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+<a name="package-Fingerprints::TopologicalAtomTorsionsFingerprints-"></a>   1 <span class="k">package </span><span class="i">Fingerprints::TopologicalAtomTorsionsFingerprints</span><span class="sc">;</span>
+   2 <span class="c">#</span>
+   3 <span class="c"># $RCSfile: TopologicalAtomTorsionsFingerprints.pm,v $</span>
+   4 <span class="c"># $Date: 2015/02/28 20:48:54 $</span>
+   5 <span class="c"># $Revision: 1.26 $</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">Fingerprints::Fingerprints</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">Molecule</span><span class="sc">;</span>
+  35 <span class="k">use</span> <span class="w">AtomTypes::AtomicInvariantsAtomTypes</span><span class="sc">;</span>
+  36 <span class="k">use</span> <span class="w">AtomTypes::DREIDINGAtomTypes</span><span class="sc">;</span>
+  37 <span class="k">use</span> <span class="w">AtomTypes::EStateAtomTypes</span><span class="sc">;</span>
+  38 <span class="k">use</span> <span class="w">AtomTypes::FunctionalClassAtomTypes</span><span class="sc">;</span>
+  39 <span class="k">use</span> <span class="w">AtomTypes::MMFF94AtomTypes</span><span class="sc">;</span>
+  40 <span class="k">use</span> <span class="w">AtomTypes::SLogPAtomTypes</span><span class="sc">;</span>
+  41 <span class="k">use</span> <span class="w">AtomTypes::SYBYLAtomTypes</span><span class="sc">;</span>
+  42 <span class="k">use</span> <span class="w">AtomTypes::TPSAAtomTypes</span><span class="sc">;</span>
+  43 <span class="k">use</span> <span class="w">AtomTypes::UFFAtomTypes</span><span class="sc">;</span>
+  44 
+  45 <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>
+  46 
+  47 <span class="i">@ISA</span> = <span class="q">qw(Fingerprints::Fingerprints Exporter)</span><span class="sc">;</span>
+  48 <span class="i">@EXPORT</span> = <span class="q">qw()</span><span class="sc">;</span>
+  49 <span class="i">@EXPORT_OK</span> = <span class="q">qw()</span><span class="sc">;</span>
+  50 
+  51 <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>
+  52 
+  53 <span class="c"># Setup class variables...</span>
+  54 <span class="k">my</span><span class="s">(</span><span class="i">$ClassName</span><span class="s">)</span><span class="sc">;</span>
+  55 <span class="i">_InitializeClass</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+  56 
+  57 <span class="c"># Overload Perl functions...</span>
+  58 <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;StringifyTopologicalAtomTorsionsFingerprints&#39;</span><span class="sc">;</span>
+  59 
+  60 <span class="c"># Class constructor...</span>
+<a name="new-"></a>  61 <span class="k">sub </span><span class="m">new</span> <span class="s">{</span>
+  62   <span class="k">my</span><span class="s">(</span><span class="i">$Class</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+  63 
+  64   <span class="c"># Initialize object...</span>
+  65   <span class="k">my</span> <span class="i">$This</span> = <span class="i">$Class</span><span class="i">-&gt;SUPER::new</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+  66   <span class="k">bless</span> <span class="i">$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>
+  67   <span class="i">$This</span><span class="i">-&gt;_InitializeTopologicalAtomTorsionsFingerprints</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+  68 
+  69   <span class="i">$This</span><span class="i">-&gt;_InitializeTopologicalAtomTorsionsFingerprintsProperties</span><span class="s">(</span><span class="i">%NamesAndValues</span><span class="s">)</span><span class="sc">;</span>
+  70 
+  71   <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
+  72 <span class="s">}</span>
+  73 
+  74 <span class="c"># Initialize object data...</span>
+  75 <span class="c">#</span>
+<a name="_InitializeTopologicalAtomTorsionsFingerprints-"></a>  76 <span class="k">sub </span><span class="m">_InitializeTopologicalAtomTorsionsFingerprints</span> <span class="s">{</span>
+  77   <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+  78 
+  79   <span class="c"># Type of fingerprint...</span>
+  80   <span class="i">$This</span>-&gt;{<span class="w">Type</span>} = <span class="q">&#39;TopologicalAtomTorsions&#39;</span><span class="sc">;</span>
+  81 
+  82   <span class="c"># Type of vector...</span>
+  83   <span class="i">$This</span>-&gt;{<span class="w">VectorType</span>} = <span class="q">&#39;FingerprintsVector&#39;</span><span class="sc">;</span>
+  84 
+  85   <span class="c"># Type of FingerprintsVector...</span>
+  86   <span class="i">$This</span>-&gt;{<span class="w">FingerprintsVectorType</span>} = <span class="q">&#39;NumericalValues&#39;</span><span class="sc">;</span>
+  87 
+  88   <span class="c"># Atom identifier type to use for atom IDs in atom torsions...</span>
+  89   <span class="c">#</span>
+  90   <span class="c"># Currently supported values are: AtomicInvariantsAtomTypes, DREIDINGAtomTypes,</span>
+  91   <span class="c"># EStateAtomTypes, FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes,</span>
+  92   <span class="c"># SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes</span>
+  93   <span class="c">#</span>
+  94   <span class="i">$This</span>-&gt;{<span class="w">AtomIdentifierType</span>} = <span class="q">&#39;&#39;</span><span class="sc">;</span>
+  95 
+  96   <span class="c"># Atom types assigned to each heavy atom...</span>
+  97   <span class="c">#</span>
+  98   <span class="i">%</span>{<span class="i">$This</span>-&gt;{<span class="w">AssignedAtomTypes</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+  99 
+ 100   <span class="c"># Final unique atom torsions...</span>
+ 101   <span class="c">#</span>
+ 102   <span class="i">@</span>{<span class="i">$This</span>-&gt;{<span class="w">AtomTorsionsIDs</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 103   <span class="i">%</span>{<span class="i">$This</span>-&gt;{<span class="w">AtomTorsionsCount</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 104 <span class="s">}</span>
+ 105 
+ 106 <span class="c"># Initialize class ...</span>
+<a name="_InitializeClass-"></a> 107 <span class="k">sub </span><span class="m">_InitializeClass</span> <span class="s">{</span>
+ 108   <span class="c">#Class name...</span>
+ 109   <span class="i">$ClassName</span> = <span class="w">__PACKAGE__</span><span class="sc">;</span>
+ 110 <span class="s">}</span>
+ 111 
+ 112 <span class="c"># Initialize object properties....</span>
+<a name="_InitializeTopologicalAtomTorsionsFingerprintsProperties-"></a> 113 <span class="k">sub </span><span class="m">_InitializeTopologicalAtomTorsionsFingerprintsProperties</span> <span class="s">{</span>
+ 114   <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+ 115 
+ 116   <span class="k">my</span><span class="s">(</span><span class="i">$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>
+ 117   <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>
+ 118     <span class="i">$MethodName</span> = <span class="q">&quot;Set${Name}&quot;</span><span class="sc">;</span>
+ 119     <span class="i">$This</span><span class="i">-&gt;$MethodName</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="sc">;</span>
+ 120   <span class="s">}</span>
+ 121 
+ 122   <span class="c"># Make sure molecule object was specified...</span>
+ 123   <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$NamesAndValues</span>{<span class="w">Molecule</span>}<span class="s">)</span> <span class="s">{</span>
+ 124     <span class="w">croak</span> <span class="q">&quot;Error: ${ClassName}-&gt;New: Object can&#39;t be instantiated without specifying molecule...&quot;</span><span class="sc">;</span>
+ 125   <span class="s">}</span>
+ 126   <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$NamesAndValues</span>{<span class="w">AtomIdentifierType</span>}<span class="s">)</span> <span class="s">{</span>
+ 127     <span class="w">croak</span> <span class="q">&quot;Error: ${ClassName}-&gt;New: Object can&#39;t be instantiated without specifying AtomIdentifierType...&quot;</span><span class="sc">;</span>
+ 128   <span class="s">}</span>
+ 129 
+ 130   <span class="i">$This</span><span class="i">-&gt;_InitializeFingerprintsVector</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 131 
+ 132   <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
+ 133 <span class="s">}</span>
+ 134 
+ 135 <span class="c"># Set atom identifier type..</span>
+ 136 <span class="c">#</span>
+<a name="SetAtomIdentifierType-"></a> 137 <span class="k">sub </span><span class="m">SetAtomIdentifierType</span> <span class="s">{</span>
+ 138   <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$IdentifierType</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+ 139 
+ 140   <span class="k">if</span> <span class="s">(</span><span class="i">$IdentifierType</span> !~ <span class="q">/^(AtomicInvariantsAtomTypes|DREIDINGAtomTypes|EStateAtomTypes|FunctionalClassAtomTypes|MMFF94AtomTypes|SLogPAtomTypes|SYBYLAtomTypes|TPSAAtomTypes|UFFAtomTypes)$/i</span><span class="s">)</span> <span class="s">{</span>
+ 141     <span class="w">croak</span> <span class="q">&quot;Error: ${ClassName}-&gt;SetAtomIdentifierType: Specified value, $IdentifierType, for AtomIdentifierType is not vaild. Supported types in current release of MayaChemTools: AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes, and UFFAtomTypes.&quot;</span><span class="sc">;</span>
+ 142   <span class="s">}</span>
+ 143 
+ 144   <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">AtomIdentifierType</span>}<span class="s">)</span> <span class="s">{</span>
+ 145     <span class="w">croak</span> <span class="q">&quot;Error: ${ClassName}-&gt;SeAtomIdentifierType: Can&#39;t change intial atom identifier type:  It&#39;s already set...&quot;</span><span class="sc">;</span>
+ 146   <span class="s">}</span>
+ 147 
+ 148   <span class="i">$This</span>-&gt;{<span class="w">AtomIdentifierType</span>} = <span class="i">$IdentifierType</span><span class="sc">;</span>
+ 149 
+ 150   <span class="c"># Initialize atom identifier type information...</span>
+ 151   <span class="i">$This</span><span class="i">-&gt;_InitializeAtomIdentifierTypeInformation</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 152 
+ 153   <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
+ 154 <span class="s">}</span>
+ 155 
+ 156 <span class="c"># Generate fingerprints description...</span>
+ 157 <span class="c">#</span>
+<a name="GetDescription-"></a> 158 <span class="k">sub </span><span class="m">GetDescription</span> <span class="s">{</span>
+ 159   <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+ 160 
+ 161   <span class="c"># Is description explicity set?</span>
+ 162   <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$This</span>-&gt;{<span class="w">Description</span>}<span class="s">)</span> <span class="s">{</span>
+ 163     <span class="k">return</span> <span class="i">$This</span>-&gt;{<span class="w">Description</span>}<span class="sc">;</span>
+ 164   <span class="s">}</span>
+ 165 
+ 166   <span class="c"># Generate fingerprints description...</span>
+ 167 
+ 168   <span class="k">return</span> <span class="q">&quot;$This-&gt;{Type}:$This-&gt;{AtomIdentifierType}&quot;</span><span class="sc">;</span>
+ 169 <span class="s">}</span>
+ 170 
+ 171 <span class="c"># Generate topological atom torsions [ Ref 58, Ref 72 ] fingerprints...</span>
+ 172 <span class="c">#</span>
+ 173 <span class="c"># Methodology:</span>
+ 174 <span class="c">#   . Assign atom types to all the atoms.</span>
+ 175 <span class="c">#   . Generate and count atom torsions.</span>
+ 176 <span class="c">#</span>
+ 177 <span class="c"># Notes:</span>
+ 178 <span class="c">#   . Hydrogen atoms are ignored during the fingerprint generation.</span>
+ 179 <span class="c">#</span>
+<a name="GenerateFingerprints-"></a> 180 <span class="k">sub </span><span class="m">GenerateFingerprints</span> <span class="s">{</span>
+ 181   <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+ 182 
+ 183   <span class="c"># Cache appropriate molecule data...</span>
+ 184   <span class="i">$This</span><span class="i">-&gt;_SetupMoleculeDataCache</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 185 
+ 186   <span class="c"># Assign atom types to all heavy atoms...</span>
+ 187   <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">-&gt;_AssignAtomTypes</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+ 188     <span class="w">carp</span> <span class="q">&quot;Warning: ${ClassName}-&gt;GenerateFingerprints: $This-&gt;{AtomIdentifierType} fingerprints generation didn&#39;t succeed: Couldn&#39;t assign valid $This-&gt;{AtomIdentifierType} to all atoms...&quot;</span><span class="sc">;</span>
+ 189     <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
+ 190   <span class="s">}</span>
+ 191 
+ 192   <span class="c"># Count atom torsions...</span>
+ 193   <span class="i">$This</span><span class="i">-&gt;_GenerateAndCountAtomTorsions</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 194 
+ 195   <span class="c"># Set final fingerprints...</span>
+ 196   <span class="i">$This</span><span class="i">-&gt;_SetFinalFingerprints</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 197 
+ 198   <span class="c"># Clear cached molecule data...</span>
+ 199   <span class="i">$This</span><span class="i">-&gt;_ClearMoleculeDataCache</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 200 
+ 201   <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
+ 202 <span class="s">}</span>
+ 203 
+ 204 <span class="c"># Assign appropriate atom types to all heavy atoms...</span>
+ 205 <span class="c">#</span>
+<a name="_AssignAtomTypes-"></a> 206 <span class="k">sub </span><span class="m">_AssignAtomTypes</span> <span class="s">{</span>
+ 207   <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+ 208   <span class="k">my</span><span class="s">(</span><span class="i">$SpecifiedAtomTypes</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">$IgnoreHydrogens</span><span class="s">)</span><span class="sc">;</span>
+ 209 
+ 210   <span class="i">%</span>{<span class="i">$This</span>-&gt;{<span class="w">AssignedAtomTypes</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 211   <span class="i">$IgnoreHydrogens</span> = <span class="n">1</span><span class="sc">;</span>
+ 212 
+ 213   <span class="i">$SpecifiedAtomTypes</span> = <span class="k">undef</span><span class="sc">;</span>
+ 214 
+ 215   <span class="j">IDENTIFIERTYPE:</span> <span class="s">{</span>
+ 216     <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^AtomicInvariantsAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span>
+ 217       <span class="i">$SpecifiedAtomTypes</span> = <span class="i">new</span> <span class="i">AtomTypes::AtomicInvariantsAtomTypes</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span> <span class="cm">=&gt;</span> <span class="i">$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="i">$IgnoreHydrogens</span><span class="cm">,</span> <span class="q">&#39;AtomicInvariantsToUse&#39;</span> <span class="cm">=&gt;</span> <span class="i">$This</span>-&gt;{<span class="w">AtomicInvariantsToUse</span>}<span class="s">)</span><span class="sc">;</span>
+ 218       <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span>
+ 219     <span class="s">}</span>
+ 220 
+ 221     <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^DREIDINGAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span>
+ 222       <span class="i">$SpecifiedAtomTypes</span> = <span class="i">new</span> <span class="i">AtomTypes::DREIDINGAtomTypes</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span> <span class="cm">=&gt;</span> <span class="i">$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="i">$IgnoreHydrogens</span><span class="s">)</span><span class="sc">;</span>
+ 223       <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span>
+ 224     <span class="s">}</span>
+ 225 
+ 226     <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^EStateAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span>
+ 227       <span class="i">$SpecifiedAtomTypes</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">$This</span>-&gt;{<span class="w">Molecule</span>}<span class="cm">,</span> <span class="q">&#39;IgnoreHydrogens&#39;</span> <span class="cm">=&gt;</span> <span class="i">$IgnoreHydrogens</span><span class="s">)</span><span class="sc">;</span>
+ 228       <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span>
+ 229     <span class="s">}</span>
+ 230 
+ 231     <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^FunctionalClassAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span>
+ 232       <span class="i">$SpecifiedAtomTypes</span> = <span class="i">new</span> <span class="i">AtomTypes::FunctionalClassAtomTypes</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span> <span class="cm">=&gt;</span> <span class="i">$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="i">$IgnoreHydrogens</span><span class="cm">,</span> <span class="q">&#39;FunctionalClassesToUse&#39;</span> <span class="cm">=&gt;</span> <span class="i">$This</span>-&gt;{<span class="w">FunctionalClassesToUse</span>}<span class="s">)</span><span class="sc">;</span>
+ 233       <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span>
+ 234     <span class="s">}</span>
+ 235 
+ 236     <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^MMFF94AtomTypes$/i</span><span class="s">)</span> <span class="s">{</span>
+ 237       <span class="i">$SpecifiedAtomTypes</span> = <span class="i">new</span> <span class="i">AtomTypes::MMFF94AtomTypes</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span> <span class="cm">=&gt;</span> <span class="i">$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="i">$IgnoreHydrogens</span><span class="s">)</span><span class="sc">;</span>
+ 238       <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span>
+ 239     <span class="s">}</span>
+ 240 
+ 241     <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^SLogPAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span>
+ 242       <span class="i">$SpecifiedAtomTypes</span> = <span class="i">new</span> <span class="i">AtomTypes::SLogPAtomTypes</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span> <span class="cm">=&gt;</span> <span class="i">$This</span>-&gt;{<span class="w">Molecule</span>}<span class="cm">,</span> <span class="q">&#39;IgnoreHydrogens&#39;</span> <span class="cm">=&gt;</span> <span class="i">$IgnoreHydrogens</span><span class="s">)</span><span class="sc">;</span>
+ 243       <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span>
+ 244     <span class="s">}</span>
+ 245     <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^SYBYLAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span>
+ 246       <span class="i">$SpecifiedAtomTypes</span> = <span class="i">new</span> <span class="i">AtomTypes::SYBYLAtomTypes</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span> <span class="cm">=&gt;</span> <span class="i">$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="i">$IgnoreHydrogens</span><span class="s">)</span><span class="sc">;</span>
+ 247       <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span>
+ 248     <span class="s">}</span>
+ 249 
+ 250     <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^TPSAAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span>
+ 251       <span class="i">$SpecifiedAtomTypes</span> = <span class="i">new</span> <span class="i">AtomTypes::TPSAAtomTypes</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span> <span class="cm">=&gt;</span> <span class="i">$This</span>-&gt;{<span class="w">Molecule</span>}<span class="cm">,</span> <span class="q">&#39;IgnorePhosphorus&#39;</span> <span class="cm">=&gt;</span> <span class="n">0</span><span class="cm">,</span> <span class="q">&#39;IgnoreSulfur&#39;</span> <span class="cm">=&gt;</span> <span class="n">0</span><span class="s">)</span><span class="sc">;</span>
+ 252       <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span>
+ 253     <span class="s">}</span>
+ 254 
+ 255     <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^UFFAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span>
+ 256       <span class="i">$SpecifiedAtomTypes</span> = <span class="i">new</span> <span class="i">AtomTypes::UFFAtomTypes</span><span class="s">(</span><span class="q">&#39;Molecule&#39;</span> <span class="cm">=&gt;</span> <span class="i">$This</span>-&gt;{<span class="w">Molecule</span>}<span class="cm">,</span> <span class="q">&#39;IgnoreHydrogens&#39;</span> <span class="cm">=&gt;</span> <span class="i">$IgnoreHydrogens</span><span class="s">)</span><span class="sc">;</span>
+ 257       <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span>
+ 258     <span class="s">}</span>
+ 259 
+ 260     <span class="w">croak</span> <span class="q">&quot;Error: ${ClassName}-&gt;_AssignAtomTypes: Unknown atom indentifier type $This-&gt;{AtomIdentifierType}...&quot;</span><span class="sc">;</span>
+ 261   <span class="s">}</span>
+ 262 
+ 263   <span class="c"># Assign atom types...</span>
+ 264   <span class="i">$SpecifiedAtomTypes</span><span class="i">-&gt;AssignAtomTypes</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 265 
+ 266   <span class="c"># Make sure atom types assignment is successful...</span>
+ 267   <span class="k">if</span> <span class="s">(</span>!<span class="i">$SpecifiedAtomTypes</span><span class="i">-&gt;IsAtomTypesAssignmentSuccessful</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+ 268     <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
+ 269   <span class="s">}</span>
+ 270 
+ 271   <span class="c"># Collect assigned atom types...</span>
+ 272   <span class="j">ATOM:</span> <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$This</span>-&gt;{<span class="w">Atoms</span>}}<span class="s">)</span> <span class="s">{</span>
+ 273     <span class="k">if</span> <span class="s">(</span><span class="i">$Atom</span><span class="i">-&gt;IsHydrogen</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+ 274       <span class="k">next</span> <span class="j">ATOM</span><span class="sc">;</span>
+ 275     <span class="s">}</span>
+ 276     <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>
+ 277     <span class="i">$This</span>-&gt;{<span class="w">AssignedAtomTypes</span>}{<span class="i">$AtomID</span>} = <span class="i">$SpecifiedAtomTypes</span><span class="i">-&gt;GetAtomType</span><span class="s">(</span><span class="i">$Atom</span><span class="s">)</span><span class="sc">;</span>
+ 278   <span class="s">}</span>
+ 279 
+ 280   <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
+ 281 <span class="s">}</span>
+ 282 
+ 283 <span class="c"># Count atom torsions involving non-hydrogen atoms by going over the structurally</span>
+ 284 <span class="c"># unique atom torsions...</span>
+ 285 <span class="c">#</span>
+<a name="_GenerateAndCountAtomTorsions-"></a> 286 <span class="k">sub </span><span class="m">_GenerateAndCountAtomTorsions</span> <span class="s">{</span>
+ 287   <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+ 288   <span class="k">my</span><span class="s">(</span><span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="cm">,</span> <span class="i">$Atom3</span><span class="cm">,</span> <span class="i">$Atom4</span><span class="cm">,</span> <span class="i">$AtomID1</span><span class="cm">,</span> <span class="i">$AtomID2</span><span class="cm">,</span> <span class="i">$AtomID3</span><span class="cm">,</span> <span class="i">$AtomID4</span><span class="cm">,</span> <span class="i">$AtomTorsionID</span><span class="cm">,</span> <span class="i">@Atom1Neighbors</span><span class="cm">,</span> <span class="i">@Atom2Neighbors</span><span class="cm">,</span> <span class="i">@Atom3Neighbors</span><span class="s">)</span><span class="sc">;</span>
+ 289 
+ 290   <span class="c"># Setup a hash to track structurally unique atom torsions by atom IDs...</span>
+ 291   <span class="i">%</span>{<span class="i">$This</span>-&gt;{<span class="w">StructurallyUniqueAtomTorsions</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 292 
+ 293   <span class="j">ATOM1:</span> <span class="k">for</span> <span class="i">$Atom1</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$This</span>-&gt;{<span class="w">Atoms</span>}}<span class="s">)</span> <span class="s">{</span>
+ 294     <span class="k">if</span> <span class="s">(</span><span class="i">$Atom1</span><span class="i">-&gt;IsHydrogen</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+ 295       <span class="k">next</span> <span class="j">ATOM1</span><span class="sc">;</span>
+ 296     <span class="s">}</span>
+ 297     <span class="i">$AtomID1</span> = <span class="i">$Atom1</span><span class="i">-&gt;GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 298     <span class="c"># Go over Atom1 neighbors other than Atom1...</span>
+ 299     <span class="i">@Atom1Neighbors</span> = <span class="i">$Atom1</span><span class="i">-&gt;GetNeighbors</span><span class="s">(</span><span class="i">$Atom1</span><span class="s">)</span><span class="sc">;</span>
+ 300     <span class="j">ATOM2:</span> <span class="k">for</span> <span class="i">$Atom2</span> <span class="s">(</span><span class="i">@Atom1Neighbors</span><span class="s">)</span> <span class="s">{</span>
+ 301       <span class="k">if</span> <span class="s">(</span><span class="i">$Atom2</span><span class="i">-&gt;IsHydrogen</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+ 302         <span class="k">next</span> <span class="j">ATOM2</span><span class="sc">;</span>
+ 303       <span class="s">}</span>
+ 304       <span class="i">$AtomID2</span> = <span class="i">$Atom2</span><span class="i">-&gt;GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 305       <span class="c"># Go over Atom2 neighbors other than Atom1 and Atom2...</span>
+ 306       <span class="i">@Atom2Neighbors</span> = <span class="i">$Atom2</span><span class="i">-&gt;GetNeighbors</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>
+ 307       <span class="j">ATOM3:</span> <span class="k">for</span> <span class="i">$Atom3</span> <span class="s">(</span><span class="i">@Atom2Neighbors</span><span class="s">)</span> <span class="s">{</span>
+ 308         <span class="k">if</span> <span class="s">(</span><span class="i">$Atom3</span><span class="i">-&gt;IsHydrogen</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+ 309           <span class="k">next</span> <span class="j">ATOM3</span><span class="sc">;</span>
+ 310         <span class="s">}</span>
+ 311         <span class="i">$AtomID3</span> = <span class="i">$Atom3</span><span class="i">-&gt;GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 312         <span class="i">@Atom3Neighbors</span> = <span class="i">$Atom3</span><span class="i">-&gt;GetNeighbors</span><span class="s">(</span><span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="cm">,</span> <span class="i">$Atom3</span><span class="s">)</span><span class="sc">;</span>
+ 313         <span class="c"># Go over Atom3 neighbors other than Atom1, Atom2 and Atom3...</span>
+ 314         <span class="j">ATOM4:</span> <span class="k">for</span> <span class="i">$Atom4</span> <span class="s">(</span><span class="i">@Atom3Neighbors</span><span class="s">)</span> <span class="s">{</span>
+ 315           <span class="k">if</span> <span class="s">(</span><span class="i">$Atom4</span><span class="i">-&gt;IsHydrogen</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+ 316             <span class="k">next</span> <span class="j">ATOM4</span><span class="sc">;</span>
+ 317           <span class="s">}</span>
+ 318           <span class="i">$AtomID4</span> = <span class="i">$Atom4</span><span class="i">-&gt;GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 319 
+ 320           <span class="c"># Is it a structurally unique torsion?</span>
+ 321           <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">-&gt;_IsStructurallyUniqueTorsion</span><span class="s">(</span><span class="i">$AtomID1</span><span class="cm">,</span> <span class="i">$AtomID2</span><span class="cm">,</span> <span class="i">$AtomID3</span><span class="cm">,</span> <span class="i">$AtomID4</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+ 322             <span class="k">next</span> <span class="j">ATOM4</span><span class="sc">;</span>
+ 323           <span class="s">}</span>
+ 324 
+ 325           <span class="c"># Track structurally unique torsions...</span>
+ 326           <span class="i">$AtomTorsionID</span> = <span class="i">$This</span><span class="i">-&gt;_GetAtomTorsionID</span><span class="s">(</span><span class="i">$AtomID1</span><span class="cm">,</span> <span class="i">$AtomID2</span><span class="cm">,</span> <span class="i">$AtomID3</span><span class="cm">,</span> <span class="i">$AtomID4</span><span class="s">)</span><span class="sc">;</span>
+ 327           <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$This</span>-&gt;{<span class="w">AtomTorsionsCount</span>}{<span class="i">$AtomTorsionID</span>}<span class="s">)</span> <span class="s">{</span>
+ 328             <span class="i">$This</span>-&gt;{<span class="w">AtomTorsionsCount</span>}{<span class="i">$AtomTorsionID</span>} += <span class="n">1</span><span class="sc">;</span>
+ 329           <span class="s">}</span>
+ 330           <span class="k">else</span> <span class="s">{</span>
+ 331             <span class="i">$This</span>-&gt;{<span class="w">AtomTorsionsCount</span>}{<span class="i">$AtomTorsionID</span>} = <span class="n">1</span><span class="sc">;</span>
+ 332           <span class="s">}</span>
+ 333         <span class="s">}</span>
+ 334       <span class="s">}</span>
+ 335     <span class="s">}</span>
+ 336   <span class="s">}</span>
+ 337 
+ 338   <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
+ 339 <span class="s">}</span>
+ 340 
+ 341 <span class="c"># Is it a structurally unique torsions?</span>
+ 342 <span class="c">#</span>
+ 343 <span class="c"># Notes:</span>
+ 344 <span class="c">#  . For a torsion to be structurally unique which hasn&#39;t already been encountered,</span>
+ 345 <span class="c">#    all the four atoms involved in the torsion must be new atoms. And this can be</span>
+ 346 <span class="c">#    simply implemented by tracking the torsions using atom IDs and maintaining a</span>
+ 347 <span class="c">#    hash of already encountered torsions using lexicographically smaller torsion ID</span>
+ 348 <span class="c">#    consisting of four atom IDs.</span>
+ 349 <span class="c">#</span>
+<a name="_IsStructurallyUniqueTorsion-"></a> 350 <span class="k">sub </span><span class="m">_IsStructurallyUniqueTorsion</span> <span class="s">{</span>
+ 351   <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">@AtomIDs</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+ 352   <span class="k">my</span><span class="s">(</span><span class="i">$TorsionID</span><span class="cm">,</span> <span class="i">$ReverseTorsionID</span><span class="s">)</span><span class="sc">;</span>
+ 353 
+ 354   <span class="i">$TorsionID</span> = <span class="k">join</span> <span class="q">&quot;-&quot;</span><span class="cm">,</span> <span class="i">@AtomIDs</span><span class="sc">;</span>
+ 355   <span class="i">$ReverseTorsionID</span> = <span class="k">join</span> <span class="q">&quot;-&quot;</span><span class="cm">,</span> <span class="k">reverse</span> <span class="i">@AtomIDs</span><span class="sc">;</span>
+ 356 
+ 357   <span class="c"># Use lexicographically smaller string...</span>
+ 358   <span class="k">if</span> <span class="s">(</span><span class="i">$ReverseTorsionID</span> <span class="k">lt</span> <span class="i">$TorsionID</span><span class="s">)</span> <span class="s">{</span>
+ 359     <span class="i">$TorsionID</span> = <span class="i">$ReverseTorsionID</span><span class="sc">;</span>
+ 360   <span class="s">}</span>
+ 361 
+ 362   <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$This</span>-&gt;{<span class="w">StructurallyUniqueAtomTorsions</span>}{<span class="i">$TorsionID</span>}<span class="s">)</span> <span class="s">{</span>
+ 363     <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
+ 364   <span class="s">}</span>
+ 365 
+ 366   <span class="c"># Keep track...</span>
+ 367   <span class="i">$This</span>-&gt;{<span class="w">StructurallyUniqueAtomTorsions</span>}{<span class="i">$TorsionID</span>} = <span class="n">1</span><span class="sc">;</span>
+ 368 
+ 369   <span class="k">return</span> <span class="n">1</span><span class="sc">;</span>
+ 370 <span class="s">}</span>
+ 371 
+ 372 <span class="c"># Get atom torsion ID corresponding to atom types involved in torsion...</span>
+ 373 <span class="c">#</span>
+ 374 <span class="c"># Notes:</span>
+ 375 <span class="c">#  . TorsionID corresponds to assigned atom types of all the four torsion atoms</span>
+ 376 <span class="c">#    concatenated by hyphen.</span>
+ 377 <span class="c">#  . TorsionIDs are generated for both forward and backward sequence of atoms</span>
+ 378 <span class="c">#    in the torsion and keeping the lexicographically smaller TorsionID to keep TorsionID</span>
+ 379 <span class="c">#    independent of atom ordering.</span>
+ 380 <span class="c">#</span>
+<a name="_GetAtomTorsionID-"></a> 381 <span class="k">sub </span><span class="m">_GetAtomTorsionID</span> <span class="s">{</span>
+ 382   <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">@AtomIDs</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+ 383   <span class="k">my</span><span class="s">(</span><span class="i">$AtomTorsionID</span><span class="cm">,</span> <span class="i">$ReverseAtomTorsionID</span><span class="cm">,</span> <span class="i">@AtomTypes</span><span class="s">)</span><span class="sc">;</span>
+ 384 
+ 385   <span class="i">@AtomTypes</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 386   <span class="i">@AtomTypes</span> = <span class="k">map</span> <span class="s">{</span> <span class="i">$This</span>-&gt;{<span class="w">AssignedAtomTypes</span>}{<span class="i">$_</span>} <span class="s">}</span> <span class="i">@AtomIDs</span><span class="sc">;</span>
+ 387 
+ 388   <span class="i">$AtomTorsionID</span> = <span class="k">join</span> <span class="q">&quot;-&quot;</span><span class="cm">,</span> <span class="i">@AtomTypes</span><span class="sc">;</span>
+ 389   <span class="i">$ReverseAtomTorsionID</span> = <span class="k">join</span> <span class="q">&quot;-&quot;</span><span class="cm">,</span> <span class="k">reverse</span> <span class="i">@AtomTypes</span><span class="sc">;</span>
+ 390 
+ 391   <span class="c"># Use lexicographically smaller string as ID...</span>
+ 392   <span class="k">return</span> <span class="s">(</span><span class="i">$ReverseAtomTorsionID</span> <span class="k">lt</span> <span class="i">$AtomTorsionID</span><span class="s">)</span> ? <span class="i">$ReverseAtomTorsionID</span> <span class="co">:</span> <span class="i">$AtomTorsionID</span><span class="sc">;</span>
+ 393 <span class="s">}</span>
+ 394 
+ 395 <span class="c"># Set final fingerpritns vector...</span>
+ 396 <span class="c">#</span>
+<a name="_SetFinalFingerprints-"></a> 397 <span class="k">sub </span><span class="m">_SetFinalFingerprints</span> <span class="s">{</span>
+ 398   <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+ 399   <span class="k">my</span><span class="s">(</span><span class="i">$AtomTorsionID</span><span class="cm">,</span> <span class="i">$Value</span><span class="cm">,</span> <span class="i">@Values</span><span class="s">)</span><span class="sc">;</span>
+ 400 
+ 401   <span class="c"># Mark successful generation of fingerprints...</span>
+ 402   <span class="i">$This</span>-&gt;{<span class="w">FingerprintsGenerated</span>} = <span class="n">1</span><span class="sc">;</span>
+ 403 
+ 404   <span class="i">@Values</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 405   <span class="i">@</span>{<span class="i">$This</span>-&gt;{<span class="w">AtomTorsionsIDs</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 406 
+ 407   <span class="k">for</span> <span class="i">$AtomTorsionID</span> <span class="s">(</span><span class="k">sort</span> <span class="k">keys</span> <span class="i">%</span>{<span class="i">$This</span>-&gt;{<span class="w">AtomTorsionsCount</span>}}<span class="s">)</span> <span class="s">{</span>
+ 408     <span class="i">$Value</span> = <span class="i">$This</span>-&gt;{<span class="w">AtomTorsionsCount</span>}{<span class="i">$AtomTorsionID</span>}<span class="sc">;</span>
+ 409     <span class="k">push</span> <span class="i">@</span>{<span class="i">$This</span>-&gt;{<span class="w">AtomTorsionsIDs</span>}}<span class="cm">,</span> <span class="i">$AtomTorsionID</span><span class="sc">;</span>
+ 410     <span class="k">push</span> <span class="i">@Values</span><span class="cm">,</span> <span class="i">$Value</span><span class="sc">;</span>
+ 411   <span class="s">}</span>
+ 412 
+ 413   <span class="c"># Add AtomPairsIDs and values to fingerprint vector...</span>
+ 414   <span class="i">$This</span>-&gt;{<span class="w">FingerprintsVector</span>}<span class="i">-&gt;AddValueIDs</span><span class="s">(</span>\<span class="i">@</span>{<span class="i">$This</span>-&gt;{<span class="w">AtomTorsionsIDs</span>}}<span class="s">)</span><span class="sc">;</span>
+ 415   <span class="i">$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>
+ 416 
+ 417   <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
+ 418 <span class="s">}</span>
+ 419 
+ 420 <span class="c"># Get atom torsions IDs corresponding to atom torsions count values in fingerprint</span>
+ 421 <span class="c"># vector as an array or reference to an array...</span>
+ 422 <span class="c">#</span>
+ 423 <span class="c"># AtomTorsionsIDs list differes in molecules and is generated during finalization</span>
+ 424 <span class="c"># of fingerprints to make sure the fingerprint vector containing count values</span>
+ 425 <span class="c"># matches the atom torsions array.</span>
+ 426 <span class="c">#</span>
+<a name="GetAtomTorsionsIDs-"></a> 427 <span class="k">sub </span><span class="m">GetAtomTorsionsIDs</span> <span class="s">{</span>
+ 428   <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+ 429 
+ 430   <span class="k">return</span> <span class="k">wantarray</span> ? <span class="i">@</span>{<span class="i">$This</span>-&gt;{<span class="w">AtomTorsionsIDs</span>}} <span class="co">:</span> \<span class="i">@</span>{<span class="i">$This</span>-&gt;{<span class="w">AtomTorsionsIDs</span>}}<span class="sc">;</span>
+ 431 <span class="s">}</span>
+ 432 
+ 433 <span class="c"># Cache  appropriate molecule data...</span>
+ 434 <span class="c">#</span>
+<a name="_SetupMoleculeDataCache-"></a> 435 <span class="k">sub </span><span class="m">_SetupMoleculeDataCache</span> <span class="s">{</span>
+ 436   <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+ 437 
+ 438   <span class="c"># Get all atoms including hydrogens. The hydrogen atoms are ignored during processing...</span>
+ 439   <span class="i">@</span>{<span class="i">$This</span>-&gt;{<span class="w">Atoms</span>}} = <span class="i">$This</span><span class="i">-&gt;GetMolecule</span><span class="s">(</span><span class="s">)</span><span class="i">-&gt;GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 440 
+ 441   <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
+ 442 <span class="s">}</span>
+ 443 
+ 444 <span class="c"># Clear cached molecule data...</span>
+ 445 <span class="c">#</span>
+<a name="_ClearMoleculeDataCache-"></a> 446 <span class="k">sub </span><span class="m">_ClearMoleculeDataCache</span> <span class="s">{</span>
+ 447   <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+ 448 
+ 449   <span class="i">@</span>{<span class="i">$This</span>-&gt;{<span class="w">Atoms</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 450 
+ 451   <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
+ 452 <span class="s">}</span>
+ 453 
+ 454 <span class="c"># Set atomic invariants to use for atom identifiers...</span>
+ 455 <span class="c">#</span>
+<a name="SetAtomicInvariantsToUse-"></a> 456 <span class="k">sub </span><span class="m">SetAtomicInvariantsToUse</span> <span class="s">{</span>
+ 457   <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">@Values</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+ 458   <span class="k">my</span><span class="s">(</span><span class="i">$FirstValue</span><span class="cm">,</span> <span class="i">$TypeOfFirstValue</span><span class="cm">,</span> <span class="i">$AtomicInvariant</span><span class="cm">,</span> <span class="i">$SpecifiedAtomicInvariant</span><span class="cm">,</span> <span class="i">$AtomicInvariantValue</span><span class="cm">,</span> <span class="i">@SpecifiedAtomicInvariants</span><span class="cm">,</span> <span class="i">@AtomicInvariantsToUse</span><span class="s">)</span><span class="sc">;</span>
+ 459 
+ 460   <span class="k">if</span> <span class="s">(</span>!<span class="i">@Values</span><span class="s">)</span> <span class="s">{</span>
+ 461     <span class="w">carp</span> <span class="q">&quot;Warning: ${ClassName}-&gt;SetAtomicInvariantsToUse: No values specified...&quot;</span><span class="sc">;</span>
+ 462     <span class="k">return</span><span class="sc">;</span>
+ 463   <span class="s">}</span>
+ 464 
+ 465   <span class="i">$FirstValue</span> = <span class="i">$Values</span>[<span class="n">0</span>]<span class="sc">;</span>
+ 466   <span class="i">$TypeOfFirstValue</span> = <span class="k">ref</span> <span class="i">$FirstValue</span><span class="sc">;</span>
+ 467 
+ 468   <span class="i">@SpecifiedAtomicInvariants</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 469   <span class="i">@AtomicInvariantsToUse</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 470 
+ 471   <span class="k">if</span> <span class="s">(</span><span class="i">$TypeOfFirstValue</span> =~ <span class="q">/^ARRAY/</span><span class="s">)</span> <span class="s">{</span>
+ 472     <span class="k">push</span> <span class="i">@SpecifiedAtomicInvariants</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$FirstValue</span>}<span class="sc">;</span>
+ 473   <span class="s">}</span>
+ 474   <span class="k">else</span> <span class="s">{</span>
+ 475     <span class="k">push</span> <span class="i">@SpecifiedAtomicInvariants</span><span class="cm">,</span> <span class="i">@Values</span><span class="sc">;</span>
+ 476   <span class="s">}</span>
+ 477 
+ 478   <span class="c"># Make sure specified AtomicInvariants are valid...</span>
+ 479   <span class="k">for</span> <span class="i">$SpecifiedAtomicInvariant</span> <span class="s">(</span><span class="i">@SpecifiedAtomicInvariants</span><span class="s">)</span> <span class="s">{</span>
+ 480     <span class="k">if</span> <span class="s">(</span>!<span class="i">AtomTypes::AtomicInvariantsAtomTypes::IsAtomicInvariantAvailable</span><span class="s">(</span><span class="i">$SpecifiedAtomicInvariant</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+ 481       <span class="w">croak</span> <span class="q">&quot;Error: ${ClassName}-&gt;SetAtomicInvariantsToUse: Specified atomic invariant, $SpecifiedAtomicInvariant, is not supported...\n &quot;</span><span class="sc">;</span>
+ 482     <span class="s">}</span>
+ 483     <span class="i">$AtomicInvariant</span> = <span class="i">$SpecifiedAtomicInvariant</span><span class="sc">;</span>
+ 484     <span class="k">push</span> <span class="i">@AtomicInvariantsToUse</span><span class="cm">,</span> <span class="i">$AtomicInvariant</span><span class="sc">;</span>
+ 485   <span class="s">}</span>
+ 486 
+ 487   <span class="c"># Set atomic invariants to use...</span>
+ 488   <span class="i">@</span>{<span class="i">$This</span>-&gt;{<span class="w">AtomicInvariantsToUse</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 489   <span class="k">push</span> <span class="i">@</span>{<span class="i">$This</span>-&gt;{<span class="w">AtomicInvariantsToUse</span>}}<span class="cm">,</span> <span class="i">@AtomicInvariantsToUse</span><span class="sc">;</span>
+ 490 
+ 491   <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
+ 492 <span class="s">}</span>
+ 493 
+ 494 <span class="c"># Set functional classes to use for atom identifiers...</span>
+ 495 <span class="c">#</span>
+<a name="SetFunctionalClassesToUse-"></a> 496 <span class="k">sub </span><span class="m">SetFunctionalClassesToUse</span> <span class="s">{</span>
+ 497   <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">@Values</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+ 498   <span class="k">my</span><span class="s">(</span><span class="i">$FirstValue</span><span class="cm">,</span> <span class="i">$TypeOfFirstValue</span><span class="cm">,</span> <span class="i">$FunctionalClass</span><span class="cm">,</span> <span class="i">$SpecifiedFunctionalClass</span><span class="cm">,</span> <span class="i">@SpecifiedFunctionalClasses</span><span class="cm">,</span> <span class="i">@FunctionalClassesToUse</span><span class="s">)</span><span class="sc">;</span>
+ 499 
+ 500   <span class="k">if</span> <span class="s">(</span>!<span class="i">@Values</span><span class="s">)</span> <span class="s">{</span>
+ 501     <span class="w">carp</span> <span class="q">&quot;Warning: ${ClassName}-&gt;SetFunctionalClassesToUse: No values specified...&quot;</span><span class="sc">;</span>
+ 502     <span class="k">return</span><span class="sc">;</span>
+ 503   <span class="s">}</span>
+ 504 
+ 505   <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">AtomIdentifierType</span>} !~ <span class="q">/^FunctionalClassAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span>
+ 506     <span class="w">carp</span> <span class="q">&quot;Warning: ${ClassName}-&gt;SetFunctionalClassesToUse: FunctionalClassesToUse can&#39;t be set for InitialAtomIdentifierType of $This-&gt;{AtomIdentifierType}...&quot;</span><span class="sc">;</span>
+ 507     <span class="k">return</span><span class="sc">;</span>
+ 508   <span class="s">}</span>
+ 509 
+ 510   <span class="i">$FirstValue</span> = <span class="i">$Values</span>[<span class="n">0</span>]<span class="sc">;</span>
+ 511   <span class="i">$TypeOfFirstValue</span> = <span class="k">ref</span> <span class="i">$FirstValue</span><span class="sc">;</span>
+ 512 
+ 513   <span class="i">@SpecifiedFunctionalClasses</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 514   <span class="i">@FunctionalClassesToUse</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 515 
+ 516   <span class="k">if</span> <span class="s">(</span><span class="i">$TypeOfFirstValue</span> =~ <span class="q">/^ARRAY/</span><span class="s">)</span> <span class="s">{</span>
+ 517     <span class="k">push</span> <span class="i">@SpecifiedFunctionalClasses</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$FirstValue</span>}<span class="sc">;</span>
+ 518   <span class="s">}</span>
+ 519   <span class="k">else</span> <span class="s">{</span>
+ 520     <span class="k">push</span> <span class="i">@SpecifiedFunctionalClasses</span><span class="cm">,</span> <span class="i">@Values</span><span class="sc">;</span>
+ 521   <span class="s">}</span>
+ 522 
+ 523   <span class="c"># Make sure specified FunctionalClasses are valid...</span>
+ 524   <span class="k">for</span> <span class="i">$SpecifiedFunctionalClass</span> <span class="s">(</span><span class="i">@SpecifiedFunctionalClasses</span><span class="s">)</span> <span class="s">{</span>
+ 525     <span class="k">if</span> <span class="s">(</span>!<span class="i">AtomTypes::FunctionalClassAtomTypes::IsFunctionalClassAvailable</span><span class="s">(</span><span class="i">$SpecifiedFunctionalClass</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+ 526       <span class="w">croak</span> <span class="q">&quot;Error: ${ClassName}-&gt;SetFunctionalClassesToUse: Specified functional class, $SpecifiedFunctionalClass, is not supported...\n &quot;</span><span class="sc">;</span>
+ 527     <span class="s">}</span>
+ 528     <span class="k">push</span> <span class="i">@FunctionalClassesToUse</span><span class="cm">,</span> <span class="i">$SpecifiedFunctionalClass</span><span class="sc">;</span>
+ 529   <span class="s">}</span>
+ 530 
+ 531   <span class="c"># Set functional classes to use...</span>
+ 532   <span class="i">@</span>{<span class="i">$This</span>-&gt;{<span class="w">FunctionalClassesToUse</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 533   <span class="k">push</span> <span class="i">@</span>{<span class="i">$This</span>-&gt;{<span class="w">FunctionalClassesToUse</span>}}<span class="cm">,</span> <span class="i">@FunctionalClassesToUse</span><span class="sc">;</span>
+ 534 
+ 535   <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
+ 536 <span class="s">}</span>
+ 537 
+ 538 <span class="c"># Initialize atom indentifier type information...</span>
+ 539 <span class="c">#</span>
+ 540 <span class="c"># Current supported values:</span>
+ 541 <span class="c">#</span>
+ 542 <span class="c"># AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, FunctionalClassAtomTypes,</span>
+ 543 <span class="c"># MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes</span>
+ 544 <span class="c">#</span>
+<a name="_InitializeAtomIdentifierTypeInformation-"></a> 545 <span class="k">sub </span><span class="m">_InitializeAtomIdentifierTypeInformation</span> <span class="s">{</span>
+ 546   <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+ 547 
+ 548   <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^AtomicInvariantsAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span>
+ 549     <span class="i">$This</span><span class="i">-&gt;_InitializeAtomicInvariantsAtomTypesInformation</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 550   <span class="s">}</span>
+ 551   <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^FunctionalClassAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span>
+ 552     <span class="i">$This</span><span class="i">-&gt;_InitializeFunctionalClassAtomTypesInformation</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 553   <span class="s">}</span>
+ 554   <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^(DREIDINGAtomTypes|EStateAtomTypes|MMFF94AtomTypes|SLogPAtomTypes|SYBYLAtomTypes|TPSAAtomTypes|UFFAtomTypes)$/i</span><span class="s">)</span> <span class="s">{</span>
+ 555     <span class="c"># Nothing to do for now...</span>
+ 556   <span class="s">}</span>
+ 557   <span class="k">else</span> <span class="s">{</span>
+ 558     <span class="w">croak</span> <span class="q">&quot;Error: ${ClassName}-&gt;_InitializeAtomIdentifierTypeInformation: Unknown atom indentifier type $This-&gt;{AtomIdentifierType}...&quot;</span><span class="sc">;</span>
+ 559   <span class="s">}</span>
+ 560 
+ 561   <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
+ 562 <span class="s">}</span>
+ 563 
+ 564 <span class="c"># Initialize atomic invariants to use for generating atom IDs in atom torsions...</span>
+ 565 <span class="c">#</span>
+ 566 <span class="c"># Let:</span>
+ 567 <span class="c">#   AS = Atom symbol corresponding to element symbol</span>
+ 568 <span class="c">#</span>
+ 569 <span class="c">#   X&lt;n&gt;   = Number of non-hydrogen atom neighbors or heavy atoms attached to atom</span>
+ 570 <span class="c">#   BO&lt;n&gt; = Sum of bond orders to non-hydrogen atom neighbors or heavy atoms attached to atom</span>
+ 571 <span class="c">#   LBO&lt;n&gt; = Largest bond order of non-hydrogen atom neighbors or heavy atoms attached to atom</span>
+ 572 <span class="c">#   SB&lt;n&gt; = Number of single bonds to non-hydrogen atom neighbors or heavy atoms attached to atom</span>
+ 573 <span class="c">#   DB&lt;n&gt; = Number of double bonds to non-hydrogen atom neighbors or heavy atoms attached to atom</span>
+ 574 <span class="c">#   TB&lt;n&gt; = Number of triple bonds to non-hydrogen atom neighbors or heavy atoms attached to atom</span>
+ 575 <span class="c">#   H&lt;n&gt;   = Number of implicit and explicit hydrogens for atom</span>
+ 576 <span class="c">#   Ar     = Aromatic annotation indicating whether atom is aromatic</span>
+ 577 <span class="c">#   RA     = Ring atom annotation indicating whether atom is a ring</span>
+ 578 <span class="c">#   FC&lt;+n/-n&gt; = Formal charge assigned to atom</span>
+ 579 <span class="c">#   MN&lt;n&gt; = Mass number indicating isotope other than most abundant isotope</span>
+ 580 <span class="c">#   SM&lt;n&gt; = Spin multiplicity of atom. Possible values: 1 (singlet), 2 (doublet) or 3 (triplet)</span>
+ 581 <span class="c">#</span>
+ 582 <span class="c">#   AtomTypeIDx = Atomic invariants atom type for atom x</span>
+ 583 <span class="c">#   AtomTypeIDy = Atomic invariants atom type for atom y</span>
+ 584 <span class="c">#   AtomTypeIDz = Atomic invariants atom type for atom z</span>
+ 585 <span class="c">#   AtomTypeIDw = Atomic invariants atom type for atom w</span>
+ 586 <span class="c">#</span>
+ 587 <span class="c"># Then:</span>
+ 588 <span class="c">#</span>
+ 589 <span class="c">#   Atom torsion AtomID generated by AtomTypes::AtomicInvariantsAtomTypes class corresponds to:</span>
+ 590 <span class="c">#</span>
+ 591 <span class="c">#     AS.X&lt;n&gt;.BO&lt;n&gt;.LBO&lt;n&gt;.&lt;SB&gt;&lt;n&gt;.&lt;DB&gt;&lt;n&gt;.&lt;TB&gt;&lt;n&gt;.H&lt;n&gt;.Ar.RA.FC&lt;+n/-n&gt;.MN&lt;n&gt;.SM&lt;n&gt;</span>
+ 592 <span class="c">#</span>
+ 593 <span class="c">#  AtomTorsion ID corresponds to:</span>
+ 594 <span class="c">#</span>
+ 595 <span class="c">#    AtomTypeIDx-AtomTypeIDy-AtomTypeIDz-AtomTypeIDw</span>
+ 596 <span class="c">#</span>
+ 597 <span class="c"># Except for AS which is a required atomic invariant in atom torsions AtomIDs, all other atomic invariants are</span>
+ 598 <span class="c"># optional. Default atomic invariants used for AtomID are: AS, X&lt;n&gt;, BO&lt;n&gt;, H&lt;n&gt;, FC&lt;+n/-n&gt;.</span>
+ 599 <span class="c"># AtomID specification doesn&#39;t include atomic invariants with zero or undefined values.</span>
+ 600 <span class="c">#</span>
+ 601 <span class="c"># Examples of atom torsion AtomIDs in Aspirin using default atomic invariants:</span>
+ 602 <span class="c">#</span>
+ 603 <span class="c">#  C.X1.BO1.H3-C.X3.BO4-O.X2.BO2-C.X3.BO4</span>
+ 604 <span class="c">#  C.X2.BO3.H1-C.X2.BO3.H1-C.X2.BO3.H1-C.X2.BO3.H1</span>
+ 605 <span class="c">#  C.X3.BO4-C.X3.BO4-O.X2.BO2-C.X3.BO4</span>
+ 606 <span class="c">#  C.X3.BO4-O.X2.BO2-C.X3.BO4-O.X1.BO2</span>
+ 607 <span class="c">#</span>
+ 608 <span class="c"># Examples of atom torsion AtomIDs in Aspirin using AS, X and BO atomic invariants:</span>
+ 609 <span class="c">#</span>
+ 610 <span class="c">#  C.X1.BO1-C.X3.BO4-O.X2.BO2-C.X3.BO4</span>
+ 611 <span class="c">#  C.X2.BO3-C.X2.BO3-C.X2.BO3-C.X2.BO3</span>
+ 612 <span class="c">#  C.X3.BO4-C.X3.BO4-O.X2.BO2-C.X3.BO4</span>
+ 613 <span class="c">#  C.X3.BO4-O.X2.BO2-C.X3.BO4-O.X1.BO2</span>
+ 614 <span class="c">#</span>
+<a name="_InitializeAtomicInvariantsAtomTypesInformation-"></a> 615 <span class="k">sub </span><span class="m">_InitializeAtomicInvariantsAtomTypesInformation</span> <span class="s">{</span>
+ 616   <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+ 617 
+ 618   <span class="c"># Default atomic invariants to use for generating atom torsions atom IDs: AS, X, BO, H, FC</span>
+ 619   <span class="c">#</span>
+ 620   <span class="i">@</span>{<span class="i">$This</span>-&gt;{<span class="w">AtomicInvariantsToUse</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 621   <span class="i">@</span>{<span class="i">$This</span>-&gt;{<span class="w">AtomicInvariantsToUse</span>}} = <span class="s">(</span><span class="q">&#39;AS&#39;</span><span class="cm">,</span> <span class="q">&#39;X&#39;</span><span class="cm">,</span> <span class="q">&#39;BO&#39;</span><span class="cm">,</span> <span class="q">&#39;H&#39;</span><span class="cm">,</span> <span class="q">&#39;FC&#39;</span><span class="s">)</span><span class="sc">;</span>
+ 622 
+ 623   <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
+ 624 <span class="s">}</span>
+ 625 
+ 626 <span class="c"># Initialize functional class atom types, generated by AtomTypes::FunctionalClassAtomTypes</span>
+ 627 <span class="c"># class, to use for generating atom identifiers...</span>
+ 628 <span class="c">#</span>
+ 629 <span class="c"># Let:</span>
+ 630 <span class="c">#   HBD: HydrogenBondDonor</span>
+ 631 <span class="c">#   HBA: HydrogenBondAcceptor</span>
+ 632 <span class="c">#   PI :  PositivelyIonizable</span>
+ 633 <span class="c">#   NI : NegativelyIonizable</span>
+ 634 <span class="c">#   Ar : Aromatic</span>
+ 635 <span class="c">#   Hal : Halogen</span>
+ 636 <span class="c">#   H : Hydrophobic</span>
+ 637 <span class="c">#   RA : RingAtom</span>
+ 638 <span class="c">#   CA : ChainAtom</span>
+ 639 <span class="c">#</span>
+ 640 <span class="c"># Then:</span>
+ 641 <span class="c">#</span>
+ 642 <span class="c">#   Functiononal class atom type specification for an atom corresponds to:</span>
+ 643 <span class="c">#</span>
+ 644 <span class="c">#     Ar.CA.H.HBA.HBD.Hal.NI.PI.RA</span>
+ 645 <span class="c">#</span>
+ 646 <span class="c">#   Default functional classes used are: HBD, HBA, PI, NI, Ar, Hal</span>
+ 647 <span class="c">#</span>
+ 648 <span class="c">#   FunctionalAtomTypes are assigned using the following definitions [ Ref 60-61, Ref 65-66 ]:</span>
+ 649 <span class="c">#</span>
+ 650 <span class="c">#     HydrogenBondDonor: NH, NH2, OH</span>
+ 651 <span class="c">#     HydrogenBondAcceptor: N[!H], O</span>
+ 652 <span class="c">#     PositivelyIonizable: +, NH2</span>
+ 653 <span class="c">#     NegativelyIonizable: -, C(=O)OH, S(=O)OH, P(=O)OH</span>
+ 654 <span class="c">#</span>
+<a name="_InitializeFunctionalClassAtomTypesInformation-"></a> 655 <span class="k">sub </span><span class="m">_InitializeFunctionalClassAtomTypesInformation</span> <span class="s">{</span>
+ 656   <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+ 657 
+ 658   <span class="c"># Default functional class atom typess to use for generating atom identifiers</span>
+ 659   <span class="c"># are: HBD, HBA, PI, NI, Ar, Hal</span>
+ 660   <span class="c">#</span>
+ 661   <span class="i">@</span>{<span class="i">$This</span>-&gt;{<span class="w">FunctionalClassesToUse</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 662   <span class="i">@</span>{<span class="i">$This</span>-&gt;{<span class="w">FunctionalClassesToUse</span>}} = <span class="s">(</span><span class="q">&#39;HBD&#39;</span><span class="cm">,</span> <span class="q">&#39;HBA&#39;</span><span class="cm">,</span> <span class="q">&#39;PI&#39;</span><span class="cm">,</span> <span class="q">&#39;NI&#39;</span><span class="cm">,</span> <span class="q">&#39;Ar&#39;</span><span class="cm">,</span> <span class="q">&#39;Hal&#39;</span><span class="s">)</span><span class="sc">;</span>
+ 663 
+ 664   <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
+ 665 <span class="s">}</span>
+ 666 
+ 667 <span class="c"># Return a string containg data for TopologicalAtomTorsionsFingerprints object...</span>
+ 668 <span class="c">#</span>
+<a name="StringifyTopologicalAtomTorsionsFingerprints-"></a> 669 <span class="k">sub </span><span class="m">StringifyTopologicalAtomTorsionsFingerprints</span> <span class="s">{</span>
+ 670   <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+ 671   <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsString</span><span class="s">)</span><span class="sc">;</span>
+ 672 
+ 673   <span class="c"># Type of fingerprint...</span>
+ 674   <span class="i">$FingerprintsString</span> = <span class="q">&quot;Fingerprint type: $This-&gt;{Type}; AtomIdentifierType: $This-&gt;{AtomIdentifierType}&quot;</span><span class="sc">;</span>
+ 675 
+ 676   <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^AtomicInvariantsAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span>
+ 677     <span class="k">my</span><span class="s">(</span><span class="i">$AtomicInvariant</span><span class="cm">,</span> <span class="i">@AtomicInvariants</span><span class="cm">,</span> <span class="i">@AtomicInvariantsOrder</span><span class="cm">,</span> <span class="i">%AvailableAtomicInvariants</span><span class="s">)</span><span class="sc">;</span>
+ 678 
+ 679     <span class="i">@AtomicInvariantsOrder</span> = <span class="i">AtomTypes::AtomicInvariantsAtomTypes::GetAtomicInvariantsOrder</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 680     <span class="i">%AvailableAtomicInvariants</span> = <span class="i">AtomTypes::AtomicInvariantsAtomTypes::GetAvailableAtomicInvariants</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 681 
+ 682     <span class="k">for</span> <span class="i">$AtomicInvariant</span> <span class="s">(</span><span class="i">@AtomicInvariantsOrder</span><span class="s">)</span> <span class="s">{</span>
+ 683       <span class="k">push</span> <span class="i">@AtomicInvariants</span><span class="cm">,</span> <span class="q">&quot;$AtomicInvariant: $AvailableAtomicInvariants{$AtomicInvariant}&quot;</span><span class="sc">;</span>
+ 684     <span class="s">}</span>
+ 685 
+ 686     <span class="i">$FingerprintsString</span> .= <span class="q">&quot;; AtomicInvariantsToUse: &lt;&quot;</span> . <span class="i">TextUtil::JoinWords</span><span class="s">(</span>\<span class="i">@</span>{<span class="i">$This</span>-&gt;{<span class="w">AtomicInvariantsToUse</span>}}<span class="cm">,</span> <span class="q">&quot;, &quot;</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span> . <span class="q">&quot;&gt;&quot;</span><span class="sc">;</span>
+ 687     <span class="i">$FingerprintsString</span> .= <span class="q">&quot;; AtomicInvariantsOrder: &lt;&quot;</span> . <span class="i">TextUtil::JoinWords</span><span class="s">(</span>\<span class="i">@AtomicInvariantsOrder</span><span class="cm">,</span> <span class="q">&quot;, &quot;</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span> . <span class="q">&quot;&gt;&quot;</span><span class="sc">;</span>
+ 688     <span class="i">$FingerprintsString</span> .= <span class="q">&quot;; AvailableAtomicInvariants: &lt;&quot;</span> . <span class="i">TextUtil::JoinWords</span><span class="s">(</span>\<span class="i">@AtomicInvariants</span><span class="cm">,</span> <span class="q">&quot;, &quot;</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span> . <span class="q">&quot;&gt;&quot;</span><span class="sc">;</span>
+ 689   <span class="s">}</span>
+ 690   <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^FunctionalClassAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span>
+ 691     <span class="k">my</span><span class="s">(</span><span class="i">$FunctionalClass</span><span class="cm">,</span> <span class="i">@FunctionalClasses</span><span class="cm">,</span> <span class="i">@FunctionalClassesOrder</span><span class="cm">,</span> <span class="i">%AvailableFunctionalClasses</span><span class="s">)</span><span class="sc">;</span>
+ 692 
+ 693     <span class="i">@FunctionalClassesOrder</span> = <span class="i">AtomTypes::FunctionalClassAtomTypes::GetFunctionalClassesOrder</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 694     <span class="i">%AvailableFunctionalClasses</span> = <span class="i">AtomTypes::FunctionalClassAtomTypes::GetAvailableFunctionalClasses</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 695 
+ 696     <span class="k">for</span> <span class="i">$FunctionalClass</span> <span class="s">(</span><span class="i">@FunctionalClassesOrder</span><span class="s">)</span> <span class="s">{</span>
+ 697       <span class="k">push</span> <span class="i">@FunctionalClasses</span><span class="cm">,</span> <span class="q">&quot;$FunctionalClass: $AvailableFunctionalClasses{$FunctionalClass}&quot;</span><span class="sc">;</span>
+ 698     <span class="s">}</span>
+ 699 
+ 700     <span class="i">$FingerprintsString</span> .= <span class="q">&quot;; FunctionalClassesToUse: &lt;&quot;</span> . <span class="i">TextUtil::JoinWords</span><span class="s">(</span>\<span class="i">@</span>{<span class="i">$This</span>-&gt;{<span class="w">FunctionalClassesToUse</span>}}<span class="cm">,</span> <span class="q">&quot;, &quot;</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span> . <span class="q">&quot;&gt;&quot;</span><span class="sc">;</span>
+ 701     <span class="i">$FingerprintsString</span> .= <span class="q">&quot;; FunctionalClassesOrder: &lt;&quot;</span> . <span class="i">TextUtil::JoinWords</span><span class="s">(</span>\<span class="i">@FunctionalClassesOrder</span><span class="cm">,</span> <span class="q">&quot;, &quot;</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span> . <span class="q">&quot;&gt;&quot;</span><span class="sc">;</span>
+ 702     <span class="i">$FingerprintsString</span> .= <span class="q">&quot;; AvailableFunctionalClasses: &lt;&quot;</span> . <span class="i">TextUtil::JoinWords</span><span class="s">(</span>\<span class="i">@FunctionalClasses</span><span class="cm">,</span> <span class="q">&quot;, &quot;</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span> . <span class="q">&quot;&gt;&quot;</span><span class="sc">;</span>
+ 703   <span class="s">}</span>
+ 704 
+ 705   <span class="c"># Total number of atom torsions...</span>
+ 706   <span class="i">$FingerprintsString</span> .= <span class="q">&quot;; NumOfAtomTorsions: &quot;</span> . <span class="i">$This</span>-&gt;{<span class="w">FingerprintsVector</span>}<span class="i">-&gt;GetNumOfValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 707 
+ 708   <span class="c"># FingerprintsVector...</span>
+ 709   <span class="i">$FingerprintsString</span> .= <span class="q">&quot;; FingerprintsVector: &lt; $This-&gt;{FingerprintsVector} &gt;&quot;</span><span class="sc">;</span>
+ 710 
+ 711   <span class="k">return</span> <span class="i">$FingerprintsString</span><span class="sc">;</span>
+ 712 <span class="s">}</span>
+ 713 
+<a name="EOF-"></a></pre>
+<p>&nbsp;</p>
+<br />
+<center>
+<img src="../../../images/h2o2.png">
+</center>
+</body>
+</html>