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

Uploaded
author deepakjadmin
date Wed, 20 Jan 2016 11:55:01 -0500
parents
children
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mayachemtools/docs/modules/html/code/EStateValuesDescriptors.html	Wed Jan 20 11:55:01 2016 -0500
@@ -0,0 +1,496 @@
+<html>
+<head>
+<title>MayaChemTools:Code:AtomicDescriptors::EStateValuesDescriptors.pm</title>
+<meta http-equiv="content-type" content="text/html;charset=utf-8">
+<link rel="stylesheet" type="text/css" href="../../../css/MayaChemToolsCode.css">
+</head>
+<body leftmargin="20" rightmargin="20" topmargin="10" bottommargin="10">
+<br/>
+<center>
+<a href="http://www.mayachemtools.org" title="MayaChemTools Home"><img src="../../../images/MayaChemToolsLogo.gif" border="0" alt="MayaChemTools"></a>
+</center>
+<br/>
+<pre>
+<a name="package-AtomicDescriptors::EStateValuesDescriptors-"></a>   1 <span class="k">package </span><span class="i">AtomicDescriptors::EStateValuesDescriptors</span><span class="sc">;</span>
+   2 <span class="c">#</span>
+   3 <span class="c"># $RCSfile: EStateValuesDescriptors.pm,v $</span>
+   4 <span class="c"># $Date: 2015/02/28 20:47:49 $</span>
+   5 <span class="c"># $Revision: 1.16 $</span>
+   6 <span class="c">#</span>
+   7 <span class="c"># Author: Manish Sud &lt;msud@san.rr.com&gt;</span>
+   8 <span class="c">#</span>
+   9 <span class="c"># Copyright (C) 2015 Manish Sud. All rights reserved.</span>
+  10 <span class="c">#</span>
+  11 <span class="c"># This file is part of MayaChemTools.</span>
+  12 <span class="c">#</span>
+  13 <span class="c"># MayaChemTools is free software; you can redistribute it and/or modify it under</span>
+  14 <span class="c"># the terms of the GNU Lesser General Public License as published by the Free</span>
+  15 <span class="c"># Software Foundation; either version 3 of the License, or (at your option) any</span>
+  16 <span class="c"># later version.</span>
+  17 <span class="c">#</span>
+  18 <span class="c"># MayaChemTools is distributed in the hope that it will be useful, but without</span>
+  19 <span class="c"># any warranty; without even the implied warranty of merchantability of fitness</span>
+  20 <span class="c"># for a particular purpose.  See the GNU Lesser General Public License for more</span>
+  21 <span class="c"># details.</span>
+  22 <span class="c">#</span>
+  23 <span class="c"># You should have received a copy of the GNU Lesser General Public License</span>
+  24 <span class="c"># along with MayaChemTools; if not, see &lt;http://www.gnu.org/licenses/&gt; or</span>
+  25 <span class="c"># write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,</span>
+  26 <span class="c"># Boston, MA, 02111-1307, USA.</span>
+  27 <span class="c">#</span>
+  28 
+  29 <span class="k">use</span> <span class="w">strict</span><span class="sc">;</span>
+  30 <span class="k">use</span> <span class="w">Carp</span><span class="sc">;</span>
+  31 <span class="k">use</span> <span class="w">Exporter</span><span class="sc">;</span>
+  32 <span class="k">use</span> <span class="w">Scalar::Util</span> <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+  33 <span class="k">use</span> <span class="w">Matrix</span><span class="sc">;</span>
+  34 <span class="k">use</span> <span class="w">Constants</span><span class="sc">;</span>
+  35 <span class="k">use</span> <span class="w">TextUtil</span> <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+  36 <span class="k">use</span> <span class="w">MathUtil</span> <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+  37 <span class="k">use</span> <span class="w">StatisticsUtil</span> <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+  38 <span class="k">use</span> <span class="w">Atom</span><span class="sc">;</span>
+  39 <span class="k">use</span> <span class="w">Molecule</span><span class="sc">;</span>
+  40 <span class="k">use</span> <span class="w">AtomicDescriptors::AtomicDescriptors</span><span class="sc">;</span>
+  41 
+  42 <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>
+  43 
+  44 <span class="i">@ISA</span> = <span class="q">qw(AtomicDescriptors::AtomicDescriptors Exporter)</span><span class="sc">;</span>
+  45 <span class="i">@EXPORT</span> = <span class="q">qw()</span><span class="sc">;</span>
+  46 <span class="i">@EXPORT_OK</span> = <span class="q">qw()</span><span class="sc">;</span>
+  47 
+  48 <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>
+  49 
+  50 <span class="c"># Setup class variables...</span>
+  51 <span class="k">my</span><span class="s">(</span><span class="i">$ClassName</span><span class="s">)</span><span class="sc">;</span>
+  52 <span class="i">_InitializeClass</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+  53 
+  54 <span class="c"># Overload Perl functions...</span>
+  55 <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;StringifyEStateValuesDescriptors&#39;</span><span class="sc">;</span>
+  56 
+  57 <span class="c"># Class constructor...</span>
+<a name="new-"></a>  58 <span class="k">sub </span><span class="m">new</span> <span class="s">{</span>
+  59   <span class="k">my</span><span class="s">(</span><span class="i">$Class</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+  60 
+  61   <span class="c"># Initialize object...</span>
+  62   <span class="k">my</span> <span class="i">$This</span> = <span class="i">$Class</span><span class="i">-&gt;SUPER::new</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+  63   <span class="k">bless</span> <span class="i">$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>
+  64   <span class="i">$This</span><span class="i">-&gt;_InitializeEStateValuesDescriptors</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+  65 
+  66   <span class="i">$This</span><span class="i">-&gt;_InitializeEStateValuesDescriptorsProperties</span><span class="s">(</span><span class="i">%NamesAndValues</span><span class="s">)</span><span class="sc">;</span>
+  67 
+  68   <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
+  69 <span class="s">}</span>
+  70 
+  71 <span class="c"># Initialize class ...</span>
+<a name="_InitializeClass-"></a>  72 <span class="k">sub </span><span class="m">_InitializeClass</span> <span class="s">{</span>
+  73   <span class="c">#Class name...</span>
+  74   <span class="i">$ClassName</span> = <span class="w">__PACKAGE__</span><span class="sc">;</span>
+  75 <span class="s">}</span>
+  76 
+  77 
+  78 <span class="c"># Initialize object data...</span>
+  79 <span class="c">#</span>
+<a name="_InitializeEStateValuesDescriptors-"></a>  80 <span class="k">sub </span><span class="m">_InitializeEStateValuesDescriptors</span> <span class="s">{</span>
+  81   <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+  82 
+  83   <span class="c"># Type of AtomicDescriptor...</span>
+  84   <span class="i">$This</span>-&gt;{<span class="w">Type</span>} = <span class="q">&#39;EStateValue&#39;</span><span class="sc">;</span>
+  85 
+  86   <span class="c"># Intrinsic state values calculated for non-hydrogen atom...</span>
+  87   <span class="c">#</span>
+  88   <span class="i">%</span>{<span class="i">$This</span>-&gt;{<span class="w">IStateValues</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+  89 
+  90   <span class="c"># Calculatetion of E-state values for types for hydrogens is not supported...</span>
+  91   <span class="i">$This</span>-&gt;{<span class="w">IgnoreHydrogens</span>} = <span class="n">1</span><span class="sc">;</span>
+  92 
+  93   <span class="c"># Perturbation to intrinsic state values of atoms corresponding to all non-hydrogen</span>
+  94   <span class="c"># atom pairs...</span>
+  95   <span class="c">#</span>
+  96   <span class="i">%</span>{<span class="i">$This</span>-&gt;{<span class="w">DeltaIStateMatrix</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+  97 
+  98   <span class="c"># E-state values calculated for non-hydrogen atoms...</span>
+  99   <span class="c">#</span>
+ 100   <span class="i">%</span>{<span class="i">$This</span>-&gt;{<span class="w">EStateValues</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 101 
+ 102   <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
+ 103 <span class="s">}</span>
+ 104 
+ 105 <span class="c"># Initialize object properties...</span>
+ 106 <span class="c">#</span>
+<a name="_InitializeEStateValuesDescriptorsProperties-"></a> 107 <span class="k">sub </span><span class="m">_InitializeEStateValuesDescriptorsProperties</span> <span class="s">{</span>
+ 108   <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+ 109 
+ 110   <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">$MethodName</span><span class="s">)</span><span class="sc">;</span>
+ 111   <span class="k">while</span> <span class="s">(</span><span class="s">(</span><span class="i">$Name</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="k">each</span>  <span class="i">%NamesAndValues</span><span class="s">)</span> <span class="s">{</span>
+ 112     <span class="i">$MethodName</span> = <span class="q">&quot;Set${Name}&quot;</span><span class="sc">;</span>
+ 113     <span class="i">$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>
+ 114   <span class="s">}</span>
+ 115 
+ 116   <span class="c"># Make sure molecule object was specified...</span>
+ 117   <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>
+ 118     <span class="w">croak</span> <span class="q">&quot;Error: ${ClassName}-&gt;New: Object can&#39;t be instantiated without specifying molecule...&quot;</span><span class="sc">;</span>
+ 119   <span class="s">}</span>
+ 120 
+ 121   <span class="c"># Intialize atomic descriptor values...</span>
+ 122   <span class="i">$This</span><span class="i">-&gt;_InitializeDescriptorValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 123 
+ 124   <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
+ 125 <span class="s">}</span>
+ 126 
+ 127 <span class="c"># Disable change of ignore hydrogens...</span>
+ 128 <span class="c">#</span>
+<a name="SetIgnoreHydrogens-"></a> 129 <span class="k">sub </span><span class="m">SetIgnoreHydrogens</span> <span class="s">{</span>
+ 130   <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$IgnoreHydrogens</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+ 131 
+ 132   <span class="w">carp</span> <span class="q">&quot;Warning: ${ClassName}-&gt;SetIgnoreHydrogens: Ignore hydrogens value can&#39;t be changed: It&#39;s not supported...&quot;</span><span class="sc">;</span>
+ 133 
+ 134   <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
+ 135 <span class="s">}</span>
+ 136 
+ 137 <span class="c"># Generate electrotopological state (E-state) values [ Ref 75-78 ] for all atoms</span>
+ 138 <span class="c"># in the molecule...</span>
+ 139 <span class="c">#</span>
+ 140 <span class="c"># Calculation of E-state values for non-hydrogen atoms:</span>
+ 141 <span class="c">#</span>
+ 142 <span class="c"># Let:</span>
+ 143 <span class="c">#</span>
+ 144 <span class="c">#   N = Principal quantum number or period number corresponding to element symbol</span>
+ 145 <span class="c">#</span>
+ 146 <span class="c">#   Sigma = Number of sigma electrons involves in bonds to hydrogen and non-hydrogen atoms</span>
+ 147 <span class="c">#           attached to atom</span>
+ 148 <span class="c">#         = Number of sigma bonds to hydrogen and non-hydrogen atoms attached to atom</span>
+ 149 <span class="c">#   PI = Number of PI electrons involved in bonds to non-hydrogen atoms attached to atom</span>
+ 150 <span class="c">#       = Number of PI bonds to non-hydrogen atoms attached to atom</span>
+ 151 <span class="c">#</span>
+ 152 <span class="c">#   LP = Number of lone pair electrons on atom</span>
+ 153 <span class="c">#</span>
+ 154 <span class="c">#   Zv = Number of electrons in valence shell of atom</span>
+ 155 <span class="c">#</span>
+ 156 <span class="c">#   X = Number of non-hydrogen atom neighbors or heavy atoms attached to atom</span>
+ 157 <span class="c">#   H = Number of implicit and explicit hydrogens for atom</span>
+ 158 <span class="c">#</span>
+ 159 <span class="c">#   Delta = Number of sigma electrons involved to bonds to non-hydrogen atoms</span>
+ 160 <span class="c">#   DeltaV = ValenceDelta = Number of valence shell electrons not involved in bonding to hydrogen atoms</span>
+ 161 <span class="c">#</span>
+ 162 <span class="c">#   Ii = Intrinsic state value for atom i</span>
+ 163 <span class="c">#</span>
+ 164 <span class="c">#   DeltaIi = Sum of perturbations to intrinsic state value Ii of atom i by all other atoms besides atom i</span>
+ 165 <span class="c">#</span>
+ 166 <span class="c">#   DeltaIij = Perturbation to intrinsic state value Ii of atom i by atom j</span>
+ 167 <span class="c">#</span>
+ 168 <span class="c">#   Dij = Graph/bond distance between atom i and j</span>
+ 169 <span class="c">#   Rij = Dij + 1</span>
+ 170 <span class="c">#</span>
+ 171 <span class="c">#   Si = E-state value for atom i</span>
+ 172 <span class="c">#</span>
+ 173 <span class="c">#</span>
+ 174 <span class="c"># Then:</span>
+ 175 <span class="c">#</span>
+ 176 <span class="c">#   Delta = Sigma - H = X</span>
+ 177 <span class="c">#</span>
+ 178 <span class="c">#   DeltaV = Zv - H</span>
+ 179 <span class="c">#      = Sigma + PI + LP - H</span>
+ 180 <span class="c">#</span>
+ 181 <span class="c">#   Ii = ( ( ( 2 / N ) ** 2 ) * DeltaV + 1 ) / Delta</span>
+ 182 <span class="c">#</span>
+ 183 <span class="c">#   Si = Ii + DeltaIi</span>
+ 184 <span class="c">#</span>
+ 185 <span class="c">#   DeltaIij = (Ii - Ij) / (Rij ** 2) for j not equal to i</span>
+ 186 <span class="c">#</span>
+ 187 <span class="c">#   DeltaIji = - DeltaIij</span>
+ 188 <span class="c">#</span>
+ 189 <span class="c">#   DeltaIi = SUM ( (Ii - Ij) / (Rij ** 2) ) for j = 1 to num of atoms skipping atom i</span>
+ 190 <span class="c">#</span>
+ 191 <span class="c"># Methodology:</span>
+ 192 <span class="c">#   . Calculate intrinsic state values for atoms.</span>
+ 193 <span class="c">#   . Generate a distance matrix.</span>
+ 194 <span class="c">#   . Use distance matrix to calculate DeltaIij matrix with each row i containing</span>
+ 195 <span class="c">#     DeltaIij values corresponding to perturbation to intrinsic state value of atom</span>
+ 196 <span class="c">#     i by atom j.</span>
+ 197 <span class="c">#   . Calculate E-state values using DeltaIij matrix.</span>
+ 198 <span class="c">#   . Assign E-state values to atoms.</span>
+ 199 <span class="c">#</span>
+ 200 <span class="c"># Notes:</span>
+ 201 <span class="c">#   . The current release of MayaChemTools doesn&#39;t support calculation of Hydrogen</span>
+ 202 <span class="c">#     E-state values.</span>
+ 203 <span class="c">#</span>
+<a name="GenerateDescriptors-"></a> 204 <span class="k">sub </span><span class="m">GenerateDescriptors</span> <span class="s">{</span>
+ 205   <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+ 206 
+ 207   <span class="c"># Cache appropriate molecule data...</span>
+ 208   <span class="i">$This</span><span class="i">-&gt;_SetupMoleculeDataCache</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 209 
+ 210   <span class="c"># Generate distance matrix...</span>
+ 211   <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>
+ 212     <span class="w">carp</span> <span class="q">&quot;Warning: ${ClassName}-&gt;GenerateDescriptors: E-state values description generation didn&#39;t succeed: Couldn&#39;t generate a distance matrix...&quot;</span><span class="sc">;</span>
+ 213     <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
+ 214   <span class="s">}</span>
+ 215 
+ 216   <span class="c"># Calculate EState values..</span>
+ 217   <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">-&gt;_CalculateEStateValuesDescriptors</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+ 218     <span class="w">carp</span> <span class="q">&quot;Warning: ${ClassName}-&gt;GenerateDescriptors: E-state values description generation didn&#39;t succeed: Couldn&#39;t calculate IState values for all atoms...&quot;</span><span class="sc">;</span>
+ 219     <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
+ 220   <span class="s">}</span>
+ 221 
+ 222   <span class="c"># Set final descriptor values...</span>
+ 223   <span class="i">$This</span><span class="i">-&gt;_SetFinalValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 224 
+ 225   <span class="c"># Clear cached molecule data...</span>
+ 226   <span class="i">$This</span><span class="i">-&gt;_ClearMoleculeDataCache</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 227 
+ 228   <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
+ 229 <span class="s">}</span>
+ 230 
+ 231 <span class="c"># Calculate E-state values for non-hydrogen atoms...</span>
+ 232 <span class="c">#</span>
+<a name="_CalculateEStateValuesDescriptors-"></a> 233 <span class="k">sub </span><span class="m">_CalculateEStateValuesDescriptors</span> <span class="s">{</span>
+ 234   <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+ 235   <span class="k">my</span><span class="s">(</span><span class="i">$DeltaIStateMatrix</span><span class="cm">,</span> <span class="i">$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">$AtomID</span><span class="cm">,</span> <span class="i">$EStateValue</span><span class="cm">,</span> <span class="i">$IStateValue</span><span class="cm">,</span> <span class="i">$DeltaIStateValue</span><span class="cm">,</span> <span class="i">@DeltaIStateMatrixRowValues</span><span class="s">)</span><span class="sc">;</span>
+ 236 
+ 237   <span class="i">%</span>{<span class="i">$This</span>-&gt;{<span class="w">EStateValues</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 238 
+ 239   <span class="c"># Calculate intrinsic state values for non-hydrogen atoms...</span>
+ 240   <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">-&gt;_CalculateIStateValues</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+ 241     <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
+ 242   <span class="s">}</span>
+ 243 
+ 244   <span class="c"># Calculate delta intrinsic state matrix for non-hydrogen atoms...</span>
+ 245   <span class="i">$This</span><span class="i">-&gt;_CalculateDeltaIStateMatrix</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 246 
+ 247   <span class="c"># Get DeltaIState matrix information...</span>
+ 248   <span class="i">$DeltaIStateMatrix</span> = <span class="i">$This</span>-&gt;{<span class="w">DeltaIStateMatrix</span>}<span class="sc">;</span>
+ 249   <span class="s">(</span><span class="i">$NumOfRows</span><span class="cm">,</span> <span class="i">$NumOfCols</span><span class="s">)</span> = <span class="i">$DeltaIStateMatrix</span><span class="i">-&gt;GetSize</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 250 
+ 251   <span class="c"># Calculate EState values...</span>
+ 252   <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>
+ 253     <span class="i">$AtomID</span> = <span class="i">$This</span>-&gt;{<span class="w">AtomIndexToID</span>}{<span class="i">$RowIndex</span>}<span class="sc">;</span>
+ 254     <span class="k">if</span> <span class="s">(</span> !<span class="s">(</span><span class="k">exists</span><span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">IStateValues</span>}{<span class="i">$AtomID</span>}<span class="s">)</span><span class="s">)</span> <span class="s">)</span> <span class="s">{</span>
+ 255       <span class="k">next</span> <span class="j">ROWINDEX</span><span class="sc">;</span>
+ 256     <span class="s">}</span>
+ 257     <span class="i">$IStateValue</span> = <span class="i">$This</span>-&gt;{<span class="w">IStateValues</span>}{<span class="i">$AtomID</span>}<span class="sc">;</span>
+ 258 
+ 259     <span class="i">@DeltaIStateMatrixRowValues</span> = <span class="i">$DeltaIStateMatrix</span><span class="i">-&gt;GetRowValues</span><span class="s">(</span><span class="i">$RowIndex</span><span class="s">)</span><span class="sc">;</span>
+ 260     <span class="i">$DeltaIStateValue</span> = <span class="i">StatisticsUtil::Sum</span><span class="s">(</span>\<span class="i">@DeltaIStateMatrixRowValues</span><span class="s">)</span><span class="sc">;</span>
+ 261 
+ 262     <span class="i">$EStateValue</span> = <span class="i">$IStateValue</span> + <span class="i">$DeltaIStateValue</span><span class="sc">;</span>
+ 263 
+ 264     <span class="i">$This</span>-&gt;{<span class="w">EStateValues</span>}{<span class="i">$AtomID</span>} = <span class="i">$EStateValue</span><span class="sc">;</span>
+ 265   <span class="s">}</span>
+ 266   <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
+ 267 <span class="s">}</span>
+ 268 
+ 269 <span class="c"># Calculate intrinsic state values for non-hydrogen atoms...</span>
+ 270 <span class="c">#</span>
+<a name="_CalculateIStateValues-"></a> 271 <span class="k">sub </span><span class="m">_CalculateIStateValues</span> <span class="s">{</span>
+ 272   <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+ 273   <span class="k">my</span><span class="s">(</span><span class="i">$Atom</span><span class="cm">,</span> <span class="i">$AtomID</span><span class="s">)</span><span class="sc">;</span>
+ 274 
+ 275   <span class="i">%</span>{<span class="i">$This</span>-&gt;{<span class="w">IStateValues</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 276 
+ 277   <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>
+ 278     <span class="c"># Irrespective of IgoreHydrogens value, just ignore hydrogens...</span>
+ 279     <span class="k">if</span> <span class="s">(</span><span class="i">$Atom</span><span class="i">-&gt;IsHydrogen</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+ 280       <span class="k">next</span> <span class="j">ATOM</span><span class="sc">;</span>
+ 281     <span class="s">}</span>
+ 282     <span class="i">$AtomID</span> = <span class="i">$Atom</span><span class="i">-&gt;GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 283     <span class="i">$This</span>-&gt;{<span class="w">IStateValues</span>}{<span class="i">$AtomID</span>} = <span class="i">$This</span><span class="i">-&gt;_CalculateIStateValue</span><span class="s">(</span><span class="i">$Atom</span><span class="s">)</span><span class="sc">;</span>
+ 284     <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span><span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">IStateValues</span>}{<span class="i">$AtomID</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+ 285       <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
+ 286     <span class="s">}</span>
+ 287   <span class="s">}</span>
+ 288   <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
+ 289 <span class="s">}</span>
+ 290 
+ 291 <span class="c"># Calculation intrinsic state value for non-hydrogen...</span>
+ 292 <span class="c">#</span>
+<a name="_CalculateIStateValue-"></a> 293 <span class="k">sub </span><span class="m">_CalculateIStateValue</span> <span class="s">{</span>
+ 294   <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Atom</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+ 295   <span class="k">my</span><span class="s">(</span><span class="i">$IStateValue</span><span class="cm">,</span> <span class="i">$Delta</span><span class="cm">,</span> <span class="i">$DeltaV</span><span class="cm">,</span> <span class="i">$PeriodNumber</span><span class="s">)</span><span class="sc">;</span>
+ 296 
+ 297   <span class="i">$PeriodNumber</span> = <span class="i">$Atom</span><span class="i">-&gt;GetPeriodNumber</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 298   <span class="s">(</span><span class="i">$Delta</span><span class="cm">,</span> <span class="i">$DeltaV</span><span class="s">)</span> = <span class="i">$This</span><span class="i">-&gt;_GetDeltaValues</span><span class="s">(</span><span class="i">$Atom</span><span class="s">)</span><span class="sc">;</span>
+ 299 
+ 300   <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$Delta</span><span class="s">)</span> &amp;&amp; <span class="k">defined</span><span class="s">(</span><span class="i">$PeriodNumber</span><span class="s">)</span> &amp;&amp; <span class="k">defined</span><span class="s">(</span><span class="i">$DeltaV</span><span class="s">)</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+ 301     <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
+ 302   <span class="s">}</span>
+ 303 
+ 304   <span class="i">$IStateValue</span> = <span class="s">(</span><span class="i">$PeriodNumber</span> &amp;&amp; <span class="i">$Delta</span><span class="s">)</span> ? <span class="s">(</span><span class="s">(</span><span class="s">(</span><span class="n">2</span>/<span class="i">$PeriodNumber</span><span class="s">)</span>**<span class="n">2</span><span class="s">)</span>*<span class="i">$DeltaV</span> + <span class="n">1</span><span class="s">)</span>/<span class="i">$Delta</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
+ 305 
+ 306   <span class="k">return</span> <span class="i">$IStateValue</span><span class="sc">;</span>
+ 307 <span class="s">}</span>
+ 308 
+ 309 <span class="c"># Get Delta and DeltaV values for atom...</span>
+ 310 <span class="c">#</span>
+<a name="_GetDeltaValues-"></a> 311 <span class="k">sub </span><span class="m">_GetDeltaValues</span> <span class="s">{</span>
+ 312   <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Atom</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+ 313   <span class="k">my</span><span class="s">(</span><span class="i">$Delta</span><span class="cm">,</span> <span class="i">$DeltaV</span><span class="cm">,</span> <span class="i">$ValenceElectrons</span><span class="cm">,</span> <span class="i">$NumOfHydrogens</span><span class="s">)</span><span class="sc">;</span>
+ 314 
+ 315   <span class="s">(</span><span class="i">$Delta</span><span class="cm">,</span> <span class="i">$DeltaV</span><span class="s">)</span> = <span class="s">(</span><span class="k">undef</span><span class="cm">,</span> <span class="k">undef</span><span class="s">)</span><span class="sc">;</span>
+ 316 
+ 317   <span class="i">$ValenceElectrons</span> = <span class="i">$Atom</span><span class="i">-&gt;GetValenceElectrons</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 318   <span class="i">$NumOfHydrogens</span> = <span class="i">$Atom</span><span class="i">-&gt;GetAtomicInvariantValue</span><span class="s">(</span><span class="q">&#39;H&#39;</span><span class="s">)</span><span class="sc">;</span>
+ 319 
+ 320   <span class="i">$Delta</span> = <span class="i">$Atom</span><span class="i">-&gt;GetAtomicInvariantValue</span><span class="s">(</span><span class="q">&#39;X&#39;</span><span class="s">)</span><span class="sc">;</span>
+ 321   <span class="k">if</span> <span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$ValenceElectrons</span><span class="s">)</span> &amp;&amp; <span class="k">defined</span><span class="s">(</span><span class="i">$NumOfHydrogens</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+ 322     <span class="i">$DeltaV</span> = <span class="i">$ValenceElectrons</span> - <span class="i">$NumOfHydrogens</span><span class="sc">;</span>
+ 323   <span class="s">}</span>
+ 324 
+ 325   <span class="k">return</span> <span class="s">(</span><span class="i">$Delta</span><span class="cm">,</span> <span class="i">$DeltaV</span><span class="s">)</span><span class="sc">;</span>
+ 326 <span class="s">}</span>
+ 327 
+ 328 <span class="c"># Calculate DeltaIState matrix for atoms with each row i containing DeltaIij values</span>
+ 329 <span class="c"># corresponding atom atoms i and j.</span>
+ 330 <span class="c">#</span>
+ 331 <span class="c"># Notes:</span>
+ 332 <span class="c">#   . Matrix elements corresponding to hydrogen atoms or unconnected</span>
+ 333 <span class="c">#     are assigned zero value.</span>
+ 334 <span class="c">#</span>
+<a name="_CalculateDeltaIStateMatrix-"></a> 335 <span class="k">sub </span><span class="m">_CalculateDeltaIStateMatrix</span> <span class="s">{</span>
+ 336   <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+ 337   <span class="k">my</span><span class="s">(</span><span class="i">$DistanceMatrix</span><span class="cm">,</span> <span class="i">$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">$ColIndex</span><span class="cm">,</span> <span class="i">$AtomID1</span><span class="cm">,</span> <span class="i">$AtomID2</span><span class="cm">,</span> <span class="i">$DeltaIStateMatrix</span><span class="cm">,</span> <span class="i">$IStateValue1</span><span class="cm">,</span> <span class="i">$IStateValue2</span><span class="cm">,</span> <span class="i">$GraphDistance</span><span class="cm">,</span> <span class="i">$DeltaIState12</span><span class="cm">,</span> <span class="i">$DeltaIState21</span><span class="cm">,</span> <span class="i">$SkipIndexCheck</span><span class="s">)</span><span class="sc">;</span>
+ 338 
+ 339   <span class="c"># Get distance matrix information...</span>
+ 340   <span class="i">$DistanceMatrix</span> = <span class="i">$This</span>-&gt;{<span class="w">DistanceMatrix</span>}<span class="sc">;</span>
+ 341   <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">$DistanceMatrix</span><span class="i">-&gt;GetSize</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 342 
+ 343   <span class="c"># Initialize DeltaIState matrix...</span>
+ 344   <span class="i">$This</span>-&gt;{<span class="w">DeltaIStateMatrix</span>} = <span class="i">new</span> <span class="i">Matrix</span><span class="s">(</span><span class="i">$NumOfRows</span><span class="cm">,</span> <span class="i">$NumOfCols</span><span class="s">)</span><span class="sc">;</span>
+ 345   <span class="i">$DeltaIStateMatrix</span> = <span class="i">$This</span>-&gt;{<span class="w">DeltaIStateMatrix</span>}<span class="sc">;</span>
+ 346 
+ 347   <span class="i">$SkipIndexCheck</span> = <span class="n">1</span><span class="sc">;</span>
+ 348 
+ 349   <span class="c"># Calculate DeltaIState matrix values...</span>
+ 350   <span class="j">ROWINDEX:</span> <span class="k">for</span> <span class="i">$RowIndex</span> <span class="s">(</span><span class="n">0</span> .. <span class="s">(</span><span class="i">$NumOfRows</span> - <span class="n">1</span><span class="s">)</span> <span class="s">)</span> <span class="s">{</span>
+ 351     <span class="i">$AtomID1</span> = <span class="i">$This</span>-&gt;{<span class="w">AtomIndexToID</span>}{<span class="i">$RowIndex</span>}<span class="sc">;</span>
+ 352     <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span><span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">IStateValues</span>}{<span class="i">$AtomID1</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+ 353       <span class="k">next</span> <span class="j">ROWINDEX</span><span class="sc">;</span>
+ 354     <span class="s">}</span>
+ 355     <span class="i">$IStateValue1</span> = <span class="i">$This</span>-&gt;{<span class="w">IStateValues</span>}{<span class="i">$AtomID1</span>}<span class="sc">;</span>
+ 356 
+ 357     <span class="j">COLINDEX:</span> <span class="k">for</span> <span class="i">$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>
+ 358       <span class="i">$AtomID2</span> = <span class="i">$This</span>-&gt;{<span class="w">AtomIndexToID</span>}{<span class="i">$ColIndex</span>}<span class="sc">;</span>
+ 359       <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span><span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">IStateValues</span>}{<span class="i">$AtomID2</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+ 360         <span class="k">next</span> <span class="j">COLINDEX</span><span class="sc">;</span>
+ 361       <span class="s">}</span>
+ 362       <span class="i">$IStateValue2</span> = <span class="i">$This</span>-&gt;{<span class="w">IStateValues</span>}{<span class="i">$AtomID2</span>}<span class="sc">;</span>
+ 363 
+ 364       <span class="c"># Make sure it&#39;s a connected atom...</span>
+ 365       <span class="i">$GraphDistance</span> = <span class="i">$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">$SkipIndexCheck</span><span class="s">)</span><span class="sc">;</span>
+ 366       <span class="k">if</span> <span class="s">(</span><span class="i">$GraphDistance</span> &gt;= <span class="w">BigNumber</span><span class="s">)</span> <span class="s">{</span>
+ 367         <span class="k">next</span> <span class="j">COLINDEX</span><span class="sc">;</span>
+ 368       <span class="s">}</span>
+ 369 
+ 370       <span class="i">$DeltaIState12</span> = <span class="s">(</span><span class="i">$IStateValue1</span> - <span class="i">$IStateValue2</span><span class="s">)</span>/<span class="s">(</span><span class="s">(</span><span class="i">$GraphDistance</span> + <span class="n">1</span><span class="s">)</span>**<span class="n">2</span><span class="s">)</span><span class="sc">;</span>
+ 371       <span class="i">$DeltaIState21</span> = -<span class="i">$DeltaIState12</span><span class="sc">;</span>
+ 372 
+ 373       <span class="c"># Set DeltaIState values...</span>
+ 374       <span class="i">$DeltaIStateMatrix</span><span class="i">-&gt;SetValue</span><span class="s">(</span><span class="i">$RowIndex</span><span class="cm">,</span> <span class="i">$ColIndex</span><span class="cm">,</span> <span class="i">$DeltaIState12</span><span class="cm">,</span> <span class="i">$SkipIndexCheck</span><span class="s">)</span><span class="sc">;</span>
+ 375       <span class="i">$DeltaIStateMatrix</span><span class="i">-&gt;SetValue</span><span class="s">(</span><span class="i">$ColIndex</span><span class="cm">,</span> <span class="i">$RowIndex</span><span class="cm">,</span> <span class="i">$DeltaIState21</span><span class="cm">,</span> <span class="i">$SkipIndexCheck</span><span class="s">)</span><span class="sc">;</span>
+ 376     <span class="s">}</span>
+ 377   <span class="s">}</span>
+ 378 <span class="s">}</span>
+ 379 
+ 380 <span class="c"># Setup distance matrix...</span>
+ 381 <span class="c">#</span>
+<a name="_SetupDistanceMatrix-"></a> 382 <span class="k">sub </span><span class="m">_SetupDistanceMatrix</span> <span class="s">{</span>
+ 383   <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+ 384 
+ 385   <span class="i">$This</span>-&gt;{<span class="w">DistanceMatrix</span>} = <span class="i">$This</span><span class="i">-&gt;GetMolecule</span><span class="s">(</span><span class="s">)</span><span class="i">-&gt;GetDistanceMatrix</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 386 
+ 387   <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span><span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">DistanceMatrix</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+ 388     <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
+ 389   <span class="s">}</span>
+ 390 
+ 391   <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
+ 392 <span class="s">}</span>
+ 393 
+ 394 <span class="c"># Setup final descriptor values...</span>
+ 395 <span class="c">#</span>
+<a name="_SetFinalValues-"></a> 396 <span class="k">sub </span><span class="m">_SetFinalValues</span> <span class="s">{</span>
+ 397   <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+ 398   <span class="k">my</span><span class="s">(</span><span class="i">$Atom</span><span class="cm">,</span> <span class="i">$AtomID</span><span class="cm">,</span> <span class="i">$EStateValue</span><span class="s">)</span><span class="sc">;</span>
+ 399 
+ 400   <span class="j">ATOM:</span> <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$This</span>-&gt;{<span class="w">Atoms</span>}}<span class="s">)</span> <span class="s">{</span>
+ 401     <span class="i">$AtomID</span> = <span class="i">$Atom</span><span class="i">-&gt;GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 402     <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$This</span>-&gt;{<span class="w">EStateValues</span>}{<span class="i">$AtomID</span>}<span class="s">)</span> <span class="s">{</span>
+ 403       <span class="k">next</span> <span class="j">ATOM</span><span class="sc">;</span>
+ 404     <span class="s">}</span>
+ 405     <span class="i">$EStateValue</span> = <span class="i">$This</span>-&gt;{<span class="w">EStateValues</span>}{<span class="i">$AtomID</span>}<span class="sc">;</span>
+ 406     <span class="i">$This</span><span class="i">-&gt;SetDescriptorValue</span><span class="s">(</span><span class="i">$Atom</span><span class="cm">,</span> <span class="i">$EStateValue</span><span class="s">)</span><span class="sc">;</span>
+ 407   <span class="s">}</span>
+ 408 
+ 409   <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
+ 410 <span class="s">}</span>
+ 411 
+ 412 <span class="c"># Cache  appropriate molecule data...</span>
+ 413 <span class="c">#</span>
+<a name="_SetupMoleculeDataCache-"></a> 414 <span class="k">sub </span><span class="m">_SetupMoleculeDataCache</span> <span class="s">{</span>
+ 415   <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+ 416 
+ 417   <span class="c"># Get all atoms including hydrogens to correctly map atom indicies to atom IDs for</span>
+ 418   <span class="c"># usage of distance matrix.</span>
+ 419   <span class="c">#</span>
+ 420   <span class="i">@</span>{<span class="i">$This</span>-&gt;{<span class="w">Atoms</span>}} = <span class="i">$This</span><span class="i">-&gt;GetMolecule</span><span class="s">(</span><span class="s">)</span><span class="i">-&gt;GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 421 
+ 422   <span class="c"># Get all atom IDs...</span>
+ 423   <span class="k">my</span><span class="s">(</span><span class="i">@AtomIDs</span><span class="s">)</span><span class="sc">;</span>
+ 424   <span class="i">@AtomIDs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 425   <span class="i">@AtomIDs</span> =  <span class="k">map</span> <span class="s">{</span> <span class="i">$_</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">$This</span>-&gt;{<span class="w">Atoms</span>}}<span class="sc">;</span>
+ 426 
+ 427   <span class="c"># Set AtomIndex to AtomID hash...</span>
+ 428   <span class="i">%</span>{<span class="i">$This</span>-&gt;{<span class="w">AtomIndexToID</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 429   <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>
+ 430 
+ 431   <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
+ 432 <span class="s">}</span>
+ 433 
+ 434 <span class="c"># Clear cached molecule data...</span>
+ 435 <span class="c">#</span>
+<a name="_ClearMoleculeDataCache-"></a> 436 <span class="k">sub </span><span class="m">_ClearMoleculeDataCache</span> <span class="s">{</span>
+ 437   <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+ 438 
+ 439   <span class="i">@</span>{<span class="i">$This</span>-&gt;{<span class="w">Atoms</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 440 
+ 441   <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
+ 442 <span class="s">}</span>
+ 443 
+ 444 <span class="c"># Return a string containg data for EStateValuesDescriptors object...</span>
+ 445 <span class="c">#</span>
+<a name="StringifyEStateValuesDescriptors-"></a> 446 <span class="k">sub </span><span class="m">StringifyEStateValuesDescriptors</span> <span class="s">{</span>
+ 447   <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+ 448   <span class="k">my</span><span class="s">(</span><span class="i">$EStateValuesDescriptorsString</span><span class="s">)</span><span class="sc">;</span>
+ 449 
+ 450   <span class="c"># Type of AtomicValues...</span>
+ 451   <span class="i">$EStateValuesDescriptorsString</span> = <span class="q">&quot;AtomicDescriptorType: $This-&gt;{Type}; IgnoreHydrogens: &quot;</span> . <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">IgnoreHydrogens</span>} ? <span class="q">&quot;Yes&quot;</span> <span class="co">:</span> <span class="q">&quot;No&quot;</span><span class="s">)</span><span class="sc">;</span>
+ 452 
+ 453   <span class="c"># Setup atomic descriptor information...</span>
+ 454   <span class="k">my</span><span class="s">(</span><span class="i">$AtomID</span><span class="cm">,</span> <span class="i">$DescriptorValue</span><span class="cm">,</span> <span class="i">@DescriptorValuesInfo</span><span class="cm">,</span> <span class="i">%DescriptorValues</span><span class="s">)</span><span class="sc">;</span>
+ 455 
+ 456   <span class="i">@DescriptorValuesInfo</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 457   <span class="i">%DescriptorValues</span> = <span class="i">$This</span><span class="i">-&gt;GetDescriptorValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 458 
+ 459   <span class="k">for</span> <span class="i">$AtomID</span> <span class="s">(</span><span class="k">sort</span> <span class="s">{</span> <span class="i">$a</span> &lt;=&gt; <span class="i">$b</span> <span class="s">}</span> <span class="k">keys</span> <span class="i">%DescriptorValues</span><span class="s">)</span> <span class="s">{</span>
+ 460     <span class="i">$DescriptorValue</span> = <span class="i">$DescriptorValues</span>{<span class="i">$AtomID</span>}<span class="sc">;</span>
+ 461     <span class="i">$DescriptorValue</span> = <span class="s">(</span><span class="i">TextUtil::IsEmpty</span><span class="s">(</span><span class="i">$DescriptorValue</span><span class="s">)</span> || <span class="i">$DescriptorValue</span> =~ <span class="q">/^None$/i</span><span class="s">)</span> ? <span class="q">&#39;None&#39;</span> <span class="co">:</span> <span class="i">MathUtil::round</span><span class="s">(</span><span class="i">$DescriptorValue</span><span class="cm">,</span> <span class="n">3</span><span class="s">)</span> + <span class="n">0</span><span class="sc">;</span>
+ 462     <span class="k">push</span> <span class="i">@DescriptorValuesInfo</span><span class="cm">,</span> <span class="q">&quot;$AtomID:$DescriptorValue&quot;</span><span class="sc">;</span>
+ 463   <span class="s">}</span>
+ 464   <span class="i">$EStateValuesDescriptorsString</span> .= <span class="q">&quot;; AtomIDs:EStateValuesDescriptors: &lt;&quot;</span> . <span class="i">TextUtil::JoinWords</span><span class="s">(</span>\<span class="i">@DescriptorValuesInfo</span><span class="cm">,</span> <span class="q">&quot;, &quot;</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span> . <span class="q">&quot;&gt;&quot;</span><span class="sc">;</span>
+ 465 
+ 466   <span class="k">return</span> <span class="i">$EStateValuesDescriptorsString</span><span class="sc">;</span>
+ 467 <span class="s">}</span>
+ 468 
+ 469 <span class="c"># Is it a EStateValuesDescriptors object?</span>
+<a name="_IsEStateValuesDescriptors-"></a> 470 <span class="k">sub </span><span class="m">_IsEStateValuesDescriptors</span> <span class="s">{</span>
+ 471   <span class="k">my</span><span class="s">(</span><span class="i">$Object</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+ 472 
+ 473   <span class="k">return</span> <span class="s">(</span><span class="i">Scalar::Util::blessed</span><span class="s">(</span><span class="i">$Object</span><span class="s">)</span> &amp;&amp; <span class="i">$Object</span><span class="i">-&gt;isa</span><span class="s">(</span><span class="i">$ClassName</span><span class="s">)</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
+ 474 <span class="s">}</span>
+ 475 
+<a name="EOF-"></a></pre>
+<p>&nbsp;</p>
+<br />
+<center>
+<img src="../../../images/h2o2.png">
+</center>
+</body>
+</html>