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

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+<a name="package-Fingerprints::TopologicalAtomPairsFingerprints-"></a>   1 <span class="k">package </span><span class="i">Fingerprints::TopologicalAtomPairsFingerprints</span><span class="sc">;</span>
+   2 <span class="c">#</span>
+   3 <span class="c"># $RCSfile: TopologicalAtomPairsFingerprints.pm,v $</span>
+   4 <span class="c"># $Date: 2015/02/28 20:48:54 $</span>
+   5 <span class="c"># $Revision: 1.30 $</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;StringifyTopologicalAtomPairsFingerprints&#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">$This</span><span class="i">-&gt;_InitializeTopologicalAtomPairsFingerprints</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+  68 
+  69   <span class="i">$This</span><span class="i">-&gt;_InitializeTopologicalAtomPairsFingerprintsProperties</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">$This</span><span class="sc">;</span>
+  72 <span class="s">}</span>
+  73 
+  74 <span class="c"># Initialize object data...</span>
+  75 <span class="c">#</span>
+<a name="_InitializeTopologicalAtomPairsFingerprints-"></a>  76 <span class="k">sub </span><span class="m">_InitializeTopologicalAtomPairsFingerprints</span> <span class="s">{</span>
+  77   <span class="k">my</span><span class="s">(</span><span class="i">$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">$This</span>-&gt;{<span class="w">Type</span>} = <span class="q">&#39;TopologicalAtomPairs&#39;</span><span class="sc">;</span>
+  81 
+  82   <span class="c"># Type of vector...</span>
+  83   <span class="i">$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">$This</span>-&gt;{<span class="w">FingerprintsVectorType</span>} = <span class="q">&#39;NumericalValues&#39;</span><span class="sc">;</span>
+  87 
+  88   <span class="c"># Minimum and maximum bond distance between atom paris...</span>
+  89   <span class="i">$This</span>-&gt;{<span class="w">MinDistance</span>} = <span class="n">1</span><span class="sc">;</span>
+  90   <span class="i">$This</span>-&gt;{<span class="w">MaxDistance</span>} = <span class="n">10</span><span class="sc">;</span>
+  91 
+  92   <span class="c"># Atom identifier type to use for atom IDs in atom pairs...</span>
+  93   <span class="c">#</span>
+  94   <span class="c"># Currently supported values are: AtomicInvariantsAtomTypes, DREIDINGAtomTypes,</span>
+  95   <span class="c"># EStateAtomTypes, FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes,</span>
+  96   <span class="c"># SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes</span>
+  97   <span class="c">#</span>
+  98   <span class="i">$This</span>-&gt;{<span class="w">AtomIdentifierType</span>} = <span class="q">&#39;&#39;</span><span class="sc">;</span>
+  99 
+ 100   <span class="c"># Atom types assigned to each heavy atom...</span>
+ 101   <span class="c">#</span>
+ 102   <span class="i">%</span>{<span class="i">$This</span>-&gt;{<span class="w">AssignedAtomTypes</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 103 
+ 104   <span class="c"># All atom pairs between minimum and maximum distance...</span>
+ 105   <span class="c">#</span>
+ 106   <span class="i">@</span>{<span class="i">$This</span>-&gt;{<span class="w">AtomPairsIDs</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 107   <span class="i">%</span>{<span class="i">$This</span>-&gt;{<span class="w">AtomPairsCount</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 108 <span class="s">}</span>
+ 109 
+ 110 <span class="c"># Initialize class ...</span>
+<a name="_InitializeClass-"></a> 111 <span class="k">sub </span><span class="m">_InitializeClass</span> <span class="s">{</span>
+ 112   <span class="c">#Class name...</span>
+ 113   <span class="i">$ClassName</span> = <span class="w">__PACKAGE__</span><span class="sc">;</span>
+ 114 <span class="s">}</span>
+ 115 
+ 116 <span class="c"># Initialize object properties....</span>
+<a name="_InitializeTopologicalAtomPairsFingerprintsProperties-"></a> 117 <span class="k">sub </span><span class="m">_InitializeTopologicalAtomPairsFingerprintsProperties</span> <span class="s">{</span>
+ 118   <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+ 119 
+ 120   <span class="k">my</span><span class="s">(</span><span class="i">$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>
+ 121   <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>
+ 122     <span class="i">$MethodName</span> = <span class="q">&quot;Set${Name}&quot;</span><span class="sc">;</span>
+ 123     <span class="i">$This</span><span class="i">-&gt;$MethodName</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="sc">;</span>
+ 124   <span class="s">}</span>
+ 125 
+ 126   <span class="c"># Make sure molecule object was specified...</span>
+ 127   <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$NamesAndValues</span>{<span class="w">Molecule</span>}<span class="s">)</span> <span class="s">{</span>
+ 128     <span class="w">croak</span> <span class="q">&quot;Error: ${ClassName}-&gt;New: Object can&#39;t be instantiated without specifying molecule...&quot;</span><span class="sc">;</span>
+ 129   <span class="s">}</span>
+ 130   <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$NamesAndValues</span>{<span class="w">AtomIdentifierType</span>}<span class="s">)</span> <span class="s">{</span>
+ 131     <span class="w">croak</span> <span class="q">&quot;Error: ${ClassName}-&gt;New: Object can&#39;t be instantiated without specifying AtomIdentifierType...&quot;</span><span class="sc">;</span>
+ 132   <span class="s">}</span>
+ 133 
+ 134   <span class="i">$This</span><span class="i">-&gt;_InitializeFingerprintsVector</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 135 
+ 136   <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
+ 137 <span class="s">}</span>
+ 138 
+ 139 <span class="c"># Set minimum distance for atom pairs...</span>
+ 140 <span class="c">#</span>
+<a name="SetMinDistance-"></a> 141 <span class="k">sub </span><span class="m">SetMinDistance</span> <span class="s">{</span>
+ 142   <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+ 143 
+ 144   <span class="k">if</span> <span class="s">(</span>!<span class="i">TextUtil::IsPositiveInteger</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+ 145     <span class="w">croak</span> <span class="q">&quot;Error: ${ClassName}-&gt;SetMinDistance: MinDistance value, $Value, is not valid:  It must be a positive integer...&quot;</span><span class="sc">;</span>
+ 146   <span class="s">}</span>
+ 147   <span class="i">$This</span>-&gt;{<span class="w">MinDistance</span>} = <span class="i">$Value</span><span class="sc">;</span>
+ 148 
+ 149   <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
+ 150 <span class="s">}</span>
+ 151 
+ 152 <span class="c"># Set maximum distance for atom pairs...</span>
+ 153 <span class="c">#</span>
+<a name="SetMaxDistance-"></a> 154 <span class="k">sub </span><span class="m">SetMaxDistance</span> <span class="s">{</span>
+ 155   <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+ 156 
+ 157   <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>
+ 158     <span class="w">croak</span> <span class="q">&quot;Error: ${ClassName}-&gt;SetMaxDistance: MaxDistance value, $Value, is not valid:  It must be a positive integer...&quot;</span><span class="sc">;</span>
+ 159   <span class="s">}</span>
+ 160   <span class="i">$This</span>-&gt;{<span class="w">MaxDistance</span>} = <span class="i">$Value</span><span class="sc">;</span>
+ 161 
+ 162   <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
+ 163 <span class="s">}</span>
+ 164 
+ 165 <span class="c"># Set atom identifier type..</span>
+ 166 <span class="c">#</span>
+<a name="SetAtomIdentifierType-"></a> 167 <span class="k">sub </span><span class="m">SetAtomIdentifierType</span> <span class="s">{</span>
+ 168   <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>
+ 169 
+ 170   <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>
+ 171     <span class="w">croak</span> <span class="q">&quot;Error: ${ClassName}-&gt;SetAtomIdentifierType: Specified value, $IdentifierType, for AtomIdentifierType is not vaild. Supported types in current release of MayaChemTools: AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes, and UFFAtomTypes.&quot;</span><span class="sc">;</span>
+ 172   <span class="s">}</span>
+ 173 
+ 174   <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">AtomIdentifierType</span>}<span class="s">)</span> <span class="s">{</span>
+ 175     <span class="w">croak</span> <span class="q">&quot;Error: ${ClassName}-&gt;SeAtomIdentifierType: Can&#39;t change intial atom identifier type:  It&#39;s already set...&quot;</span><span class="sc">;</span>
+ 176   <span class="s">}</span>
+ 177 
+ 178   <span class="i">$This</span>-&gt;{<span class="w">AtomIdentifierType</span>} = <span class="i">$IdentifierType</span><span class="sc">;</span>
+ 179 
+ 180   <span class="c"># Initialize atom identifier type information...</span>
+ 181   <span class="i">$This</span><span class="i">-&gt;_InitializeAtomIdentifierTypeInformation</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 182 
+ 183   <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
+ 184 <span class="s">}</span>
+ 185 
+ 186 <span class="c"># Generate fingerprints description...</span>
+ 187 <span class="c">#</span>
+<a name="GetDescription-"></a> 188 <span class="k">sub </span><span class="m">GetDescription</span> <span class="s">{</span>
+ 189   <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+ 190 
+ 191   <span class="c"># Is description explicity set?</span>
+ 192   <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$This</span>-&gt;{<span class="w">Description</span>}<span class="s">)</span> <span class="s">{</span>
+ 193     <span class="k">return</span> <span class="i">$This</span>-&gt;{<span class="w">Description</span>}<span class="sc">;</span>
+ 194   <span class="s">}</span>
+ 195 
+ 196   <span class="c"># Generate fingerprints description...</span>
+ 197 
+ 198   <span class="k">return</span> <span class="q">&quot;$This-&gt;{Type}:$This-&gt;{AtomIdentifierType}:MinDistance$This-&gt;{MinDistance}:MaxDistance$This-&gt;{MaxDistance}&quot;</span><span class="sc">;</span>
+ 199 <span class="s">}</span>
+ 200 
+ 201 <span class="c"># Generate topological atom pairs [ Ref 57, Ref 59, Ref 72 ] fingerprints...</span>
+ 202 <span class="c">#</span>
+ 203 <span class="c"># Methodology:</span>
+ 204 <span class="c">#   . Generate a distance matrix.</span>
+ 205 <span class="c">#   . Assign atom types to all the atoms.</span>
+ 206 <span class="c">#   . Using distance matrix and atom types, count occurrence of</span>
+ 207 <span class="c">#     unique atom pairs within specified distance range - It corresponds to the</span>
+ 208 <span class="c">#     correlation-vector for the atom pairs.</span>
+ 209 <span class="c">#</span>
+ 210 <span class="c"># Notes:</span>
+ 211 <span class="c">#   . Hydrogen atoms are ignored during the fingerprint generation.</span>
+ 212 <span class="c">#</span>
+<a name="GenerateFingerprints-"></a> 213 <span class="k">sub </span><span class="m">GenerateFingerprints</span> <span class="s">{</span>
+ 214   <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+ 215 
+ 216   <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">MinDistance</span>} &gt; <span class="i">$This</span>-&gt;{<span class="w">MaxDistance</span>}<span class="s">)</span> <span class="s">{</span>
+ 217     <span class="w">croak</span> <span class="q">&quot;Error: ${ClassName}-&gt;GenerateTopologicalAtomPairsFingerprints: No fingerpritns generated: MinDistance, $This-&gt;{MinDistance}, must be &lt;= MaxDistance, $This-&gt;{MaxDistance}...&quot;</span><span class="sc">;</span>
+ 218   <span class="s">}</span>
+ 219 
+ 220   <span class="c"># Cache appropriate molecule data...</span>
+ 221   <span class="i">$This</span><span class="i">-&gt;_SetupMoleculeDataCache</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 222 
+ 223   <span class="c"># Generate distance matrix...</span>
+ 224   <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">-&gt;_SetupDistanceMatrix</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+ 225     <span class="w">carp</span> <span class="q">&quot;Warning: ${ClassName}-&gt;GenerateFingerprints: $This-&gt;{AtomIdentifierType} fingerprints generation didn&#39;t succeed: Couldn&#39;t generate distance matrix...&quot;</span><span class="sc">;</span>
+ 226     <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
+ 227   <span class="s">}</span>
+ 228 
+ 229   <span class="c"># Assign atom types to all heavy atoms...</span>
+ 230   <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>
+ 231     <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 $This-&gt;{AtomIdentifierType} to all atoms...&quot;</span><span class="sc">;</span>
+ 232     <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
+ 233   <span class="s">}</span>
+ 234 
+ 235   <span class="c"># Intialize values of toplogical atom pairs...</span>
+ 236   <span class="i">$This</span><span class="i">-&gt;_InitializeToplogicalAtomPairs</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 237 
+ 238   <span class="c"># Count atom pairs...</span>
+ 239   <span class="i">$This</span><span class="i">-&gt;_GenerateAndCountAtomPairs</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 240 
+ 241   <span class="c"># Set final fingerprints...</span>
+ 242   <span class="i">$This</span><span class="i">-&gt;_SetFinalFingerprints</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 243 
+ 244   <span class="c"># Clear cached molecule data...</span>
+ 245   <span class="i">$This</span><span class="i">-&gt;_ClearMoleculeDataCache</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 246 
+ 247   <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
+ 248 <span class="s">}</span>
+ 249 
+ 250 <span class="c"># Setup distance matrix...</span>
+ 251 <span class="c">#</span>
+<a name="_SetupDistanceMatrix-"></a> 252 <span class="k">sub </span><span class="m">_SetupDistanceMatrix</span> <span class="s">{</span>
+ 253   <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+ 254 
+ 255   <span class="i">$This</span>-&gt;{<span class="w">DistanceMatrix</span>} = <span class="i">$This</span><span class="i">-&gt;GetMolecule</span><span class="s">(</span><span class="s">)</span><span class="i">-&gt;GetDistanceMatrix</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 256 
+ 257   <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span>-&gt;{<span class="w">DistanceMatrix</span>}<span class="s">)</span> <span class="s">{</span>
+ 258     <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
+ 259   <span class="s">}</span>
+ 260 
+ 261   <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
+ 262 <span class="s">}</span>
+ 263 
+ 264 <span class="c"># Assign appropriate atom types to all heavy atoms...</span>
+ 265 <span class="c">#</span>
+<a name="_AssignAtomTypes-"></a> 266 <span class="k">sub </span><span class="m">_AssignAtomTypes</span> <span class="s">{</span>
+ 267   <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+ 268   <span class="k">my</span><span class="s">(</span><span class="i">$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">$IgnoreHydrogens</span><span class="s">)</span><span class="sc">;</span>
+ 269 
+ 270   <span class="i">%</span>{<span class="i">$This</span>-&gt;{<span class="w">AssignedAtomTypes</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 271   <span class="i">$IgnoreHydrogens</span> = <span class="n">1</span><span class="sc">;</span>
+ 272 
+ 273   <span class="i">$SpecifiedAtomTypes</span> = <span class="k">undef</span><span class="sc">;</span>
+ 274 
+ 275   <span class="j">IDENTIFIERTYPE:</span> <span class="s">{</span>
+ 276     <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>
+ 277       <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>
+ 278       <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span>
+ 279     <span class="s">}</span>
+ 280 
+ 281     <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>
+ 282       <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">$IgnoreHydrogens</span><span class="s">)</span><span class="sc">;</span>
+ 283       <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span>
+ 284     <span class="s">}</span>
+ 285 
+ 286     <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^EStateAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span>
+ 287       <span class="i">$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>
+ 288       <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span>
+ 289     <span class="s">}</span>
+ 290 
+ 291     <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>
+ 292       <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>
+ 293       <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span>
+ 294     <span class="s">}</span>
+ 295 
+ 296     <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>
+ 297       <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">$IgnoreHydrogens</span><span class="s">)</span><span class="sc">;</span>
+ 298       <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span>
+ 299     <span class="s">}</span>
+ 300 
+ 301     <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^SLogPAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span>
+ 302       <span class="i">$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>
+ 303       <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span>
+ 304     <span class="s">}</span>
+ 305     <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>
+ 306       <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">$IgnoreHydrogens</span><span class="s">)</span><span class="sc">;</span>
+ 307       <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span>
+ 308     <span class="s">}</span>
+ 309 
+ 310     <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^TPSAAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span>
+ 311       <span class="i">$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">$This</span>-&gt;{<span class="w">Molecule</span>}<span class="cm">,</span> <span class="q">&#39;IgnorePhosphorus&#39;</span> <span class="cm">=&gt;</span> <span class="n">0</span><span class="cm">,</span> <span class="q">&#39;IgnoreSulfur&#39;</span> <span class="cm">=&gt;</span> <span class="n">0</span><span class="s">)</span><span class="sc">;</span>
+ 312       <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span>
+ 313     <span class="s">}</span>
+ 314 
+ 315     <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^UFFAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span>
+ 316       <span class="i">$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>
+ 317       <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span>
+ 318     <span class="s">}</span>
+ 319 
+ 320     <span class="w">croak</span> <span class="q">&quot;Error: ${ClassName}-&gt;_AssignAtomTypes: Unknown atom indentifier type $This-&gt;{AtomIdentifierType}...&quot;</span><span class="sc">;</span>
+ 321   <span class="s">}</span>
+ 322 
+ 323   <span class="c"># Assign atom types...</span>
+ 324   <span class="i">$SpecifiedAtomTypes</span><span class="i">-&gt;AssignAtomTypes</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 325 
+ 326   <span class="c"># Make sure atom types assignment is successful...</span>
+ 327   <span class="k">if</span> <span class="s">(</span>!<span class="i">$SpecifiedAtomTypes</span><span class="i">-&gt;IsAtomTypesAssignmentSuccessful</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+ 328     <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
+ 329   <span class="s">}</span>
+ 330 
+ 331   <span class="c"># Collect assigned atom types...</span>
+ 332   <span class="j">ATOM:</span> <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$This</span>-&gt;{<span class="w">Atoms</span>}}<span class="s">)</span> <span class="s">{</span>
+ 333     <span class="k">if</span> <span class="s">(</span><span class="i">$Atom</span><span class="i">-&gt;IsHydrogen</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+ 334       <span class="k">next</span> <span class="j">ATOM</span><span class="sc">;</span>
+ 335     <span class="s">}</span>
+ 336     <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>
+ 337     <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>
+ 338   <span class="s">}</span>
+ 339 
+ 340   <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
+ 341 <span class="s">}</span>
+ 342 
+ 343 <span class="c"># Initialize topological atom pairs between specified distance range...</span>
+ 344 <span class="c">#</span>
+<a name="_InitializeToplogicalAtomPairs-"></a> 345 <span class="k">sub </span><span class="m">_InitializeToplogicalAtomPairs</span> <span class="s">{</span>
+ 346   <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+ 347   <span class="k">my</span><span class="s">(</span><span class="i">$Distance</span><span class="s">)</span><span class="sc">;</span>
+ 348 
+ 349   <span class="i">@</span>{<span class="i">$This</span>-&gt;{<span class="w">AtomPairsIDs</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 350   <span class="i">%</span>{<span class="i">$This</span>-&gt;{<span class="w">AtomPairsCount</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 351 
+ 352   <span class="k">for</span> <span class="i">$Distance</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">MinDistance</span>} .. <span class="i">$This</span>-&gt;{<span class="w">MaxDistance</span>}<span class="s">)</span> <span class="s">{</span>
+ 353     <span class="i">%</span>{<span class="i">$This</span>-&gt;{<span class="w">AtomPairsCount</span>}{<span class="i">$Distance</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 354   <span class="s">}</span>
+ 355 
+ 356   <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
+ 357 <span class="s">}</span>
+ 358 
+ 359 <span class="c"># Count atom pairs between mininum and maximum distance at each</span>
+ 360 <span class="c"># distance using distance matrix and atom types assiged to each heavy</span>
+ 361 <span class="c"># atom.</span>
+ 362 <span class="c">#</span>
+ 363 <span class="c"># Notes:</span>
+ 364 <span class="c">#   . The row and column indices of distance matrix correspond to atom indices.</span>
+ 365 <span class="c">#   . Distance value of BigNumber implies the atom is not connected to any other atom.</span>
+ 366 <span class="c">#   . Due to symmetric nature of distance matrix, only upper or lower triangular matrix</span>
+ 367 <span class="c">#     needs to be processed during identification and count of atom pairs.</span>
+ 368 <span class="c">#</span>
+<a name="_GenerateAndCountAtomPairs-"></a> 369 <span class="k">sub </span><span class="m">_GenerateAndCountAtomPairs</span> <span class="s">{</span>
+ 370   <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+ 371 
+ 372   <span class="k">my</span><span class="s">(</span><span class="i">$NumOfRows</span><span class="cm">,</span> <span class="i">$NumOfCols</span><span class="cm">,</span> <span class="i">$RowIndex</span><span class="cm">,</span> <span class="i">$ColIndex</span><span class="cm">,</span> <span class="i">$DistanceMatrix</span><span class="cm">,</span> <span class="i">$Distance</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">$AtomType1</span><span class="cm">,</span> <span class="i">$AtomType2</span><span class="cm">,</span> <span class="i">$SkipIndexCheck</span><span class="cm">,</span> <span class="i">$CountIncrement</span><span class="s">)</span><span class="sc">;</span>
+ 373 
+ 374   <span class="i">$DistanceMatrix</span> = <span class="i">$This</span>-&gt;{<span class="w">DistanceMatrix</span>}<span class="sc">;</span>
+ 375   <span class="s">(</span><span class="i">$NumOfRows</span><span class="cm">,</span> <span class="i">$NumOfCols</span><span class="s">)</span> = <span class="i">$DistanceMatrix</span><span class="i">-&gt;GetSize</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 376   <span class="i">$SkipIndexCheck</span> = <span class="n">0</span><span class="sc">;</span>
+ 377 
+ 378   <span class="j">ROWINDEX:</span> <span class="k">for</span> <span class="i">$RowIndex</span> <span class="s">(</span><span class="n">0</span> .. <span class="s">(</span><span class="i">$NumOfRows</span> - <span class="n">1</span><span class="s">)</span> <span class="s">)</span> <span class="s">{</span>
+ 379     <span class="i">$AtomID1</span> = <span class="i">$This</span>-&gt;{<span class="w">AtomIndexToID</span>}{<span class="i">$RowIndex</span>}<span class="sc">;</span>
+ 380     <span class="k">if</span> <span class="s">(</span> !<span class="s">(</span><span class="k">exists</span><span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">AssignedAtomTypes</span>}{<span class="i">$AtomID1</span>}<span class="s">)</span><span class="s">)</span> <span class="s">)</span> <span class="s">{</span>
+ 381       <span class="k">next</span> <span class="j">ROWINDEX</span><span class="sc">;</span>
+ 382     <span class="s">}</span>
+ 383     <span class="i">$AtomType1</span> = <span class="i">$This</span>-&gt;{<span class="w">AssignedAtomTypes</span>}{<span class="i">$AtomID1</span>}<span class="sc">;</span>
+ 384 
+ 385     <span class="j">COLINDEX:</span> <span class="k">for</span> <span class="i">$ColIndex</span> <span class="s">(</span><span class="s">(</span><span class="i">$RowIndex</span> + <span class="n">1</span><span class="s">)</span> .. <span class="s">(</span><span class="i">$NumOfCols</span> - <span class="n">1</span><span class="s">)</span> <span class="s">)</span> <span class="s">{</span>
+ 386       <span class="i">$AtomID2</span> = <span class="i">$This</span>-&gt;{<span class="w">AtomIndexToID</span>}{<span class="i">$ColIndex</span>}<span class="sc">;</span>
+ 387       <span class="k">if</span> <span class="s">(</span> !<span class="s">(</span><span class="k">exists</span><span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">AssignedAtomTypes</span>}{<span class="i">$AtomID2</span>}<span class="s">)</span><span class="s">)</span> <span class="s">)</span> <span class="s">{</span>
+ 388         <span class="k">next</span> <span class="j">COLINDEX</span><span class="sc">;</span>
+ 389       <span class="s">}</span>
+ 390       <span class="i">$Distance</span> = <span class="i">$DistanceMatrix</span><span class="i">-&gt;GetValue</span><span class="s">(</span><span class="i">$RowIndex</span><span class="cm">,</span> <span class="i">$ColIndex</span><span class="cm">,</span> <span class="i">$SkipIndexCheck</span><span class="s">)</span><span class="sc">;</span>
+ 391       <span class="k">if</span> <span class="s">(</span><span class="i">$Distance</span> &lt; <span class="i">$This</span>-&gt;{<span class="w">MinDistance</span>} || <span class="i">$Distance</span> &gt; <span class="i">$This</span>-&gt;{<span class="w">MaxDistance</span>}<span class="s">)</span> <span class="s">{</span>
+ 392         <span class="k">next</span> <span class="j">COLINDEX</span><span class="sc">;</span>
+ 393       <span class="s">}</span>
+ 394       <span class="i">$AtomType2</span> = <span class="i">$This</span>-&gt;{<span class="w">AssignedAtomTypes</span>}{<span class="i">$AtomID2</span>}<span class="sc">;</span>
+ 395 
+ 396       <span class="k">if</span> <span class="s">(</span><span class="i">$AtomType1</span> <span class="k">le</span> <span class="i">$AtomType2</span><span class="s">)</span> <span class="s">{</span>
+ 397         <span class="i">$This</span><span class="i">-&gt;_SetAtomPairsCount</span><span class="s">(</span><span class="i">$Distance</span><span class="cm">,</span> <span class="i">$AtomType1</span><span class="cm">,</span> <span class="i">$AtomType2</span><span class="s">)</span><span class="sc">;</span>
+ 398       <span class="s">}</span>
+ 399       <span class="k">else</span> <span class="s">{</span>
+ 400         <span class="i">$This</span><span class="i">-&gt;_SetAtomPairsCount</span><span class="s">(</span><span class="i">$Distance</span><span class="cm">,</span> <span class="i">$AtomType2</span><span class="cm">,</span> <span class="i">$AtomType1</span><span class="s">)</span><span class="sc">;</span>
+ 401       <span class="s">}</span>
+ 402     <span class="s">}</span>
+ 403   <span class="s">}</span>
+ 404   <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
+ 405 <span class="s">}</span>
+ 406 
+ 407 <span class="c"># Set atom paris count for a specific atom ID pair at a specific distance...</span>
+ 408 <span class="c">#</span>
+<a name="_SetAtomPairsCount-"></a> 409 <span class="k">sub </span><span class="m">_SetAtomPairsCount</span> <span class="s">{</span>
+ 410   <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Distance</span><span class="cm">,</span> <span class="i">$AtomType1</span><span class="cm">,</span> <span class="i">$AtomType2</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+ 411 
+ 412   <span class="k">if</span> <span class="s">(</span>! <span class="k">exists</span> <span class="i">$This</span>-&gt;{<span class="w">AtomPairsCount</span>}{<span class="i">$Distance</span>}{<span class="i">$AtomType1</span>}<span class="s">)</span> <span class="s">{</span>
+ 413     <span class="i">%</span>{<span class="i">$This</span>-&gt;{<span class="w">AtomPairsCount</span>}{<span class="i">$Distance</span>}{<span class="i">$AtomType1</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 414     <span class="i">$This</span>-&gt;{<span class="w">AtomPairsCount</span>}{<span class="i">$Distance</span>}{<span class="i">$AtomType1</span>}{<span class="i">$AtomType2</span>} = <span class="n">1</span><span class="sc">;</span>
+ 415     <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
+ 416   <span class="s">}</span>
+ 417 
+ 418   <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$This</span>-&gt;{<span class="w">AtomPairsCount</span>}{<span class="i">$Distance</span>}{<span class="i">$AtomType1</span>}{<span class="i">$AtomType2</span>}<span class="s">)</span> <span class="s">{</span>
+ 419     <span class="i">$This</span>-&gt;{<span class="w">AtomPairsCount</span>}{<span class="i">$Distance</span>}{<span class="i">$AtomType1</span>}{<span class="i">$AtomType2</span>} += <span class="n">1</span><span class="sc">;</span>
+ 420   <span class="s">}</span>
+ 421   <span class="k">else</span> <span class="s">{</span>
+ 422     <span class="i">$This</span>-&gt;{<span class="w">AtomPairsCount</span>}{<span class="i">$Distance</span>}{<span class="i">$AtomType1</span>}{<span class="i">$AtomType2</span>} = <span class="n">1</span><span class="sc">;</span>
+ 423   <span class="s">}</span>
+ 424 
+ 425   <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
+ 426 <span class="s">}</span>
+ 427 
+ 428 <span class="c"># Set final fingerpritns vector...</span>
+ 429 <span class="c">#</span>
+<a name="_SetFinalFingerprints-"></a> 430 <span class="k">sub </span><span class="m">_SetFinalFingerprints</span> <span class="s">{</span>
+ 431   <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+ 432   <span class="k">my</span><span class="s">(</span><span class="i">$Distance</span><span class="cm">,</span> <span class="i">$AtomType1</span><span class="cm">,</span> <span class="i">$AtomType2</span><span class="cm">,</span> <span class="i">$Value</span><span class="cm">,</span> <span class="i">@Values</span><span class="s">)</span><span class="sc">;</span>
+ 433 
+ 434   <span class="c"># Mark successful generation of fingerprints...</span>
+ 435   <span class="i">$This</span>-&gt;{<span class="w">FingerprintsGenerated</span>} = <span class="n">1</span><span class="sc">;</span>
+ 436 
+ 437   <span class="i">@Values</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 438   <span class="i">@</span>{<span class="i">$This</span>-&gt;{<span class="w">AtomPairsIDs</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 439 
+ 440   <span class="k">for</span> <span class="i">$Distance</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">MinDistance</span>} .. <span class="i">$This</span>-&gt;{<span class="w">MaxDistance</span>}<span class="s">)</span> <span class="s">{</span>
+ 441     <span class="k">for</span> <span class="i">$AtomType1</span> <span class="s">(</span><span class="k">sort</span> <span class="k">keys</span> <span class="i">%</span>{<span class="i">$This</span>-&gt;{<span class="w">AtomPairsCount</span>}{<span class="i">$Distance</span>}} <span class="s">)</span> <span class="s">{</span>
+ 442       <span class="k">for</span> <span class="i">$AtomType2</span> <span class="s">(</span><span class="k">sort</span> <span class="k">keys</span> <span class="i">%</span>{<span class="i">$This</span>-&gt;{<span class="w">AtomPairsCount</span>}{<span class="i">$Distance</span>}{<span class="i">$AtomType1</span>}} <span class="s">)</span> <span class="s">{</span>
+ 443         <span class="k">push</span> <span class="i">@</span>{<span class="i">$This</span>-&gt;{<span class="w">AtomPairsIDs</span>}}<span class="cm">,</span> <span class="q">&quot;${AtomType1}-D${Distance}-${AtomType2}&quot;</span><span class="sc">;</span>
+ 444         <span class="i">$Value</span> = <span class="i">$This</span>-&gt;{<span class="w">AtomPairsCount</span>}{<span class="i">$Distance</span>}{<span class="i">$AtomType1</span>}{<span class="i">$AtomType2</span>}<span class="sc">;</span>
+ 445         <span class="k">push</span> <span class="i">@Values</span><span class="cm">,</span> <span class="i">$Value</span><span class="sc">;</span>
+ 446       <span class="s">}</span>
+ 447     <span class="s">}</span>
+ 448   <span class="s">}</span>
+ 449 
+ 450   <span class="c"># Add AtomPairsIDs and values to fingerprint vector...</span>
+ 451   <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">AtomPairsIDs</span>}}<span class="s">)</span><span class="sc">;</span>
+ 452   <span class="i">$This</span>-&gt;{<span class="w">FingerprintsVector</span>}<span class="i">-&gt;AddValues</span><span class="s">(</span>\<span class="i">@Values</span><span class="s">)</span><span class="sc">;</span>
+ 453 
+ 454   <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
+ 455 <span class="s">}</span>
+ 456 
+ 457 <span class="c"># Get atom pair IDs corresponding to atom pairs count values in fingerprint</span>
+ 458 <span class="c"># vector as an array or reference to an array...</span>
+ 459 <span class="c">#</span>
+ 460 <span class="c"># AtomPairIDs list differes in molecules and is generated during finalization</span>
+ 461 <span class="c"># of fingerprints to make sure the fingerprint vector containing count values</span>
+ 462 <span class="c"># matches the atom pairs array.</span>
+ 463 <span class="c">#</span>
+<a name="GetAtomPairIDs-"></a> 464 <span class="k">sub </span><span class="m">GetAtomPairIDs</span> <span class="s">{</span>
+ 465   <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+ 466 
+ 467   <span class="k">return</span> <span class="k">wantarray</span> ? <span class="i">@</span>{<span class="i">$This</span>-&gt;{<span class="w">AtomPairsIDs</span>}} <span class="co">:</span> \<span class="i">@</span>{<span class="i">$This</span>-&gt;{<span class="w">AtomPairsIDs</span>}}<span class="sc">;</span>
+ 468 <span class="s">}</span>
+ 469 
+ 470 <span class="c"># Cache  appropriate molecule data...</span>
+ 471 <span class="c">#</span>
+<a name="_SetupMoleculeDataCache-"></a> 472 <span class="k">sub </span><span class="m">_SetupMoleculeDataCache</span> <span class="s">{</span>
+ 473   <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+ 474 
+ 475   <span class="c"># Get all atoms including hydrogens to correctly map atom indices to atom IDs for</span>
+ 476   <span class="c"># usage of distance matrix. The hydrogen atoms are ignored during processing...</span>
+ 477   <span class="c">#</span>
+ 478   <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>
+ 479 
+ 480   <span class="c"># Get all atom IDs...</span>
+ 481   <span class="k">my</span><span class="s">(</span><span class="i">@AtomIDs</span><span class="s">)</span><span class="sc">;</span>
+ 482   <span class="i">@AtomIDs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 483   <span class="i">@AtomIDs</span> =  <span class="k">map</span> <span class="s">{</span> <span class="i">$_</span><span class="i">-&gt;GetID</span><span class="s">(</span><span class="s">)</span> <span class="s">}</span> <span class="i">@</span>{<span class="i">$This</span>-&gt;{<span class="w">Atoms</span>}}<span class="sc">;</span>
+ 484 
+ 485   <span class="c"># Set AtomIndex to AtomID hash...</span>
+ 486   <span class="i">%</span>{<span class="i">$This</span>-&gt;{<span class="w">AtomIndexToID</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 487   <span class="i">@</span>{<span class="i">$This</span>-&gt;{<span class="w">AtomIndexToID</span>}}{ <span class="s">(</span><span class="n">0</span> .. <span class="i">$#AtomIDs</span><span class="s">)</span> } = <span class="i">@AtomIDs</span><span class="sc">;</span>
+ 488 
+ 489   <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
+ 490 <span class="s">}</span>
+ 491 
+ 492 <span class="c"># Clear cached molecule data...</span>
+ 493 <span class="c">#</span>
+<a name="_ClearMoleculeDataCache-"></a> 494 <span class="k">sub </span><span class="m">_ClearMoleculeDataCache</span> <span class="s">{</span>
+ 495   <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+ 496 
+ 497   <span class="i">@</span>{<span class="i">$This</span>-&gt;{<span class="w">Atoms</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 498 
+ 499   <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
+ 500 <span class="s">}</span>
+ 501 
+ 502 <span class="c"># Set atomic invariants to use for atom identifiers...</span>
+ 503 <span class="c">#</span>
+<a name="SetAtomicInvariantsToUse-"></a> 504 <span class="k">sub </span><span class="m">SetAtomicInvariantsToUse</span> <span class="s">{</span>
+ 505   <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">@Values</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+ 506   <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>
+ 507 
+ 508   <span class="k">if</span> <span class="s">(</span>!<span class="i">@Values</span><span class="s">)</span> <span class="s">{</span>
+ 509     <span class="w">carp</span> <span class="q">&quot;Warning: ${ClassName}-&gt;SetAtomicInvariantsToUse: No values specified...&quot;</span><span class="sc">;</span>
+ 510     <span class="k">return</span><span class="sc">;</span>
+ 511   <span class="s">}</span>
+ 512 
+ 513   <span class="i">$FirstValue</span> = <span class="i">$Values</span>[<span class="n">0</span>]<span class="sc">;</span>
+ 514   <span class="i">$TypeOfFirstValue</span> = <span class="k">ref</span> <span class="i">$FirstValue</span><span class="sc">;</span>
+ 515 
+ 516   <span class="i">@SpecifiedAtomicInvariants</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 517   <span class="i">@AtomicInvariantsToUse</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 518 
+ 519   <span class="k">if</span> <span class="s">(</span><span class="i">$TypeOfFirstValue</span> =~ <span class="q">/^ARRAY/</span><span class="s">)</span> <span class="s">{</span>
+ 520     <span class="k">push</span> <span class="i">@SpecifiedAtomicInvariants</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$FirstValue</span>}<span class="sc">;</span>
+ 521   <span class="s">}</span>
+ 522   <span class="k">else</span> <span class="s">{</span>
+ 523     <span class="k">push</span> <span class="i">@SpecifiedAtomicInvariants</span><span class="cm">,</span> <span class="i">@Values</span><span class="sc">;</span>
+ 524   <span class="s">}</span>
+ 525 
+ 526   <span class="c"># Make sure specified AtomicInvariants are valid...</span>
+ 527   <span class="k">for</span> <span class="i">$SpecifiedAtomicInvariant</span> <span class="s">(</span><span class="i">@SpecifiedAtomicInvariants</span><span class="s">)</span> <span class="s">{</span>
+ 528     <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>
+ 529       <span class="w">croak</span> <span class="q">&quot;Error: ${ClassName}-&gt;SetAtomicInvariantsToUse: Specified atomic invariant, $SpecifiedAtomicInvariant, is not supported...\n &quot;</span><span class="sc">;</span>
+ 530     <span class="s">}</span>
+ 531     <span class="i">$AtomicInvariant</span> = <span class="i">$SpecifiedAtomicInvariant</span><span class="sc">;</span>
+ 532     <span class="k">push</span> <span class="i">@AtomicInvariantsToUse</span><span class="cm">,</span> <span class="i">$AtomicInvariant</span><span class="sc">;</span>
+ 533   <span class="s">}</span>
+ 534 
+ 535   <span class="c"># Set atomic invariants to use...</span>
+ 536   <span class="i">@</span>{<span class="i">$This</span>-&gt;{<span class="w">AtomicInvariantsToUse</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 537   <span class="k">push</span> <span class="i">@</span>{<span class="i">$This</span>-&gt;{<span class="w">AtomicInvariantsToUse</span>}}<span class="cm">,</span> <span class="i">@AtomicInvariantsToUse</span><span class="sc">;</span>
+ 538 
+ 539   <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
+ 540 <span class="s">}</span>
+ 541 
+ 542 <span class="c"># Set functional classes to use for atom identifiers...</span>
+ 543 <span class="c">#</span>
+<a name="SetFunctionalClassesToUse-"></a> 544 <span class="k">sub </span><span class="m">SetFunctionalClassesToUse</span> <span class="s">{</span>
+ 545   <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">@Values</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+ 546   <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>
+ 547 
+ 548   <span class="k">if</span> <span class="s">(</span>!<span class="i">@Values</span><span class="s">)</span> <span class="s">{</span>
+ 549     <span class="w">carp</span> <span class="q">&quot;Warning: ${ClassName}-&gt;SetFunctionalClassesToUse: No values specified...&quot;</span><span class="sc">;</span>
+ 550     <span class="k">return</span><span class="sc">;</span>
+ 551   <span class="s">}</span>
+ 552 
+ 553   <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">AtomIdentifierType</span>} !~ <span class="q">/^FunctionalClassAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span>
+ 554     <span class="w">carp</span> <span class="q">&quot;Warning: ${ClassName}-&gt;SetFunctionalClassesToUse: FunctionalClassesToUse can&#39;t be set for InitialAtomIdentifierType of $This-&gt;{AtomIdentifierType}...&quot;</span><span class="sc">;</span>
+ 555     <span class="k">return</span><span class="sc">;</span>
+ 556   <span class="s">}</span>
+ 557 
+ 558   <span class="i">$FirstValue</span> = <span class="i">$Values</span>[<span class="n">0</span>]<span class="sc">;</span>
+ 559   <span class="i">$TypeOfFirstValue</span> = <span class="k">ref</span> <span class="i">$FirstValue</span><span class="sc">;</span>
+ 560 
+ 561   <span class="i">@SpecifiedFunctionalClasses</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 562   <span class="i">@FunctionalClassesToUse</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 563 
+ 564   <span class="k">if</span> <span class="s">(</span><span class="i">$TypeOfFirstValue</span> =~ <span class="q">/^ARRAY/</span><span class="s">)</span> <span class="s">{</span>
+ 565     <span class="k">push</span> <span class="i">@SpecifiedFunctionalClasses</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$FirstValue</span>}<span class="sc">;</span>
+ 566   <span class="s">}</span>
+ 567   <span class="k">else</span> <span class="s">{</span>
+ 568     <span class="k">push</span> <span class="i">@SpecifiedFunctionalClasses</span><span class="cm">,</span> <span class="i">@Values</span><span class="sc">;</span>
+ 569   <span class="s">}</span>
+ 570 
+ 571   <span class="c"># Make sure specified FunctionalClasses are valid...</span>
+ 572   <span class="k">for</span> <span class="i">$SpecifiedFunctionalClass</span> <span class="s">(</span><span class="i">@SpecifiedFunctionalClasses</span><span class="s">)</span> <span class="s">{</span>
+ 573     <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>
+ 574       <span class="w">croak</span> <span class="q">&quot;Error: ${ClassName}-&gt;SetFunctionalClassesToUse: Specified functional class, $SpecifiedFunctionalClass, is not supported...\n &quot;</span><span class="sc">;</span>
+ 575     <span class="s">}</span>
+ 576     <span class="k">push</span> <span class="i">@FunctionalClassesToUse</span><span class="cm">,</span> <span class="i">$SpecifiedFunctionalClass</span><span class="sc">;</span>
+ 577   <span class="s">}</span>
+ 578 
+ 579   <span class="c"># Set functional classes to use...</span>
+ 580   <span class="i">@</span>{<span class="i">$This</span>-&gt;{<span class="w">FunctionalClassesToUse</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 581   <span class="k">push</span> <span class="i">@</span>{<span class="i">$This</span>-&gt;{<span class="w">FunctionalClassesToUse</span>}}<span class="cm">,</span> <span class="i">@FunctionalClassesToUse</span><span class="sc">;</span>
+ 582 
+ 583   <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
+ 584 <span class="s">}</span>
+ 585 
+ 586 <span class="c"># Initialize atom indentifier type information...</span>
+ 587 <span class="c">#</span>
+ 588 <span class="c"># Current supported values:</span>
+ 589 <span class="c">#</span>
+ 590 <span class="c"># AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, FunctionalClassAtomTypes,</span>
+ 591 <span class="c"># MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes</span>
+ 592 <span class="c">#</span>
+<a name="_InitializeAtomIdentifierTypeInformation-"></a> 593 <span class="k">sub </span><span class="m">_InitializeAtomIdentifierTypeInformation</span> <span class="s">{</span>
+ 594   <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+ 595 
+ 596   <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>
+ 597     <span class="i">$This</span><span class="i">-&gt;_InitializeAtomicInvariantsAtomTypesInformation</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 598   <span class="s">}</span>
+ 599   <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^FunctionalClassAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span>
+ 600     <span class="i">$This</span><span class="i">-&gt;_InitializeFunctionalClassAtomTypesInformation</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 601   <span class="s">}</span>
+ 602   <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>
+ 603     <span class="c"># Nothing to do for now...</span>
+ 604   <span class="s">}</span>
+ 605   <span class="k">else</span> <span class="s">{</span>
+ 606     <span class="w">croak</span> <span class="q">&quot;Error: ${ClassName}-&gt;_InitializeAtomIdentifierTypeInformation: Unknown atom indentifier type $This-&gt;{AtomIdentifierType}...&quot;</span><span class="sc">;</span>
+ 607   <span class="s">}</span>
+ 608 
+ 609   <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
+ 610 <span class="s">}</span>
+ 611 
+ 612 <span class="c"># Initialize atomic invariants atom types to use for generating atom identifiers...</span>
+ 613 <span class="c">#</span>
+ 614 <span class="c"># Let:</span>
+ 615 <span class="c">#   AS = Atom symbol corresponding to element symbol</span>
+ 616 <span class="c">#</span>
+ 617 <span class="c">#   X&lt;n&gt;   = Number of non-hydrogen atom neighbors or heavy atoms attached to atom</span>
+ 618 <span class="c">#   BO&lt;n&gt; = Sum of bond orders to non-hydrogen atom neighbors or heavy atoms attached to atom</span>
+ 619 <span class="c">#   LBO&lt;n&gt; = Largest bond order of non-hydrogen atom neighbors or heavy atoms attached to atom</span>
+ 620 <span class="c">#   SB&lt;n&gt; = Number of single bonds to non-hydrogen atom neighbors or heavy atoms attached to atom</span>
+ 621 <span class="c">#   DB&lt;n&gt; = Number of double bonds to non-hydrogen atom neighbors or heavy atoms attached to atom</span>
+ 622 <span class="c">#   TB&lt;n&gt; = Number of triple bonds to non-hydrogen atom neighbors or heavy atoms attached to atom</span>
+ 623 <span class="c">#   H&lt;n&gt;   = Number of implicit and explicit hydrogens for atom</span>
+ 624 <span class="c">#   Ar     = Aromatic annotation indicating whether atom is aromatic</span>
+ 625 <span class="c">#   RA     = Ring atom annotation indicating whether atom is a ring</span>
+ 626 <span class="c">#   FC&lt;+n/-n&gt; = Formal charge assigned to atom</span>
+ 627 <span class="c">#   MN&lt;n&gt; = Mass number indicating isotope other than most abundant isotope</span>
+ 628 <span class="c">#   SM&lt;n&gt; = Spin multiplicity of atom. Possible values: 1 (singlet), 2 (doublet) or 3 (triplet)</span>
+ 629 <span class="c">#</span>
+ 630 <span class="c">#   AtomTypeIDx = Atomic invariants atom type for atom x</span>
+ 631 <span class="c">#   AtomTypeIDy = Atomic invariants atom type for atom y</span>
+ 632 <span class="c">#   Dn   = Topological distance between atom x and y</span>
+ 633 <span class="c">#</span>
+ 634 <span class="c"># Then:</span>
+ 635 <span class="c">#</span>
+ 636 <span class="c">#   Atom pair AtomID generated by AtomTypes::AtomicInvariantsAtomTypes class corresponds to:</span>
+ 637 <span class="c">#</span>
+ 638 <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>
+ 639 <span class="c">#</span>
+ 640 <span class="c">#  AtomPairID corresponds to:</span>
+ 641 <span class="c">#</span>
+ 642 <span class="c">#    AtomTypeIDx-D&lt;n&gt;-AtomTypeIDy</span>
+ 643 <span class="c">#</span>
+ 644 <span class="c"># Except for AS which is a required atomic invariant in atom pair AtomIDs, all other atomic invariants are</span>
+ 645 <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>
+ 646 <span class="c"># AtomID specification doesn&#39;t include atomic invariants with zero or undefined values.</span>
+ 647 <span class="c">#</span>
+ 648 <span class="c"># Examples of atom pair AtomIDs:</span>
+ 649 <span class="c">#</span>
+ 650 <span class="c">#   O.X1.BO1.H1 - Hydroxyl oxygen in carboxylate with attached hydrogen and no explicit charge</span>
+ 651 <span class="c">#   O.X1.BO1.FC-1 - Hydroxyl ozygen in carboxylate with explicit negative charge</span>
+ 652 <span class="c">#   O.X1.BO2 - Carbonyl oxygen in carboxylate with double bond to carbon</span>
+ 653 <span class="c">#   O.X2.BO2 - Hydroxyl ozygen in carboxylate attached to carbonyl carbon and another heavy atom</span>
+ 654 <span class="c">#</span>
+ 655 <span class="c">#   C.X2.BO3.H1.Ar - Aromatic carbon</span>
+ 656 <span class="c">#</span>
+ 657 <span class="c"># Examples of AtomPairIDs:</span>
+ 658 <span class="c">#</span>
+ 659 <span class="c">#   C.X2.BO2.H3-D1-O.X1.BO1 - Carbon with two heavy atom neighbors attached to oxygen at bond distance 1(methanol)</span>
+ 660 <span class="c">#</span>
+ 661 <span class="c">#   C.X2.BO3.H1.Ar-D3-C.X2.BO3.H1.Ar  - Two aromatic carbons at bond distance 3 where each carbon has</span>
+ 662 <span class="c">#                                       two heavy atom neighbors and bond order of 3 (benzene)</span>
+ 663 <span class="c">#</span>
+<a name="_InitializeAtomicInvariantsAtomTypesInformation-"></a> 664 <span class="k">sub </span><span class="m">_InitializeAtomicInvariantsAtomTypesInformation</span> <span class="s">{</span>
+ 665   <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+ 666 
+ 667   <span class="c"># Default atomic invariants to use for generating atom neighborhood atom IDs: AS, X, BO, H, FC</span>
+ 668   <span class="c">#</span>
+ 669   <span class="i">@</span>{<span class="i">$This</span>-&gt;{<span class="w">AtomicInvariantsToUse</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 670   <span class="i">@</span>{<span class="i">$This</span>-&gt;{<span class="w">AtomicInvariantsToUse</span>}} = <span class="s">(</span><span class="q">&#39;AS&#39;</span><span class="cm">,</span> <span class="q">&#39;X&#39;</span><span class="cm">,</span> <span class="q">&#39;BO&#39;</span><span class="cm">,</span> <span class="q">&#39;H&#39;</span><span class="cm">,</span> <span class="q">&#39;FC&#39;</span><span class="s">)</span><span class="sc">;</span>
+ 671 
+ 672   <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
+ 673 <span class="s">}</span>
+ 674 
+ 675 <span class="c"># Initialize functional class atom types, generated by AtomTypes::FunctionalClassAtomTypes</span>
+ 676 <span class="c"># class, to use for generating atom identifiers...</span>
+ 677 <span class="c">#</span>
+ 678 <span class="c"># Let:</span>
+ 679 <span class="c">#   HBD: HydrogenBondDonor</span>
+ 680 <span class="c">#   HBA: HydrogenBondAcceptor</span>
+ 681 <span class="c">#   PI :  PositivelyIonizable</span>
+ 682 <span class="c">#   NI : NegativelyIonizable</span>
+ 683 <span class="c">#   Ar : Aromatic</span>
+ 684 <span class="c">#   Hal : Halogen</span>
+ 685 <span class="c">#   H : Hydrophobic</span>
+ 686 <span class="c">#   RA : RingAtom</span>
+ 687 <span class="c">#   CA : ChainAtom</span>
+ 688 <span class="c">#</span>
+ 689 <span class="c"># Then:</span>
+ 690 <span class="c">#</span>
+ 691 <span class="c">#   Functiononal class atom type specification for an atom corresponds to:</span>
+ 692 <span class="c">#</span>
+ 693 <span class="c">#     Ar.CA.H.HBA.HBD.Hal.NI.PI.RA</span>
+ 694 <span class="c">#</span>
+ 695 <span class="c">#   Default functional classes used are: HBD, HBA, PI, NI, Ar, Hal</span>
+ 696 <span class="c">#</span>
+ 697 <span class="c">#   FunctionalAtomTypes are assigned using the following definitions [ Ref 60-61, Ref 65-66 ]:</span>
+ 698 <span class="c">#</span>
+ 699 <span class="c">#     HydrogenBondDonor: NH, NH2, OH</span>
+ 700 <span class="c">#     HydrogenBondAcceptor: N[!H], O</span>
+ 701 <span class="c">#     PositivelyIonizable: +, NH2</span>
+ 702 <span class="c">#     NegativelyIonizable: -, C(=O)OH, S(=O)OH, P(=O)OH</span>
+ 703 <span class="c">#</span>
+<a name="_InitializeFunctionalClassAtomTypesInformation-"></a> 704 <span class="k">sub </span><span class="m">_InitializeFunctionalClassAtomTypesInformation</span> <span class="s">{</span>
+ 705   <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+ 706 
+ 707   <span class="c"># Default functional class atom typess to use for generating atom identifiers</span>
+ 708   <span class="c"># are: HBD, HBA, PI, NI, Ar, Hal</span>
+ 709   <span class="c">#</span>
+ 710   <span class="i">@</span>{<span class="i">$This</span>-&gt;{<span class="w">FunctionalClassesToUse</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 711   <span class="i">@</span>{<span class="i">$This</span>-&gt;{<span class="w">FunctionalClassesToUse</span>}} = <span class="s">(</span><span class="q">&#39;HBD&#39;</span><span class="cm">,</span> <span class="q">&#39;HBA&#39;</span><span class="cm">,</span> <span class="q">&#39;PI&#39;</span><span class="cm">,</span> <span class="q">&#39;NI&#39;</span><span class="cm">,</span> <span class="q">&#39;Ar&#39;</span><span class="cm">,</span> <span class="q">&#39;Hal&#39;</span><span class="s">)</span><span class="sc">;</span>
+ 712 
+ 713   <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
+ 714 <span class="s">}</span>
+ 715 
+ 716 <span class="c"># Return a string containg data for TopologicalAtomPairsFingerprints object...</span>
+ 717 <span class="c">#</span>
+<a name="StringifyTopologicalAtomPairsFingerprints-"></a> 718 <span class="k">sub </span><span class="m">StringifyTopologicalAtomPairsFingerprints</span> <span class="s">{</span>
+ 719   <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+ 720   <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsString</span><span class="s">)</span><span class="sc">;</span>
+ 721 
+ 722   <span class="c"># Type of fingerprint...</span>
+ 723   <span class="i">$FingerprintsString</span> = <span class="q">&quot;Fingerprint type: $This-&gt;{Type}; AtomIdentifierType: $This-&gt;{AtomIdentifierType}&quot;</span><span class="sc">;</span>
+ 724 
+ 725   <span class="c"># Min and max distance...</span>
+ 726   <span class="i">$FingerprintsString</span> .= <span class="q">&quot;; MinDistance:  $This-&gt;{MinDistance}; MaxDistance: $This-&gt;{MaxDistance}&quot;</span><span class="sc">;</span>
+ 727 
+ 728   <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^AtomicInvariantsAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span>
+ 729     <span class="k">my</span><span class="s">(</span><span class="i">$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>
+ 730 
+ 731     <span class="i">@AtomicInvariantsOrder</span> = <span class="i">AtomTypes::AtomicInvariantsAtomTypes::GetAtomicInvariantsOrder</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 732     <span class="i">%AvailableAtomicInvariants</span> = <span class="i">AtomTypes::AtomicInvariantsAtomTypes::GetAvailableAtomicInvariants</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 733 
+ 734     <span class="k">for</span> <span class="i">$AtomicInvariant</span> <span class="s">(</span><span class="i">@AtomicInvariantsOrder</span><span class="s">)</span> <span class="s">{</span>
+ 735       <span class="k">push</span> <span class="i">@AtomicInvariants</span><span class="cm">,</span> <span class="q">&quot;$AtomicInvariant: $AvailableAtomicInvariants{$AtomicInvariant}&quot;</span><span class="sc">;</span>
+ 736     <span class="s">}</span>
+ 737 
+ 738     <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>
+ 739     <span class="i">$FingerprintsString</span> .= <span class="q">&quot;; AtomicInvariantsOrder: &lt;&quot;</span> . <span class="i">TextUtil::JoinWords</span><span class="s">(</span>\<span class="i">@AtomicInvariantsOrder</span><span class="cm">,</span> <span class="q">&quot;, &quot;</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span> . <span class="q">&quot;&gt;&quot;</span><span class="sc">;</span>
+ 740     <span class="i">$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>
+ 741   <span class="s">}</span>
+ 742   <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>
+ 743     <span class="k">my</span><span class="s">(</span><span class="i">$FunctionalClass</span><span class="cm">,</span> <span class="i">@FunctionalClasses</span><span class="cm">,</span> <span class="i">@FunctionalClassesOrder</span><span class="cm">,</span> <span class="i">%AvailableFunctionalClasses</span><span class="s">)</span><span class="sc">;</span>
+ 744 
+ 745     <span class="i">@FunctionalClassesOrder</span> = <span class="i">AtomTypes::FunctionalClassAtomTypes::GetFunctionalClassesOrder</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 746     <span class="i">%AvailableFunctionalClasses</span> = <span class="i">AtomTypes::FunctionalClassAtomTypes::GetAvailableFunctionalClasses</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 747 
+ 748     <span class="k">for</span> <span class="i">$FunctionalClass</span> <span class="s">(</span><span class="i">@FunctionalClassesOrder</span><span class="s">)</span> <span class="s">{</span>
+ 749       <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>
+ 750     <span class="s">}</span>
+ 751 
+ 752     <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>
+ 753     <span class="i">$FingerprintsString</span> .= <span class="q">&quot;; FunctionalClassesOrder: &lt;&quot;</span> . <span class="i">TextUtil::JoinWords</span><span class="s">(</span>\<span class="i">@FunctionalClassesOrder</span><span class="cm">,</span> <span class="q">&quot;, &quot;</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span> . <span class="q">&quot;&gt;&quot;</span><span class="sc">;</span>
+ 754     <span class="i">$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>
+ 755   <span class="s">}</span>
+ 756 
+ 757   <span class="c"># Total number of atom pairs...</span>
+ 758   <span class="i">$FingerprintsString</span> .= <span class="q">&quot;; NumOfAtomPairs: &quot;</span> . <span class="i">$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>
+ 759 
+ 760   <span class="c"># FingerprintsVector...</span>
+ 761   <span class="i">$FingerprintsString</span> .= <span class="q">&quot;; FingerprintsVector: &lt; $This-&gt;{FingerprintsVector} &gt;&quot;</span><span class="sc">;</span>
+ 762 
+ 763   <span class="k">return</span> <span class="i">$FingerprintsString</span><span class="sc">;</span>
+ 764 <span class="s">}</span>
+ 765 
+<a name="EOF-"></a></pre>
+<p>&nbsp;</p>
+<br />
+<center>
+<img src="../../../images/h2o2.png">
+</center>
+</body>
+</html>