hydrogen atoms...</span>
+ 361     <span class="k">for</span> <span class="i">$AtomType</span> <span class="s">(</span><span class="i">@</span>{<span class="i">AtomTypes::EStateAtomTypes::GetAllPossibleEStateNonHydrogenAtomTypes</span><span class="s">(</span><span class="s">)</span>}<span class="s">)</span> <span class="s">{</span>
+ 362       <span class="k">push</span> <span class="i">@IDs</span><span class="cm">,</span> <span class="q">&quot;S${AtomType}&quot;</span><span class="sc">;</span>
+ 363       <span class="k">push</span> <span class="i">@Values</span><span class="cm">,</span> <span class="k">exists</span><span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">EStateIndicies</span>}{<span class="i">$AtomType</span>}<span class="s">)</span> ? <span class="i">MathUtil::round</span><span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">EStateIndicies</span>}{<span class="i">$AtomType</span>}<span class="cm">,</span> <span class="i">$ValuesPrecision</span><span class="s">)</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
+ 364     <span class="s">}</span>
+ 365   <span class="s">}</span>
+ 366   <span class="k">else</span> <span class="s">{</span>
+ 367     <span class="k">for</span> <span class="i">$AtomType</span> <span class="s">(</span><span class="k">sort</span> <span class="k">keys</span> <span class="i">%</span>{<span class="i">$This</span>-&gt;{<span class="w">EStateIndicies</span>}}<span class="s">)</span> <span class="s">{</span>
+ 368       <span class="k">push</span> <span class="i">@IDs</span><span class="cm">,</span> <span class="q">&quot;S${AtomType}&quot;</span><span class="sc">;</span>
+ 369       <span class="k">push</span> <span class="i">@Values</span><span class="cm">,</span> <span class="i">MathUtil::round</span><span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">EStateIndicies</span>}{<span class="i">$AtomType</span>}<span class="cm">,</span> <span class="i">$ValuesPrecision</span><span class="s">)</span><span class="sc">;</span>
+ 370     <span class="s">}</span>
+ 371   <span class="s">}</span>
+ 372 
+ 373   <span class="c"># Add IDs and values to fingerprint vector...</span>
+ 374   <span class="k">if</span> <span class="s">(</span><span class="i">@IDs</span><span class="s">)</span> <span class="s">{</span>
+ 375     <span class="i">$This</span>-&gt;{<span class="w">FingerprintsVector</span>}<span class="i">-&gt;AddValueIDs</span><span class="s">(</span>\<span class="i">@IDs</span><span class="s">)</span><span class="sc">;</span>
+ 376   <span class="s">}</span>
+ 377   <span class="i">$This</span>-&gt;{<span class="w">FingerprintsVector</span>}<span class="i">-&gt;AddValues</span><span class="s">(</span>\<span class="i">@Values</span><span class="s">)</span><span class="sc">;</span>
+ 378 
+ 379   <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
+ 380 <span class="s">}</span>
+ 381 
+ 382 <span class="c"># Cache  appropriate molecule data...</span>
+ 383 <span class="c">#</span>
+<a name="_SetupMoleculeDataCache-"></a> 384 <span class="k">sub </span><span class="m">_SetupMoleculeDataCache</span> <span class="s">{</span>
+ 385   <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+ 386 
+ 387   <span class="c"># Get all non-hydrogen atoms...</span>
+ 388   <span class="k">my</span><span class="s">(</span><span class="i">$NegateAtomCheckMethod</span><span class="s">)</span><span class="sc">;</span>
+ 389   <span class="i">$NegateAtomCheckMethod</span> = <span class="n">1</span><span class="sc">;</span>
+ 390   <span class="i">@</span>{<span class="i">$This</span>-&gt;{<span class="w">Atoms</span>}} = <span class="i">$This</span><span class="i">-&gt;GetMolecule</span><span class="s">(</span><span class="s">)</span><span class="i">-&gt;GetAtoms</span><span class="s">(</span><span class="q">&quot;IsHydrogen&quot;</span><span class="cm">,</span> <span class="i">$NegateAtomCheckMethod</span><span class="s">)</span><span class="sc">;</span>
+ 391 
+ 392   <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
+ 393 <span class="s">}</span>
+ 394 
+ 395 <span class="c"># Clear cached molecule data...</span>
+ 396 <span class="c">#</span>
+<a name="_ClearMoleculeDataCache-"></a> 397 <span class="k">sub </span><span class="m">_ClearMoleculeDataCache</span> <span class="s">{</span>
+ 398   <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+ 399 
+ 400   <span class="i">@</span>{<span class="i">$This</span>-&gt;{<span class="w">Atoms</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 401 
+ 402   <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
+ 403 <span class="s">}</span>
+ 404 
+ 405 <span class="c"># Return a string containg data for EStateIndiciesFingerprints object...</span>
+<a name="StringifyEStateIndiciesFingerprints-"></a> 406 <span class="k">sub </span><span class="m">StringifyEStateIndiciesFingerprints</span> <span class="s">{</span>
+ 407   <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+ 408   <span class="k">my</span><span class="s">(</span><span class="i">$EStateIndiciesFingerprintsString</span><span class="s">)</span><span class="sc">;</span>
+ 409 
+ 410   <span class="c"># Type of Keys...</span>
+ 411   <span class="i">$EStateIndiciesFingerprintsString</span> = <span class="q">&quot;Type: $This-&gt;{Type}; EStateAtomTypesSetToUse: $This-&gt;{EStateAtomTypesSetToUse}&quot;</span><span class="sc">;</span>
+ 412 
+ 413   <span class="c"># Fingerprint vector...</span>
+ 414   <span class="i">$EStateIndiciesFingerprintsString</span> .= <span class="q">&quot;; FingerprintsVector: &lt; $This-&gt;{FingerprintsVector} &gt;&quot;</span><span class="sc">;</span>
+ 415 
+ 416   <span class="k">return</span> <span class="i">$EStateIndiciesFingerprintsString</span><span class="sc">;</span>
+ 417 <span class="s">}</span>
+ 418 
+<a name="EOF-"></a></pre>
+<p>&nbsp;</p>
+<br />
+<center>
+<img src="../../../images/h2o2.png">
+</center>
+</body>
+</html>