annotate mayachemtools/docs/modules/html/code/ExtendedConnectivityFingerprints.html @ 3:e420415a1799 draft

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1 <html>
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2 <head>
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3 <title>MayaChemTools:Code:Fingerprints::ExtendedConnectivityFingerprints.pm</title>
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4 <meta http-equiv="content-type" content="text/html;charset=utf-8">
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5 <link rel="stylesheet" type="text/css" href="../../../css/MayaChemToolsCode.css">
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6 </head>
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7 <body leftmargin="20" rightmargin="20" topmargin="10" bottommargin="10">
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8 <br/>
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9 <center>
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10 <a href="http://www.mayachemtools.org" title="MayaChemTools Home"><img src="../../../images/MayaChemToolsLogo.gif" border="0" alt="MayaChemTools"></a>
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11 </center>
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12 <br/>
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13 <pre>
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14 <a name="package-Fingerprints::ExtendedConnectivityFingerprints-"></a> 1 <span class="k">package </span><span class="i">Fingerprints::ExtendedConnectivityFingerprints</span><span class="sc">;</span>
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15 2 <span class="c">#</span>
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16 3 <span class="c"># $RCSfile: ExtendedConnectivityFingerprints.pm,v $</span>
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17 4 <span class="c"># $Date: 2015/02/28 20:48:54 $</span>
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18 5 <span class="c"># $Revision: 1.39 $</span>
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19 6 <span class="c">#</span>
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20 7 <span class="c"># Author: Manish Sud &lt;msud@san.rr.com&gt;</span>
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21 8 <span class="c">#</span>
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22 9 <span class="c"># Copyright (C) 2015 Manish Sud. All rights reserved.</span>
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23 10 <span class="c">#</span>
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24 11 <span class="c"># This file is part of MayaChemTools.</span>
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25 12 <span class="c">#</span>
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26 13 <span class="c"># MayaChemTools is free software; you can redistribute it and/or modify it under</span>
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27 14 <span class="c"># the terms of the GNU Lesser General Public License as published by the Free</span>
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28 15 <span class="c"># Software Foundation; either version 3 of the License, or (at your option) any</span>
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29 16 <span class="c"># later version.</span>
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30 17 <span class="c">#</span>
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31 18 <span class="c"># MayaChemTools is distributed in the hope that it will be useful, but without</span>
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32 19 <span class="c"># any warranty; without even the implied warranty of merchantability of fitness</span>
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33 20 <span class="c"># for a particular purpose. See the GNU Lesser General Public License for more</span>
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34 21 <span class="c"># details.</span>
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35 22 <span class="c">#</span>
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36 23 <span class="c"># You should have received a copy of the GNU Lesser General Public License</span>
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37 24 <span class="c"># along with MayaChemTools; if not, see &lt;http://www.gnu.org/licenses/&gt; or</span>
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38 25 <span class="c"># write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,</span>
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39 26 <span class="c"># Boston, MA, 02111-1307, USA.</span>
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40 27 <span class="c">#</span>
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41 28
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42 29 <span class="k">use</span> <span class="w">strict</span><span class="sc">;</span>
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43 30 <span class="k">use</span> <span class="w">Carp</span><span class="sc">;</span>
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44 31 <span class="k">use</span> <span class="w">Exporter</span><span class="sc">;</span>
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45 32 <span class="k">use</span> <span class="w">TextUtil</span> <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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46 33 <span class="k">use</span> <span class="w">MathUtil</span> <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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47 34 <span class="k">use</span> <span class="w">Fingerprints::Fingerprints</span><span class="sc">;</span>
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48 35 <span class="k">use</span> <span class="w">Molecule</span><span class="sc">;</span>
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49 36 <span class="k">use</span> <span class="w">AtomTypes::AtomicInvariantsAtomTypes</span><span class="sc">;</span>
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50 37 <span class="k">use</span> <span class="w">AtomTypes::FunctionalClassAtomTypes</span><span class="sc">;</span>
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51 38 <span class="k">use</span> <span class="w">AtomTypes::DREIDINGAtomTypes</span><span class="sc">;</span>
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52 39 <span class="k">use</span> <span class="w">AtomTypes::EStateAtomTypes</span><span class="sc">;</span>
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53 40 <span class="k">use</span> <span class="w">AtomTypes::MMFF94AtomTypes</span><span class="sc">;</span>
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54 41 <span class="k">use</span> <span class="w">AtomTypes::SLogPAtomTypes</span><span class="sc">;</span>
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55 42 <span class="k">use</span> <span class="w">AtomTypes::SYBYLAtomTypes</span><span class="sc">;</span>
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56 43 <span class="k">use</span> <span class="w">AtomTypes::TPSAAtomTypes</span><span class="sc">;</span>
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57 44 <span class="k">use</span> <span class="w">AtomTypes::UFFAtomTypes</span><span class="sc">;</span>
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58 45
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59 46 <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>
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60 47
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61 48 <span class="i">@ISA</span> = <span class="q">qw(Fingerprints::Fingerprints Exporter)</span><span class="sc">;</span>
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62 49 <span class="i">@EXPORT</span> = <span class="q">qw()</span><span class="sc">;</span>
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63 50 <span class="i">@EXPORT_OK</span> = <span class="q">qw()</span><span class="sc">;</span>
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64 51
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65 52 <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>
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66 53
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67 54 <span class="c"># Setup class variables...</span>
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68 55 <span class="k">my</span><span class="s">(</span><span class="i">$ClassName</span><span class="s">)</span><span class="sc">;</span>
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69 56 <span class="i">_InitializeClass</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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70 57
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71 58 <span class="c"># Overload Perl functions...</span>
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72 59 <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;StringifyExtendedConnectivityFingerprints&#39;</span><span class="sc">;</span>
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73 60
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74 61 <span class="c"># Class constructor...</span>
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75 <a name="new-"></a> 62 <span class="k">sub </span><span class="m">new</span> <span class="s">{</span>
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76 63 <span class="k">my</span><span class="s">(</span><span class="i">$Class</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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77 64
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78 65 <span class="c"># Initialize object...</span>
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79 66 <span class="k">my</span> <span class="i">$This</span> = <span class="i">$Class</span><span class="i">-&gt;SUPER::new</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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80 67 <span class="k">bless</span> <span class="i">$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>
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81 68 <span class="i">$This</span><span class="i">-&gt;_InitializeExtendedConnectivityFingerprints</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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82 69
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83 70 <span class="i">$This</span><span class="i">-&gt;_InitializeExtendedConnectivityFingerprintsProperties</span><span class="s">(</span><span class="i">%NamesAndValues</span><span class="s">)</span><span class="sc">;</span>
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84 71
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85 72 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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86 73 <span class="s">}</span>
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87 74
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88 75 <span class="c"># Initialize object data...</span>
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89 76 <span class="c">#</span>
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90 <a name="_InitializeExtendedConnectivityFingerprints-"></a> 77 <span class="k">sub </span><span class="m">_InitializeExtendedConnectivityFingerprints</span> <span class="s">{</span>
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91 78 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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92 79
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93 80 <span class="c"># Type of fingerprint to generate:</span>
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94 81 <span class="c">#</span>
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95 82 <span class="c"># ExtendedConnectivity - Set of integer identifiers corresponding to structurally unique features</span>
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96 83 <span class="c"># ExtendedConnectivityCount - Set of integer identifiers corresponding to structurally unique features and their count</span>
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97 84 <span class="c"># ExtendedConnectivityBits - A bit vector indicating presence/absence of structurally unique features</span>
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98 85 <span class="c">#</span>
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99 86 <span class="i">$This</span>-&gt;{<span class="w">Type</span>} = <span class="q">&#39;ExtendedConnectivity&#39;</span><span class="sc">;</span>
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100 87
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101 88 <span class="c"># Atomic neighborhoods radius for extended connectivity...</span>
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102 89 <span class="i">$This</span>-&gt;{<span class="w">NeighborhoodRadius</span>} = <span class="n">2</span><span class="sc">;</span>
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103 90
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104 91 <span class="c"># Size of bit bector to use during generation of ExtendedConnectivityBits fingerprints...</span>
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105 92 <span class="i">$This</span>-&gt;{<span class="w">Size</span>} = <span class="n">1024</span><span class="sc">;</span>
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106 93
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107 94 <span class="c"># Min and max size of bit bector to use during generation of ExtendedConnectivityBits fingerprints...</span>
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108 95 <span class="i">$This</span>-&gt;{<span class="w">MinSize</span>} = <span class="n">32</span><span class="sc">;</span>
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109 96 <span class="i">$This</span>-&gt;{<span class="w">MaxSize</span>} = <span class="n">2</span>**<span class="n">32</span><span class="sc">;</span>
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110 97
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111 98 <span class="c"># Type of atom attributes to use for initial identifier assignment to non-hydrogen atoms</span>
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112 99 <span class="c"># during the calculation of extended connectivity fingerprints [ Ref 48, Ref 52 ]...</span>
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113 100 <span class="c">#</span>
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114 101 <span class="c"># Currently supported values are: AtomicInvariantsAtomTypes, FunctionalClassAtomTypes,</span>
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115 102 <span class="c"># DREIDINGAtomTypes, EStateAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes,</span>
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116 103 <span class="c"># TPSAAtomTypes, UFFAtomTypes</span>
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117 104 <span class="c">#</span>
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118 105 <span class="i">$This</span>-&gt;{<span class="w">AtomIdentifierType</span>} = <span class="q">&#39;&#39;</span><span class="sc">;</span>
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119 106
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120 107 <span class="c"># Random number generator to use during generation of fingerprints bit-vector</span>
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121 108 <span class="c"># string: Perl CORE::rand or MayaChemTools MathUtil::random function.</span>
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122 109 <span class="c">#</span>
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123 110 <span class="c"># The random number generator implemented in MayaChemTools is a variant of</span>
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124 111 <span class="c"># linear congruential generator (LCG) as described by Miller et al. [ Ref 120 ].</span>
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125 112 <span class="c"># It is also referred to as Lehmer random number generator or Park-Miller</span>
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126 113 <span class="c"># random number generator.</span>
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127 114 <span class="c">#</span>
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128 115 <span class="c"># Unlike Perl&#39;s core random number generator function rand, the random number</span>
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129 116 <span class="c"># generator implemented in MayaChemTools, MathUtil::random, generates consistent</span>
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130 117 <span class="c"># random values across different platformsfor a specific random seed and leads</span>
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131 118 <span class="c"># to generation of portable fingerprints bit-vector strings.</span>
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132 119 <span class="c">#</span>
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133 120 <span class="i">$This</span>-&gt;{<span class="w">UsePerlCoreRandom</span>} = <span class="n">1</span><span class="sc">;</span>
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134 121
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135 122 <span class="c"># Atom neighorhoods up to specified neighborhood radius...</span>
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136 123 <span class="i">%</span>{<span class="i">$This</span>-&gt;{<span class="w">AtomNeighborhoods</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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137 124
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138 125 <span class="c"># Atom identifiers at different neighborhoods up to specified neighborhood radius...</span>
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139 126 <span class="i">%</span>{<span class="i">$This</span>-&gt;{<span class="w">AtomIdentifiers</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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140 127
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141 128 <span class="c"># Structurally unique atom identifiers at different neighborhoods up to specified neighborhood radius...</span>
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142 129 <span class="i">%</span>{<span class="i">$This</span>-&gt;{<span class="w">UniqueAtomIdentifiers</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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143 130 <span class="i">%</span>{<span class="i">$This</span>-&gt;{<span class="w">UniqueAtomIdentifiersCount</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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144 131
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145 132 <span class="c"># Unique atom identifiers at different neighborhoods up to specified neighborhood radius...</span>
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146 133 <span class="i">%</span>{<span class="i">$This</span>-&gt;{<span class="w">StructurallyUniqueAtomIdentifiers</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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147 134 <span class="i">%</span>{<span class="i">$This</span>-&gt;{<span class="w">StructurallyUniqueAtomIdentifiersCount</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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148 135
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149 136 <span class="c"># Structure feature information at different neighborhoods up to specified neighborhood</span>
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150 137 <span class="c"># radius used during removal of atom indentifiers which are structually equivalent...</span>
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151 138 <span class="i">%</span>{<span class="i">$This</span>-&gt;{<span class="w">StructureFeatures</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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152 139 <span class="s">}</span>
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153 140
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154 141 <span class="c"># Initialize class ...</span>
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155 <a name="_InitializeClass-"></a> 142 <span class="k">sub </span><span class="m">_InitializeClass</span> <span class="s">{</span>
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156 143 <span class="c">#Class name...</span>
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157 144 <span class="i">$ClassName</span> = <span class="w">__PACKAGE__</span><span class="sc">;</span>
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158 145 <span class="s">}</span>
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159 146
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160 147 <span class="c"># Initialize object properties....</span>
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161 <a name="_InitializeExtendedConnectivityFingerprintsProperties-"></a> 148 <span class="k">sub </span><span class="m">_InitializeExtendedConnectivityFingerprintsProperties</span> <span class="s">{</span>
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162 149 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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163 150
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164 151 <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">$MethodName</span><span class="s">)</span><span class="sc">;</span>
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165 152 <span class="k">while</span> <span class="s">(</span><span class="s">(</span><span class="i">$Name</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="k">each</span> <span class="i">%NamesAndValues</span><span class="s">)</span> <span class="s">{</span>
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166 153 <span class="i">$MethodName</span> = <span class="q">&quot;Set${Name}&quot;</span><span class="sc">;</span>
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167 154 <span class="i">$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>
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168 155 <span class="s">}</span>
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169 156
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170 157 <span class="c"># Make sure molecule object was specified...</span>
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171 158 <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>
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172 159 <span class="w">croak</span> <span class="q">&quot;Error: ${ClassName}-&gt;New: Object can&#39;t be instantiated without specifying molecule...&quot;</span><span class="sc">;</span>
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173 160 <span class="s">}</span>
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174 161
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175 162 <span class="c"># Make sure AtomIdentifierType was specified...</span>
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176 163 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$NamesAndValues</span>{<span class="w">AtomIdentifierType</span>}<span class="s">)</span> <span class="s">{</span>
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177 164 <span class="w">croak</span> <span class="q">&quot;Error: ${ClassName}-&gt;New: Object can&#39;t be instantiated without specifying AtomIdentifierType...&quot;</span><span class="sc">;</span>
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178 165 <span class="s">}</span>
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179 166
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180 167 <span class="c"># Make sure it&#39;s power of 2...</span>
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181 168 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$NamesAndValues</span>{<span class="w">Size</span>}<span class="s">)</span> <span class="s">{</span>
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182 169 <span class="k">if</span> <span class="s">(</span>!<span class="i">TextUtil::IsNumberPowerOfNumber</span><span class="s">(</span><span class="i">$NamesAndValues</span>{<span class="w">Size</span>}<span class="cm">,</span> <span class="n">2</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
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183 170 <span class="w">croak</span> <span class="q">&quot;Error: ${ClassName}-&gt;New: Specified size value, $NamesAndValues{Size}, must be power of 2...&quot;</span><span class="sc">;</span>
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184 171 <span class="s">}</span>
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185 172 <span class="s">}</span>
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186 173
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187 174 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">Type</span>} =~ <span class="q">/^ExtendedConnectivity$/i</span><span class="s">)</span> <span class="s">{</span>
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188 175 <span class="i">$This</span><span class="i">-&gt;_InitializeExtendedConnectivityFingerprintsVector</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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189 176 <span class="s">}</span>
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190 177 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">Type</span>} =~ <span class="q">/^ExtendedConnectivityCount$/i</span><span class="s">)</span> <span class="s">{</span>
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191 178 <span class="i">$This</span><span class="i">-&gt;_InitializeExtendedConnectivityCountFingerprintsVector</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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192 179 <span class="s">}</span>
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193 180 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">Type</span>} =~ <span class="q">/^ExtendedConnectivityBits$/i</span><span class="s">)</span> <span class="s">{</span>
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194 181 <span class="i">$This</span><span class="i">-&gt;_InitializeExtendedConnectivityBitsFingerprintsBitVector</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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195 182 <span class="s">}</span>
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196 183 <span class="k">else</span> <span class="s">{</span>
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197 184 <span class="w">croak</span> <span class="q">&quot;Error: ${ClassName}-&gt;_InitializeExtendedConnectivityFingerprintsProperties: Unknown ExtendedConnectivity fingerprints type: $This-&gt;{Type}; Supported fingerprints types: ExtendedConnectivity, ExtendedConnectivityCount or ExtendedConnectivityBits...&quot;</span><span class="sc">;</span>
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198 185 <span class="s">}</span>
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199 186
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200 187 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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201 188 <span class="s">}</span>
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202 189
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203 190 <span class="c"># Initialize extended connectivity fingerprints vector...</span>
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204 191 <span class="c">#</span>
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205 <a name="_InitializeExtendedConnectivityFingerprintsVector-"></a> 192 <span class="k">sub </span><span class="m">_InitializeExtendedConnectivityFingerprintsVector</span> <span class="s">{</span>
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206 193 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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207 194
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208 195 <span class="c"># Type of vector...</span>
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209 196 <span class="i">$This</span>-&gt;{<span class="w">VectorType</span>} = <span class="q">&#39;FingerprintsVector&#39;</span><span class="sc">;</span>
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210 197
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211 198 <span class="c"># Type of FingerprintsVector...</span>
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212 199 <span class="i">$This</span>-&gt;{<span class="w">FingerprintsVectorType</span>} = <span class="q">&#39;AlphaNumericalValues&#39;</span><span class="sc">;</span>
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213 200
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214 201 <span class="i">$This</span><span class="i">-&gt;_InitializeFingerprintsVector</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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215 202
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216 203 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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217 204 <span class="s">}</span>
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218 205
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219 206 <span class="c"># Initialize extended connectivity count fingerprints vector...</span>
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220 207 <span class="c">#</span>
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221 <a name="_InitializeExtendedConnectivityCountFingerprintsVector-"></a> 208 <span class="k">sub </span><span class="m">_InitializeExtendedConnectivityCountFingerprintsVector</span> <span class="s">{</span>
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222 209 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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223 210
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224 211 <span class="c"># Type of vector...</span>
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225 212 <span class="i">$This</span>-&gt;{<span class="w">VectorType</span>} = <span class="q">&#39;FingerprintsVector&#39;</span><span class="sc">;</span>
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226 213
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227 214 <span class="c"># Type of FingerprintsVector...</span>
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228 215 <span class="i">$This</span>-&gt;{<span class="w">FingerprintsVectorType</span>} = <span class="q">&#39;NumericalValues&#39;</span><span class="sc">;</span>
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229 216
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230 217 <span class="i">$This</span><span class="i">-&gt;_InitializeFingerprintsVector</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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231 218
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232 219 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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233 220 <span class="s">}</span>
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234 221
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235 222 <span class="c"># Initialize extended connectivity bit fingerprints vector...</span>
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236 223 <span class="c">#</span>
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237 <a name="_InitializeExtendedConnectivityBitsFingerprintsBitVector-"></a> 224 <span class="k">sub </span><span class="m">_InitializeExtendedConnectivityBitsFingerprintsBitVector</span> <span class="s">{</span>
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238 225 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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239 226
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240 227 <span class="c"># Type of vector...</span>
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241 228 <span class="i">$This</span>-&gt;{<span class="w">VectorType</span>} = <span class="q">&#39;FingerprintsBitVector&#39;</span><span class="sc">;</span>
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242 229
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243 230 <span class="i">$This</span><span class="i">-&gt;_InitializeFingerprintsBitVector</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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244 231
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245 232 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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246 233 <span class="s">}</span>
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247 234
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248 235 <span class="c"># Set type...</span>
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249 236 <span class="c">#</span>
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250 <a name="SetType-"></a> 237 <span class="k">sub </span><span class="m">SetType</span> <span class="s">{</span>
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251 238 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Type</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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252 239
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253 240 <span class="k">if</span> <span class="s">(</span><span class="i">$Type</span> =~ <span class="q">/^ExtendedConnectivity$/i</span><span class="s">)</span> <span class="s">{</span>
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254 241 <span class="i">$This</span>-&gt;{<span class="w">Type</span>} = <span class="q">&#39;ExtendedConnectivity&#39;</span><span class="sc">;</span><span class="sc">;</span>
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255 242 <span class="s">}</span>
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256 243 <span class="k">elsif</span> <span class="s">(</span><span class="i">$Type</span> =~ <span class="q">/^ExtendedConnectivityCount$/i</span><span class="s">)</span> <span class="s">{</span>
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257 244 <span class="i">$This</span>-&gt;{<span class="w">Type</span>} = <span class="q">&#39;ExtendedConnectivityCount&#39;</span><span class="sc">;</span><span class="sc">;</span>
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258 245 <span class="s">}</span>
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259 246 <span class="k">elsif</span> <span class="s">(</span><span class="i">$Type</span> =~ <span class="q">/^ExtendedConnectivityBits$/i</span><span class="s">)</span> <span class="s">{</span>
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260 247 <span class="i">$This</span>-&gt;{<span class="w">Type</span>} = <span class="q">&#39;ExtendedConnectivityBits&#39;</span><span class="sc">;</span><span class="sc">;</span>
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261 248 <span class="s">}</span>
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262 249 <span class="k">else</span> <span class="s">{</span>
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263 250 <span class="w">croak</span> <span class="q">&quot;Error: ${ClassName}-&gt;SetType: Unknown ExtendedConnectivity fingerprints type: $This-&gt;{Type}; Supported fingerprints types: ExtendedConnectivity, ExtendedConnectivityCount or ExtendedConnectivityBits...&quot;</span><span class="sc">;</span>
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264 251 <span class="s">}</span>
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265 252 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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266 253 <span class="s">}</span>
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267 254
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268 255 <span class="c"># Disable vector type change...</span>
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269 256 <span class="c">#</span>
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270 <a name="SetVectorType-"></a> 257 <span class="k">sub </span><span class="m">SetVectorType</span> <span class="s">{</span>
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271 258 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Type</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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272 259
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273 260 <span class="w">croak</span> <span class="q">&quot;Error: ${ClassName}-&gt;SetVectorType: Can&#39;t change vector type...&quot;</span><span class="sc">;</span>
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274 261
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275 262 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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276 263 <span class="s">}</span>
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277 264
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278 265 <span class="c"># Disable vector type change...</span>
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279 266 <span class="c">#</span>
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280 <a name="SetFingerprintsVectorType-"></a> 267 <span class="k">sub </span><span class="m">SetFingerprintsVectorType</span> <span class="s">{</span>
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281 268 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Type</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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282 269
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283 270 <span class="w">croak</span> <span class="q">&quot;Error: ${ClassName}-&gt;SetFingerprintsVectorType: Can&#39;t change fingerprints vector type...&quot;</span><span class="sc">;</span>
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284 271
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285 272 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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286 273 <span class="s">}</span>
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287 274
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288 275 <span class="c"># Set intial atom identifier type..</span>
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289 276 <span class="c">#</span>
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290 <a name="SetAtomIdentifierType-"></a> 277 <span class="k">sub </span><span class="m">SetAtomIdentifierType</span> <span class="s">{</span>
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291 278 <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>
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292 279
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293 280 <span class="k">if</span> <span class="s">(</span><span class="i">$IdentifierType</span> !~ <span class="q">/^(AtomicInvariantsAtomTypes|FunctionalClassAtomTypes|DREIDINGAtomTypes|EStateAtomTypes|MMFF94AtomTypes|SLogPAtomTypes|SYBYLAtomTypes|TPSAAtomTypes|UFFAtomTypes)$/i</span><span class="s">)</span> <span class="s">{</span>
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294 281 <span class="w">croak</span> <span class="q">&quot;Error: ${ClassName}-&gt;SetAtomIdentifierType: Specified value, $IdentifierType, for AtomIdentifierType is not vaild. Supported types in current release of MayaChemTools: AtomicInvariantsAtomTypes, FunctionalClassAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes and UFFAtomTypes.&quot;</span><span class="sc">;</span>
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295 282 <span class="s">}</span>
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296 283
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297 284 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">AtomIdentifierType</span>}<span class="s">)</span> <span class="s">{</span>
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298 285 <span class="w">croak</span> <span class="q">&quot;Error: ${ClassName}-&gt;SetAtomIdentifierType: Can&#39;t change intial atom identifier type: It&#39;s already set...&quot;</span><span class="sc">;</span>
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299 286 <span class="s">}</span>
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300 287
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301 288 <span class="i">$This</span>-&gt;{<span class="w">AtomIdentifierType</span>} = <span class="i">$IdentifierType</span><span class="sc">;</span>
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302 289
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303 290 <span class="c"># Initialize identifier type information...</span>
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304 291 <span class="i">$This</span><span class="i">-&gt;_InitializeAtomIdentifierTypeInformation</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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305 292
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306 293 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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307 294 <span class="s">}</span>
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308 295
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309 296 <span class="c"># Set atom neighborhood radius...</span>
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310 297 <span class="c">#</span>
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311 <a name="SetNeighborhoodRadius-"></a> 298 <span class="k">sub </span><span class="m">SetNeighborhoodRadius</span> <span class="s">{</span>
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312 299 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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313 300
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314 301 <span class="k">if</span> <span class="s">(</span>!<span class="i">TextUtil::IsInteger</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
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315 302 <span class="w">croak</span> <span class="q">&quot;Error: ${ClassName}-&gt;SetNeighborhoodRadius: NeighborhoodRadius value, $Value, is not valid: It must be an integer...&quot;</span><span class="sc">;</span>
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316 303 <span class="s">}</span>
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317 304
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318 305 <span class="k">if</span> <span class="s">(</span><span class="i">$Value</span> &lt; <span class="n">0</span> <span class="s">)</span> <span class="s">{</span>
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319 306 <span class="w">croak</span> <span class="q">&quot;Error: ${ClassName}-&gt;SetNeighborhoodRadius: NeighborhoodRadius value, $Value, is not valid: It must be &gt;= 0...&quot;</span><span class="sc">;</span>
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320 307 <span class="s">}</span>
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321 308 <span class="i">$This</span>-&gt;{<span class="w">NeighborhoodRadius</span>} = <span class="i">$Value</span><span class="sc">;</span>
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322 309
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323 310 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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324 311 <span class="s">}</span>
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325 312
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326 313 <span class="c"># Generate fingerprints description...</span>
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327 314 <span class="c">#</span>
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328 <a name="GetDescription-"></a> 315 <span class="k">sub </span><span class="m">GetDescription</span> <span class="s">{</span>
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329 316 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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330 317
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331 318 <span class="c"># Is description explicity set?</span>
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332 319 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$This</span>-&gt;{<span class="w">Description</span>}<span class="s">)</span> <span class="s">{</span>
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333 320 <span class="k">return</span> <span class="i">$This</span>-&gt;{<span class="w">Description</span>}<span class="sc">;</span>
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334 321 <span class="s">}</span>
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335 322
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336 323 <span class="c"># Generate fingerprints description...</span>
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337 324
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338 325 <span class="k">return</span> <span class="q">&quot;$This-&gt;{Type}:$This-&gt;{AtomIdentifierType}:Radius$This-&gt;{NeighborhoodRadius}&quot;</span><span class="sc">;</span>
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339 326 <span class="s">}</span>
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340 327
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341 328 <span class="c"># Generate fingerprints...</span>
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342 329 <span class="c">#</span>
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343 330 <span class="c"># Methodology:</span>
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344 331 <span class="c"># . Assign initial atom identfiers to all non-hydrogen atoms in the molecule</span>
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345 332 <span class="c">#</span>
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346 333 <span class="c"># . Remove duplicates from the initial identifiers and add them to list corresponding</span>
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347 334 <span class="c"># to molecule fingerprint</span>
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348 335 <span class="c">#</span>
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349 336 <span class="c"># . For NeighborhoodRadius value of 0, just return the molecule fingerprint list</span>
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350 337 <span class="c">#</span>
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351 338 <span class="c"># . For each NeighborhoodRadius level</span>
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352 339 <span class="c"># . For each non-hydrogen CentralAtom at this NeighborhoodRadius level</span>
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353 340 <span class="c"># . For each non-hydrogen SuccessorNeighborAtom</span>
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354 341 <span class="c"># . Collect (BondOrder AtomIdentifier) pair of values corresponding to</span>
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355 342 <span class="c"># (CentralAtom SuccessorNeighborAtom) and add it to a list</span>
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356 343 <span class="c">#</span>
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357 344 <span class="c"># . Sort list containing (BondOrder AtomIdentifier) pairs first by BondOrder followed</span>
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358 345 <span class="c"># by AtomIdendifiers to make these values graph invariant</span>
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359 346 <span class="c"># . Generate a hash code for the values in the list</span>
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360 347 <span class="c"># . Assign hash code as new atom identifier at the current NeighborhoodRadius level</span>
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361 348 <span class="c"># . Save all atoms and bonds corresponding to the substructure involved in</span>
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362 349 <span class="c"># generating the hash code to be used for identifying structural duplicate hash code</span>
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363 350 <span class="c">#</span>
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364 351 <span class="c"># . Add the new identifier to the molecule fingerprint list making sure it&#39;s not a duplicate</span>
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365 352 <span class="c"># identifier</span>
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366 353 <span class="c">#</span>
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367 354 <span class="c"># Hash code atom identifier deduplication:</span>
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368 355 <span class="c"># . Track/remove the identifier generated at higher neighborhood radius level</span>
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369 356 <span class="c">#</span>
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370 357 <span class="c"># Structural atom identifier deduplication:</span>
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371 358 <span class="c"># . For equivalent atoms and bonds corresponding to substructure at a NeighborhoodRadius level,</span>
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372 359 <span class="c"># track/remove the atom identifier with largest value</span>
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373 360 <span class="c">#</span>
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374 361 <span class="c">#</span>
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375 <a name="GenerateFingerprints-"></a> 362 <span class="k">sub </span><span class="m">GenerateFingerprints</span> <span class="s">{</span>
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376 363 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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377 364
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378 365 <span class="c"># Cache appropriate molecule data...</span>
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379 366 <span class="i">$This</span><span class="i">-&gt;_SetupMoleculeDataCache</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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380 367
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381 368 <span class="c"># Assign intial atom identifers...</span>
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382 369 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">-&gt;_AssignInitialAtomIdentifiers</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
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383 370 <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 $This-&gt;{AtomIdentifierType} to all atoms...&quot;</span><span class="sc">;</span>
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384 371 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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385 372 <span class="s">}</span>
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386 373
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387 374 <span class="c"># Identify atom neighborhoods up to specified radius...</span>
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388 375 <span class="i">$This</span><span class="i">-&gt;_GetAtomNeighborhoods</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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389 376
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390 377 <span class="c"># Assign atom identifiers to central atoms considering atom neighborhoods at each</span>
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391 378 <span class="c"># radius level...</span>
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392 379 <span class="i">$This</span><span class="i">-&gt;_AssignAtomIdentifiersToAtomNeighborhoods</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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393 380
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394 381 <span class="c"># Remove duplicates identifiers...</span>
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395 382 <span class="i">$This</span><span class="i">-&gt;_RemoveDuplicateAtomIdentifiers</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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396 383
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397 384 <span class="c"># Set final fingerprints...</span>
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398 385 <span class="i">$This</span><span class="i">-&gt;_SetFinalFingerprints</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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399 386
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400 387 <span class="c"># Clear cached molecule data...</span>
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401 388 <span class="i">$This</span><span class="i">-&gt;_ClearMoleculeDataCache</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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402 389
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403 390 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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404 391 <span class="s">}</span>
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405 392
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406 393 <span class="c"># Assign appropriate initial atom identifiers...</span>
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407 394 <span class="c">#</span>
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408 395 <span class="c"># Generation of initial identifier for a specific atom involves:</span>
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409 396 <span class="c"># . Values of the specified atom attributes are appended in a specific order to</span>
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410 397 <span class="c"># generate an initial atom identifier string</span>
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411 398 <span class="c"># . A 32 bit unsigned integer hash key, using TextUtil::HashCode function, is</span>
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412 399 <span class="c"># generated for the atom indentifier and assigned to the atom as initial</span>
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413 400 <span class="c"># atom identifier.</span>
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414 401 <span class="c">#</span>
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415 <a name="_AssignInitialAtomIdentifiers-"></a> 402 <span class="k">sub </span><span class="m">_AssignInitialAtomIdentifiers</span> <span class="s">{</span>
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416 403 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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417 404 <span class="k">my</span><span class="s">(</span><span class="i">$Atom</span><span class="cm">,</span> <span class="i">$AtomID</span><span class="cm">,</span> <span class="i">$Radius</span><span class="cm">,</span> <span class="i">$SpecifiedAtomTypes</span><span class="cm">,</span> <span class="i">$IgnoreHydrogens</span><span class="cm">,</span> <span class="i">$AtomType</span><span class="cm">,</span> <span class="i">$InitialAtomTypeString</span><span class="cm">,</span> <span class="i">$InitialAtomIdentifier</span><span class="s">)</span><span class="sc">;</span>
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418 405
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419 406 <span class="c"># Initialize atom identifiers...</span>
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420 407 <span class="i">$This</span><span class="i">-&gt;_InitializeAtomIdentifiers</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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421 408
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422 409 <span class="c"># Set up atom types...</span>
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423 410 <span class="i">$IgnoreHydrogens</span> = <span class="n">1</span><span class="sc">;</span>
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424 411 <span class="i">$SpecifiedAtomTypes</span> = <span class="k">undef</span><span class="sc">;</span>
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425 412
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426 413 <span class="j">IDENTIFIERTYPE:</span> <span class="s">{</span>
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427 414 <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>
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428 415 <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>
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429 416 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span>
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430 417 <span class="s">}</span>
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431 418
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432 419 <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>
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433 420 <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>
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434 421 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span>
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435 422 <span class="s">}</span>
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436 423
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437 424 <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>
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438 425 <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">$IgnoreHydrogens</span><span class="s">)</span><span class="sc">;</span>
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439 426 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span>
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440 427 <span class="s">}</span>
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441 428
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442 429 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^EStateAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span>
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443 430 <span class="i">$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>
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444 431 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span>
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445 432 <span class="s">}</span>
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446 433
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447 434 <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>
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448 435 <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">$IgnoreHydrogens</span><span class="s">)</span><span class="sc">;</span>
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449 436 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span>
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450 437 <span class="s">}</span>
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451 438
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452 439 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^SLogPAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span>
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453 440 <span class="i">$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>
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454 441 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span>
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455 442 <span class="s">}</span>
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456 443
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457 444 <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>
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458 445 <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">$IgnoreHydrogens</span><span class="s">)</span><span class="sc">;</span>
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459 446 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span>
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460 447 <span class="s">}</span>
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461 448
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462 449 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^TPSAAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span>
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463 450 <span class="i">$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">$This</span>-&gt;{<span class="w">Molecule</span>}<span class="cm">,</span> <span class="q">&#39;IgnorePhosphorus&#39;</span> <span class="cm">=&gt;</span> <span class="n">0</span><span class="cm">,</span> <span class="q">&#39;IgnoreSulfur&#39;</span> <span class="cm">=&gt;</span> <span class="n">0</span><span class="s">)</span><span class="sc">;</span>
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464 451 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span>
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465 452 <span class="s">}</span>
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466 453
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467 454 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^UFFAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span>
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468 455 <span class="i">$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>
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469 456 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span>
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470 457 <span class="s">}</span>
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471 458
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472 459 <span class="w">croak</span> <span class="q">&quot;Error: ${ClassName}-&gt;_AssignInitialAtomIdentifiers: Couldn&#39;t assign intial atom identifiers: InitialAtomIdentifierType $This-&gt;{AtomIdentifierType} is not supported...&quot;</span><span class="sc">;</span>
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473 460 <span class="s">}</span>
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474 461
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475 462 <span class="c"># Assign atom types...</span>
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476 463 <span class="i">$SpecifiedAtomTypes</span><span class="i">-&gt;AssignAtomTypes</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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477 464
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478 465 <span class="c"># Make sure atom types assignment is successful...</span>
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479 466 <span class="k">if</span> <span class="s">(</span>!<span class="i">$SpecifiedAtomTypes</span><span class="i">-&gt;IsAtomTypesAssignmentSuccessful</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
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480 467 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
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481 468 <span class="s">}</span>
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482 469
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483 470 <span class="c"># Assign atom identifiers at radius 0...</span>
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484 471 <span class="i">$Radius</span> = <span class="n">0</span><span class="sc">;</span>
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485 472 <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>
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486 473 <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>
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487 474
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488 475 <span class="i">$AtomType</span> = <span class="i">$SpecifiedAtomTypes</span><span class="i">-&gt;GetAtomType</span><span class="s">(</span><span class="i">$Atom</span><span class="s">)</span><span class="sc">;</span>
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489 476 <span class="i">$InitialAtomTypeString</span> = <span class="i">$AtomType</span> ? <span class="i">$AtomType</span> <span class="co">:</span> <span class="q">&#39;None&#39;</span><span class="sc">;</span>
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490 477
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491 478 <span class="i">$InitialAtomIdentifier</span> = <span class="i">TextUtil::HashCode</span><span class="s">(</span><span class="i">$InitialAtomTypeString</span><span class="s">)</span><span class="sc">;</span>
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492 479 <span class="i">$This</span>-&gt;{<span class="w">AtomIdentifiers</span>}{<span class="i">$Radius</span>}{<span class="i">$AtomID</span>} = <span class="i">$InitialAtomIdentifier</span><span class="sc">;</span>
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493 480 <span class="s">}</span>
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494 481
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495 482 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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496 483 <span class="s">}</span>
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497 484
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498 485 <span class="c"># Initialize atom identifiers...</span>
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499 486 <span class="c">#</span>
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500 <a name="_InitializeAtomIdentifiers-"></a> 487 <span class="k">sub </span><span class="m">_InitializeAtomIdentifiers</span> <span class="s">{</span>
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501 488 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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502 489 <span class="k">my</span><span class="s">(</span><span class="i">$Radius</span><span class="cm">,</span> <span class="i">$CurrentRadius</span><span class="s">)</span><span class="sc">;</span>
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503 490
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504 491 <span class="i">$Radius</span> = <span class="i">$This</span>-&gt;{<span class="w">NeighborhoodRadius</span>}<span class="sc">;</span>
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505 492
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506 493 <span class="i">%</span>{<span class="i">$This</span>-&gt;{<span class="w">AtomIdentifiers</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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507 494 <span class="k">for</span> <span class="i">$CurrentRadius</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$Radius</span><span class="s">)</span> <span class="s">{</span>
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508 495 <span class="c"># Atom idenfiers key and value correspond to AtomID and AtomIdentifier</span>
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509 496 <span class="i">%</span>{<span class="i">$This</span>-&gt;{<span class="w">AtomIdentifiers</span>}{<span class="i">$CurrentRadius</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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510 497
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511 498 <span class="c"># Unique and strcuturally unique idenfiers key and value correspond to AtomIdentifier and AtomID</span>
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512 499 <span class="i">%</span>{<span class="i">$This</span>-&gt;{<span class="w">UniqueAtomIdentifiers</span>}{<span class="i">$CurrentRadius</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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513 500 <span class="i">%</span>{<span class="i">$This</span>-&gt;{<span class="w">UniqueAtomIdentifiersCount</span>}{<span class="i">$CurrentRadius</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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514 501
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515 502 <span class="i">%</span>{<span class="i">$This</span>-&gt;{<span class="w">StructurallyUniqueAtomIdentifiers</span>}{<span class="i">$CurrentRadius</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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516 503 <span class="i">%</span>{<span class="i">$This</span>-&gt;{<span class="w">StructurallyUniqueAtomIdentifiersCount</span>}{<span class="i">$CurrentRadius</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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517 504 <span class="s">}</span>
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518 505
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519 506 <span class="s">}</span>
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520 507
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521 508 <span class="c"># Collect atom neighborhoods upto specified neighborhood radius...</span>
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522 509 <span class="c">#</span>
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523 <a name="_GetAtomNeighborhoods-"></a> 510 <span class="k">sub </span><span class="m">_GetAtomNeighborhoods</span> <span class="s">{</span>
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524 511 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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525 512 <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">$Radius</span><span class="cm">,</span> <span class="i">$CurrentRadius</span><span class="cm">,</span> <span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span>
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526 513
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527 514 <span class="i">%</span>{<span class="i">$This</span>-&gt;{<span class="w">AtomNeighborhoods</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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528 515
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529 516 <span class="i">$Radius</span> = <span class="i">$This</span>-&gt;{<span class="w">NeighborhoodRadius</span>}<span class="sc">;</span>
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530 517 <span class="k">if</span> <span class="s">(</span><span class="i">$Radius</span> &lt; <span class="n">1</span><span class="s">)</span> <span class="s">{</span>
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parents:
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531 518 <span class="c"># At radius level 0, it&#39;s just the atoms...</span>
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532 519 <span class="k">return</span><span class="sc">;</span>
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533 520 <span class="s">}</span>
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534 521
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parents:
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535 522 <span class="c"># Initialize neighborhood at different radii...</span>
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536 523 <span class="k">for</span> <span class="i">$CurrentRadius</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$Radius</span><span class="s">)</span> <span class="s">{</span>
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537 524 <span class="i">%</span>{<span class="i">$This</span>-&gt;{<span class="w">AtomNeighborhoods</span>}{<span class="i">$CurrentRadius</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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538 525 <span class="s">}</span>
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539 526
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540 527 <span class="i">$Molecule</span> = <span class="i">$This</span><span class="i">-&gt;GetMolecule</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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541 528
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542 529 <span class="c"># Collect available atom neighborhoods at different at different neighborhood level for each atom...</span>
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543 530 <span class="k">my</span><span class="s">(</span><span class="i">$AtomsNeighborhoodWithSuccessorAtomsRef</span><span class="s">)</span><span class="sc">;</span>
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544 531
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545 532 <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>
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546 533 <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>
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parents:
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547 534 <span class="i">$CurrentRadius</span> = <span class="n">0</span><span class="sc">;</span>
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548 535 <span class="k">for</span> <span class="i">$AtomsNeighborhoodWithSuccessorAtomsRef</span> <span class="s">(</span><span class="i">$Molecule</span><span class="i">-&gt;GetAtomNeighborhoodsWithSuccessorAtomsAndRadiusUpto</span><span class="s">(</span><span class="i">$Atom</span><span class="cm">,</span> <span class="i">$Radius</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
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parents:
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549 536 <span class="i">$This</span>-&gt;{<span class="w">AtomNeighborhoods</span>}{<span class="i">$CurrentRadius</span>}{<span class="i">$AtomID</span>} = <span class="i">$AtomsNeighborhoodWithSuccessorAtomsRef</span><span class="sc">;</span>
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parents:
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550 537 <span class="i">$CurrentRadius</span>++<span class="sc">;</span>
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parents:
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551 538 <span class="s">}</span>
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parents:
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552 539 <span class="s">}</span>
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parents:
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553 540 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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parents:
diff changeset
554 541 <span class="s">}</span>
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555 542
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parents:
diff changeset
556 543 <span class="c"># Assign atom identifiers to central atom at each neighborhood radius level...</span>
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parents:
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557 544 <span class="c">#</span>
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parents:
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558 <a name="_AssignAtomIdentifiersToAtomNeighborhoods-"></a> 545 <span class="k">sub </span><span class="m">_AssignAtomIdentifiersToAtomNeighborhoods</span> <span class="s">{</span>
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559 546 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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parents:
diff changeset
560 547 <span class="k">my</span><span class="s">(</span><span class="i">$Radius</span><span class="cm">,</span> <span class="i">$NextRadius</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">$NeighborhoodAtom</span><span class="cm">,</span> <span class="i">$SuccessorAtom</span><span class="cm">,</span> <span class="i">$SuccessorAtomID</span><span class="cm">,</span> <span class="i">$NeighborhoodAtomSuccessorAtomsRef</span><span class="cm">,</span> <span class="i">$NeighborhoodAtomsWithSuccessorAtomsRef</span><span class="cm">,</span> <span class="i">$Bond</span><span class="cm">,</span> <span class="i">$BondOrder</span><span class="cm">,</span> <span class="i">$SuccessorAtomCount</span><span class="s">)</span><span class="sc">;</span>
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561 548
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parents:
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562 549 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">NeighborhoodRadius</span>} &lt; <span class="n">1</span><span class="s">)</span> <span class="s">{</span>
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parents:
diff changeset
563 550 <span class="k">return</span><span class="sc">;</span>
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parents:
diff changeset
564 551 <span class="s">}</span>
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parents:
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565 552
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parents:
diff changeset
566 553 <span class="c"># Go over the atom neighborhoods at each radius upto specified radius and assign atom</span>
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parents:
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567 554 <span class="c"># indentifiers using their connected successor atoms and their identifiers.</span>
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parents:
diff changeset
568 555 <span class="c">#</span>
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parents:
diff changeset
569 556 <span class="c"># For a neighborhood atom at a specified radius, the successor connected atoms correpond</span>
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parents:
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570 557 <span class="c"># to next radius level and the last set of neighorhood atoms don&#39;t have any successor connected</span>
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parents:
diff changeset
571 558 <span class="c"># atoms. Additionally, radius level 0 just correspond to initial atom identifiers.</span>
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parents:
diff changeset
572 559 <span class="c">#</span>
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parents:
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573 560 <span class="c"># So in order to process atom neighborhood upto specified radius level, the last atom neighborhood</span>
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parents:
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574 561 <span class="c"># doesn&#39;t need to be processed: it gets processed at previous radius level as successor connected</span>
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parents:
diff changeset
575 562 <span class="c"># atoms.</span>
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parents:
diff changeset
576 563 <span class="c">#</span>
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parents:
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577 564 <span class="j">RADIUS:</span> <span class="k">for</span> <span class="i">$Radius</span> <span class="s">(</span><span class="n">0</span> .. <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">NeighborhoodRadius</span>} - <span class="n">1</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
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578 565 <span class="j">ATOM:</span> <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$This</span>-&gt;{<span class="w">Atoms</span>}}<span class="s">)</span> <span class="s">{</span>
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parents:
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579 566 <span class="i">$AtomID</span> = <span class="i">$Atom</span><span class="i">-&gt;GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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580 567
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parents:
diff changeset
581 568 <span class="c"># Are there any available atom neighborhoods at this radius?</span>
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parents:
diff changeset
582 569 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$This</span>-&gt;{<span class="w">AtomNeighborhoods</span>}{<span class="i">$Radius</span>}{<span class="i">$AtomID</span>}<span class="s">)</span> <span class="s">{</span>
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diff changeset
583 570 <span class="k">next</span> <span class="j">ATOM</span><span class="sc">;</span>
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parents:
diff changeset
584 571 <span class="s">}</span>
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parents:
diff changeset
585 572 <span class="i">$NextRadius</span> = <span class="i">$Radius</span> + <span class="n">1</span><span class="sc">;</span>
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diff changeset
586 573
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parents:
diff changeset
587 574 <span class="c"># Go over neighborhood atoms and their successor connected atoms at this radius and collect</span>
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parents:
diff changeset
588 575 <span class="c"># (BondOrder AtomIdentifier) values for bonded atom pairs. Additionally, keep track of atom and bonds</span>
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parents:
diff changeset
589 576 <span class="c"># for the neighorhoods to remove identifieres generated from structurally duplicate features.</span>
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parents:
diff changeset
590 577 <span class="c">#</span>
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parents:
diff changeset
591 578 <span class="k">my</span><span class="s">(</span><span class="i">%BondOrdersAndAtomIdentifiers</span><span class="s">)</span><span class="sc">;</span>
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parents:
diff changeset
592 579
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diff changeset
593 580 <span class="i">%BondOrdersAndAtomIdentifiers</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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parents:
diff changeset
594 581 <span class="i">$SuccessorAtomCount</span> = <span class="n">0</span><span class="sc">;</span>
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parents:
diff changeset
595 582
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596 583 <span class="j">NEIGHBORHOODS:</span> <span class="k">for</span> <span class="i">$NeighborhoodAtomsWithSuccessorAtomsRef</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$This</span>-&gt;{<span class="w">AtomNeighborhoods</span>}{<span class="i">$Radius</span>}{<span class="i">$AtomID</span>}}<span class="s">)</span> <span class="s">{</span>
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diff changeset
597 584 <span class="s">(</span><span class="i">$NeighborhoodAtom</span><span class="cm">,</span> <span class="i">$NeighborhoodAtomSuccessorAtomsRef</span><span class="s">)</span> = <span class="i">@</span>{<span class="i">$NeighborhoodAtomsWithSuccessorAtomsRef</span>}<span class="sc">;</span>
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diff changeset
598 585
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parents:
diff changeset
599 586 <span class="c"># Any connected successors for the NeighborhoodAtom?</span>
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diff changeset
600 587 <span class="k">if</span> <span class="s">(</span>!<span class="i">@</span>{<span class="i">$NeighborhoodAtomSuccessorAtomsRef</span>}<span class="s">)</span> <span class="s">{</span>
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parents:
diff changeset
601 588 <span class="k">next</span> <span class="j">NEIGHBORHOODS</span><span class="sc">;</span>
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parents:
diff changeset
602 589 <span class="s">}</span>
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diff changeset
603 590 <span class="j">SUCCESSORATOM:</span> <span class="k">for</span> <span class="i">$SuccessorAtom</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$NeighborhoodAtomSuccessorAtomsRef</span>}<span class="s">)</span> <span class="s">{</span>
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parents:
diff changeset
604 591 <span class="k">if</span> <span class="s">(</span><span class="i">$SuccessorAtom</span><span class="i">-&gt;IsHydrogen</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
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parents:
diff changeset
605 592 <span class="c"># Skip successor hydrogen atom...</span>
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parents:
diff changeset
606 593 <span class="k">next</span> <span class="j">SUCCESSORATOM</span><span class="sc">;</span>
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parents:
diff changeset
607 594 <span class="s">}</span>
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608 595 <span class="i">$SuccessorAtomID</span> = <span class="i">$SuccessorAtom</span><span class="i">-&gt;GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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parents:
diff changeset
609 596 <span class="i">$SuccessorAtomCount</span>++<span class="sc">;</span>
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parents:
diff changeset
610 597
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611 598 <span class="i">$Bond</span> = <span class="i">$NeighborhoodAtom</span><span class="i">-&gt;GetBondToAtom</span><span class="s">(</span><span class="i">$SuccessorAtom</span><span class="s">)</span><span class="sc">;</span>
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612 599 <span class="i">$BondOrder</span> = <span class="i">$Bond</span><span class="i">-&gt;IsAromatic</span><span class="s">(</span><span class="s">)</span> ? <span class="q">&quot;1.5&quot;</span> <span class="co">:</span> <span class="i">$Bond</span><span class="i">-&gt;GetBondOrder</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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613 600
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614 601 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$BondOrdersAndAtomIdentifiers</span>{<span class="i">$BondOrder</span>}<span class="s">)</span> <span class="s">{</span>
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diff changeset
615 602 <span class="i">@</span>{<span class="i">$BondOrdersAndAtomIdentifiers</span>{<span class="i">$BondOrder</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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diff changeset
616 603 <span class="s">}</span>
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diff changeset
617 604 <span class="k">push</span> <span class="i">@</span>{<span class="i">$BondOrdersAndAtomIdentifiers</span>{<span class="i">$BondOrder</span>}}<span class="cm">,</span> <span class="i">$This</span>-&gt;{<span class="w">AtomIdentifiers</span>}{<span class="i">$Radius</span>}{<span class="i">$SuccessorAtomID</span>}<span class="sc">;</span>
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diff changeset
618 605 <span class="s">}</span>
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619 606 <span class="s">}</span>
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620 607 <span class="k">if</span> <span class="s">(</span>!<span class="i">$SuccessorAtomCount</span><span class="s">)</span> <span class="s">{</span>
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diff changeset
621 608 <span class="k">next</span> <span class="j">ATOM</span><span class="sc">;</span>
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622 609 <span class="s">}</span>
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623 610 <span class="c"># Assign a new atom identifier at the NextRadius level...</span>
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diff changeset
624 611 <span class="i">$This</span><span class="i">-&gt;_AssignAtomIdentifierToAtomNeighborhood</span><span class="s">(</span><span class="i">$AtomID</span><span class="cm">,</span> <span class="i">$Radius</span><span class="cm">,</span> \<span class="i">%BondOrdersAndAtomIdentifiers</span><span class="s">)</span><span class="sc">;</span>
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625 612 <span class="s">}</span>
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626 613 <span class="s">}</span>
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627 614 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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diff changeset
628 615 <span class="s">}</span>
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629 616
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630 617 <span class="c"># Generate and assign atom indentifier for AtomID using atom neighborhood at next radius level...</span>
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diff changeset
631 618 <span class="c">#</span>
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diff changeset
632 <a name="_AssignAtomIdentifierToAtomNeighborhood-"></a> 619 <span class="k">sub </span><span class="m">_AssignAtomIdentifierToAtomNeighborhood</span> <span class="s">{</span>
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633 620 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$AtomID</span><span class="cm">,</span> <span class="i">$Radius</span><span class="cm">,</span> <span class="i">$BondOrdersAndAtomIdentifiersRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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diff changeset
634 621 <span class="k">my</span><span class="s">(</span><span class="i">$NextRadius</span><span class="cm">,</span> <span class="i">$AtomIdentifier</span><span class="cm">,</span> <span class="i">$SuccessorAtomIdentifier</span><span class="cm">,</span> <span class="i">$BondOrder</span><span class="cm">,</span> <span class="i">$AtomIdentifierString</span><span class="cm">,</span> <span class="i">@AtomIndentifiersInfo</span><span class="s">)</span><span class="sc">;</span>
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635 622
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636 623 <span class="i">$NextRadius</span> = <span class="i">$Radius</span> + <span class="n">1</span><span class="sc">;</span>
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637 624
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638 625 <span class="i">@AtomIndentifiersInfo</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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639 626
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640 627 <span class="i">$AtomIdentifier</span> = <span class="i">$This</span>-&gt;{<span class="w">AtomIdentifiers</span>}{<span class="i">$Radius</span>}{<span class="i">$AtomID</span>}<span class="sc">;</span>
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diff changeset
641 628 <span class="k">push</span> <span class="i">@AtomIndentifiersInfo</span><span class="cm">,</span> <span class="s">(</span><span class="i">$NextRadius</span><span class="cm">,</span> <span class="i">$AtomIdentifier</span><span class="s">)</span><span class="sc">;</span>
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diff changeset
642 629
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643 630 <span class="c"># Sort out successor atom bond order and identifier pairs by bond order followed by atom identifiers</span>
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644 631 <span class="c"># in order to make the final atom identifier graph invariant...</span>
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645 632 <span class="c">#</span>
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parents:
diff changeset
646 633 <span class="k">for</span> <span class="i">$BondOrder</span> <span class="s">(</span><span class="k">sort</span> <span class="s">{</span> <span class="i">$a</span> &lt;=&gt; <span class="i">$b</span> <span class="s">}</span> <span class="k">keys</span> <span class="i">%</span>{<span class="i">$BondOrdersAndAtomIdentifiersRef</span>}<span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
647 634 <span class="k">for</span> <span class="i">$SuccessorAtomIdentifier</span> <span class="s">(</span><span class="k">sort</span> <span class="s">{</span> <span class="i">$a</span> &lt;=&gt; <span class="i">$b</span> <span class="s">}</span> <span class="i">@</span>{<span class="i">$BondOrdersAndAtomIdentifiersRef</span>-&gt;{<span class="i">$BondOrder</span>}}<span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
648 635 <span class="k">push</span> <span class="i">@AtomIndentifiersInfo</span><span class="cm">,</span> <span class="s">(</span><span class="i">$BondOrder</span><span class="cm">,</span> <span class="i">$SuccessorAtomIdentifier</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
649 636 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
650 637 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
651 638 <span class="i">$AtomIdentifierString</span> = <span class="k">join</span><span class="s">(</span><span class="q">&quot;&quot;</span><span class="cm">,</span> <span class="i">@AtomIndentifiersInfo</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
652 639 <span class="i">$AtomIdentifier</span> = <span class="i">TextUtil::HashCode</span><span class="s">(</span><span class="i">$AtomIdentifierString</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
653 640
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
654 641 <span class="c"># Assign atom identifier to the atom at next radius level...</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
655 642 <span class="i">$This</span>-&gt;{<span class="w">AtomIdentifiers</span>}{<span class="i">$NextRadius</span>}{<span class="i">$AtomID</span>} = <span class="i">$AtomIdentifier</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
656 643
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
657 644 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
658 645 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
659 646
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
660 647 <span class="c"># Remove duplicates atom identifiers...</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
661 648 <span class="c">#</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
662 <a name="_RemoveDuplicateAtomIdentifiers-"></a> 649 <span class="k">sub </span><span class="m">_RemoveDuplicateAtomIdentifiers</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
663 650 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
664 651
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
665 652 <span class="i">$This</span><span class="i">-&gt;_RemoveDuplicateIdentifiersByValue</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
666 653 <span class="i">$This</span><span class="i">-&gt;_RemoveStructurallyDuplicateIdenfiers</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
667 654
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
668 655 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
669 656 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
670 657
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
671 658 <span class="c"># Remove duplicate identifiers at each radius level by just using their value...</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
672 659 <span class="c">#</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
673 <a name="_RemoveDuplicateIdentifiersByValue-"></a> 660 <span class="k">sub </span><span class="m">_RemoveDuplicateIdentifiersByValue</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
674 661 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
675 662 <span class="k">my</span><span class="s">(</span><span class="i">$Radius</span><span class="cm">,</span> <span class="i">$Atom</span><span class="cm">,</span> <span class="i">$AtomID</span><span class="cm">,</span> <span class="i">$AtomIdentifier</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
676 663
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
677 664 <span class="k">for</span> <span class="i">$Radius</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$This</span>-&gt;{<span class="w">NeighborhoodRadius</span>}<span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
678 665 <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>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
679 666 <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>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
680 667 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$This</span>-&gt;{<span class="w">AtomIdentifiers</span>}{<span class="i">$Radius</span>}{<span class="i">$AtomID</span>}<span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
681 668 <span class="k">next</span> <span class="j">ATOM</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
682 669 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
683 670 <span class="i">$AtomIdentifier</span> = <span class="i">$This</span>-&gt;{<span class="w">AtomIdentifiers</span>}{<span class="i">$Radius</span>}{<span class="i">$AtomID</span>}<span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
684 671 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$This</span>-&gt;{<span class="w">UniqueAtomIdentifiers</span>}{<span class="i">$Radius</span>}{<span class="i">$AtomIdentifier</span>}<span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
685 672 <span class="c"># It&#39;s a duplicate atom idenfier at this radius level...</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
686 673 <span class="i">$This</span>-&gt;{<span class="w">UniqueAtomIdentifiersCount</span>}{<span class="i">$Radius</span>}{<span class="i">$AtomIdentifier</span>} += <span class="n">1</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
687 674 <span class="k">next</span> <span class="j">ATOM</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
688 675 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
689 676 <span class="i">$This</span>-&gt;{<span class="w">UniqueAtomIdentifiers</span>}{<span class="i">$Radius</span>}{<span class="i">$AtomIdentifier</span>} = <span class="i">$AtomID</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
690 677 <span class="i">$This</span>-&gt;{<span class="w">UniqueAtomIdentifiersCount</span>}{<span class="i">$Radius</span>}{<span class="i">$AtomIdentifier</span>} = <span class="n">1</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
691 678 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
692 679 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
693 680 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
694 681 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
695 682
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
696 683 <span class="c"># Remove structurally duplicate identifiers at each radius level...</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
697 684 <span class="c">#</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
698 685 <span class="c"># Methodology:</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
699 686 <span class="c"># . For unquie atom identifiers at each radius level, assign complete structure features</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
700 687 <span class="c"># in terms all the bonds involved to generate that identifier</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
701 688 <span class="c"># . Use the complete structure features to remover atom identifiers which are</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
702 689 <span class="c"># structurally equivalent which can also be at earlier radii levels</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
703 690 <span class="c">#</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
704 691 <span class="c">#</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
705 <a name="_RemoveStructurallyDuplicateIdenfiers-"></a> 692 <span class="k">sub </span><span class="m">_RemoveStructurallyDuplicateIdenfiers</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
706 693 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
707 694 <span class="k">my</span><span class="s">(</span><span class="i">$Radius</span><span class="cm">,</span> <span class="i">$AtomID</span><span class="cm">,</span> <span class="i">$AtomIdentifier</span><span class="cm">,</span> <span class="i">$SimilarAtomIdentifierRadius</span><span class="cm">,</span> <span class="i">$SimilarAtomIdentifier</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
708 695
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
709 696 <span class="c"># Setup structure features...</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
710 697 <span class="i">$This</span><span class="i">-&gt;_SetupStructureFeaturesForAtomIDsInvolvedInUniqueIdentifiers</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
711 698
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
712 699 <span class="c"># Identify structurally unqiue identifiers...</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
713 700 <span class="k">for</span> <span class="i">$Radius</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$This</span>-&gt;{<span class="w">NeighborhoodRadius</span>}<span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
714 701 <span class="j">ATOMIDENTIFIER:</span> <span class="k">for</span> <span class="i">$AtomIdentifier</span> <span class="s">(</span><span class="k">sort</span> <span class="s">{</span> <span class="i">$a</span> &lt;=&gt; <span class="i">$b</span> <span class="s">}</span> <span class="k">keys</span> <span class="i">%</span>{<span class="i">$This</span>-&gt;{<span class="w">UniqueAtomIdentifiers</span>}{<span class="i">$Radius</span>}}<span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
715 702 <span class="i">$AtomID</span> = <span class="i">$This</span>-&gt;{<span class="w">UniqueAtomIdentifiers</span>}{<span class="i">$Radius</span>}{<span class="i">$AtomIdentifier</span>}<span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
716 703
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
717 704 <span class="s">(</span><span class="i">$SimilarAtomIdentifierRadius</span><span class="cm">,</span> <span class="i">$SimilarAtomIdentifier</span><span class="s">)</span> = <span class="i">$This</span><span class="i">-&gt;_FindStructurallySimilarAtomIdentifier</span><span class="s">(</span><span class="i">$Radius</span><span class="cm">,</span> <span class="i">$AtomID</span><span class="cm">,</span> <span class="i">$AtomIdentifier</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
718 705 <span class="k">if</span> <span class="s">(</span><span class="i">$SimilarAtomIdentifier</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
719 706 <span class="c"># Current atom identifier is similar to an earlier structurally unique atom identifier...</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
720 707 <span class="i">$This</span>-&gt;{<span class="w">StructurallyUniqueAtomIdentifiersCount</span>}{<span class="i">$SimilarAtomIdentifierRadius</span>}{<span class="i">$SimilarAtomIdentifier</span>} += <span class="i">$This</span>-&gt;{<span class="w">UniqueAtomIdentifiersCount</span>}{<span class="i">$Radius</span>}{<span class="i">$AtomIdentifier</span>}<span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
721 708 <span class="k">next</span> <span class="j">ATOMIDENTIFIER</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
722 709 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
723 710 <span class="i">$This</span>-&gt;{<span class="w">StructurallyUniqueAtomIdentifiers</span>}{<span class="i">$Radius</span>}{<span class="i">$AtomIdentifier</span>} = <span class="i">$AtomID</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
724 711
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
725 712 <span class="c"># Set structurally unique atom identifier count to the unique atom identifiers count...</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
726 713 <span class="i">$This</span>-&gt;{<span class="w">StructurallyUniqueAtomIdentifiersCount</span>}{<span class="i">$Radius</span>}{<span class="i">$AtomIdentifier</span>} = <span class="i">$This</span>-&gt;{<span class="w">UniqueAtomIdentifiersCount</span>}{<span class="i">$Radius</span>}{<span class="i">$AtomIdentifier</span>}<span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
727 714 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
728 715 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
729 716 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
730 717 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
731 718
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
732 719 <span class="c"># Set final fingerpritns vector...</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
733 720 <span class="c">#</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
734 <a name="_SetFinalFingerprints-"></a> 721 <span class="k">sub </span><span class="m">_SetFinalFingerprints</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
735 722 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
736 723
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
737 724 <span class="c"># Mark successful generation of fingerprints...</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
738 725 <span class="i">$This</span>-&gt;{<span class="w">FingerprintsGenerated</span>} = <span class="n">1</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
739 726
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
740 727 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">Type</span>} =~ <span class="q">/^ExtendedConnectivity$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
741 728 <span class="i">$This</span><span class="i">-&gt;_SetFinalExtendedConnectivityFingerprints</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
742 729 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
743 730 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">Type</span>} =~ <span class="q">/^ExtendedConnectivityCount$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
744 731 <span class="i">$This</span><span class="i">-&gt;_SetFinalExtendedConnectivityCountFingerprints</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
745 732 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
746 733 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">Type</span>} =~ <span class="q">/^ExtendedConnectivityBits$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
747 734 <span class="i">$This</span><span class="i">-&gt;_SetFinalExtendedConnectivityBitsFingerprints</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
748 735 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
749 736
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
750 737 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
751 738 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
752 739
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
753 740 <span class="c"># Set final extended connectivity fingerpritns vector...</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
754 741 <span class="c">#</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
755 <a name="_SetFinalExtendedConnectivityFingerprints-"></a> 742 <span class="k">sub </span><span class="m">_SetFinalExtendedConnectivityFingerprints</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
756 743 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
757 744 <span class="k">my</span><span class="s">(</span><span class="i">$Radius</span><span class="cm">,</span> <span class="i">$AtomIdentifier</span><span class="cm">,</span> <span class="i">@AtomIdentifiers</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
758 745
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
759 746 <span class="i">@AtomIdentifiers</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
760 747
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
761 748 <span class="k">for</span> <span class="i">$Radius</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$This</span>-&gt;{<span class="w">NeighborhoodRadius</span>}<span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
762 749 <span class="k">for</span> <span class="i">$AtomIdentifier</span> <span class="s">(</span><span class="k">sort</span> <span class="s">{</span> <span class="i">$a</span> &lt;=&gt; <span class="i">$b</span> <span class="s">}</span> <span class="k">keys</span> <span class="i">%</span>{<span class="i">$This</span>-&gt;{<span class="w">StructurallyUniqueAtomIdentifiers</span>}{<span class="i">$Radius</span>}}<span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
763 750 <span class="k">push</span> <span class="i">@AtomIdentifiers</span><span class="cm">,</span> <span class="i">$AtomIdentifier</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
764 751 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
765 752 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
766 753 <span class="c"># Add atom identifiers to fingerprint vector...</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
767 754 <span class="i">$This</span>-&gt;{<span class="w">FingerprintsVector</span>}<span class="i">-&gt;AddValues</span><span class="s">(</span>\<span class="i">@AtomIdentifiers</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
768 755
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
769 756 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
770 757 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
771 758
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
772 759 <span class="c"># Set final extended connectivity count fingerpritns vector...</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
773 760 <span class="c">#</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
774 <a name="_SetFinalExtendedConnectivityCountFingerprints-"></a> 761 <span class="k">sub </span><span class="m">_SetFinalExtendedConnectivityCountFingerprints</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
775 762 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
776 763 <span class="k">my</span><span class="s">(</span><span class="i">$Radius</span><span class="cm">,</span> <span class="i">$AtomIdentifier</span><span class="cm">,</span> <span class="i">$AtomIdentifierCount</span><span class="cm">,</span> <span class="i">@AtomIdentifiers</span><span class="cm">,</span> <span class="i">@AtomIdentifiersCount</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
777 764
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
778 765 <span class="i">@AtomIdentifiers</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> <span class="i">@AtomIdentifiersCount</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
779 766
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
780 767 <span class="k">for</span> <span class="i">$Radius</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$This</span>-&gt;{<span class="w">NeighborhoodRadius</span>}<span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
781 768 <span class="k">for</span> <span class="i">$AtomIdentifier</span> <span class="s">(</span><span class="k">sort</span> <span class="s">{</span> <span class="i">$a</span> &lt;=&gt; <span class="i">$b</span> <span class="s">}</span> <span class="k">keys</span> <span class="i">%</span>{<span class="i">$This</span>-&gt;{<span class="w">StructurallyUniqueAtomIdentifiers</span>}{<span class="i">$Radius</span>}}<span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
782 769 <span class="i">$AtomIdentifierCount</span> = <span class="i">$This</span>-&gt;{<span class="w">StructurallyUniqueAtomIdentifiersCount</span>}{<span class="i">$Radius</span>}{<span class="i">$AtomIdentifier</span>}<span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
783 770 <span class="k">push</span> <span class="i">@AtomIdentifiers</span><span class="cm">,</span> <span class="i">$AtomIdentifier</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
784 771 <span class="k">push</span> <span class="i">@AtomIdentifiersCount</span><span class="cm">,</span> <span class="i">$AtomIdentifierCount</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
785 772 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
786 773 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
787 774 <span class="c"># Add atom identifiers to fingerprint vector as value IDs...</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
788 775 <span class="i">$This</span>-&gt;{<span class="w">FingerprintsVector</span>}<span class="i">-&gt;AddValueIDs</span><span class="s">(</span>\<span class="i">@AtomIdentifiers</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
789 776
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
790 777 <span class="c"># Add atom identifiers to count to fingerprint vector as values...</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
791 778 <span class="i">$This</span>-&gt;{<span class="w">FingerprintsVector</span>}<span class="i">-&gt;AddValues</span><span class="s">(</span>\<span class="i">@AtomIdentifiersCount</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
792 779
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
793 780 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
794 781 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
795 782
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
796 783 <span class="c"># Set final extended connectivity bits fingerpritns vector...</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
797 784 <span class="c">#</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
798 <a name="_SetFinalExtendedConnectivityBitsFingerprints-"></a> 785 <span class="k">sub </span><span class="m">_SetFinalExtendedConnectivityBitsFingerprints</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
799 786 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
800 787 <span class="k">my</span><span class="s">(</span><span class="i">$Radius</span><span class="cm">,</span> <span class="i">$AtomIdentifier</span><span class="cm">,</span> <span class="i">$FingerprintsBitVector</span><span class="cm">,</span> <span class="i">$Size</span><span class="cm">,</span> <span class="i">$SkipBitPosCheck</span><span class="cm">,</span> <span class="i">$AtomIdentifierBitPos</span><span class="cm">,</span> <span class="i">$SetBitNum</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
801 788
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
802 789 <span class="i">$FingerprintsBitVector</span> = <span class="i">$This</span>-&gt;{<span class="w">FingerprintsBitVector</span>}<span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
803 790
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
804 791 <span class="i">$Size</span> = <span class="i">$This</span>-&gt;{<span class="w">Size</span>}<span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
805 792
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
806 793 <span class="i">$SkipBitPosCheck</span> = <span class="n">1</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
807 794
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
808 795 <span class="k">for</span> <span class="i">$Radius</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$This</span>-&gt;{<span class="w">NeighborhoodRadius</span>}<span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
809 796 <span class="k">for</span> <span class="i">$AtomIdentifier</span> <span class="s">(</span><span class="k">keys</span> <span class="i">%</span>{<span class="i">$This</span>-&gt;{<span class="w">StructurallyUniqueAtomIdentifiers</span>}{<span class="i">$Radius</span>}}<span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
810 797 <span class="c"># Set random number seed...</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
811 798 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">UsePerlCoreRandom</span>}<span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
812 799 <span class="i">CORE::</span><span class="k">srand</span><span class="s">(</span><span class="i">$AtomIdentifier</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
813 800 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
814 801 <span class="k">else</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
815 802 <span class="i">MathUtil::srandom</span><span class="s">(</span><span class="i">$AtomIdentifier</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
816 803 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
817 804
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
818 805 <span class="c"># Set bit position...</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
819 806 <span class="i">$AtomIdentifierBitPos</span> = <span class="i">$This</span>-&gt;{<span class="w">UsePerlCoreRandom</span>} ? <span class="k">int</span><span class="s">(</span><span class="i">CORE::</span><span class="k">rand</span><span class="s">(</span><span class="i">$Size</span><span class="s">)</span><span class="s">)</span> <span class="co">:</span> <span class="k">int</span><span class="s">(</span><span class="i">MathUtil::random</span><span class="s">(</span><span class="i">$Size</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
820 807 <span class="i">$FingerprintsBitVector</span><span class="i">-&gt;SetBit</span><span class="s">(</span><span class="i">$AtomIdentifierBitPos</span><span class="cm">,</span> <span class="i">$SkipBitPosCheck</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
821 808 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
822 809 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
823 810 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
824 811 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
825 812
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
826 813
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
827 814 <span class="c"># Identify structurally unique identifiers by comparing structure features involved in</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
828 815 <span class="c"># generating identifiear by comparing it agains all the previous structurally unique</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
829 816 <span class="c"># identifiers...</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
830 817 <span class="c">#</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
831 <a name="_FindStructurallySimilarAtomIdentifier-"></a> 818 <span class="k">sub </span><span class="m">_FindStructurallySimilarAtomIdentifier</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
832 819 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$SpecifiedRadius</span><span class="cm">,</span> <span class="i">$SpecifiedAtomID</span><span class="cm">,</span> <span class="i">$SpecifiedAtomIdentifier</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
833 820 <span class="k">my</span><span class="s">(</span><span class="i">$Radius</span><span class="cm">,</span> <span class="i">$AtomID</span><span class="cm">,</span> <span class="i">$AtomIdentifier</span><span class="cm">,</span> <span class="i">$FeatureAtomCount</span><span class="cm">,</span> <span class="i">$FeatureAtomIDsRef</span><span class="cm">,</span> <span class="i">$SpecifiedFeatureAtomID</span><span class="cm">,</span> <span class="i">$SpecifiedFeatureAtomCount</span><span class="cm">,</span> <span class="i">$SpecifiedFeatureAtomIDsRef</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
834 821
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
835 822 <span class="k">if</span> <span class="s">(</span><span class="i">$SpecifiedRadius</span> == <span class="n">0</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
836 823 <span class="c"># After duplicate removal by value, all identifier at radius level 0 would be structurally unique...</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
837 824 <span class="k">return</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>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
838 825 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
839 826
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
840 827 <span class="i">$SpecifiedFeatureAtomCount</span> = <span class="i">$This</span>-&gt;{<span class="w">StructureFeatures</span>}{<span class="w">AtomCount</span>}{<span class="i">$SpecifiedRadius</span>}{<span class="i">$SpecifiedAtomID</span>}<span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
841 828 <span class="i">$SpecifiedFeatureAtomIDsRef</span> = <span class="i">$This</span>-&gt;{<span class="w">StructureFeatures</span>}{<span class="w">AtomIDs</span>}{<span class="i">$SpecifiedRadius</span>}{<span class="i">$SpecifiedAtomID</span>}<span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
842 829
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
843 830 <span class="c"># No need to compare features at radius 0...</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
844 831 <span class="k">for</span> <span class="i">$Radius</span> <span class="s">(</span><span class="n">1</span> .. <span class="i">$SpecifiedRadius</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
845 832 <span class="j">ATOMIDENTIFIER:</span> <span class="k">for</span> <span class="i">$AtomIdentifier</span> <span class="s">(</span><span class="k">keys</span> <span class="i">%</span>{<span class="i">$This</span>-&gt;{<span class="w">StructurallyUniqueAtomIdentifiers</span>}{<span class="i">$Radius</span>}}<span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
846 833 <span class="i">$AtomID</span> = <span class="i">$This</span>-&gt;{<span class="w">StructurallyUniqueAtomIdentifiers</span>}{<span class="i">$Radius</span>}{<span class="i">$AtomIdentifier</span>}<span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
847 834
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
848 835 <span class="i">$FeatureAtomCount</span> = <span class="i">$This</span>-&gt;{<span class="w">StructureFeatures</span>}{<span class="w">AtomCount</span>}{<span class="i">$Radius</span>}{<span class="i">$AtomID</span>}<span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
849 836 <span class="i">$FeatureAtomIDsRef</span> = <span class="i">$This</span>-&gt;{<span class="w">StructureFeatures</span>}{<span class="w">AtomIDs</span>}{<span class="i">$Radius</span>}{<span class="i">$AtomID</span>}<span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
850 837
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
851 838 <span class="k">if</span> <span class="s">(</span><span class="i">$SpecifiedFeatureAtomCount</span> != <span class="i">$FeatureAtomCount</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
852 839 <span class="c"># Couldn&#39;t be structurally equivalent...</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
853 840 <span class="k">next</span> <span class="j">ATOMIDENTIFIER</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
854 841 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
855 842 <span class="k">for</span> <span class="i">$SpecifiedFeatureAtomID</span> <span class="s">(</span><span class="k">keys</span> <span class="i">%</span> {<span class="i">$SpecifiedFeatureAtomIDsRef</span>}<span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
856 843 <span class="k">if</span> <span class="s">(</span>! <span class="k">exists</span> <span class="i">$FeatureAtomIDsRef</span>-&gt;{<span class="i">$SpecifiedFeatureAtomID</span>}<span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
857 844 <span class="c"># For structural equivalency, all atom in specified feature must also be present in a previously</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
858 845 <span class="c"># identified structurally unique structure feature...</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
859 846 <span class="k">next</span> <span class="j">ATOMIDENTIFIER</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
860 847 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
861 848 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
862 849 <span class="c"># Found structurally equivalent feature...</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
863 850 <span class="k">return</span> <span class="s">(</span><span class="i">$Radius</span><span class="cm">,</span> <span class="i">$AtomIdentifier</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
864 851 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
865 852 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
866 853 <span class="k">return</span> <span class="s">(</span><span class="k">undef</span><span class="cm">,</span> <span class="k">undef</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
867 854 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
868 855
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
869 856 <span class="c"># Setup structure features for atom IDs involved in unique atom identifiers at all</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
870 857 <span class="c"># radii level...</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
871 858 <span class="c">#</span>
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parents:
diff changeset
872 <a name="_SetupStructureFeaturesForAtomIDsInvolvedInUniqueIdentifiers-"></a> 859 <span class="k">sub </span><span class="m">_SetupStructureFeaturesForAtomIDsInvolvedInUniqueIdentifiers</span> <span class="s">{</span>
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parents:
diff changeset
873 860 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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diff changeset
874 861 <span class="k">my</span><span class="s">(</span><span class="i">$Radius</span><span class="cm">,</span> <span class="i">$PreviousRadius</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">$AtomIdentifier</span><span class="cm">,</span> <span class="i">$NeighborhoodAtomID</span><span class="cm">,</span> <span class="i">$NeighborhoodAtomsWithSuccessorAtomsRef</span><span class="cm">,</span> <span class="i">$NeighborhoodAtom</span><span class="cm">,</span> <span class="i">$NeighborhoodAtomSuccessorAtomsRef</span><span class="cm">,</span> <span class="i">%AtomIDs</span><span class="s">)</span><span class="sc">;</span>
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diff changeset
875 862
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diff changeset
876 863 <span class="i">$This</span><span class="i">-&gt;_InitializeStructureFeatures</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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diff changeset
877 864
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diff changeset
878 865 <span class="c"># Collect atom IDs involved in unique atom identifiers...</span>
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diff changeset
879 866 <span class="i">%AtomIDs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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diff changeset
880 867 <span class="k">for</span> <span class="i">$Radius</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$This</span>-&gt;{<span class="w">NeighborhoodRadius</span>}<span class="s">)</span> <span class="s">{</span>
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881 868 <span class="k">for</span> <span class="i">$AtomIdentifier</span> <span class="s">(</span><span class="k">keys</span> <span class="i">%</span>{<span class="i">$This</span>-&gt;{<span class="w">UniqueAtomIdentifiers</span>}{<span class="i">$Radius</span>}}<span class="s">)</span> <span class="s">{</span>
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882 869 <span class="i">$AtomID</span> = <span class="i">$This</span>-&gt;{<span class="w">UniqueAtomIdentifiers</span>}{<span class="i">$Radius</span>}{<span class="i">$AtomIdentifier</span>}<span class="sc">;</span>
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883 870 <span class="i">$AtomIDs</span>{<span class="i">$AtomID</span>} = <span class="i">$AtomID</span><span class="sc">;</span>
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diff changeset
884 871 <span class="s">}</span>
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885 872 <span class="s">}</span>
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886 873
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887 874 <span class="c"># Setup structure features...</span>
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diff changeset
888 875 <span class="k">for</span> <span class="i">$Radius</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$This</span>-&gt;{<span class="w">NeighborhoodRadius</span>}<span class="s">)</span> <span class="s">{</span>
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889 876 <span class="k">for</span> <span class="i">$AtomID</span> <span class="s">(</span><span class="k">keys</span> <span class="i">%AtomIDs</span><span class="s">)</span> <span class="s">{</span>
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890 877 <span class="k">my</span><span class="s">(</span><span class="i">$StructureFeatureAtomCount</span><span class="cm">,</span> <span class="i">%StructureFeatureAtomIDs</span><span class="s">)</span><span class="sc">;</span>
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diff changeset
891 878
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diff changeset
892 879 <span class="i">$StructureFeatureAtomCount</span> = <span class="n">0</span><span class="sc">;</span>
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parents:
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893 880 <span class="i">%StructureFeatureAtomIDs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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parents:
diff changeset
894 881
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diff changeset
895 882 <span class="c"># Get partial structure features for the atom at previous radius level...</span>
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parents:
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896 883 <span class="i">$PreviousRadius</span> = <span class="i">$Radius</span> - <span class="n">1</span><span class="sc">;</span>
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897 884 <span class="k">if</span> <span class="s">(</span><span class="i">$PreviousRadius</span> &gt;= <span class="n">0</span><span class="s">)</span> <span class="s">{</span>
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parents:
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898 885 <span class="i">$StructureFeatureAtomCount</span> += <span class="i">$This</span>-&gt;{<span class="w">StructureFeatures</span>}{<span class="w">AtomCount</span>}{<span class="i">$PreviousRadius</span>}{<span class="i">$AtomID</span>}<span class="sc">;</span>
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899 886 <span class="i">%StructureFeatureAtomIDs</span> = <span class="i">%</span>{<span class="i">$This</span>-&gt;{<span class="w">StructureFeatures</span>}{<span class="w">AtomIDs</span>}{<span class="i">$PreviousRadius</span>}{<span class="i">$AtomID</span>}}<span class="sc">;</span>
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diff changeset
900 887 <span class="s">}</span>
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diff changeset
901 888
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diff changeset
902 889 <span class="c"># Get all neighborhood atom at this radius level...</span>
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diff changeset
903 890 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span><span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">AtomNeighborhoods</span>}{<span class="i">$Radius</span>}<span class="s">)</span> &amp;&amp; <span class="k">exists</span><span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">AtomNeighborhoods</span>}{<span class="i">$Radius</span>}{<span class="i">$AtomID</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
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parents:
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904 891 <span class="j">NEIGHBORHOODS:</span> <span class="k">for</span> <span class="i">$NeighborhoodAtomsWithSuccessorAtomsRef</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$This</span>-&gt;{<span class="w">AtomNeighborhoods</span>}{<span class="i">$Radius</span>}{<span class="i">$AtomID</span>}}<span class="s">)</span> <span class="s">{</span>
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905 892 <span class="s">(</span><span class="i">$NeighborhoodAtom</span><span class="cm">,</span> <span class="i">$NeighborhoodAtomSuccessorAtomsRef</span><span class="s">)</span> = <span class="i">@</span>{<span class="i">$NeighborhoodAtomsWithSuccessorAtomsRef</span>}<span class="sc">;</span>
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906 893 <span class="k">if</span> <span class="s">(</span><span class="i">$NeighborhoodAtom</span><span class="i">-&gt;IsHydrogen</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
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parents:
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907 894 <span class="k">next</span> <span class="j">NEIGHBORHOODS</span><span class="sc">;</span>
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parents:
diff changeset
908 895 <span class="s">}</span>
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diff changeset
909 896 <span class="i">$NeighborhoodAtomID</span> = <span class="i">$NeighborhoodAtom</span><span class="i">-&gt;GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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910 897 <span class="i">$StructureFeatureAtomCount</span>++<span class="sc">;</span>
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diff changeset
911 898 <span class="i">$StructureFeatureAtomIDs</span>{<span class="i">$NeighborhoodAtomID</span>} = <span class="i">$NeighborhoodAtomID</span><span class="sc">;</span>
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parents:
diff changeset
912 899 <span class="s">}</span>
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diff changeset
913 900 <span class="s">}</span>
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diff changeset
914 901
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diff changeset
915 902 <span class="c"># Assign structure features to atom at this radius level...</span>
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diff changeset
916 903 <span class="i">$This</span>-&gt;{<span class="w">StructureFeatures</span>}{<span class="w">AtomCount</span>}{<span class="i">$Radius</span>}{<span class="i">$AtomID</span>} = <span class="i">$StructureFeatureAtomCount</span><span class="sc">;</span>
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diff changeset
917 904 <span class="i">$This</span>-&gt;{<span class="w">StructureFeatures</span>}{<span class="w">AtomIDs</span>}{<span class="i">$Radius</span>}{<span class="i">$AtomID</span>} = \<span class="i">%StructureFeatureAtomIDs</span><span class="sc">;</span>
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diff changeset
918 905 <span class="s">}</span>
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parents:
diff changeset
919 906 <span class="s">}</span>
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diff changeset
920 907 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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parents:
diff changeset
921 908 <span class="s">}</span>
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diff changeset
922 909
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diff changeset
923 910 <span class="c"># Intialize structure features at each radius level...</span>
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parents:
diff changeset
924 911 <span class="c">#</span>
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parents:
diff changeset
925 <a name="_InitializeStructureFeatures-"></a> 912 <span class="k">sub </span><span class="m">_InitializeStructureFeatures</span> <span class="s">{</span>
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diff changeset
926 913 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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parents:
diff changeset
927 914 <span class="k">my</span><span class="s">(</span><span class="i">$Radius</span><span class="cm">,</span> <span class="i">$CurrentRadius</span><span class="cm">,</span> <span class="i">$Atom</span><span class="cm">,</span> <span class="i">$AtomID</span><span class="s">)</span><span class="sc">;</span>
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diff changeset
928 915
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diff changeset
929 916 <span class="c"># Initialize all structure features...</span>
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parents:
diff changeset
930 917
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diff changeset
931 918 <span class="i">%</span>{<span class="i">$This</span>-&gt;{<span class="w">StructureFeatures</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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932 919 <span class="i">%</span>{<span class="i">$This</span>-&gt;{<span class="w">StructureFeatures</span>}{<span class="w">AtomCount</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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parents:
diff changeset
933 920 <span class="i">%</span>{<span class="i">$This</span>-&gt;{<span class="w">StructureFeatures</span>}{<span class="w">AtomIDs</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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diff changeset
934 921
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diff changeset
935 922 <span class="i">$Radius</span> = <span class="i">$This</span>-&gt;{<span class="w">NeighborhoodRadius</span>}<span class="sc">;</span>
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parents:
diff changeset
936 923 <span class="k">for</span> <span class="i">$CurrentRadius</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$Radius</span><span class="s">)</span> <span class="s">{</span>
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parents:
diff changeset
937 924 <span class="c"># Structure features for at specific radii accessed using atom IDs...</span>
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diff changeset
938 925 <span class="i">%</span>{<span class="i">$This</span>-&gt;{<span class="w">StructureFeatures</span>}{<span class="w">AtomCount</span>}{<span class="i">$CurrentRadius</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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parents:
diff changeset
939 926 <span class="i">%</span>{<span class="i">$This</span>-&gt;{<span class="w">StructureFeatures</span>}{<span class="w">AtomIDs</span>}{<span class="i">$CurrentRadius</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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parents:
diff changeset
940 927 <span class="s">}</span>
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diff changeset
941 928 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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diff changeset
942 929 <span class="s">}</span>
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diff changeset
943 930
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diff changeset
944 931 <span class="c"># Cache appropriate molecule data...</span>
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diff changeset
945 932 <span class="c">#</span>
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diff changeset
946 <a name="_SetupMoleculeDataCache-"></a> 933 <span class="k">sub </span><span class="m">_SetupMoleculeDataCache</span> <span class="s">{</span>
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parents:
diff changeset
947 934 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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diff changeset
948 935
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diff changeset
949 936 <span class="c"># Get all non-hydrogen atoms...</span>
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parents:
diff changeset
950 937 <span class="k">my</span><span class="s">(</span><span class="i">$NegateAtomCheckMethod</span><span class="s">)</span><span class="sc">;</span>
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parents:
diff changeset
951 938 <span class="i">$NegateAtomCheckMethod</span> = <span class="n">1</span><span class="sc">;</span>
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parents:
diff changeset
952 939 <span class="i">@</span>{<span class="i">$This</span>-&gt;{<span class="w">Atoms</span>}} = <span class="i">$This</span><span class="i">-&gt;GetMolecule</span><span class="s">(</span><span class="s">)</span><span class="i">-&gt;GetAtoms</span><span class="s">(</span><span class="q">&quot;IsHydrogen&quot;</span><span class="cm">,</span> <span class="i">$NegateAtomCheckMethod</span><span class="s">)</span><span class="sc">;</span>
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diff changeset
953 940
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diff changeset
954 941 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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diff changeset
955 942 <span class="s">}</span>
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diff changeset
956 943
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parents:
diff changeset
957 944 <span class="c"># Clear cached molecule data...</span>
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parents:
diff changeset
958 945 <span class="c">#</span>
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diff changeset
959 <a name="_ClearMoleculeDataCache-"></a> 946 <span class="k">sub </span><span class="m">_ClearMoleculeDataCache</span> <span class="s">{</span>
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parents:
diff changeset
960 947 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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parents:
diff changeset
961 948
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diff changeset
962 949 <span class="i">@</span>{<span class="i">$This</span>-&gt;{<span class="w">Atoms</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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diff changeset
963 950
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diff changeset
964 951 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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parents:
diff changeset
965 952 <span class="s">}</span>
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diff changeset
966 953
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diff changeset
967 954 <span class="c"># Initialize atom indentifier type information...</span>
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parents:
diff changeset
968 955 <span class="c">#</span>
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parents:
diff changeset
969 956 <span class="c"># Current supported values:</span>
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diff changeset
970 957 <span class="c">#</span>
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diff changeset
971 958 <span class="c"># AtomicInvariantsAtomTypes, FunctionalClassAtomTypes, DREIDINGAtomTypes, EStateAtomTypes,</span>
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parents:
diff changeset
972 959 <span class="c"># MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes</span>
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parents:
diff changeset
973 960 <span class="c">#</span>
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parents:
diff changeset
974 <a name="_InitializeAtomIdentifierTypeInformation-"></a> 961 <span class="k">sub </span><span class="m">_InitializeAtomIdentifierTypeInformation</span> <span class="s">{</span>
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parents:
diff changeset
975 962 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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976 963
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977 964 <span class="j">IDENTIFIERTYPE:</span> <span class="s">{</span>
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diff changeset
978 965 <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>
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parents:
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979 966 <span class="i">$This</span><span class="i">-&gt;_InitializeAtomicInvariantsAtomTypesInformation</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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diff changeset
980 967 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span>
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parents:
diff changeset
981 968 <span class="s">}</span>
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parents:
diff changeset
982 969 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^FunctionalClassAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span>
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parents:
diff changeset
983 970 <span class="i">$This</span><span class="i">-&gt;_InitializeFunctionalClassAtomTypesInformation</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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984 971 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span>
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985 972 <span class="s">}</span>
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986 973 <span class="k">if</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>
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987 974 <span class="c"># Nothing to do for now...</span>
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988 975 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span>
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989 976 <span class="s">}</span>
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990 977 <span class="w">carp</span> <span class="q">&quot;Warning: ${ClassName}-&gt;_InitializeAtomIdentifierTypeInformation: Unknown atom indentifier type $This-&gt;{AtomIdentifierType}...&quot;</span><span class="sc">;</span>
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991 978 <span class="s">}</span>
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992 979 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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993 980 <span class="s">}</span>
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994 981
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995 982 <span class="c"># Initialize atomic invariants atom types, generated by AtomTypes::AtomicInvariantsAtomTypes</span>
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996 983 <span class="c"># class, to use for generating initial atom identifiers...</span>
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997 984 <span class="c">#</span>
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998 985 <span class="c"># Let:</span>
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999 986 <span class="c"># AS = Atom symbol corresponding to element symbol</span>
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1000 987 <span class="c">#</span>
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1001 988 <span class="c"># X&lt;n&gt; = Number of non-hydrogen atom neighbors or heavy atoms attached to atom</span>
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1002 989 <span class="c"># BO&lt;n&gt; = Sum of bond orders to non-hydrogen atom neighbors or heavy atoms attached to atom</span>
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1003 990 <span class="c"># LBO&lt;n&gt; = Largest bond order of non-hydrogen atom neighbors or heavy atoms attached to atom</span>
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1004 991 <span class="c"># SB&lt;n&gt; = Number of single bonds to non-hydrogen atom neighbors or heavy atoms attached to atom</span>
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1005 992 <span class="c"># DB&lt;n&gt; = Number of double bonds to non-hydrogen atom neighbors or heavy atoms attached to atom</span>
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1006 993 <span class="c"># TB&lt;n&gt; = Number of triple bonds to non-hydrogen atom neighbors or heavy atoms attached to atom</span>
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1007 994 <span class="c"># H&lt;n&gt; = Number of implicit and explicit hydrogens for atom</span>
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1008 995 <span class="c"># Ar = Aromatic annotation indicating whether atom is aromatic</span>
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1009 996 <span class="c"># RA = Ring atom annotation indicating whether atom is a ring</span>
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1010 997 <span class="c"># FC&lt;+n/-n&gt; = Formal charge assigned to atom</span>
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1011 998 <span class="c"># MN&lt;n&gt; = Mass number indicating isotope other than most abundant isotope</span>
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1012 999 <span class="c"># SM&lt;n&gt; = Spin multiplicity of atom. Possible values: 1 (singlet), 2 (doublet) or 3 (triplet)</span>
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1013 1000 <span class="c">#</span>
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1014 1001 <span class="c"># Then:</span>
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1015 1002 <span class="c">#</span>
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1016 1003 <span class="c"># Atom type generated by AtomTypes::AtomicInvariantsAtomTypes class corresponds to:</span>
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1017 1004 <span class="c">#</span>
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1018 1005 <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>
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1019 1006 <span class="c">#</span>
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1020 1007 <span class="c"># Except for AS which is a required atomic invariant in atom types, all other atomic invariants are</span>
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1021 1008 <span class="c"># optional.</span>
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1022 1009 <span class="c">#</span>
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1023 1010 <span class="c"># Default atomic invariants used for generating inital atom identifiers are [ Ref 24 ]:</span>
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1024 1011 <span class="c">#</span>
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1025 1012 <span class="c"># AS, X&lt;n&gt;, BO&lt;n&gt;, H&lt;n&gt;, FC&lt;+n/-n&gt;, MN&lt;n&gt;</span>
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1026 1013 <span class="c">#</span>
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1027 1014 <span class="c"># In addition to usage of abbreviations for specifying atomic invariants, the following descriptive words</span>
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1028 1015 <span class="c"># are also allowed:</span>
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1029 1016 <span class="c">#</span>
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1030 1017 <span class="c"># X : NumOfNonHydrogenAtomNeighbors or NumOfHeavyAtomNeighbors</span>
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1031 1018 <span class="c"># BO : SumOfBondOrdersToNonHydrogenAtoms or SumOfBondOrdersToHeavyAtoms</span>
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1032 1019 <span class="c"># LBO : LargestBondOrderToNonHydrogenAtoms or LargestBondOrderToHeavyAtoms</span>
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1033 1020 <span class="c"># SB : NumOfSingleBondsToNonHydrogenAtoms or NumOfSingleBondsToHeavyAtoms</span>
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1034 1021 <span class="c"># DB : NumOfDoubleBondsToNonHydrogenAtoms or NumOfDoubleBondsToHeavyAtoms</span>
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1035 1022 <span class="c"># TB : NumOfTripleBondsToNonHydrogenAtoms or NumOfTripleBondsToHeavyAtoms</span>
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1036 1023 <span class="c"># H : NumOfImplicitAndExplicitHydrogens</span>
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1037 1024 <span class="c"># Ar : Aromatic</span>
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1038 1025 <span class="c"># RA : RingAtom</span>
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1039 1026 <span class="c"># FC : FormalCharge</span>
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1040 1027 <span class="c"># MN : MassNumber</span>
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1041 1028 <span class="c"># SM : SpinMultiplicity</span>
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1042 1029 <span class="c">#</span>
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1043 <a name="_InitializeAtomicInvariantsAtomTypesInformation-"></a>1030 <span class="k">sub </span><span class="m">_InitializeAtomicInvariantsAtomTypesInformation</span> <span class="s">{</span>
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1044 1031 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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1045 1032
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1046 1033 <span class="c"># Default atomic invariants to use for generating initial atom identifiers are: AS, X, BO, LBO, H, FC</span>
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1047 1034 <span class="c">#</span>
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1048 1035 <span class="i">@</span>{<span class="i">$This</span>-&gt;{<span class="w">AtomicInvariantsToUse</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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1049 1036 <span class="i">@</span>{<span class="i">$This</span>-&gt;{<span class="w">AtomicInvariantsToUse</span>}} = <span class="s">(</span><span class="q">&#39;AS&#39;</span><span class="cm">,</span> <span class="q">&#39;X&#39;</span><span class="cm">,</span> <span class="q">&#39;BO&#39;</span><span class="cm">,</span> <span class="q">&#39;H&#39;</span><span class="cm">,</span> <span class="q">&#39;FC&#39;</span><span class="cm">,</span> <span class="q">&#39;MN&#39;</span><span class="s">)</span><span class="sc">;</span>
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1050 1037
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1051 1038 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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1052 1039 <span class="s">}</span>
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1053 1040
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1054 1041 <span class="c"># Initialize functional class atom types, generated by AtomTypes::FunctionalClassAtomTypes</span>
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1055 1042 <span class="c"># class, to use for generating initial atom identifiers...</span>
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1056 1043 <span class="c">#</span>
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1057 1044 <span class="c"># Let:</span>
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1058 1045 <span class="c"># HBD: HydrogenBondDonor</span>
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1059 1046 <span class="c"># HBA: HydrogenBondAcceptor</span>
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1060 1047 <span class="c"># PI : PositivelyIonizable</span>
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1061 1048 <span class="c"># NI : NegativelyIonizable</span>
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1062 1049 <span class="c"># Ar : Aromatic</span>
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1063 1050 <span class="c"># Hal : Halogen</span>
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1064 1051 <span class="c"># H : Hydrophobic</span>
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1065 1052 <span class="c"># RA : RingAtom</span>
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1066 1053 <span class="c"># CA : ChainAtom</span>
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1067 1054 <span class="c">#</span>
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1068 1055 <span class="c"># Then:</span>
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1069 1056 <span class="c">#</span>
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1070 1057 <span class="c"># Functiononal class atom type specification for an atom corresponds to:</span>
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1071 1058 <span class="c">#</span>
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1072 1059 <span class="c"># Ar.CA.H.HBA.HBD.Hal.NI.PI.RA</span>
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1073 1060 <span class="c">#</span>
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1074 1061 <span class="c"># Default functional classes used are: HBD, HBA, PI, NI, Ar, Hal</span>
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1075 1062 <span class="c">#</span>
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1076 1063 <span class="c"># FunctionalAtomTypes are assigned using the following definitions [ Ref 60-61, Ref 65-66 ]:</span>
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1077 1064 <span class="c">#</span>
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1078 1065 <span class="c"># HydrogenBondDonor: NH, NH2, OH</span>
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1079 1066 <span class="c"># HydrogenBondAcceptor: N[!H], O</span>
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1080 1067 <span class="c"># PositivelyIonizable: +, NH2</span>
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1081 1068 <span class="c"># NegativelyIonizable: -, C(=O)OH, S(=O)OH, P(=O)OH</span>
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1082 1069 <span class="c">#</span>
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1083 <a name="_InitializeFunctionalClassAtomTypesInformation-"></a>1070 <span class="k">sub </span><span class="m">_InitializeFunctionalClassAtomTypesInformation</span> <span class="s">{</span>
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1084 1071 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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1085 1072
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1086 1073 <span class="c"># Default functional class atom typess to use for generating initial atom identifiers</span>
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1087 1074 <span class="c"># are: HBD, HBA, PI, NI, Ar, Hal</span>
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1088 1075 <span class="c">#</span>
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1089 1076 <span class="i">@</span>{<span class="i">$This</span>-&gt;{<span class="w">FunctionalClassesToUse</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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1090 1077 <span class="i">@</span>{<span class="i">$This</span>-&gt;{<span class="w">FunctionalClassesToUse</span>}} = <span class="s">(</span><span class="q">&#39;HBD&#39;</span><span class="cm">,</span> <span class="q">&#39;HBA&#39;</span><span class="cm">,</span> <span class="q">&#39;PI&#39;</span><span class="cm">,</span> <span class="q">&#39;NI&#39;</span><span class="cm">,</span> <span class="q">&#39;Ar&#39;</span><span class="cm">,</span> <span class="q">&#39;Hal&#39;</span><span class="s">)</span><span class="sc">;</span>
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1091 1078
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1092 1079 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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1093 1080 <span class="s">}</span>
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1094 1081
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1095 1082 <span class="c"># Set atomic invariants to use for generation of intial atom indentifiers...</span>
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1096 1083 <span class="c">#</span>
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1097 <a name="SetAtomicInvariantsToUse-"></a>1084 <span class="k">sub </span><span class="m">SetAtomicInvariantsToUse</span> <span class="s">{</span>
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1098 1085 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">@Values</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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1099 1086 <span class="k">my</span><span class="s">(</span><span class="i">$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">@SpecifiedAtomicInvariants</span><span class="cm">,</span> <span class="i">@AtomicInvariantsToUse</span><span class="s">)</span><span class="sc">;</span>
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1100 1087
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1101 1088 <span class="k">if</span> <span class="s">(</span>!<span class="i">@Values</span><span class="s">)</span> <span class="s">{</span>
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1102 1089 <span class="w">carp</span> <span class="q">&quot;Warning: ${ClassName}-&gt;SetAtomicInvariantsToUse: No values specified...&quot;</span><span class="sc">;</span>
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1103 1090 <span class="k">return</span><span class="sc">;</span>
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1104 1091 <span class="s">}</span>
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1105 1092
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1106 1093 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">AtomIdentifierType</span>} !~ <span class="q">/^AtomicInvariantsAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span>
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1107 1094 <span class="w">carp</span> <span class="q">&quot;Warning: ${ClassName}-&gt;SetFunctionalAtomTypesToUse: AtomicInvariantsToUse can&#39;t be set for InitialAtomIdentifierType of $This-&gt;{AtomIdentifierType}...&quot;</span><span class="sc">;</span>
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1108 1095 <span class="k">return</span><span class="sc">;</span>
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1109 1096 <span class="s">}</span>
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1110 1097
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1111 1098 <span class="i">$FirstValue</span> = <span class="i">$Values</span>[<span class="n">0</span>]<span class="sc">;</span>
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1112 1099 <span class="i">$TypeOfFirstValue</span> = <span class="k">ref</span> <span class="i">$FirstValue</span><span class="sc">;</span>
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1113 1100
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1114 1101 <span class="i">@SpecifiedAtomicInvariants</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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1115 1102 <span class="i">@AtomicInvariantsToUse</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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1116 1103
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1117 1104 <span class="k">if</span> <span class="s">(</span><span class="i">$TypeOfFirstValue</span> =~ <span class="q">/^ARRAY/</span><span class="s">)</span> <span class="s">{</span>
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1118 1105 <span class="k">push</span> <span class="i">@SpecifiedAtomicInvariants</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$FirstValue</span>}<span class="sc">;</span>
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parents:
diff changeset
1119 1106 <span class="s">}</span>
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parents:
diff changeset
1120 1107 <span class="k">else</span> <span class="s">{</span>
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parents:
diff changeset
1121 1108 <span class="k">push</span> <span class="i">@SpecifiedAtomicInvariants</span><span class="cm">,</span> <span class="i">@Values</span><span class="sc">;</span>
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parents:
diff changeset
1122 1109 <span class="s">}</span>
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diff changeset
1123 1110
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parents:
diff changeset
1124 1111 <span class="c"># Make sure specified AtomicInvariants are valid...</span>
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parents:
diff changeset
1125 1112 <span class="k">for</span> <span class="i">$SpecifiedAtomicInvariant</span> <span class="s">(</span><span class="i">@SpecifiedAtomicInvariants</span><span class="s">)</span> <span class="s">{</span>
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parents:
diff changeset
1126 1113 <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>
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parents:
diff changeset
1127 1114 <span class="w">croak</span> <span class="q">&quot;Error: ${ClassName}-&gt;SetAtomicInvariantsToUse: Specified atomic invariant, $SpecifiedAtomicInvariant, is not supported...\n &quot;</span><span class="sc">;</span>
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parents:
diff changeset
1128 1115 <span class="s">}</span>
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diff changeset
1129 1116 <span class="i">$AtomicInvariant</span> = <span class="i">$SpecifiedAtomicInvariant</span><span class="sc">;</span>
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parents:
diff changeset
1130 1117 <span class="k">push</span> <span class="i">@AtomicInvariantsToUse</span><span class="cm">,</span> <span class="i">$AtomicInvariant</span><span class="sc">;</span>
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parents:
diff changeset
1131 1118 <span class="s">}</span>
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parents:
diff changeset
1132 1119
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diff changeset
1133 1120 <span class="c"># Set atomic invariants to use...</span>
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parents:
diff changeset
1134 1121 <span class="i">@</span>{<span class="i">$This</span>-&gt;{<span class="w">AtomicInvariantsToUse</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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parents:
diff changeset
1135 1122 <span class="k">push</span> <span class="i">@</span>{<span class="i">$This</span>-&gt;{<span class="w">AtomicInvariantsToUse</span>}}<span class="cm">,</span> <span class="i">@AtomicInvariantsToUse</span><span class="sc">;</span>
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parents:
diff changeset
1136 1123
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diff changeset
1137 1124 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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parents:
diff changeset
1138 1125 <span class="s">}</span>
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parents:
diff changeset
1139 1126
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diff changeset
1140 1127 <span class="c"># Set functional classes to use for generation of intial atom indentifiers...</span>
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parents:
diff changeset
1141 1128 <span class="c">#</span>
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parents:
diff changeset
1142 <a name="SetFunctionalClassesToUse-"></a>1129 <span class="k">sub </span><span class="m">SetFunctionalClassesToUse</span> <span class="s">{</span>
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1143 1130 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">@Values</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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1144 1131 <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>
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diff changeset
1145 1132
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diff changeset
1146 1133 <span class="k">if</span> <span class="s">(</span>!<span class="i">@Values</span><span class="s">)</span> <span class="s">{</span>
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parents:
diff changeset
1147 1134 <span class="w">carp</span> <span class="q">&quot;Warning: ${ClassName}-&gt;SetFunctionalClassesToUse: No values specified...&quot;</span><span class="sc">;</span>
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parents:
diff changeset
1148 1135 <span class="k">return</span><span class="sc">;</span>
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parents:
diff changeset
1149 1136 <span class="s">}</span>
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parents:
diff changeset
1150 1137
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diff changeset
1151 1138 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">AtomIdentifierType</span>} !~ <span class="q">/^FunctionalClassAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span>
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parents:
diff changeset
1152 1139 <span class="w">carp</span> <span class="q">&quot;Warning: ${ClassName}-&gt;SetFunctionalClassesToUse: FunctionalClassesToUse can&#39;t be set for InitialAtomIdentifierType of $This-&gt;{AtomIdentifierType}...&quot;</span><span class="sc">;</span>
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parents:
diff changeset
1153 1140 <span class="k">return</span><span class="sc">;</span>
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parents:
diff changeset
1154 1141 <span class="s">}</span>
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diff changeset
1155 1142
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diff changeset
1156 1143 <span class="i">$FirstValue</span> = <span class="i">$Values</span>[<span class="n">0</span>]<span class="sc">;</span>
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diff changeset
1157 1144 <span class="i">$TypeOfFirstValue</span> = <span class="k">ref</span> <span class="i">$FirstValue</span><span class="sc">;</span>
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parents:
diff changeset
1158 1145
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diff changeset
1159 1146 <span class="i">@SpecifiedFunctionalClasses</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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parents:
diff changeset
1160 1147 <span class="i">@FunctionalClassesToUse</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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diff changeset
1161 1148
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diff changeset
1162 1149 <span class="k">if</span> <span class="s">(</span><span class="i">$TypeOfFirstValue</span> =~ <span class="q">/^ARRAY/</span><span class="s">)</span> <span class="s">{</span>
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parents:
diff changeset
1163 1150 <span class="k">push</span> <span class="i">@SpecifiedFunctionalClasses</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$FirstValue</span>}<span class="sc">;</span>
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parents:
diff changeset
1164 1151 <span class="s">}</span>
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parents:
diff changeset
1165 1152 <span class="k">else</span> <span class="s">{</span>
73ae111cf86f Uploaded
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parents:
diff changeset
1166 1153 <span class="k">push</span> <span class="i">@SpecifiedFunctionalClasses</span><span class="cm">,</span> <span class="i">@Values</span><span class="sc">;</span>
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deepakjadmin
parents:
diff changeset
1167 1154 <span class="s">}</span>
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parents:
diff changeset
1168 1155
73ae111cf86f Uploaded
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parents:
diff changeset
1169 1156 <span class="c"># Make sure specified FunctionalClasses are valid...</span>
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parents:
diff changeset
1170 1157 <span class="k">for</span> <span class="i">$SpecifiedFunctionalClass</span> <span class="s">(</span><span class="i">@SpecifiedFunctionalClasses</span><span class="s">)</span> <span class="s">{</span>
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parents:
diff changeset
1171 1158 <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>
73ae111cf86f Uploaded
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parents:
diff changeset
1172 1159 <span class="w">croak</span> <span class="q">&quot;Error: ${ClassName}-&gt;SetFunctionalClassesToUse: Specified functional class, $SpecifiedFunctionalClass, is not supported...\n &quot;</span><span class="sc">;</span>
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parents:
diff changeset
1173 1160 <span class="s">}</span>
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parents:
diff changeset
1174 1161 <span class="k">push</span> <span class="i">@FunctionalClassesToUse</span><span class="cm">,</span> <span class="i">$SpecifiedFunctionalClass</span><span class="sc">;</span>
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parents:
diff changeset
1175 1162 <span class="s">}</span>
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parents:
diff changeset
1176 1163
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diff changeset
1177 1164 <span class="c"># Set functional classes to use...</span>
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parents:
diff changeset
1178 1165 <span class="i">@</span>{<span class="i">$This</span>-&gt;{<span class="w">FunctionalClassesToUse</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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parents:
diff changeset
1179 1166 <span class="k">push</span> <span class="i">@</span>{<span class="i">$This</span>-&gt;{<span class="w">FunctionalClassesToUse</span>}}<span class="cm">,</span> <span class="i">@FunctionalClassesToUse</span><span class="sc">;</span>
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parents:
diff changeset
1180 1167
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diff changeset
1181 1168 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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parents:
diff changeset
1182 1169 <span class="s">}</span>
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parents:
diff changeset
1183 1170
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diff changeset
1184 1171 <span class="c"># Return a string containg data for ExtendedConnectivityFingerprints object...</span>
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parents:
diff changeset
1185 <a name="StringifyExtendedConnectivityFingerprints-"></a>1172 <span class="k">sub </span><span class="m">StringifyExtendedConnectivityFingerprints</span> <span class="s">{</span>
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parents:
diff changeset
1186 1173 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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parents:
diff changeset
1187 1174 <span class="k">my</span><span class="s">(</span><span class="i">$ExtendedConnectivityFingerprintsString</span><span class="s">)</span><span class="sc">;</span>
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parents:
diff changeset
1188 1175
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diff changeset
1189 1176 <span class="i">$ExtendedConnectivityFingerprintsString</span> = <span class="q">&quot;InitialAtomIdentifierType: $This-&gt;{AtomIdentifierType}; NeighborhoodRadius: $This-&gt;{NeighborhoodRadius}&quot;</span><span class="sc">;</span>
73ae111cf86f Uploaded
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parents:
diff changeset
1190 1177
73ae111cf86f Uploaded
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diff changeset
1191 1178 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^AtomicInvariantsAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span>
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parents:
diff changeset
1192 1179 <span class="k">my</span><span class="s">(</span><span class="i">$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>
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diff changeset
1193 1180
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diff changeset
1194 1181 <span class="i">@AtomicInvariantsOrder</span> = <span class="i">AtomTypes::AtomicInvariantsAtomTypes::GetAtomicInvariantsOrder</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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diff changeset
1195 1182 <span class="i">%AvailableAtomicInvariants</span> = <span class="i">AtomTypes::AtomicInvariantsAtomTypes::GetAvailableAtomicInvariants</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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parents:
diff changeset
1196 1183
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diff changeset
1197 1184 <span class="k">for</span> <span class="i">$AtomicInvariant</span> <span class="s">(</span><span class="i">@AtomicInvariantsOrder</span><span class="s">)</span> <span class="s">{</span>
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parents:
diff changeset
1198 1185 <span class="k">push</span> <span class="i">@AtomicInvariants</span><span class="cm">,</span> <span class="q">&quot;$AtomicInvariant: $AvailableAtomicInvariants{$AtomicInvariant}&quot;</span><span class="sc">;</span>
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parents:
diff changeset
1199 1186 <span class="s">}</span>
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diff changeset
1200 1187
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parents:
diff changeset
1201 1188 <span class="i">$ExtendedConnectivityFingerprintsString</span> .= <span class="q">&quot;; AtomicInvariantsToUse: &lt;&quot;</span> . <span class="i">TextUtil::JoinWords</span><span class="s">(</span>\<span class="i">@</span>{<span class="i">$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>
73ae111cf86f Uploaded
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parents:
diff changeset
1202 1189 <span class="i">$ExtendedConnectivityFingerprintsString</span> .= <span class="q">&quot;; AtomicInvariantsOrder: &lt;&quot;</span> . <span class="i">TextUtil::JoinWords</span><span class="s">(</span>\<span class="i">@AtomicInvariantsOrder</span><span class="cm">,</span> <span class="q">&quot;, &quot;</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span> . <span class="q">&quot;&gt;&quot;</span><span class="sc">;</span>
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parents:
diff changeset
1203 1190 <span class="i">$ExtendedConnectivityFingerprintsString</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>
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parents:
diff changeset
1204 1191 <span class="s">}</span>
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parents:
diff changeset
1205 1192 <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>
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parents:
diff changeset
1206 1193 <span class="k">my</span><span class="s">(</span><span class="i">$FunctionalClass</span><span class="cm">,</span> <span class="i">@FunctionalClasses</span><span class="cm">,</span> <span class="i">@FunctionalClassesOrder</span><span class="cm">,</span> <span class="i">%AvailableFunctionalClasses</span><span class="s">)</span><span class="sc">;</span>
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parents:
diff changeset
1207 1194
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diff changeset
1208 1195 <span class="i">@FunctionalClassesOrder</span> = <span class="i">AtomTypes::FunctionalClassAtomTypes::GetFunctionalClassesOrder</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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diff changeset
1209 1196 <span class="i">%AvailableFunctionalClasses</span> = <span class="i">AtomTypes::FunctionalClassAtomTypes::GetAvailableFunctionalClasses</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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parents:
diff changeset
1210 1197
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diff changeset
1211 1198 <span class="k">for</span> <span class="i">$FunctionalClass</span> <span class="s">(</span><span class="i">@FunctionalClassesOrder</span><span class="s">)</span> <span class="s">{</span>
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parents:
diff changeset
1212 1199 <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>
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parents:
diff changeset
1213 1200 <span class="s">}</span>
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parents:
diff changeset
1214 1201
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parents:
diff changeset
1215 1202 <span class="i">$ExtendedConnectivityFingerprintsString</span> .= <span class="q">&quot;; FunctionalClassesToUse: &lt;&quot;</span> . <span class="i">TextUtil::JoinWords</span><span class="s">(</span>\<span class="i">@</span>{<span class="i">$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>
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parents:
diff changeset
1216 1203 <span class="i">$ExtendedConnectivityFingerprintsString</span> .= <span class="q">&quot;; FunctionalClassesOrder: &lt;&quot;</span> . <span class="i">TextUtil::JoinWords</span><span class="s">(</span>\<span class="i">@FunctionalClassesOrder</span><span class="cm">,</span> <span class="q">&quot;, &quot;</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span> . <span class="q">&quot;&gt;&quot;</span><span class="sc">;</span>
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parents:
diff changeset
1217 1204 <span class="i">$ExtendedConnectivityFingerprintsString</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>
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parents:
diff changeset
1218 1205 <span class="s">}</span>
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diff changeset
1219 1206
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diff changeset
1220 1207 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">Type</span>} =~ <span class="q">/^ExtendedConnectivityBits$/i</span><span class="s">)</span> <span class="s">{</span>
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parents:
diff changeset
1221 1208 <span class="c"># Size...</span>
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parents:
diff changeset
1222 1209 <span class="i">$ExtendedConnectivityFingerprintsString</span> .= <span class="q">&quot;; Size: $This-&gt;{Size}; MinSize: $This-&gt;{MinSize}; MaxSize: $This-&gt;{MaxSize}&quot;</span><span class="sc">;</span>
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parents:
diff changeset
1223 1210
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parents:
diff changeset
1224 1211 <span class="c"># Fingerprint bit density and num of bits set...</span>
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diff changeset
1225 1212 <span class="k">my</span><span class="s">(</span><span class="i">$NumOfSetBits</span><span class="cm">,</span> <span class="i">$BitDensity</span><span class="s">)</span><span class="sc">;</span>
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1226 1213 <span class="i">$NumOfSetBits</span> = <span class="i">$This</span>-&gt;{<span class="w">FingerprintsBitVector</span>}<span class="i">-&gt;GetNumOfSetBits</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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1227 1214 <span class="i">$BitDensity</span> = <span class="i">$This</span>-&gt;{<span class="w">FingerprintsBitVector</span>}<span class="i">-&gt;GetFingerprintsBitDensity</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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1228 1215 <span class="i">$ExtendedConnectivityFingerprintsString</span> .= <span class="q">&quot;; NumOfOnBits: $NumOfSetBits; BitDensity: $BitDensity&quot;</span><span class="sc">;</span>
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1229 1216
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1230 1217 <span class="i">$ExtendedConnectivityFingerprintsString</span> .= <span class="q">&quot;; FingerprintsBitVector: &lt; $This-&gt;{FingerprintsBitVector} &gt;&quot;</span><span class="sc">;</span>
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1231 1218 <span class="s">}</span>
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1232 1219 <span class="k">else</span> <span class="s">{</span>
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1233 1220 <span class="c"># Number of identifiers...</span>
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1234 1221 <span class="i">$ExtendedConnectivityFingerprintsString</span> .= <span class="q">&quot;; NumOfIdentifiers: &quot;</span> . <span class="i">$This</span>-&gt;{<span class="w">FingerprintsVector</span>}<span class="i">-&gt;GetNumOfValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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1235 1222
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1236 1223 <span class="c"># FingerprintsVector...</span>
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1237 1224 <span class="i">$ExtendedConnectivityFingerprintsString</span> .= <span class="q">&quot;; FingerprintsVector: &lt; $This-&gt;{FingerprintsVector} &gt;&quot;</span><span class="sc">;</span>
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1238 1225 <span class="s">}</span>
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1239 1226
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1240 1227 <span class="k">return</span> <span class="i">$ExtendedConnectivityFingerprintsString</span><span class="sc">;</span>
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1241 1228 <span class="s">}</span>
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1242 1229
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1243 <a name="EOF-"></a></pre>
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1244 <p>&nbsp;</p>
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1245 <br />
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1246 <center>
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1247 <img src="../../../images/h2o2.png">
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1248 </center>
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1249 </body>
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1250 </html>