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1 <html>
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2 <head>
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3 <title>MayaChemTools:Code:Fingerprints::PathLengthFingerprints.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::PathLengthFingerprints-"></a> 1 <span class="k">package </span><span class="i">Fingerprints::PathLengthFingerprints</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: PathLengthFingerprints.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::DREIDINGAtomTypes</span><span class="sc">;</span>
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51 38 <span class="k">use</span> <span class="w">AtomTypes::EStateAtomTypes</span><span class="sc">;</span>
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52 39 <span class="k">use</span> <span class="w">AtomTypes::FunctionalClassAtomTypes</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;StringifyPathLengthFingerprints&#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">$This</span><span class="i">-&gt;_InitializePathLengthFingerprints</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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82 69
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83 70 <span class="i">$This</span><span class="i">-&gt;_InitializePathLengthFingerprintsProperties</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">$This</span><span class="sc">;</span>
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86 73 <span class="s">}</span>
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87 74
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88 75 <span class="c"># Initialize object data...</span>
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89 76 <span class="c">#</span>
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90 <a name="_InitializePathLengthFingerprints-"></a> 77 <span class="k">sub </span><span class="m">_InitializePathLengthFingerprints</span> <span class="s">{</span>
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91 78 <span class="k">my</span><span class="s">(</span><span class="i">$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"># PathLengthBits - A bit vector indicating presence/absence of atom paths</span>
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96 83 <span class="c"># PathLengthCount - A vector containing count of atom paths</span>
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97 84 <span class="c">#</span>
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98 85 <span class="i">$This</span>-&gt;{<span class="w">Type</span>} = <span class="q">&#39;&#39;</span><span class="sc">;</span>
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99 86
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100 87 <span class="c"># Type of vector: FingerprintsBitVector or FingerprintsVector</span>
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101 88 <span class="i">$This</span>-&gt;{<span class="w">VectorType</span>} = <span class="q">&#39;&#39;</span><span class="sc">;</span>
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102 89
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103 90 <span class="c"># Set default mininum, maximum, and default size. Although any arbitrary size can</span>
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104 91 <span class="c"># be specified, bit vector used to store bits work on a vector size which is</span>
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105 92 <span class="c"># power of 2 and additonal bits are automatically added and cleared.</span>
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106 93 <span class="c">#</span>
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107 94 <span class="i">$This</span>-&gt;{<span class="w">Size</span>} = <span class="n">1024</span><span class="sc">;</span>
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108 95
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109 96 <span class="i">$This</span>-&gt;{<span class="w">MinSize</span>} = <span class="n">32</span><span class="sc">;</span>
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110 97 <span class="i">$This</span>-&gt;{<span class="w">MaxSize</span>} = <span class="n">2</span>**<span class="n">32</span><span class="sc">;</span>
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111 98
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112 99 <span class="c"># Minimum and maximum path lengths to use for fingerprints generation...</span>
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113 100 <span class="i">$This</span>-&gt;{<span class="w">MinLength</span>} = <span class="n">1</span><span class="sc">;</span>
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114 101 <span class="i">$This</span>-&gt;{<span class="w">MaxLength</span>} = <span class="n">8</span><span class="sc">;</span>
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115 102
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116 103 <span class="c"># Numner of bits to set for each atom path for FingerprintsBitVector...</span>
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117 104 <span class="i">$This</span>-&gt;{<span class="w">NumOfBitsToSetPerPath</span>} = <span class="n">1</span><span class="sc">;</span>
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118 105
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119 106 <span class="c"># Atom identifier type to use for path atoms during fingerprints generation...</span>
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120 107 <span class="c">#</span>
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121 108 <span class="c"># Currently supported values are: AtomicInvariantsAtomTypes, DREIDINGAtomTypes,</span>
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122 109 <span class="c"># EStateAtomTypes, FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes,</span>
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123 110 <span class="c"># SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes</span>
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124 111 <span class="c">#</span>
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125 112 <span class="i">$This</span>-&gt;{<span class="w">AtomIdentifierType</span>} = <span class="q">&#39;&#39;</span><span class="sc">;</span>
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126 113
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127 114 <span class="c"># Atom types assigned to atoms...</span>
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128 115 <span class="i">%</span>{<span class="i">$This</span>-&gt;{<span class="w">AssignedAtomTypes</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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129 116
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130 117 <span class="c"># For molecules containing rings, atom paths starting from each atom can be traversed in four</span>
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131 118 <span class="c"># different ways:</span>
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132 119 <span class="c">#</span>
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133 120 <span class="c"># . Atom paths without any rings and sharing of bonds in traversed paths.</span>
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134 121 <span class="c"># . Atom paths containing rings and without any sharing of bonds in traversed paths</span>
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135 122 <span class="c"># . All possible atom paths without any rings and sharing of bonds in traversed paths</span>
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136 123 <span class="c"># . All possible atom paths containing rings and with sharing of bonds in traversed paths.</span>
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137 124 <span class="c">#</span>
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138 125 <span class="c"># Atom path traversal is terminated at the last ring atom. For molecules containing no rings,</span>
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139 126 <span class="c"># first two and last two types described above are equivalent.</span>
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140 127 <span class="c">#</span>
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141 128 <span class="c"># AllowSharedBonds and AllowRings variables allow generation of differen types of paths</span>
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142 129 <span class="c"># to be used for fingerprints generation.</span>
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143 130 <span class="c">#</span>
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144 131 <span class="c"># In addition to atom symbols, bond symbols are also used to generate a string</span>
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145 132 <span class="c"># for atom paths. These atom paths strings are hased to a 32 bit integer key which</span>
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146 133 <span class="c"># in turn is used as a seed for a random number generation in range of 1 to fingerprint</span>
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147 134 <span class="c"># size for setting corresponding bit in bit vector.</span>
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148 135 <span class="c">#</span>
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149 136 <span class="c"># UseBondSymbols variable allow generation of atom path strings and consequently fingerprints.</span>
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150 137 <span class="c">#</span>
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151 138 <span class="c"># Combination of AllowSharedBonds, AllowRings, and UseBondSymbols allow generation of</span>
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152 139 <span class="c"># 8 different types of path length fingerprints:</span>
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153 140 <span class="c">#</span>
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154 141 <span class="c"># AllowSharedBonds AllowRings UseBondSymbols PathLengthFingerprintsType</span>
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155 142 <span class="c">#</span>
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156 143 <span class="c"># No No Yes AtomPathsNoCyclesWithBondSymbols</span>
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157 144 <span class="c"># No Yes Yes AtomPathsWithCyclesWithBondSymbols</span>
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158 145 <span class="c">#</span>
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159 146 <span class="c"># Yes No Yes AllAtomPathsNoCyclesWithBondSymbols</span>
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160 147 <span class="c"># Yes Yes Yes AllAtomPathsWithCyclesWithBondSymbols [ DEFAULT ]</span>
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161 148 <span class="c">#</span>
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162 149 <span class="c"># No No No AtomPathsNoCyclesNoBondSymbols</span>
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163 150 <span class="c"># No Yes No AtomPathsWithCyclesNoBondSymbols</span>
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164 151 <span class="c">#</span>
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165 152 <span class="c"># Yes No No AllAtomPathsNoCyclesNoBondSymbols</span>
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166 153 <span class="c"># Yes Yes No AllAtomPathsWithCyclesNoWithBondSymbols</span>
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167 154 <span class="c">#</span>
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168 155 <span class="c">#</span>
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169 156
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170 157 <span class="c"># By default, atom paths starting from atoms are allowed to share bonds already traversed...</span>
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171 158 <span class="i">$This</span>-&gt;{<span class="w">AllowSharedBonds</span>} = <span class="n">1</span><span class="sc">;</span>
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172 159
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173 160 <span class="c"># By default rings are included in paths...</span>
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174 161 <span class="i">$This</span>-&gt;{<span class="w">AllowRings</span>} = <span class="n">1</span><span class="sc">;</span>
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175 162
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176 163 <span class="c"># By default bond symbols are included in atom path strings...</span>
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177 164 <span class="i">$This</span>-&gt;{<span class="w">UseBondSymbols</span>} = <span class="n">1</span><span class="sc">;</span>
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178 165
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179 166 <span class="c"># By default only structurally unique atom paths are used for generation</span>
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180 167 <span class="c"># atom path strings...</span>
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181 168 <span class="i">$This</span>-&gt;{<span class="w">UseUniquePaths</span>} = <span class="n">1</span><span class="sc">;</span>
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182 169
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183 170 <span class="c"># Random number generator to use during generation of fingerprints bit-vector</span>
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184 171 <span class="c"># string: Perl CORE::rand or MayaChemTools MathUtil::random function.</span>
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185 172 <span class="c">#</span>
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186 173 <span class="c"># The random number generator implemented in MayaChemTools is a variant of</span>
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187 174 <span class="c"># linear congruential generator (LCG) as described by Miller et al. [ Ref 120 ].</span>
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188 175 <span class="c"># It is also referred to as Lehmer random number generator or Park-Miller</span>
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189 176 <span class="c"># random number generator.</span>
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190 177 <span class="c">#</span>
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191 178 <span class="c"># Unlike Perl&#39;s core random number generator function rand, the random number</span>
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192 179 <span class="c"># generator implemented in MayaChemTools, MathUtil::random, generates consistent</span>
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193 180 <span class="c"># random values across different platformsfor a specific random seed and leads</span>
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194 181 <span class="c"># to generation of portable fingerprints bit-vector strings.</span>
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195 182 <span class="c">#</span>
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196 183 <span class="i">$This</span>-&gt;{<span class="w">UsePerlCoreRandom</span>} = <span class="n">1</span><span class="sc">;</span>
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197 184
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198 185 <span class="c"># Bond symbols to use during generation of atom path strings...</span>
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199 186 <span class="i">%</span>{<span class="i">$This</span>-&gt;{<span class="w">BondOrderToSymbol</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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200 187 <span class="i">%</span>{<span class="i">$This</span>-&gt;{<span class="w">BondOrderToSymbol</span>}} = <span class="s">(</span><span class="q">&#39;1&#39;</span> <span class="cm">=&gt;</span> <span class="q">&#39;&#39;</span><span class="cm">,</span> <span class="q">&#39;1.5&#39;</span> <span class="cm">=&gt;</span> <span class="q">&#39;:&#39;</span><span class="cm">,</span> <span class="q">&#39;2&#39;</span> <span class="cm">=&gt;</span> <span class="q">&#39;=&#39;</span><span class="cm">,</span> <span class="q">&#39;3&#39;</span> <span class="cm">=&gt;</span> <span class="q">&#39;#&#39;</span><span class="s">)</span><span class="sc">;</span>
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201 188
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202 189 <span class="c"># BondSymbols map to use for bonded atom IDs to use during atom path strings...</span>
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203 190 <span class="i">%</span>{<span class="i">$This</span>-&gt;{<span class="w">BondSymbols</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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204 191
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205 192 <span class="c"># Path atom IDs to remove duplicate paths...</span>
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206 193 <span class="i">%</span>{<span class="i">$This</span>-&gt;{<span class="w">UniqueLinearAtomPathsIDs</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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207 194 <span class="i">%</span>{<span class="i">$This</span>-&gt;{<span class="w">UniqueCyclicAtomPathsIDs</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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208 195
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209 196 <span class="c"># Reference to all the atom paths upto specified path length...</span>
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210 197 <span class="i">$This</span>-&gt;{<span class="w">AtomPathsRef</span>} = <span class="q">&#39;&#39;</span><span class="sc">;</span>
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211 198
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212 199 <span class="c"># Atom paths strings created using specified atom types and bond symbols...</span>
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213 200 <span class="i">%</span>{<span class="i">$This</span>-&gt;{<span class="w">AtomPathsStrings</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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214 201 <span class="s">}</span>
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215 202
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216 203 <span class="c"># Initialize class ...</span>
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217 <a name="_InitializeClass-"></a> 204 <span class="k">sub </span><span class="m">_InitializeClass</span> <span class="s">{</span>
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218 205 <span class="c">#Class name...</span>
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219 206 <span class="i">$ClassName</span> = <span class="w">__PACKAGE__</span><span class="sc">;</span>
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220 207 <span class="s">}</span>
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221 208
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222 209 <span class="c"># Initialize object properties....</span>
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223 <a name="_InitializePathLengthFingerprintsProperties-"></a> 210 <span class="k">sub </span><span class="m">_InitializePathLengthFingerprintsProperties</span> <span class="s">{</span>
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224 211 <span class="k">my</span><span class="s">(</span><span class="i">$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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225 212
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226 213 <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">$MethodName</span><span class="s">)</span><span class="sc">;</span>
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227 214 <span class="k">while</span> <span class="s">(</span><span class="s">(</span><span class="i">$Name</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="k">each</span> <span class="i">%NamesAndValues</span><span class="s">)</span> <span class="s">{</span>
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228 215 <span class="i">$MethodName</span> = <span class="q">&quot;Set${Name}&quot;</span><span class="sc">;</span>
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229 216 <span class="i">$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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230 217 <span class="s">}</span>
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231 218
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232 219 <span class="c"># Make sure molecule object was specified...</span>
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233 220 <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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234 221 <span class="w">croak</span> <span class="q">&quot;Error: ${ClassName}-&gt;New: Object can&#39;t be instantiated without specifying molecule...&quot;</span><span class="sc">;</span>
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235 222 <span class="s">}</span>
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236 223
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237 224 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$NamesAndValues</span>{<span class="w">Type</span>}<span class="s">)</span> <span class="s">{</span>
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238 225 <span class="w">croak</span> <span class="q">&quot;Error: ${ClassName}-&gt;New: Object can&#39;t be instantiated without specifying Type...&quot;</span><span class="sc">;</span>
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239 226 <span class="s">}</span>
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240 227
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241 228 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$NamesAndValues</span>{<span class="w">AtomIdentifierType</span>}<span class="s">)</span> <span class="s">{</span>
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242 229 <span class="w">croak</span> <span class="q">&quot;Error: ${ClassName}-&gt;New: Object can&#39;t be instantiated without specifying AtomIdentifierType...&quot;</span><span class="sc">;</span>
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243 230 <span class="s">}</span>
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244 231
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245 232 <span class="c"># Make sure it&#39;s power of 2...</span>
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246 233 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$NamesAndValues</span>{<span class="w">Size</span>}<span class="s">)</span> <span class="s">{</span>
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247 234 <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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248 235 <span class="w">croak</span> <span class="q">&quot;Error: ${ClassName}-&gt;New: Specified size value, $NamesAndValues{Size}, must be power of 2...&quot;</span><span class="sc">;</span>
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249 236 <span class="s">}</span>
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250 237 <span class="s">}</span>
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251 238
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252 239 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">Type</span>} =~ <span class="q">/^PathLengthBits$/i</span><span class="s">)</span> <span class="s">{</span>
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253 240 <span class="i">$This</span><span class="i">-&gt;_InitializePathLengthBits</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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254 241 <span class="s">}</span>
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255 242 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">Type</span>} =~ <span class="q">/^PathLengthCount$/i</span><span class="s">)</span> <span class="s">{</span>
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256 243 <span class="i">$This</span><span class="i">-&gt;_InitializePathLengthCount</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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257 244 <span class="s">}</span>
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258 245 <span class="k">else</span> <span class="s">{</span>
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259 246 <span class="w">croak</span> <span class="q">&quot;Error: ${ClassName}-&gt;_InitializePathLengthFingerprintsProperties: Unknown PathLength type: $This-&gt;{Type}; Supported PathLength type : PathLengthBits or PathLengthCount......&quot;</span><span class="sc">;</span>
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260 247 <span class="s">}</span>
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261 248
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262 249 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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263 250 <span class="s">}</span>
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264 251
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265 252 <span class="c"># Initialize PathLength bits...</span>
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266 253 <span class="c">#</span>
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267 <a name="_InitializePathLengthBits-"></a> 254 <span class="k">sub </span><span class="m">_InitializePathLengthBits</span> <span class="s">{</span>
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268 255 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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269 256
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270 257 <span class="c"># Vector type...</span>
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271 258 <span class="i">$This</span>-&gt;{<span class="w">VectorType</span>} = <span class="q">&#39;FingerprintsBitVector&#39;</span><span class="sc">;</span>
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272 259
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273 260 <span class="i">$This</span><span class="i">-&gt;_InitializeFingerprintsBitVector</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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274 261
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275 262 <span class="k">return</span> <span class="i">$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"># Initialize PathLength key count...</span>
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279 266 <span class="c">#</span>
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280 <a name="_InitializePathLengthCount-"></a> 267 <span class="k">sub </span><span class="m">_InitializePathLengthCount</span> <span class="s">{</span>
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281 268 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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282 269
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283 270 <span class="c"># Vector type and type of values...</span>
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284 271 <span class="i">$This</span>-&gt;{<span class="w">VectorType</span>} = <span class="q">&#39;FingerprintsVector&#39;</span><span class="sc">;</span>
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285 272 <span class="i">$This</span>-&gt;{<span class="w">FingerprintsVectorType</span>} = <span class="q">&#39;NumericalValues&#39;</span><span class="sc">;</span>
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286 273
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287 274 <span class="i">$This</span><span class="i">-&gt;_InitializeFingerprintsVector</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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288 275
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289 276 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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290 277 <span class="s">}</span>
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291 278
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292 279 <span class="c"># Set type...</span>
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293 280 <span class="c">#</span>
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294 <a name="SetType-"></a> 281 <span class="k">sub </span><span class="m">SetType</span> <span class="s">{</span>
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295 282 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Type</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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296 283
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297 284 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">Type</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: ${ClassName}-&gt;SetType: Can&#39;t change type: It&#39;s already set...&quot;</span><span class="sc">;</span>
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299 286 <span class="s">}</span>
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300 287
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301 288 <span class="k">if</span> <span class="s">(</span><span class="i">$Type</span> =~ <span class="q">/^PathLengthBits$/i</span><span class="s">)</span> <span class="s">{</span>
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302 289 <span class="i">$This</span>-&gt;{<span class="w">Type</span>} = <span class="q">&#39;PathLengthBits&#39;</span><span class="sc">;</span><span class="sc">;</span>
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303 290 <span class="s">}</span>
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304 291 <span class="k">elsif</span> <span class="s">(</span><span class="i">$Type</span> =~ <span class="q">/^PathLengthCount$/i</span><span class="s">)</span> <span class="s">{</span>
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305 292 <span class="i">$This</span>-&gt;{<span class="w">Type</span>} = <span class="q">&#39;PathLengthCount&#39;</span><span class="sc">;</span><span class="sc">;</span>
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306 293 <span class="s">}</span>
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307 294 <span class="k">else</span> <span class="s">{</span>
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308 295 <span class="w">croak</span> <span class="q">&quot;Error: ${ClassName}-&gt;SetType: Unknown PathLength keys: $Type; Supported PathLength types: PathLengthBits or PathLengthCount...&quot;</span><span class="sc">;</span>
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309 296 <span class="s">}</span>
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310 297 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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311 298 <span class="s">}</span>
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312 299
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313 300 <span class="c"># Disable vector type change...</span>
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314 301 <span class="c">#</span>
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315 <a name="SetVectorType-"></a> 302 <span class="k">sub </span><span class="m">SetVectorType</span> <span class="s">{</span>
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316 303 <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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317 304
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318 305 <span class="w">croak</span> <span class="q">&quot;Error: ${ClassName}-&gt;SetVectorType: Can&#39;t change vector type...&quot;</span><span class="sc">;</span>
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319 306
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320 307 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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321 308 <span class="s">}</span>
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322 309
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323 310 <span class="c"># Disable vector type change...</span>
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324 311 <span class="c">#</span>
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325 <a name="SetFingerprintsVectorType-"></a> 312 <span class="k">sub </span><span class="m">SetFingerprintsVectorType</span> <span class="s">{</span>
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326 313 <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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327 314
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328 315 <span class="w">croak</span> <span class="q">&quot;Error: ${ClassName}-&gt;SetFingerprintsVectorType: Can&#39;t change fingerprints vector type...&quot;</span><span class="sc">;</span>
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329 316
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330 317 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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331 318 <span class="s">}</span>
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332 319
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333 320 <span class="c"># Set atom identifier type to use for path length atom identifiers...</span>
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334 321 <span class="c">#</span>
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335 <a name="SetAtomIdentifierType-"></a> 322 <span class="k">sub </span><span class="m">SetAtomIdentifierType</span> <span class="s">{</span>
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336 323 <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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337 324
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338 325 <span class="k">if</span> <span class="s">(</span><span class="i">$IdentifierType</span> !~ <span class="q">/^(AtomicInvariantsAtomTypes|DREIDINGAtomTypes|EStateAtomTypes|FunctionalClassAtomTypes|MMFF94AtomTypes|SLogPAtomTypes|SYBYLAtomTypes|TPSAAtomTypes|UFFAtomTypes)$/i</span><span class="s">)</span> <span class="s">{</span>
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339 326 <span class="w">croak</span> <span class="q">&quot;Error: ${ClassName}-&gt;SetAtomIdentifierType: Specified value, $IdentifierType, for AtomIdentifierType is not vaild. Supported types in current release of MayaChemTools: AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes, and UFFAtomTypes.&quot;</span><span class="sc">;</span>
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340 327 <span class="s">}</span>
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341 328
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342 329 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">AtomIdentifierType</span>}<span class="s">)</span> <span class="s">{</span>
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343 330 <span class="w">croak</span> <span class="q">&quot;Error: ${ClassName}-&gt;SetAtomIdentifierType: Can&#39;t change atom identifier type: It&#39;s already set...&quot;</span><span class="sc">;</span>
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344 331 <span class="s">}</span>
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345 332
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346 333 <span class="i">$This</span>-&gt;{<span class="w">AtomIdentifierType</span>} = <span class="i">$IdentifierType</span><span class="sc">;</span>
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347 334
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348 335 <span class="c"># Initialize atom identifier type information...</span>
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349 336 <span class="i">$This</span><span class="i">-&gt;_InitializeAtomIdentifierTypeInformation</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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350 337
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351 338 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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352 339 <span class="s">}</span>
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353 340
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354 341 <span class="c"># Set minimum path length...</span>
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355 342 <span class="c">#</span>
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356 <a name="SetMinLength-"></a> 343 <span class="k">sub </span><span class="m">SetMinLength</span> <span class="s">{</span>
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357 344 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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358 345
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359 346 <span class="k">if</span> <span class="s">(</span>!<span class="i">TextUtil::IsPositiveInteger</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
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360 347 <span class="w">croak</span> <span class="q">&quot;Error: ${ClassName}-&gt;SetMinLength: MinLength value, $Value, is not valid: It must be a positive integer...&quot;</span><span class="sc">;</span>
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361 348 <span class="s">}</span>
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362 349 <span class="i">$This</span>-&gt;{<span class="w">MinLength</span>} = <span class="i">$Value</span><span class="sc">;</span>
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363 350
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364 351 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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365 352 <span class="s">}</span>
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366 353
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367 354 <span class="c"># Set maximum path length...</span>
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368 355 <span class="c">#</span>
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369 <a name="SetMaxLength-"></a> 356 <span class="k">sub </span><span class="m">SetMaxLength</span> <span class="s">{</span>
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370 357 <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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371 358
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372 359 <span class="k">if</span> <span class="s">(</span>!<span class="i">TextUtil::IsPositiveInteger</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
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373 360 <span class="w">croak</span> <span class="q">&quot;Error: ${ClassName}-&gt;SetMaxLength: MaxLength value, $Value, is not valid: It must be a positive integer...&quot;</span><span class="sc">;</span>
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374 361 <span class="s">}</span>
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375 362 <span class="i">$This</span>-&gt;{<span class="w">MaxLength</span>} = <span class="i">$Value</span><span class="sc">;</span>
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376 363
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377 364 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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378 365 <span class="s">}</span>
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379 366
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380 367 <span class="c"># Set number of bits to set for each path...</span>
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381 368 <span class="c">#</span>
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382 <a name="SetNumOfBitsToSetPerPath-"></a> 369 <span class="k">sub </span><span class="m">SetNumOfBitsToSetPerPath</span> <span class="s">{</span>
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383 370 <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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384 371
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385 372 <span class="k">if</span> <span class="s">(</span>!<span class="i">TextUtil::IsPositiveInteger</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
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386 373 <span class="w">croak</span> <span class="q">&quot;Error: ${ClassName}-&gt;SetNumOfBitsToSetPerPath: NumOfBitsToSetPerPath value, $Value, is not valid: It must be a positive integer...&quot;</span><span class="sc">;</span>
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387 374 <span class="s">}</span>
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388 375 <span class="i">$This</span>-&gt;{<span class="w">NumOfBitsToSetPerPath</span>} = <span class="i">$Value</span><span class="sc">;</span>
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389 376
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390 377 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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391 378 <span class="s">}</span>
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392 379
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393 380 <span class="c"># Generate fingerprints description...</span>
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394 381 <span class="c">#</span>
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395 <a name="GetDescription-"></a> 382 <span class="k">sub </span><span class="m">GetDescription</span> <span class="s">{</span>
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396 383 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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397 384
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398 385 <span class="c"># Is description explicity set?</span>
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399 386 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$This</span>-&gt;{<span class="w">Description</span>}<span class="s">)</span> <span class="s">{</span>
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400 387 <span class="k">return</span> <span class="i">$This</span>-&gt;{<span class="w">Description</span>}<span class="sc">;</span>
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401 388 <span class="s">}</span>
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402 389
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403 390 <span class="c"># Generate fingerprints description...</span>
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404 391
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405 392 <span class="k">return</span> <span class="q">&quot;$This-&gt;{Type}:$This-&gt;{AtomIdentifierType}:MinLength$This-&gt;{MinLength}:MaxLength$This-&gt;{MaxLength}&quot;</span><span class="sc">;</span>
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406 393 <span class="s">}</span>
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407 394
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408 395 <span class="c"># Generate path length fingerprints...</span>
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409 396 <span class="c">#</span>
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410 <a name="GenerateFingerprints-"></a> 397 <span class="k">sub </span><span class="m">GenerateFingerprints</span> <span class="s">{</span>
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411 398 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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412 399
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413 400 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">MinLength</span>} &gt; <span class="i">$This</span>-&gt;{<span class="w">MaxLength</span>}<span class="s">)</span> <span class="s">{</span>
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414 401 <span class="w">croak</span> <span class="q">&quot;Error: ${ClassName}-&gt;GenerateFingerprints: No fingerpritns generated: MinLength, $This-&gt;{MinLength}, must be &lt;= MaxLength, $This-&gt;{MaxLength}...&quot;</span><span class="sc">;</span>
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415 402 <span class="s">}</span>
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416 403
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417 404 <span class="c"># Cache appropriate molecule data...</span>
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418 405 <span class="i">$This</span><span class="i">-&gt;_SetupMoleculeDataCache</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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419 406
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420 407 <span class="c"># Assign atom types to all atoms...</span>
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421 408 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">-&gt;_AssignAtomTypes</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
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422 409 <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 $This-&gt;{AtomIdentifierType} to all atoms...&quot;</span><span class="sc">;</span>
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423 410 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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424 411 <span class="s">}</span>
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425 412
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426 413 <span class="c"># Setup bond symbol map...</span>
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427 414 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">UseBondSymbols</span>}<span class="s">)</span> <span class="s">{</span>
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428 415 <span class="i">$This</span><span class="i">-&gt;_InitializeBondSymbols</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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429 416 <span class="s">}</span>
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430 417
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431 418 <span class="c"># Generate appropriate atom paths...</span>
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432 419 <span class="i">$This</span><span class="i">-&gt;_GenerateAtomPathsUpToMaxLength</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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433 420
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434 421 <span class="c"># Initialize atom path strings...</span>
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435 422 <span class="i">$This</span><span class="i">-&gt;_InitializeAtomPathsStrings</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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436 423
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437 424 <span class="c"># Generate appropriate atom path strings for unique atom paths...</span>
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438 425 <span class="i">$This</span><span class="i">-&gt;_GenerateAtomPathsStrings</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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439 426
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440 427 <span class="c"># Set final fingerprints...</span>
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441 428 <span class="i">$This</span><span class="i">-&gt;_SetFinalFingerprints</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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442 429
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443 430 <span class="c"># Clear cached molecule data...</span>
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444 431 <span class="i">$This</span><span class="i">-&gt;_ClearMoleculeDataCache</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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445 432
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446 433 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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447 434 <span class="s">}</span>
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448 435
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449 436 <span class="c"># Assign appropriate atom types to all atoms...</span>
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450 437 <span class="c">#</span>
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451 <a name="_AssignAtomTypes-"></a> 438 <span class="k">sub </span><span class="m">_AssignAtomTypes</span> <span class="s">{</span>
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452 439 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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453 440 <span class="k">my</span><span class="s">(</span><span class="i">$SpecifiedAtomTypes</span><span class="cm">,</span> <span class="i">$Atom</span><span class="cm">,</span> <span class="i">$AtomID</span><span class="cm">,</span> <span class="i">$IgnoreHydrogens</span><span class="s">)</span><span class="sc">;</span>
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454 441
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455 442 <span class="i">%</span>{<span class="i">$This</span>-&gt;{<span class="w">AssignedAtomTypes</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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456 443 <span class="i">$IgnoreHydrogens</span> = <span class="n">0</span><span class="sc">;</span>
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457 444
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458 445 <span class="i">$SpecifiedAtomTypes</span> = <span class="k">undef</span><span class="sc">;</span>
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459 446
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460 447 <span class="j">IDENTIFIERTYPE:</span> <span class="s">{</span>
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461 448 <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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462 449 <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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463 450 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span>
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464 451 <span class="s">}</span>
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465 452
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466 453 <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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467 454 <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">$IgnoreHydrogens</span><span class="s">)</span><span class="sc">;</span>
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468 455 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span>
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469 456 <span class="s">}</span>
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470 457
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471 458 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^EStateAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span>
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472 459 <span class="i">$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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473 460 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span>
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474 461 <span class="s">}</span>
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475 462
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476 463 <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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477 464 <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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478 465 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span>
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479 466 <span class="s">}</span>
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480 467
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481 468 <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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482 469 <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">$IgnoreHydrogens</span><span class="s">)</span><span class="sc">;</span>
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483 470 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span>
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484 471 <span class="s">}</span>
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485 472
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486 473 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^SLogPAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span>
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487 474 <span class="i">$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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488 475 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span>
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489 476 <span class="s">}</span>
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490 477 <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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491 478 <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">$IgnoreHydrogens</span><span class="s">)</span><span class="sc">;</span>
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492 479 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span>
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493 480 <span class="s">}</span>
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494 481
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495 482 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^TPSAAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span>
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496 483 <span class="i">$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">$This</span>-&gt;{<span class="w">Molecule</span>}<span class="cm">,</span> <span class="q">&#39;IgnorePhosphorus&#39;</span> <span class="cm">=&gt;</span> <span class="n">0</span><span class="cm">,</span> <span class="q">&#39;IgnoreSulfur&#39;</span> <span class="cm">=&gt;</span> <span class="n">0</span><span class="s">)</span><span class="sc">;</span>
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497 484 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span>
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498 485 <span class="s">}</span>
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499 486
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500 487 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^UFFAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span>
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501 488 <span class="i">$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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502 489 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span>
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503 490 <span class="s">}</span>
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504 491
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505 492 <span class="w">croak</span> <span class="q">&quot;Error: ${ClassName}-&gt;_AssignAtomTypes: Unknown atom indentifier type $This-&gt;{AtomIdentifierType}...&quot;</span><span class="sc">;</span>
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506 493 <span class="s">}</span>
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507 494
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508 495 <span class="c"># Assign atom types...</span>
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509 496 <span class="i">$SpecifiedAtomTypes</span><span class="i">-&gt;AssignAtomTypes</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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510 497
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511 498 <span class="c"># Make sure atom types assignment is successful...</span>
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512 499 <span class="k">if</span> <span class="s">(</span>!<span class="i">$SpecifiedAtomTypes</span><span class="i">-&gt;IsAtomTypesAssignmentSuccessful</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
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513 500 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
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514 501 <span class="s">}</span>
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515 502
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516 503 <span class="c"># Collect assigned atom types...</span>
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517 504 <span class="j">ATOM:</span> <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$This</span>-&gt;{<span class="w">Atoms</span>}}<span class="s">)</span> <span class="s">{</span>
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518 505 <span class="i">$AtomID</span> = <span class="i">$Atom</span><span class="i">-&gt;GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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519 506 <span class="i">$This</span>-&gt;{<span class="w">AssignedAtomTypes</span>}{<span class="i">$AtomID</span>} = <span class="i">$SpecifiedAtomTypes</span><span class="i">-&gt;GetAtomType</span><span class="s">(</span><span class="i">$Atom</span><span class="s">)</span><span class="sc">;</span>
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520 507 <span class="s">}</span>
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521 508
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522 509 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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523 510 <span class="s">}</span>
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524 511
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525 512 <span class="c"># Setup bond symbol map for atoms to speed up generation of path length identifiers</span>
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526 513 <span class="c"># during fingerprints generation...</span>
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527 514 <span class="c">#</span>
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528 <a name="_InitializeBondSymbols-"></a> 515 <span class="k">sub </span><span class="m">_InitializeBondSymbols</span> <span class="s">{</span>
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529 516 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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530 517 <span class="k">my</span><span class="s">(</span><span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="cm">,</span> <span class="i">$AtomID1</span><span class="cm">,</span> <span class="i">$AtomID2</span><span class="cm">,</span> <span class="i">$Bond</span><span class="cm">,</span> <span class="i">$BondSymbol</span><span class="cm">,</span> <span class="i">$BondOrder</span><span class="s">)</span><span class="sc">;</span>
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531 518
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532 519 <span class="i">%</span>{<span class="i">$This</span>-&gt;{<span class="w">BondSymbols</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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diff changeset
533 520
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534 521 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span>-&gt;{<span class="w">UseBondSymbols</span>}<span class="s">)</span> <span class="s">{</span>
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diff changeset
535 522 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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deepakjadmin
parents:
diff changeset
536 523 <span class="s">}</span>
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diff changeset
537 524
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538 525 <span class="k">for</span> <span class="i">$Bond</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">Molecule</span>}<span class="i">-&gt;GetBonds</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
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parents:
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539 526 <span class="i">$BondOrder</span> = <span class="i">$Bond</span><span class="i">-&gt;GetBondOrder</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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parents:
diff changeset
540 527 <span class="i">$BondSymbol</span> = <span class="i">$Bond</span><span class="i">-&gt;IsAromatic</span><span class="s">(</span><span class="s">)</span> ? <span class="q">&#39;:&#39;</span> <span class="co">:</span> <span class="s">(</span><span class="k">exists</span><span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">BondOrderToSymbol</span>}{<span class="i">$BondOrder</span>}<span class="s">)</span> ? <span class="i">$This</span>-&gt;{<span class="w">BondOrderToSymbol</span>}{<span class="i">$BondOrder</span>} <span class="co">:</span> <span class="i">$BondOrder</span><span class="s">)</span><span class="sc">;</span>
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parents:
diff changeset
541 528 <span class="s">(</span><span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">)</span> = <span class="i">$Bond</span><span class="i">-&gt;GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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parents:
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542 529 <span class="i">$AtomID1</span> = <span class="i">$Atom1</span><span class="i">-&gt;GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> <span class="i">$AtomID2</span> = <span class="i">$Atom2</span><span class="i">-&gt;GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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parents:
diff changeset
543 530 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomID1</span> &gt; <span class="i">$AtomID2</span><span class="s">)</span> <span class="s">{</span>
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parents:
diff changeset
544 531 <span class="s">(</span><span class="i">$AtomID1</span><span class="cm">,</span> <span class="i">$AtomID2</span><span class="s">)</span> = <span class="s">(</span><span class="i">$AtomID2</span><span class="cm">,</span> <span class="i">$AtomID1</span><span class="s">)</span><span class="sc">;</span>
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parents:
diff changeset
545 532 <span class="s">}</span>
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parents:
diff changeset
546 533
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parents:
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547 534 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$This</span>-&gt;{<span class="w">BondSymbols</span>}{<span class="i">$AtomID1</span>}<span class="s">)</span> <span class="s">{</span>
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parents:
diff changeset
548 535 <span class="i">%</span>{<span class="i">$This</span>-&gt;{<span class="w">BondSymbols</span>}{<span class="i">$AtomID1</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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parents:
diff changeset
549 536 <span class="s">}</span>
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parents:
diff changeset
550 537 <span class="i">$This</span>-&gt;{<span class="w">BondSymbols</span>}{<span class="i">$AtomID1</span>}{<span class="i">$AtomID2</span>} = <span class="i">$BondSymbol</span><span class="sc">;</span>
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deepakjadmin
parents:
diff changeset
551 538 <span class="s">}</span>
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parents:
diff changeset
552 539 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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parents:
diff changeset
553 540 <span class="s">}</span>
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deepakjadmin
parents:
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554 541
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parents:
diff changeset
555 542 <span class="c"># Get appropriate atom paths with length up to MaxLength...</span>
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parents:
diff changeset
556 543 <span class="c">#</span>
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parents:
diff changeset
557 <a name="_GenerateAtomPathsUpToMaxLength-"></a> 544 <span class="k">sub </span><span class="m">_GenerateAtomPathsUpToMaxLength</span> <span class="s">{</span>
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parents:
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558 545 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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parents:
diff changeset
559 546 <span class="k">my</span><span class="s">(</span><span class="i">$PathLength</span><span class="cm">,</span> <span class="i">$AllowRings</span><span class="cm">,</span> <span class="i">$Molecule</span><span class="cm">,</span> <span class="i">$AtomPathsRef</span><span class="s">)</span><span class="sc">;</span>
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parents:
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560 547
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parents:
diff changeset
561 548 <span class="i">$PathLength</span> = <span class="i">$This</span>-&gt;{<span class="w">MaxLength</span>}<span class="sc">;</span>
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deepakjadmin
parents:
diff changeset
562 549 <span class="i">$AllowRings</span> = <span class="i">$This</span>-&gt;{<span class="w">AllowRings</span>}<span class="sc">;</span>
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parents:
diff changeset
563 550 <span class="i">$Molecule</span> = <span class="i">$This</span>-&gt;{<span class="w">Molecule</span>}<span class="sc">;</span>
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parents:
diff changeset
564 551
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parents:
diff changeset
565 552 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">AllowSharedBonds</span>}<span class="s">)</span> <span class="s">{</span>
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parents:
diff changeset
566 553 <span class="i">$AtomPathsRef</span> = <span class="i">$Molecule</span><span class="i">-&gt;GetAllAtomPathsWithLengthUpto</span><span class="s">(</span><span class="i">$PathLength</span><span class="cm">,</span> <span class="i">$AllowRings</span><span class="s">)</span><span class="sc">;</span>
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deepakjadmin
parents:
diff changeset
567 554 <span class="s">}</span>
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deepakjadmin
parents:
diff changeset
568 555 <span class="k">else</span> <span class="s">{</span>
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deepakjadmin
parents:
diff changeset
569 556 <span class="i">$AtomPathsRef</span> = <span class="i">$Molecule</span><span class="i">-&gt;GetAtomPathsWithLengthUpto</span><span class="s">(</span><span class="i">$PathLength</span><span class="cm">,</span> <span class="i">$AllowRings</span><span class="s">)</span><span class="sc">;</span>
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deepakjadmin
parents:
diff changeset
570 557 <span class="s">}</span>
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parents:
diff changeset
571 558 <span class="i">$This</span>-&gt;{<span class="w">AtomPathsRef</span>} = <span class="i">$AtomPathsRef</span><span class="sc">;</span>
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deepakjadmin
parents:
diff changeset
572 559
73ae111cf86f Uploaded
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parents:
diff changeset
573 560 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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deepakjadmin
parents:
diff changeset
574 561 <span class="s">}</span>
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deepakjadmin
parents:
diff changeset
575 562
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
576 563 <span class="c"># Initialize atom paths strings at various pathlength levels...</span>
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deepakjadmin
parents:
diff changeset
577 564 <span class="c">#</span>
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deepakjadmin
parents:
diff changeset
578 <a name="_InitializeAtomPathsStrings-"></a> 565 <span class="k">sub </span><span class="m">_InitializeAtomPathsStrings</span> <span class="s">{</span>
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parents:
diff changeset
579 566 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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deepakjadmin
parents:
diff changeset
580 567 <span class="k">my</span><span class="s">(</span><span class="i">$PathLength</span><span class="s">)</span><span class="sc">;</span>
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parents:
diff changeset
581 568
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parents:
diff changeset
582 569 <span class="i">%</span>{<span class="i">$This</span>-&gt;{<span class="w">AtomPathsStrings</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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parents:
diff changeset
583 570
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parents:
diff changeset
584 571 <span class="k">for</span> <span class="i">$PathLength</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">MinLength</span>} .. <span class="i">$This</span>-&gt;{<span class="w">MaxLength</span>}<span class="s">)</span> <span class="s">{</span>
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deepakjadmin
parents:
diff changeset
585 572 <span class="i">%</span>{<span class="i">$This</span>-&gt;{<span class="w">AtomPathsStrings</span>}{<span class="i">$PathLength</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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parents:
diff changeset
586 573 <span class="s">}</span>
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deepakjadmin
parents:
diff changeset
587 574
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
588 575 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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deepakjadmin
parents:
diff changeset
589 576 <span class="s">}</span>
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deepakjadmin
parents:
diff changeset
590 577
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parents:
diff changeset
591 578 <span class="c"># Generate appropriate atom path strings for unique atom paths...</span>
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deepakjadmin
parents:
diff changeset
592 579 <span class="c">#</span>
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parents:
diff changeset
593 <a name="_GenerateAtomPathsStrings-"></a> 580 <span class="k">sub </span><span class="m">_GenerateAtomPathsStrings</span> <span class="s">{</span>
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parents:
diff changeset
594 581 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$PathAtomsRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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deepakjadmin
parents:
diff changeset
595 582 <span class="k">my</span><span class="s">(</span><span class="i">$PathLength</span><span class="cm">,</span> <span class="i">$MinPathLength</span><span class="cm">,</span> <span class="i">$UseUniquePaths</span><span class="s">)</span><span class="sc">;</span>
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parents:
diff changeset
596 583
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parents:
diff changeset
597 584 <span class="i">$MinPathLength</span> = <span class="i">$This</span>-&gt;{<span class="w">MinLength</span>}<span class="sc">;</span>
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parents:
diff changeset
598 585 <span class="i">$UseUniquePaths</span> = <span class="i">$This</span>-&gt;{<span class="w">UseUniquePaths</span>}<span class="sc">;</span>
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deepakjadmin
parents:
diff changeset
599 586
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parents:
diff changeset
600 587 <span class="j">PATHATOMS:</span> <span class="k">for</span> <span class="i">$PathAtomsRef</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$This</span>-&gt;{<span class="w">AtomPathsRef</span>}}<span class="s">)</span> <span class="s">{</span>
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parents:
diff changeset
601 588 <span class="i">$PathLength</span> = <span class="k">scalar</span> <span class="i">@</span>{<span class="i">$PathAtomsRef</span>}<span class="sc">;</span>
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parents:
diff changeset
602 589 <span class="k">if</span> <span class="s">(</span><span class="i">$PathLength</span> &lt; <span class="i">$MinPathLength</span><span class="s">)</span> <span class="s">{</span>
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parents:
diff changeset
603 590 <span class="k">next</span> <span class="j">PATHATOMS</span><span class="sc">;</span>
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deepakjadmin
parents:
diff changeset
604 591 <span class="s">}</span>
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parents:
diff changeset
605 592 <span class="k">if</span> <span class="s">(</span><span class="i">$UseUniquePaths</span><span class="s">)</span> <span class="s">{</span>
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deepakjadmin
parents:
diff changeset
606 593 <span class="i">$This</span><span class="i">-&gt;_GenerateAtomPathStringUsingUniquePath</span><span class="s">(</span><span class="i">$PathAtomsRef</span><span class="s">)</span><span class="sc">;</span>
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deepakjadmin
parents:
diff changeset
607 594 <span class="s">}</span>
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deepakjadmin
parents:
diff changeset
608 595 <span class="k">else</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
609 596 <span class="i">$This</span><span class="i">-&gt;_GenerateAtomPathString</span><span class="s">(</span><span class="i">$PathAtomsRef</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
610 597 <span class="s">}</span>
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deepakjadmin
parents:
diff changeset
611 598 <span class="s">}</span>
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deepakjadmin
parents:
diff changeset
612 599 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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parents:
diff changeset
613 600 <span class="s">}</span>
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parents:
diff changeset
614 601
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parents:
diff changeset
615 602 <span class="c"># Generate atom path string using unique path...</span>
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parents:
diff changeset
616 603 <span class="c">#</span>
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parents:
diff changeset
617 <a name="_GenerateAtomPathStringUsingUniquePath-"></a> 604 <span class="k">sub </span><span class="m">_GenerateAtomPathStringUsingUniquePath</span> <span class="s">{</span>
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diff changeset
618 605 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$PathAtomsRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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diff changeset
619 606
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diff changeset
620 607 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">AllowRings</span>} &amp;&amp; <span class="i">$This</span><span class="i">-&gt;_DoesAtomPathContainsCycle</span><span class="s">(</span><span class="i">$PathAtomsRef</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
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parents:
diff changeset
621 608 <span class="i">$This</span><span class="i">-&gt;_GenerateAtomPathStringUsingUniquePathContainingCycle</span><span class="s">(</span><span class="i">$PathAtomsRef</span><span class="s">)</span><span class="sc">;</span>
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parents:
diff changeset
622 609 <span class="s">}</span>
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diff changeset
623 610 <span class="k">else</span> <span class="s">{</span>
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diff changeset
624 611 <span class="i">$This</span><span class="i">-&gt;_GenerateAtomPathStringUsingUniqueLinearPath</span><span class="s">(</span><span class="i">$PathAtomsRef</span><span class="s">)</span><span class="sc">;</span>
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parents:
diff changeset
625 612 <span class="s">}</span>
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parents:
diff changeset
626 613 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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parents:
diff changeset
627 614 <span class="s">}</span>
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diff changeset
628 615
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parents:
diff changeset
629 616 <span class="c"># Generate atom path string for specified path containing no cycle...</span>
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parents:
diff changeset
630 617 <span class="c">#</span>
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diff changeset
631 <a name="_GenerateAtomPathStringUsingUniqueLinearPath-"></a> 618 <span class="k">sub </span><span class="m">_GenerateAtomPathStringUsingUniqueLinearPath</span> <span class="s">{</span>
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diff changeset
632 619 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$PathAtomsRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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diff changeset
633 620
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diff changeset
634 621 <span class="c"># Is it a unique linear atom path?</span>
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diff changeset
635 622 <span class="c">#</span>
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diff changeset
636 623 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">-&gt;_IsUniqueLinearAtomPath</span><span class="s">(</span><span class="i">$PathAtomsRef</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
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diff changeset
637 624 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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parents:
diff changeset
638 625 <span class="s">}</span>
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parents:
diff changeset
639 626 <span class="i">$This</span><span class="i">-&gt;_GenerateAtomPathString</span><span class="s">(</span><span class="i">$PathAtomsRef</span><span class="s">)</span><span class="sc">;</span>
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diff changeset
640 627
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diff changeset
641 628 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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parents:
diff changeset
642 629 <span class="s">}</span>
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diff changeset
643 630
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diff changeset
644 631 <span class="c"># Is it a structurally unique linear path?</span>
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diff changeset
645 632 <span class="c">#</span>
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diff changeset
646 633 <span class="c"># For a path to be structurally unique, all of its atom IDs must be diffferent from any</span>
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diff changeset
647 634 <span class="c"># earlier path atom IDs. In order to generate atom path atom ID invariant of the atom</span>
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parents:
diff changeset
648 635 <span class="c"># order in the molecule, atom IDs are sorted numerically before generating the path ID.</span>
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diff changeset
649 636 <span class="c">#</span>
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650 637 <span class="c"># Notes:</span>
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diff changeset
651 638 <span class="c"># . Atom path ID doesn&#39;t reflect the order of atoms in the atom path.</span>
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diff changeset
652 639 <span class="c">#</span>
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deepakjadmin
parents:
diff changeset
653 <a name="_IsUniqueLinearAtomPath-"></a> 640 <span class="k">sub </span><span class="m">_IsUniqueLinearAtomPath</span> <span class="s">{</span>
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parents:
diff changeset
654 641 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$PathAtomsRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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deepakjadmin
parents:
diff changeset
655 642 <span class="k">my</span><span class="s">(</span><span class="i">$AtomPathID</span><span class="cm">,</span> <span class="i">$PathLength</span><span class="cm">,</span> <span class="i">@PathAtomIDs</span><span class="s">)</span><span class="sc">;</span>
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deepakjadmin
parents:
diff changeset
656 643
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parents:
diff changeset
657 644 <span class="i">@PathAtomIDs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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deepakjadmin
parents:
diff changeset
658 645 <span class="i">@PathAtomIDs</span> = <span class="k">map</span> <span class="s">{</span> <span class="i">$_</span><span class="i">-&gt;GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> <span class="s">}</span> <span class="i">@</span>{<span class="i">$PathAtomsRef</span>}<span class="sc">;</span>
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parents:
diff changeset
659 646
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diff changeset
660 647 <span class="i">$AtomPathID</span> = <span class="k">join</span> <span class="q">&#39;-&#39;</span><span class="cm">,</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">@PathAtomIDs</span><span class="sc">;</span>
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parents:
diff changeset
661 648 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$This</span>-&gt;{<span class="w">UniqueLinearAtomPathsIDs</span>}{<span class="i">$AtomPathID</span>}<span class="s">)</span> <span class="s">{</span>
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deepakjadmin
parents:
diff changeset
662 649 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
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deepakjadmin
parents:
diff changeset
663 650 <span class="s">}</span>
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deepakjadmin
parents:
diff changeset
664 651
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parents:
diff changeset
665 652 <span class="c"># It&#39;s a unique atom path...</span>
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parents:
diff changeset
666 653 <span class="i">$This</span>-&gt;{<span class="w">UniqueLinearAtomPathsIDs</span>}{<span class="i">$AtomPathID</span>} = <span class="n">1</span><span class="sc">;</span>
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deepakjadmin
parents:
diff changeset
667 654
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
668 655 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span>
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deepakjadmin
parents:
diff changeset
669 656 <span class="s">}</span>
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parents:
diff changeset
670 657
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parents:
diff changeset
671 658 <span class="c"># Generate atom path string for specified path containing a cycle...</span>
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deepakjadmin
parents:
diff changeset
672 659 <span class="c">#</span>
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parents:
diff changeset
673 <a name="_GenerateAtomPathStringUsingUniquePathContainingCycle-"></a> 660 <span class="k">sub </span><span class="m">_GenerateAtomPathStringUsingUniquePathContainingCycle</span> <span class="s">{</span>
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deepakjadmin
parents:
diff changeset
674 661 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$PathAtomsRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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deepakjadmin
parents:
diff changeset
675 662
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deepakjadmin
parents:
diff changeset
676 663 <span class="c"># Is it a unique atom path containing a cycle?</span>
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deepakjadmin
parents:
diff changeset
677 664 <span class="c">#</span>
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deepakjadmin
parents:
diff changeset
678 665 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">-&gt;_IsUniqueAtomPathContainingCycle</span><span class="s">(</span><span class="i">$PathAtomsRef</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
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deepakjadmin
parents:
diff changeset
679 666 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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deepakjadmin
parents:
diff changeset
680 667 <span class="s">}</span>
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parents:
diff changeset
681 668
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deepakjadmin
parents:
diff changeset
682 669 <span class="k">my</span><span class="s">(</span><span class="i">$CycleClosingPathAtomIndex</span><span class="s">)</span><span class="sc">;</span>
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deepakjadmin
parents:
diff changeset
683 670 <span class="s">(</span><span class="i">$CycleClosingPathAtomIndex</span><span class="s">)</span> = <span class="i">$This</span><span class="i">-&gt;_GetAtomPathCycleClosingAtomIndex</span><span class="s">(</span><span class="i">$PathAtomsRef</span><span class="s">)</span><span class="sc">;</span>
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parents:
diff changeset
684 671
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parents:
diff changeset
685 672 <span class="k">if</span> <span class="s">(</span><span class="i">$CycleClosingPathAtomIndex</span> == <span class="n">0</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
686 673 <span class="i">$This</span><span class="i">-&gt;_GenerateUniqueAtomPathStringForPathCycle</span><span class="s">(</span><span class="i">$PathAtomsRef</span><span class="s">)</span><span class="sc">;</span>
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deepakjadmin
parents:
diff changeset
687 674 <span class="s">}</span>
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deepakjadmin
parents:
diff changeset
688 675 <span class="k">else</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
689 676 <span class="i">$This</span><span class="i">-&gt;_GenerateUniqueAtomPathStringForPathContainingCycle</span><span class="s">(</span><span class="i">$PathAtomsRef</span><span class="cm">,</span> <span class="i">$CycleClosingPathAtomIndex</span><span class="s">)</span><span class="sc">;</span>
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deepakjadmin
parents:
diff changeset
690 677 <span class="s">}</span>
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deepakjadmin
parents:
diff changeset
691 678 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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deepakjadmin
parents:
diff changeset
692 679 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
693 680
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
694 681 <span class="c"># Generate a unique atom path string for a cyclic path by generating atom path</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
695 682 <span class="c"># strings for all possible paths in the cycle and keeping the lexicographically smallest</span>
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deepakjadmin
parents:
diff changeset
696 683 <span class="c"># one.</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
697 684 <span class="c">#</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
698 685 <span class="c"># Although all the paths enumerated during atom path string generation are also</span>
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deepakjadmin
parents:
diff changeset
699 686 <span class="c"># present in the intial paths list, but structural uniqueness check would detect</span>
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deepakjadmin
parents:
diff changeset
700 687 <span class="c"># &#39;em earlier and this method ends being invoked only once for the first cyclic path.</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
701 688 <span class="c">#</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
702 689 <span class="c"># For atom paths containg same atom types and bond symbols, atom path strings</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
703 690 <span class="c"># would be same for the paths.</span>
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deepakjadmin
parents:
diff changeset
704 691 <span class="c">#</span>
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deepakjadmin
parents:
diff changeset
705 <a name="_GenerateUniqueAtomPathStringForPathCycle-"></a> 692 <span class="k">sub </span><span class="m">_GenerateUniqueAtomPathStringForPathCycle</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">$This</span><span class="cm">,</span> <span class="i">$PathAtomsRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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deepakjadmin
parents:
diff changeset
707 694
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
708 695 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span><span class="i">-&gt;_AreAllPathAtomsSymbolsSame</span><span class="s">(</span><span class="i">$PathAtomsRef</span><span class="s">)</span> &amp;&amp; <span class="i">$This</span><span class="i">-&gt;_AreAllPathBondSymbolsSame</span><span class="s">(</span><span class="i">$PathAtomsRef</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
709 696 <span class="k">return</span> <span class="i">$This</span><span class="i">-&gt;_GenerateAtomPathString</span><span class="s">(</span><span class="i">$PathAtomsRef</span><span class="s">)</span><span class="sc">;</span>
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deepakjadmin
parents:
diff changeset
710 697 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
711 698
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
712 699 <span class="c"># Generate all possible atom path strings and select the lexicographically smallest one...</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
713 700 <span class="k">my</span><span class="s">(</span><span class="i">$Index</span><span class="cm">,</span> <span class="i">$PathLength</span><span class="cm">,</span> <span class="i">$FinalAtomPathString</span><span class="cm">,</span> <span class="i">$FirstAtomPathString</span><span class="cm">,</span> <span class="i">$LastIndex</span><span class="cm">,</span> <span class="i">$FirstPartIndex</span><span class="cm">,</span> <span class="i">$FirstPartStartIndex</span><span class="cm">,</span> <span class="i">$FirstPartEndIndex</span><span class="cm">,</span> <span class="i">$SecondPartIndex</span><span class="cm">,</span> <span class="i">$SecondPartStartIndex</span><span class="cm">,</span> <span class="i">$SecondPartEndIndex</span><span class="cm">,</span> <span class="i">$AtomPathSymbolsRef</span><span class="cm">,</span> <span class="i">$AtomPathString</span><span class="cm">,</span> <span class="i">$ReverseAtomPathString</span><span class="cm">,</span> <span class="i">@FirstPartPathAtoms</span><span class="cm">,</span> <span class="i">@SecondPartPathAtoms</span><span class="cm">,</span> <span class="i">@PathAtoms</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
714 701
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
715 702 <span class="i">$PathLength</span> = <span class="k">scalar</span> <span class="i">@</span>{<span class="i">$PathAtomsRef</span>}<span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
716 703 <span class="i">$LastIndex</span> = <span class="i">$PathLength</span> - <span class="n">1</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
717 704
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
718 705 <span class="i">$FinalAtomPathString</span> = <span class="q">&#39;&#39;</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
719 706 <span class="i">$FirstAtomPathString</span> = <span class="n">1</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
720 707
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
721 708 <span class="i">@FirstPartPathAtoms</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> <span class="i">@SecondPartPathAtoms</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> <span class="i">@PathAtoms</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
722 709
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
723 710 <span class="k">for</span> <span class="i">$Index</span> <span class="s">(</span><span class="n">0</span> .. <span class="s">(</span><span class="i">$LastIndex</span> - <span class="n">1</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
724 711 <span class="i">@FirstPartPathAtoms</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> <span class="i">@SecondPartPathAtoms</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> <span class="i">@PathAtoms</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
725 712
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
726 713 <span class="i">$FirstPartStartIndex</span> = <span class="n">0</span><span class="sc">;</span> <span class="i">$FirstPartEndIndex</span> = <span class="i">$Index</span> - <span class="n">1</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
727 714 <span class="i">$SecondPartStartIndex</span> = <span class="i">$Index</span><span class="sc">;</span> <span class="i">$SecondPartEndIndex</span> = <span class="i">$LastIndex</span> - <span class="n">1</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
728 715
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
729 716 <span class="c"># Get first part atoms...</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
730 717 <span class="k">for</span> <span class="i">$FirstPartIndex</span> <span class="s">(</span><span class="i">$FirstPartStartIndex</span> .. <span class="i">$FirstPartEndIndex</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
731 718 <span class="k">push</span> <span class="i">@FirstPartPathAtoms</span><span class="cm">,</span> <span class="i">$PathAtomsRef</span>-&gt;[<span class="i">$FirstPartIndex</span>]<span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
732 719 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
733 720
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
734 721 <span class="c"># Get second part atoms...</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
735 722 <span class="k">for</span> <span class="i">$SecondPartIndex</span> <span class="s">(</span><span class="i">$SecondPartStartIndex</span> .. <span class="i">$SecondPartEndIndex</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
736 723 <span class="k">push</span> <span class="i">@SecondPartPathAtoms</span><span class="cm">,</span> <span class="i">$PathAtomsRef</span>-&gt;[<span class="i">$SecondPartIndex</span>]<span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
737 724 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
738 725
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
739 726 <span class="c"># Get final list of path atoms...</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
740 727 <span class="k">if</span> <span class="s">(</span><span class="i">@SecondPartPathAtoms</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
741 728 <span class="k">push</span> <span class="i">@PathAtoms</span><span class="cm">,</span> <span class="i">@SecondPartPathAtoms</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
742 729 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
743 730 <span class="k">if</span> <span class="s">(</span><span class="i">@FirstPartPathAtoms</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
744 731 <span class="k">push</span> <span class="i">@PathAtoms</span><span class="cm">,</span> <span class="i">@FirstPartPathAtoms</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
745 732 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
746 733
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
747 734 <span class="c"># Complete the cycle by adding first atom as the last atom...</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
748 735 <span class="k">push</span> <span class="i">@PathAtoms</span><span class="cm">,</span> <span class="i">$PathAtomsRef</span>-&gt;[<span class="i">$SecondPartStartIndex</span>]<span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
749 736
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
750 737 <span class="c"># Generate atom path string...</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
751 738 <span class="i">$AtomPathSymbolsRef</span> = <span class="i">$This</span><span class="i">-&gt;_GenerateAtomPathSymbols</span><span class="s">(</span>\<span class="i">@PathAtoms</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
752 739
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
753 740 <span class="i">$AtomPathString</span> = <span class="k">join</span> <span class="q">&#39;&#39;</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$AtomPathSymbolsRef</span>}<span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
754 741 <span class="i">$ReverseAtomPathString</span> = <span class="k">join</span> <span class="q">&#39;&#39;</span><span class="cm">,</span> <span class="k">reverse</span> <span class="i">@</span>{<span class="i">$AtomPathSymbolsRef</span>}<span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
755 742
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
756 743 <span class="k">if</span> <span class="s">(</span><span class="i">$ReverseAtomPathString</span> <span class="k">le</span> <span class="i">$AtomPathString</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
757 744 <span class="i">$AtomPathString</span> = <span class="i">$ReverseAtomPathString</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
758 745 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
759 746
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
760 747 <span class="c"># Update final atom path string...</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
761 748
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
762 749 <span class="k">if</span> <span class="s">(</span><span class="i">$FirstAtomPathString</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
763 750 <span class="i">$FirstAtomPathString</span> = <span class="n">0</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
764 751 <span class="i">$FinalAtomPathString</span> = <span class="i">$AtomPathString</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
765 752 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
766 753 <span class="k">else</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
767 754 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomPathString</span> <span class="k">le</span> <span class="i">$FinalAtomPathString</span><span class="s">)</span> <span class="s">{</span>
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parents:
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768 755 <span class="i">$FinalAtomPathString</span> = <span class="i">$AtomPathString</span><span class="sc">;</span>
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parents:
diff changeset
769 756 <span class="s">}</span>
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parents:
diff changeset
770 757 <span class="s">}</span>
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parents:
diff changeset
771 758 <span class="s">}</span>
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parents:
diff changeset
772 759
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parents:
diff changeset
773 760 <span class="c"># Set final atom path string...</span>
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parents:
diff changeset
774 761 <span class="c">#</span>
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parents:
diff changeset
775 762 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$This</span>-&gt;{<span class="w">AtomPathsStrings</span>}{<span class="i">$PathLength</span>}{<span class="i">$FinalAtomPathString</span>}<span class="s">)</span> <span class="s">{</span>
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parents:
diff changeset
776 763 <span class="i">$This</span>-&gt;{<span class="w">AtomPathsStrings</span>}{<span class="i">$PathLength</span>}{<span class="i">$FinalAtomPathString</span>} += <span class="n">1</span><span class="sc">;</span>
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deepakjadmin
parents:
diff changeset
777 764 <span class="s">}</span>
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parents:
diff changeset
778 765 <span class="k">else</span> <span class="s">{</span>
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parents:
diff changeset
779 766 <span class="i">$This</span>-&gt;{<span class="w">AtomPathsStrings</span>}{<span class="i">$PathLength</span>}{<span class="i">$FinalAtomPathString</span>} = <span class="n">1</span><span class="sc">;</span>
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deepakjadmin
parents:
diff changeset
780 767 <span class="s">}</span>
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parents:
diff changeset
781 768
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parents:
diff changeset
782 769 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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parents:
diff changeset
783 770 <span class="s">}</span>
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parents:
diff changeset
784 771
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parents:
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785 772 <span class="c">#</span>
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parents:
diff changeset
786 773 <span class="c"># Generate a unique atom path string for paths containing a cycle closed by</span>
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deepakjadmin
parents:
diff changeset
787 774 <span class="c"># the specified atom index and the last atom index.</span>
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deepakjadmin
parents:
diff changeset
788 775 <span class="c">#</span>
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parents:
diff changeset
789 776 <span class="c"># The following methodology is used to generate atom path string which is</span>
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deepakjadmin
parents:
diff changeset
790 777 <span class="c"># independemt of initial atom ordering:</span>
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deepakjadmin
parents:
diff changeset
791 778 <span class="c"># . Generate atom paths string from first atom to the atom before the first cycle</span>
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parents:
diff changeset
792 779 <span class="c"># closing atom.</span>
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deepakjadmin
parents:
diff changeset
793 780 <span class="c"># . Generate atom path string from atoms from first cycle closing atom index to</span>
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deepakjadmin
parents:
diff changeset
794 781 <span class="c"># the last path atom in both forward and reverse order. And select the lexicographically</span>
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deepakjadmin
parents:
diff changeset
795 782 <span class="c"># smallest atom path string.</span>
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deepakjadmin
parents:
diff changeset
796 783 <span class="c"># . Combine atom path string generated in first step with second step to generate</span>
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deepakjadmin
parents:
diff changeset
797 784 <span class="c"># final atom path string.</span>
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deepakjadmin
parents:
diff changeset
798 785 <span class="c">#</span>
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parents:
diff changeset
799 <a name="_GenerateUniqueAtomPathStringForPathContainingCycle-"></a> 786 <span class="k">sub </span><span class="m">_GenerateUniqueAtomPathStringForPathContainingCycle</span> <span class="s">{</span>
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parents:
diff changeset
800 787 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$PathAtomsRef</span><span class="cm">,</span> <span class="i">$CycleClosingAtomIndex</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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parents:
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801 788 <span class="k">my</span><span class="s">(</span><span class="i">$Index</span><span class="cm">,</span> <span class="i">$PathLength</span><span class="cm">,</span> <span class="i">$LastIndex</span><span class="cm">,</span> <span class="i">$LinearPartStartIndex</span><span class="cm">,</span> <span class="i">$LinearPartEndIndex</span><span class="cm">,</span> <span class="i">$CyclicPartStartIndex</span><span class="cm">,</span> <span class="i">$CyclicPartEndIndex</span><span class="cm">,</span> <span class="i">$CyclicPartAtomPathSymbolsRef</span><span class="cm">,</span> <span class="i">$CyclicPartAtomPathString</span><span class="cm">,</span> <span class="i">$ReverseCyclicPartAtomPathString</span><span class="cm">,</span> <span class="i">$AtomPathString</span><span class="cm">,</span> <span class="i">$AtomPathSymbolsRef</span><span class="cm">,</span> <span class="i">@CyclicPartPathAtoms</span><span class="cm">,</span> <span class="i">@PathAtoms</span><span class="s">)</span><span class="sc">;</span>
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deepakjadmin
parents:
diff changeset
802 789
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parents:
diff changeset
803 790 <span class="i">$PathLength</span> = <span class="k">scalar</span> <span class="i">@</span>{<span class="i">$PathAtomsRef</span>}<span class="sc">;</span>
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parents:
diff changeset
804 791 <span class="i">$LastIndex</span> = <span class="i">$PathLength</span> - <span class="n">1</span><span class="sc">;</span>
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parents:
diff changeset
805 792
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deepakjadmin
parents:
diff changeset
806 793 <span class="i">@PathAtoms</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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parents:
diff changeset
807 794
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parents:
diff changeset
808 795 <span class="c"># Get path atoms corresponding to linear part of the path...</span>
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parents:
diff changeset
809 796 <span class="i">$LinearPartStartIndex</span> = <span class="n">0</span><span class="sc">;</span> <span class="i">$LinearPartEndIndex</span> = <span class="i">$CycleClosingAtomIndex</span> - <span class="n">1</span><span class="sc">;</span>
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parents:
diff changeset
810 797
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parents:
diff changeset
811 798 <span class="k">for</span> <span class="i">$Index</span> <span class="s">(</span><span class="i">$LinearPartStartIndex</span> .. <span class="i">$LinearPartEndIndex</span><span class="s">)</span> <span class="s">{</span>
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deepakjadmin
parents:
diff changeset
812 799 <span class="k">push</span> <span class="i">@PathAtoms</span><span class="cm">,</span> <span class="i">$PathAtomsRef</span>-&gt;[<span class="i">$Index</span>]<span class="sc">;</span>
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deepakjadmin
parents:
diff changeset
813 800 <span class="s">}</span>
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deepakjadmin
parents:
diff changeset
814 801
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deepakjadmin
parents:
diff changeset
815 802 <span class="c"># Get atoms correcponding to cyclic part of the path...</span>
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deepakjadmin
parents:
diff changeset
816 803 <span class="i">@CyclicPartPathAtoms</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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deepakjadmin
parents:
diff changeset
817 804 <span class="i">$CyclicPartStartIndex</span> = <span class="i">$CycleClosingAtomIndex</span><span class="sc">;</span> <span class="i">$CyclicPartEndIndex</span> = <span class="i">$LastIndex</span><span class="sc">;</span>
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deepakjadmin
parents:
diff changeset
818 805
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deepakjadmin
parents:
diff changeset
819 806 <span class="k">for</span> <span class="i">$Index</span> <span class="s">(</span><span class="i">$CyclicPartStartIndex</span> .. <span class="i">$CyclicPartEndIndex</span><span class="s">)</span> <span class="s">{</span>
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deepakjadmin
parents:
diff changeset
820 807 <span class="k">push</span> <span class="i">@CyclicPartPathAtoms</span><span class="cm">,</span> <span class="i">$PathAtomsRef</span>-&gt;[<span class="i">$Index</span>]<span class="sc">;</span>
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deepakjadmin
parents:
diff changeset
821 808 <span class="s">}</span>
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deepakjadmin
parents:
diff changeset
822 809
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
823 810 <span class="c"># Setup a lexicographically smaller atom path string for cyclic part...</span>
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deepakjadmin
parents:
diff changeset
824 811
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parents:
diff changeset
825 812 <span class="i">$CyclicPartAtomPathSymbolsRef</span> = <span class="i">$This</span><span class="i">-&gt;_GenerateAtomPathSymbols</span><span class="s">(</span>\<span class="i">@CyclicPartPathAtoms</span><span class="s">)</span><span class="sc">;</span>
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deepakjadmin
parents:
diff changeset
826 813 <span class="i">$CyclicPartAtomPathString</span> = <span class="k">join</span> <span class="q">&#39;&#39;</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$CyclicPartAtomPathSymbolsRef</span>}<span class="sc">;</span>
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deepakjadmin
parents:
diff changeset
827 814 <span class="i">$ReverseCyclicPartAtomPathString</span> = <span class="k">join</span> <span class="q">&#39;&#39;</span><span class="cm">,</span> <span class="k">reverse</span> <span class="i">@</span>{<span class="i">$CyclicPartAtomPathSymbolsRef</span>}<span class="sc">;</span>
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deepakjadmin
parents:
diff changeset
828 815
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deepakjadmin
parents:
diff changeset
829 816 <span class="c"># Setup atom path corresponding to linear part and lexigraphicall smaller cyclic part...</span>
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deepakjadmin
parents:
diff changeset
830 817
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parents:
diff changeset
831 818 <span class="k">if</span> <span class="s">(</span><span class="i">$ReverseCyclicPartAtomPathString</span> <span class="k">le</span> <span class="i">$CyclicPartAtomPathString</span><span class="s">)</span> <span class="s">{</span>
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parents:
diff changeset
832 819 <span class="k">push</span> <span class="i">@PathAtoms</span><span class="cm">,</span> <span class="k">reverse</span> <span class="i">@CyclicPartPathAtoms</span><span class="sc">;</span>
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deepakjadmin
parents:
diff changeset
833 820 <span class="s">}</span>
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parents:
diff changeset
834 821 <span class="k">else</span> <span class="s">{</span>
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deepakjadmin
parents:
diff changeset
835 822 <span class="k">push</span> <span class="i">@PathAtoms</span><span class="cm">,</span> <span class="i">@CyclicPartPathAtoms</span><span class="sc">;</span>
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deepakjadmin
parents:
diff changeset
836 823 <span class="s">}</span>
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deepakjadmin
parents:
diff changeset
837 824
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deepakjadmin
parents:
diff changeset
838 825 <span class="c"># Setup final atom path string...</span>
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deepakjadmin
parents:
diff changeset
839 826
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parents:
diff changeset
840 827 <span class="i">$AtomPathSymbolsRef</span> = <span class="i">$This</span><span class="i">-&gt;_GenerateAtomPathSymbols</span><span class="s">(</span>\<span class="i">@PathAtoms</span><span class="s">)</span><span class="sc">;</span>
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deepakjadmin
parents:
diff changeset
841 828 <span class="i">$AtomPathString</span> = <span class="k">join</span> <span class="q">&#39;&#39;</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$AtomPathSymbolsRef</span>}<span class="sc">;</span>
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parents:
diff changeset
842 829
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parents:
diff changeset
843 830 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$This</span>-&gt;{<span class="w">AtomPathsStrings</span>}{<span class="i">$PathLength</span>}{<span class="i">$AtomPathString</span>}<span class="s">)</span> <span class="s">{</span>
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parents:
diff changeset
844 831 <span class="i">$This</span>-&gt;{<span class="w">AtomPathsStrings</span>}{<span class="i">$PathLength</span>}{<span class="i">$AtomPathString</span>} += <span class="n">1</span><span class="sc">;</span>
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deepakjadmin
parents:
diff changeset
845 832 <span class="s">}</span>
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deepakjadmin
parents:
diff changeset
846 833 <span class="k">else</span> <span class="s">{</span>
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parents:
diff changeset
847 834 <span class="i">$This</span>-&gt;{<span class="w">AtomPathsStrings</span>}{<span class="i">$PathLength</span>}{<span class="i">$AtomPathString</span>} = <span class="n">1</span><span class="sc">;</span>
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deepakjadmin
parents:
diff changeset
848 835 <span class="s">}</span>
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parents:
diff changeset
849 836
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deepakjadmin
parents:
diff changeset
850 837 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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deepakjadmin
parents:
diff changeset
851 838 <span class="s">}</span>
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deepakjadmin
parents:
diff changeset
852 839
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
853 840 <span class="c"># Does atom path contain a cycle?</span>
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deepakjadmin
parents:
diff changeset
854 841 <span class="c">#</span>
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deepakjadmin
parents:
diff changeset
855 842 <span class="c"># For an atom path to contain cycle, it must satisfy the following conditions:</span>
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deepakjadmin
parents:
diff changeset
856 843 <span class="c"># . Pathlength &gt;= 3</span>
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deepakjadmin
parents:
diff changeset
857 844 <span class="c"># . Last atom ID is equal to first atom ID or some other atom ID besides itself</span>
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deepakjadmin
parents:
diff changeset
858 845 <span class="c">#</span>
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deepakjadmin
parents:
diff changeset
859 <a name="_DoesAtomPathContainsCycle-"></a> 846 <span class="k">sub </span><span class="m">_DoesAtomPathContainsCycle</span> <span class="s">{</span>
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parents:
diff changeset
860 847 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$PathAtomsRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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parents:
diff changeset
861 848 <span class="k">my</span><span class="s">(</span><span class="i">$PathLength</span><span class="s">)</span><span class="sc">;</span>
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parents:
diff changeset
862 849
73ae111cf86f Uploaded
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parents:
diff changeset
863 850 <span class="i">$PathLength</span> = <span class="k">scalar</span> <span class="i">@</span>{<span class="i">$PathAtomsRef</span>}<span class="sc">;</span>
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parents:
diff changeset
864 851 <span class="k">if</span> <span class="s">(</span><span class="i">$PathLength</span> &lt;= <span class="n">2</span><span class="s">)</span> <span class="s">{</span>
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parents:
diff changeset
865 852 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
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deepakjadmin
parents:
diff changeset
866 853 <span class="s">}</span>
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parents:
diff changeset
867 854
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parents:
diff changeset
868 855 <span class="k">my</span><span class="s">(</span><span class="i">$AtomIndex</span><span class="cm">,</span> <span class="i">$LastAtomIndex</span><span class="cm">,</span> <span class="i">$Atom</span><span class="cm">,</span> <span class="i">$AtomID</span><span class="cm">,</span> <span class="i">$LastAtom</span><span class="cm">,</span> <span class="i">$LastAtomID</span><span class="s">)</span><span class="sc">;</span>
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parents:
diff changeset
869 856
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parents:
diff changeset
870 857 <span class="i">$LastAtomIndex</span> = <span class="i">$PathLength</span> - <span class="n">1</span><span class="sc">;</span>
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deepakjadmin
parents:
diff changeset
871 858 <span class="i">$LastAtom</span> = <span class="i">$PathAtomsRef</span>-&gt;[<span class="i">$LastAtomIndex</span>]<span class="sc">;</span>
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parents:
diff changeset
872 859 <span class="i">$LastAtomID</span> = <span class="i">$LastAtom</span><span class="i">-&gt;GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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deepakjadmin
parents:
diff changeset
873 860
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deepakjadmin
parents:
diff changeset
874 861 <span class="c"># Look for atomID similar to last atom ID...</span>
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parents:
diff changeset
875 862 <span class="k">for</span> <span class="i">$AtomIndex</span> <span class="s">(</span><span class="n">0</span> .. <span class="s">(</span><span class="i">$LastAtomIndex</span> - <span class="n">1</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
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parents:
diff changeset
876 863 <span class="i">$Atom</span> = <span class="i">$PathAtomsRef</span>-&gt;[<span class="i">$AtomIndex</span>]<span class="sc">;</span>
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parents:
diff changeset
877 864 <span class="i">$AtomID</span> = <span class="i">$Atom</span><span class="i">-&gt;GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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parents:
diff changeset
878 865
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parents:
diff changeset
879 866 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomID</span> == <span class="i">$LastAtomID</span><span class="s">)</span> <span class="s">{</span>
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parents:
diff changeset
880 867 <span class="c"># It&#39;s a cycle...</span>
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parents:
diff changeset
881 868 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span>
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parents:
diff changeset
882 869 <span class="s">}</span>
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parents:
diff changeset
883 870 <span class="s">}</span>
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deepakjadmin
parents:
diff changeset
884 871 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
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deepakjadmin
parents:
diff changeset
885 872 <span class="s">}</span>
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deepakjadmin
parents:
diff changeset
886 873
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parents:
diff changeset
887 874 <span class="c"># Get atom path cycle closing atom index...</span>
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deepakjadmin
parents:
diff changeset
888 875 <span class="c">#</span>
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parents:
diff changeset
889 <a name="_GetAtomPathCycleClosingAtomIndex-"></a> 876 <span class="k">sub </span><span class="m">_GetAtomPathCycleClosingAtomIndex</span> <span class="s">{</span>
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parents:
diff changeset
890 877 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$PathAtomsRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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parents:
diff changeset
891 878 <span class="k">my</span><span class="s">(</span><span class="i">$AtomIndex</span><span class="cm">,</span> <span class="i">$LastAtomIndex</span><span class="cm">,</span> <span class="i">$Atom</span><span class="cm">,</span> <span class="i">$AtomID</span><span class="cm">,</span> <span class="i">$LastAtom</span><span class="cm">,</span> <span class="i">$LastAtomID</span><span class="cm">,</span> <span class="i">$PathLength</span><span class="s">)</span><span class="sc">;</span>
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deepakjadmin
parents:
diff changeset
892 879
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
893 880 <span class="i">$PathLength</span> = <span class="k">scalar</span> <span class="i">@</span>{<span class="i">$PathAtomsRef</span>}<span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
894 881
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
895 882 <span class="i">$LastAtomIndex</span> = <span class="i">$PathLength</span> - <span class="n">1</span><span class="sc">;</span>
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deepakjadmin
parents:
diff changeset
896 883 <span class="i">$LastAtom</span> = <span class="i">$PathAtomsRef</span>-&gt;[<span class="i">$LastAtomIndex</span>]<span class="sc">;</span> <span class="i">$LastAtomID</span> = <span class="i">$LastAtom</span><span class="i">-&gt;GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
897 884
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
898 885 <span class="c"># Look for atomID similar to last atom ID...</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
899 886 <span class="k">for</span> <span class="i">$AtomIndex</span> <span class="s">(</span><span class="n">0</span> .. <span class="s">(</span><span class="i">$LastAtomIndex</span> - <span class="n">1</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
900 887 <span class="i">$Atom</span> = <span class="i">$PathAtomsRef</span>-&gt;[<span class="i">$AtomIndex</span>]<span class="sc">;</span> <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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deepakjadmin
parents:
diff changeset
901 888
73ae111cf86f Uploaded
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parents:
diff changeset
902 889 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomID</span> == <span class="i">$LastAtomID</span><span class="s">)</span> <span class="s">{</span>
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deepakjadmin
parents:
diff changeset
903 890 <span class="c"># It&#39;s a cycle closing atom...</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
904 891 <span class="k">return</span> <span class="i">$AtomIndex</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
905 892 <span class="s">}</span>
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deepakjadmin
parents:
diff changeset
906 893 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
907 894 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
908 895 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
909 896
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
910 897 <span class="c"># Is it a structurally unique path containing a cycle?</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
911 898 <span class="c">#</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
912 899 <span class="c"># For atom paths containing cycles, last atom ID is either equal to first atom ID or</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
913 900 <span class="c"># some other atom ID besides itself.</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
914 901 <span class="c">#</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
915 902 <span class="c"># In order to determine its structurally unqiue independent of initial atom ordering,</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
916 903 <span class="c"># the following methodolgy is used:</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
917 904 <span class="c">#</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
918 905 <span class="c"># . For paths with same first and atom IDs:</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
919 906 <span class="c"># . Remove the last atom ID from atom path</span>
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deepakjadmin
parents:
diff changeset
920 907 <span class="c"># . Sort atom IDs in the path</span>
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deepakjadmin
parents:
diff changeset
921 908 <span class="c"># . Add first atom ID from the sorted list to the end of list to complete the cycle</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
922 909 <span class="c"># . Generate a atom path ID</span>
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deepakjadmin
parents:
diff changeset
923 910 <span class="c"># . Use final path ID to track uniqueness of path containing cycle.</span>
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deepakjadmin
parents:
diff changeset
924 911 <span class="c">#</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
925 912 <span class="c"># . For paths with last atom ID equal to some other atom ID besidies itself:</span>
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deepakjadmin
parents:
diff changeset
926 913 <span class="c"># . Sort atom IDs in atom path</span>
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deepakjadmin
parents:
diff changeset
927 914 <span class="c"># . Generate atom path ID and use it to track unqiueness of atom paths.</span>
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deepakjadmin
parents:
diff changeset
928 915 <span class="c">#</span>
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deepakjadmin
parents:
diff changeset
929 <a name="_IsUniqueAtomPathContainingCycle-"></a> 916 <span class="k">sub </span><span class="m">_IsUniqueAtomPathContainingCycle</span> <span class="s">{</span>
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deepakjadmin
parents:
diff changeset
930 917 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$PathAtomsRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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deepakjadmin
parents:
diff changeset
931 918 <span class="k">my</span><span class="s">(</span><span class="i">$PathLength</span><span class="cm">,</span> <span class="i">$AtomPathID</span><span class="cm">,</span> <span class="i">$FirstAtom</span><span class="cm">,</span> <span class="i">$LastAtom</span><span class="cm">,</span> <span class="i">$FirstAtomID</span><span class="cm">,</span> <span class="i">$LastAtomID</span><span class="cm">,</span> <span class="i">@PathAtomIDs</span><span class="cm">,</span> <span class="i">@SortedPathAtomIDs</span><span class="s">)</span><span class="sc">;</span>
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deepakjadmin
parents:
diff changeset
932 919
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parents:
diff changeset
933 920 <span class="i">@PathAtomIDs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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deepakjadmin
parents:
diff changeset
934 921 <span class="i">@PathAtomIDs</span> = <span class="k">map</span> <span class="s">{</span> <span class="i">$_</span><span class="i">-&gt;GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> <span class="s">}</span> <span class="i">@</span>{<span class="i">$PathAtomsRef</span>}<span class="sc">;</span>
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deepakjadmin
parents:
diff changeset
935 922
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
936 923 <span class="i">$PathLength</span> = <span class="k">scalar</span> <span class="i">@</span>{<span class="i">$PathAtomsRef</span>}<span class="sc">;</span>
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deepakjadmin
parents:
diff changeset
937 924
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deepakjadmin
parents:
diff changeset
938 925 <span class="i">$FirstAtom</span> = <span class="i">$PathAtomsRef</span>-&gt;[<span class="n">0</span>]<span class="sc">;</span> <span class="i">$FirstAtomID</span> = <span class="i">$FirstAtom</span><span class="i">-&gt;GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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parents:
diff changeset
939 926 <span class="i">$LastAtom</span> = <span class="i">$PathAtomsRef</span>-&gt;[<span class="i">$PathLength</span> - <span class="n">1</span>]<span class="sc">;</span> <span class="i">$LastAtomID</span> = <span class="i">$LastAtom</span><span class="i">-&gt;GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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deepakjadmin
parents:
diff changeset
940 927
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
941 928 <span class="k">if</span> <span class="s">(</span><span class="i">$FirstAtomID</span> == <span class="i">$LastAtomID</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
942 929 <span class="k">pop</span> <span class="i">@PathAtomIDs</span><span class="sc">;</span>
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deepakjadmin
parents:
diff changeset
943 930
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
944 931 <span class="i">@SortedPathAtomIDs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
945 932 <span class="i">@SortedPathAtomIDs</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">@PathAtomIDs</span><span class="sc">;</span>
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deepakjadmin
parents:
diff changeset
946 933
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
947 934 <span class="k">push</span> <span class="i">@SortedPathAtomIDs</span><span class="cm">,</span> <span class="i">$SortedPathAtomIDs</span>[<span class="n">0</span>]<span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
948 935
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
949 936 <span class="i">$AtomPathID</span> = <span class="k">join</span> <span class="q">&#39;-&#39;</span><span class="cm">,</span> <span class="i">@SortedPathAtomIDs</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
950 937 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
951 938 <span class="k">else</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
952 939 <span class="i">$AtomPathID</span> = <span class="k">join</span> <span class="q">&#39;-&#39;</span><span class="cm">,</span> <span class="k">sort</span> <span class="s">{</span> <span class="i">$a</span> &lt;=&gt; <span class="i">$b</span> <span class="s">}</span> <span class="i">@PathAtomIDs</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
953 940 <span class="s">}</span>
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deepakjadmin
parents:
diff changeset
954 941
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
955 942 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$This</span>-&gt;{<span class="w">UniqueCyclicAtomPathsIDs</span>}{<span class="i">$AtomPathID</span>}<span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
956 943 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
957 944 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
958 945
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
959 946 <span class="c"># It&#39;s a unique atom path containing a cycle...</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
960 947 <span class="i">$This</span>-&gt;{<span class="w">UniqueCyclicAtomPathsIDs</span>}{<span class="i">$AtomPathID</span>} = <span class="n">1</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
961 948
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
962 949 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
963 950 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
964 951
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
965 952 <span class="c"># Generate atom path string for specified atom path...</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
966 953 <span class="c">#</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
967 <a name="_GenerateAtomPathString-"></a> 954 <span class="k">sub </span><span class="m">_GenerateAtomPathString</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
968 955 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$PathAtomsRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
969 956 <span class="k">my</span><span class="s">(</span><span class="i">$PathLength</span><span class="cm">,</span> <span class="i">$AtomPathString</span><span class="cm">,</span> <span class="i">$ReverseAtomPathString</span><span class="cm">,</span> <span class="i">$AtomPathSymbolsRef</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
970 957
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
971 958 <span class="i">$PathLength</span> = <span class="k">scalar</span> <span class="i">@</span>{<span class="i">$PathAtomsRef</span>}<span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
972 959
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
973 960 <span class="c"># Generate path atom and bond symbols...</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
974 961 <span class="c">#</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
975 962 <span class="i">$AtomPathSymbolsRef</span> = <span class="i">$This</span><span class="i">-&gt;_GenerateAtomPathSymbols</span><span class="s">(</span><span class="i">$PathAtomsRef</span><span class="s">)</span><span class="sc">;</span>
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deepakjadmin
parents:
diff changeset
976 963
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
977 964 <span class="c"># Check presence of path using path ID created by atom path symbols...</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
978 965 <span class="i">$AtomPathString</span> = <span class="k">join</span> <span class="q">&#39;&#39;</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$AtomPathSymbolsRef</span>}<span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
979 966 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$This</span>-&gt;{<span class="w">AtomPathsStrings</span>}{<span class="i">$PathLength</span>}{<span class="i">$AtomPathString</span>}<span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
980 967 <span class="i">$This</span>-&gt;{<span class="w">AtomPathsStrings</span>}{<span class="i">$PathLength</span>}{<span class="i">$AtomPathString</span>} += <span class="n">1</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
981 968 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
982 969 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
983 970
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
984 971 <span class="c"># Check presence of reverse path using path ID created by atom path symbols...</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
985 972 <span class="c">#</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
986 973 <span class="i">$ReverseAtomPathString</span> = <span class="k">join</span> <span class="q">&#39;&#39;</span><span class="cm">,</span> <span class="k">reverse</span> <span class="i">@</span>{<span class="i">$AtomPathSymbolsRef</span>}<span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
987 974 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$This</span>-&gt;{<span class="w">AtomPathsStrings</span>}{<span class="i">$PathLength</span>}{<span class="i">$ReverseAtomPathString</span>}<span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
988 975 <span class="i">$This</span>-&gt;{<span class="w">AtomPathsStrings</span>}{<span class="i">$PathLength</span>}{<span class="i">$ReverseAtomPathString</span>} += <span class="n">1</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
989 976 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
990 977 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
991 978
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
992 979 <span class="c"># Use lexicographically smaller atom path string as PathID...</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
993 980 <span class="c">#</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
994 981 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomPathString</span> <span class="k">le</span> <span class="i">$ReverseAtomPathString</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
995 982 <span class="i">$This</span>-&gt;{<span class="w">AtomPathsStrings</span>}{<span class="i">$PathLength</span>}{<span class="i">$AtomPathString</span>} = <span class="n">1</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
996 983 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
997 984 <span class="k">else</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
998 985 <span class="i">$This</span>-&gt;{<span class="w">AtomPathsStrings</span>}{<span class="i">$PathLength</span>}{<span class="i">$ReverseAtomPathString</span>} = <span class="n">1</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
999 986 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1000 987 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1001 988 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1002 989
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1003 990 <span class="c"># Are atom types for all path atoms same?</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1004 991 <span class="c">#</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1005 <a name="_AreAllPathAtomsSymbolsSame-"></a> 992 <span class="k">sub </span><span class="m">_AreAllPathAtomsSymbolsSame</span> <span class="s">{</span>
73ae111cf86f Uploaded
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parents:
diff changeset
1006 993 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$PathAtomsRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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parents:
diff changeset
1007 994 <span class="k">my</span><span class="s">(</span><span class="i">$Index</span><span class="cm">,</span> <span class="i">$Atom</span><span class="cm">,</span> <span class="i">$AtomID</span><span class="cm">,</span> <span class="i">$AtomType</span><span class="cm">,</span> <span class="i">$FirstAtomType</span><span class="s">)</span><span class="sc">;</span>
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parents:
diff changeset
1008 995
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parents:
diff changeset
1009 996 <span class="i">$Atom</span> = <span class="i">$PathAtomsRef</span>-&gt;[<span class="n">0</span>]<span class="sc">;</span> <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:
diff changeset
1010 997 <span class="i">$FirstAtomType</span> = <span class="i">$This</span>-&gt;{<span class="w">AssignedAtomTypes</span>}{<span class="i">$AtomID</span>}<span class="sc">;</span>
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parents:
diff changeset
1011 998
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parents:
diff changeset
1012 999 <span class="k">for</span> <span class="i">$Index</span> <span class="s">(</span><span class="n">1</span> .. <span class="i">$#</span>{<span class="i">$PathAtomsRef</span>}<span class="s">)</span> <span class="s">{</span>
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parents:
diff changeset
1013 1000 <span class="i">$Atom</span> = <span class="i">$PathAtomsRef</span>-&gt;[<span class="i">$Index</span>]<span class="sc">;</span> <span class="i">$AtomID</span> = <span class="i">$Atom</span><span class="i">-&gt;GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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parents:
diff changeset
1014 1001 <span class="i">$AtomType</span> = <span class="i">$This</span>-&gt;{<span class="w">AssignedAtomTypes</span>}{<span class="i">$AtomID</span>}<span class="sc">;</span>
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parents:
diff changeset
1015 1002
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parents:
diff changeset
1016 1003 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomType</span> <span class="k">ne</span> <span class="i">$FirstAtomType</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1017 1004 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
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deepakjadmin
parents:
diff changeset
1018 1005 <span class="s">}</span>
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deepakjadmin
parents:
diff changeset
1019 1006 <span class="s">}</span>
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parents:
diff changeset
1020 1007 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span>
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parents:
diff changeset
1021 1008 <span class="s">}</span>
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parents:
diff changeset
1022 1009
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1023 1010 <span class="c"># Are bond symbols for all path bonds same?</span>
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parents:
diff changeset
1024 1011 <span class="c">#</span>
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parents:
diff changeset
1025 <a name="_AreAllPathBondSymbolsSame-"></a>1012 <span class="k">sub </span><span class="m">_AreAllPathBondSymbolsSame</span> <span class="s">{</span>
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parents:
diff changeset
1026 1013 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$PathAtomsRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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parents:
diff changeset
1027 1014 <span class="k">my</span><span class="s">(</span><span class="i">$Index</span><span class="cm">,</span> <span class="i">$Atom</span><span class="cm">,</span> <span class="i">$BondedAtom</span><span class="cm">,</span> <span class="i">$AtomID</span><span class="cm">,</span> <span class="i">$BondedAtomID</span><span class="cm">,</span> <span class="i">$BondAtomID1</span><span class="cm">,</span> <span class="i">$BondAtomID2</span><span class="cm">,</span> <span class="i">$FirstBondSymbol</span><span class="cm">,</span> <span class="i">$BondSymbol</span><span class="s">)</span><span class="sc">;</span>
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parents:
diff changeset
1028 1015
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parents:
diff changeset
1029 1016 <span class="c"># During no usage of bond symbols, just ignore them and assume they are same...</span>
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parents:
diff changeset
1030 1017 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span>-&gt;{<span class="w">UseBondSymbols</span>}<span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1031 1018 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span>
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deepakjadmin
parents:
diff changeset
1032 1019 <span class="s">}</span>
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parents:
diff changeset
1033 1020
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diff changeset
1034 1021 <span class="i">$Atom</span> = <span class="i">$PathAtomsRef</span>-&gt;[<span class="n">0</span>]<span class="sc">;</span> <span class="i">$BondedAtom</span> = <span class="i">$PathAtomsRef</span>-&gt;[<span class="n">1</span>]<span class="sc">;</span>
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parents:
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1035 1022 <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> <span class="i">$BondedAtomID</span> = <span class="i">$BondedAtom</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
1036 1023
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diff changeset
1037 1024 <span class="s">(</span><span class="i">$BondAtomID1</span><span class="cm">,</span> <span class="i">$BondAtomID2</span><span class="s">)</span> = <span class="s">(</span><span class="i">$AtomID</span> &lt; <span class="i">$BondedAtomID</span><span class="s">)</span> ? <span class="s">(</span><span class="i">$AtomID</span><span class="cm">,</span> <span class="i">$BondedAtomID</span><span class="s">)</span> <span class="co">:</span> <span class="s">(</span><span class="i">$BondedAtomID</span><span class="cm">,</span> <span class="i">$AtomID</span><span class="s">)</span><span class="sc">;</span>
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parents:
diff changeset
1038 1025 <span class="i">$FirstBondSymbol</span> = <span class="i">$This</span>-&gt;{<span class="w">BondSymbols</span>}{<span class="i">$BondAtomID1</span>}{<span class="i">$BondAtomID2</span>}<span class="sc">;</span>
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parents:
diff changeset
1039 1026
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parents:
diff changeset
1040 1027 <span class="k">for</span> <span class="i">$Index</span> <span class="s">(</span><span class="n">1</span> .. <span class="s">(</span><span class="i">$#</span>{<span class="i">$PathAtomsRef</span>} - <span class="n">1</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
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parents:
diff changeset
1041 1028 <span class="i">$Atom</span> = <span class="i">$PathAtomsRef</span>-&gt;[<span class="i">$Index</span>]<span class="sc">;</span> <span class="i">$BondedAtom</span> = <span class="i">$PathAtomsRef</span>-&gt;[<span class="i">$Index</span> + <span class="n">1</span>]<span class="sc">;</span>
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parents:
diff changeset
1042 1029 <span class="i">$AtomID</span> = <span class="i">$Atom</span><span class="i">-&gt;GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> <span class="i">$BondedAtomID</span> = <span class="i">$BondedAtom</span><span class="i">-&gt;GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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parents:
diff changeset
1043 1030
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diff changeset
1044 1031 <span class="s">(</span><span class="i">$BondAtomID1</span><span class="cm">,</span> <span class="i">$BondAtomID2</span><span class="s">)</span> = <span class="s">(</span><span class="i">$AtomID</span> &lt; <span class="i">$BondedAtomID</span><span class="s">)</span> ? <span class="s">(</span><span class="i">$AtomID</span><span class="cm">,</span> <span class="i">$BondedAtomID</span><span class="s">)</span> <span class="co">:</span> <span class="s">(</span><span class="i">$BondedAtomID</span><span class="cm">,</span> <span class="i">$AtomID</span><span class="s">)</span><span class="sc">;</span>
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parents:
diff changeset
1045 1032 <span class="i">$BondSymbol</span> = <span class="i">$This</span>-&gt;{<span class="w">BondSymbols</span>}{<span class="i">$BondAtomID1</span>}{<span class="i">$BondAtomID2</span>}<span class="sc">;</span>
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parents:
diff changeset
1046 1033
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diff changeset
1047 1034 <span class="k">if</span> <span class="s">(</span><span class="i">$BondSymbol</span> <span class="k">ne</span> <span class="i">$FirstBondSymbol</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
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parents:
diff changeset
1048 1035 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
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deepakjadmin
parents:
diff changeset
1049 1036 <span class="s">}</span>
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deepakjadmin
parents:
diff changeset
1050 1037 <span class="s">}</span>
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parents:
diff changeset
1051 1038 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span>
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deepakjadmin
parents:
diff changeset
1052 1039 <span class="s">}</span>
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deepakjadmin
parents:
diff changeset
1053 1040
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deepakjadmin
parents:
diff changeset
1054 1041 <span class="c"># Generate atom path symbols...</span>
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deepakjadmin
parents:
diff changeset
1055 1042 <span class="c">#</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1056 <a name="_GenerateAtomPathSymbols-"></a>1043 <span class="k">sub </span><span class="m">_GenerateAtomPathSymbols</span> <span class="s">{</span>
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parents:
diff changeset
1057 1044 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$PathAtomsRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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deepakjadmin
parents:
diff changeset
1058 1045 <span class="k">my</span><span class="s">(</span><span class="i">$Atom</span><span class="cm">,</span> <span class="i">$AtomID</span><span class="cm">,</span> <span class="i">@AtomPathSymbols</span><span class="s">)</span><span class="sc">;</span>
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deepakjadmin
parents:
diff changeset
1059 1046
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1060 1047 <span class="i">@AtomPathSymbols</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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parents:
diff changeset
1061 1048
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1062 1049 <span class="k">if</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$PathAtomsRef</span>} == <span class="n">1</span><span class="s">)</span> <span class="s">{</span>
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parents:
diff changeset
1063 1050 <span class="i">$Atom</span> = <span class="i">$PathAtomsRef</span>-&gt;[<span class="n">0</span>]<span class="sc">;</span> <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
1064 1051 <span class="k">push</span> <span class="i">@AtomPathSymbols</span><span class="cm">,</span> <span class="i">$This</span>-&gt;{<span class="w">AssignedAtomTypes</span>}{<span class="i">$AtomID</span>}<span class="sc">;</span>
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deepakjadmin
parents:
diff changeset
1065 1052 <span class="k">return</span> \<span class="i">@AtomPathSymbols</span><span class="sc">;</span>
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deepakjadmin
parents:
diff changeset
1066 1053 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1067 1054
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1068 1055 <span class="c"># Ignore bond information...</span>
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deepakjadmin
parents:
diff changeset
1069 1056 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span>-&gt;{<span class="w">UseBondSymbols</span>}<span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1070 1057 <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$PathAtomsRef</span>}<span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1071 1058 <span class="i">$AtomID</span> = <span class="i">$Atom</span><span class="i">-&gt;GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1072 1059 <span class="k">push</span> <span class="i">@AtomPathSymbols</span><span class="cm">,</span> <span class="i">$This</span>-&gt;{<span class="w">AssignedAtomTypes</span>}{<span class="i">$AtomID</span>}<span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1073 1060 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1074 1061 <span class="k">return</span> \<span class="i">@AtomPathSymbols</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1075 1062 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1076 1063
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1077 1064 <span class="c"># Use atoms and bonds to generate atom path string...</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1078 1065 <span class="k">my</span><span class="s">(</span><span class="i">$Index</span><span class="cm">,</span> <span class="i">$BondedAtom</span><span class="cm">,</span> <span class="i">$BondedAtomID</span><span class="cm">,</span> <span class="i">$BondAtomID1</span><span class="cm">,</span> <span class="i">$BondAtomID2</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1079 1066
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deepakjadmin
parents:
diff changeset
1080 1067 <span class="c"># Process atom type of first atom in path...</span>
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deepakjadmin
parents:
diff changeset
1081 1068 <span class="i">$Atom</span> = <span class="i">$PathAtomsRef</span>-&gt;[<span class="n">0</span>]<span class="sc">;</span> <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
1082 1069 <span class="k">push</span> <span class="i">@AtomPathSymbols</span><span class="cm">,</span> <span class="i">$This</span>-&gt;{<span class="w">AssignedAtomTypes</span>}{<span class="i">$AtomID</span>}<span class="sc">;</span>
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parents:
diff changeset
1083 1070
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parents:
diff changeset
1084 1071 <span class="k">for</span> <span class="i">$Index</span> <span class="s">(</span><span class="n">0</span> .. <span class="s">(</span><span class="i">$#</span>{<span class="i">$PathAtomsRef</span>} - <span class="n">1</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded
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parents:
diff changeset
1085 1072 <span class="i">$Atom</span> = <span class="i">$PathAtomsRef</span>-&gt;[<span class="i">$Index</span>]<span class="sc">;</span> <span class="i">$BondedAtom</span> = <span class="i">$PathAtomsRef</span>-&gt;[<span class="i">$Index</span> + <span class="n">1</span>]<span class="sc">;</span>
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parents:
diff changeset
1086 1073 <span class="i">$AtomID</span> = <span class="i">$Atom</span><span class="i">-&gt;GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> <span class="i">$BondedAtomID</span> = <span class="i">$BondedAtom</span><span class="i">-&gt;GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded
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parents:
diff changeset
1087 1074
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parents:
diff changeset
1088 1075 <span class="s">(</span><span class="i">$BondAtomID1</span><span class="cm">,</span> <span class="i">$BondAtomID2</span><span class="s">)</span> = <span class="s">(</span><span class="i">$AtomID</span> &lt; <span class="i">$BondedAtomID</span><span class="s">)</span> ? <span class="s">(</span><span class="i">$AtomID</span><span class="cm">,</span> <span class="i">$BondedAtomID</span><span class="s">)</span> <span class="co">:</span> <span class="s">(</span><span class="i">$BondedAtomID</span><span class="cm">,</span> <span class="i">$AtomID</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded
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parents:
diff changeset
1089 1076 <span class="k">push</span> <span class="i">@AtomPathSymbols</span><span class="cm">,</span> <span class="i">$This</span>-&gt;{<span class="w">BondSymbols</span>}{<span class="i">$BondAtomID1</span>}{<span class="i">$BondAtomID2</span>}<span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1090 1077
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1091 1078 <span class="c"># Process atom type of next atom in path...</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1092 1079 <span class="k">push</span> <span class="i">@AtomPathSymbols</span><span class="cm">,</span> <span class="i">$This</span>-&gt;{<span class="w">AssignedAtomTypes</span>}{<span class="i">$BondedAtomID</span>}<span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1093 1080 <span class="s">}</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1094 1081 <span class="k">return</span> \<span class="i">@AtomPathSymbols</span><span class="sc">;</span>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1095 1082 <span class="s">}</span>
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deepakjadmin
parents:
diff changeset
1096 1083
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parents:
diff changeset
1097 1084 <span class="c"># Set final fingerprits...</span>
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parents:
diff changeset
1098 1085 <span class="c">#</span>
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parents:
diff changeset
1099 <a name="_SetFinalFingerprints-"></a>1086 <span class="k">sub </span><span class="m">_SetFinalFingerprints</span> <span class="s">{</span>
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parents:
diff changeset
1100 1087 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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deepakjadmin
parents:
diff changeset
1101 1088
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deepakjadmin
parents:
diff changeset
1102 1089 <span class="c"># Mark successful generation of fingerprints...</span>
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deepakjadmin
parents:
diff changeset
1103 1090 <span class="i">$This</span>-&gt;{<span class="w">FingerprintsGenerated</span>} = <span class="n">1</span><span class="sc">;</span>
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parents:
diff changeset
1104 1091
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parents:
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1105 1092 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">Type</span>} =~ <span class="q">/^PathLengthBits$/i</span><span class="s">)</span> <span class="s">{</span>
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1106 1093 <span class="i">$This</span><span class="i">-&gt;_SetFinalFingerprintsBitVector</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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parents:
diff changeset
1107 1094 <span class="s">}</span>
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parents:
diff changeset
1108 1095 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">Type</span>} =~ <span class="q">/^PathLengthCount$/i</span><span class="s">)</span> <span class="s">{</span>
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1109 1096 <span class="i">$This</span><span class="i">-&gt;_SetFinalFingerprintsVector</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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diff changeset
1110 1097 <span class="s">}</span>
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diff changeset
1111 1098
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diff changeset
1112 1099 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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diff changeset
1113 1100 <span class="s">}</span>
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diff changeset
1114 1101
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diff changeset
1115 1102 <span class="c"># Set final fingerprits bit vector...</span>
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diff changeset
1116 1103 <span class="c">#</span>
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diff changeset
1117 <a name="_SetFinalFingerprintsBitVector-"></a>1104 <span class="k">sub </span><span class="m">_SetFinalFingerprintsBitVector</span> <span class="s">{</span>
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1118 1105 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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1119 1106 <span class="k">my</span><span class="s">(</span><span class="i">$PathLength</span><span class="cm">,</span> <span class="i">$Size</span><span class="cm">,</span> <span class="i">$AtomPathString</span><span class="cm">,</span> <span class="i">$AtomPathHashCode</span><span class="cm">,</span> <span class="i">$AtomPathBitPos</span><span class="cm">,</span> <span class="i">$FingerprintsBitVector</span><span class="cm">,</span> <span class="i">$SkipBitPosCheck</span><span class="cm">,</span> <span class="i">$NumOfBitsToSetPerPath</span><span class="cm">,</span> <span class="i">$SetBitNum</span><span class="s">)</span><span class="sc">;</span>
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diff changeset
1120 1107
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1121 1108 <span class="i">$FingerprintsBitVector</span> = <span class="i">$This</span>-&gt;{<span class="w">FingerprintsBitVector</span>}<span class="sc">;</span>
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diff changeset
1122 1109
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1123 1110 <span class="i">$Size</span> = <span class="i">$This</span>-&gt;{<span class="w">Size</span>}<span class="sc">;</span>
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diff changeset
1124 1111
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1125 1112 <span class="i">$SkipBitPosCheck</span> = <span class="n">1</span><span class="sc">;</span>
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1126 1113 <span class="i">$NumOfBitsToSetPerPath</span> = <span class="i">$This</span>-&gt;{<span class="w">NumOfBitsToSetPerPath</span>}<span class="sc">;</span>
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1127 1114
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1128 1115 <span class="k">for</span> <span class="i">$PathLength</span> <span class="s">(</span><span class="k">keys</span> <span class="i">%</span>{<span class="i">$This</span>-&gt;{<span class="w">AtomPathsStrings</span>}}<span class="s">)</span> <span class="s">{</span>
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1129 1116 <span class="k">for</span> <span class="i">$AtomPathString</span> <span class="s">(</span><span class="k">keys</span> <span class="i">%</span>{<span class="i">$This</span>-&gt;{<span class="w">AtomPathsStrings</span>}{<span class="i">$PathLength</span>}}<span class="s">)</span> <span class="s">{</span>
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1130 1117 <span class="i">$AtomPathHashCode</span> = <span class="i">TextUtil::HashCode</span><span class="s">(</span><span class="i">$AtomPathString</span><span class="s">)</span><span class="sc">;</span>
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1131 1118
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1132 1119 <span class="c"># Set random number seed...</span>
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1133 1120 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">UsePerlCoreRandom</span>}<span class="s">)</span> <span class="s">{</span>
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1134 1121 <span class="i">CORE::</span><span class="k">srand</span><span class="s">(</span><span class="i">$AtomPathHashCode</span><span class="s">)</span><span class="sc">;</span>
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diff changeset
1135 1122 <span class="s">}</span>
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diff changeset
1136 1123 <span class="k">else</span> <span class="s">{</span>
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parents:
diff changeset
1137 1124 <span class="i">MathUtil::srandom</span><span class="s">(</span><span class="i">$AtomPathHashCode</span><span class="s">)</span><span class="sc">;</span>
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diff changeset
1138 1125 <span class="s">}</span>
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1139 1126
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1140 1127 <span class="k">for</span> <span class="i">$SetBitNum</span> <span class="s">(</span><span class="n">1</span> .. <span class="i">$NumOfBitsToSetPerPath</span><span class="s">)</span> <span class="s">{</span>
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1141 1128 <span class="i">$AtomPathBitPos</span> = <span class="i">$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>
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1142 1129 <span class="i">$FingerprintsBitVector</span><span class="i">-&gt;SetBit</span><span class="s">(</span><span class="i">$AtomPathBitPos</span><span class="cm">,</span> <span class="i">$SkipBitPosCheck</span><span class="s">)</span><span class="sc">;</span>
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parents:
diff changeset
1143 1130 <span class="s">}</span>
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diff changeset
1144 1131 <span class="s">}</span>
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parents:
diff changeset
1145 1132 <span class="s">}</span>
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diff changeset
1146 1133 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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parents:
diff changeset
1147 1134 <span class="s">}</span>
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diff changeset
1148 1135
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diff changeset
1149 1136 <span class="c"># Set final fingerprits vector...</span>
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parents:
diff changeset
1150 1137 <span class="c">#</span>
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diff changeset
1151 <a name="_SetFinalFingerprintsVector-"></a>1138 <span class="k">sub </span><span class="m">_SetFinalFingerprintsVector</span> <span class="s">{</span>
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diff changeset
1152 1139 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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diff changeset
1153 1140 <span class="k">my</span><span class="s">(</span><span class="i">$PathLength</span><span class="cm">,</span> <span class="i">$AtomPathString</span><span class="cm">,</span> <span class="i">$FingerprintsVector</span><span class="cm">,</span> <span class="i">$AtomPathCount</span><span class="cm">,</span> <span class="i">@Values</span><span class="cm">,</span> <span class="i">@ValueIDs</span><span class="s">)</span><span class="sc">;</span>
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diff changeset
1154 1141
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diff changeset
1155 1142 <span class="i">@Values</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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1156 1143 <span class="i">@ValueIDs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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parents:
diff changeset
1157 1144
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diff changeset
1158 1145 <span class="k">for</span> <span class="i">$PathLength</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">$This</span>-&gt;{<span class="w">AtomPathsStrings</span>}}<span class="s">)</span> <span class="s">{</span>
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diff changeset
1159 1146 <span class="k">for</span> <span class="i">$AtomPathString</span> <span class="s">(</span><span class="k">sort</span> <span class="k">keys</span> <span class="i">%</span>{<span class="i">$This</span>-&gt;{<span class="w">AtomPathsStrings</span>}{<span class="i">$PathLength</span>}}<span class="s">)</span> <span class="s">{</span>
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diff changeset
1160 1147 <span class="i">$AtomPathCount</span> = <span class="i">$This</span>-&gt;{<span class="w">AtomPathsStrings</span>}{<span class="i">$PathLength</span>}{<span class="i">$AtomPathString</span>}<span class="sc">;</span>
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diff changeset
1161 1148
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parents:
diff changeset
1162 1149 <span class="k">push</span> <span class="i">@Values</span><span class="cm">,</span> <span class="i">$AtomPathCount</span><span class="sc">;</span>
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parents:
diff changeset
1163 1150 <span class="k">push</span> <span class="i">@ValueIDs</span><span class="cm">,</span> <span class="i">$AtomPathString</span><span class="sc">;</span>
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deepakjadmin
parents:
diff changeset
1164 1151 <span class="s">}</span>
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parents:
diff changeset
1165 1152 <span class="s">}</span>
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parents:
diff changeset
1166 1153
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diff changeset
1167 1154 <span class="c"># Add PathLengthIDs and values to fingerprint vector...</span>
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parents:
diff changeset
1168 1155 <span class="i">$This</span>-&gt;{<span class="w">FingerprintsVector</span>}<span class="i">-&gt;AddValueIDs</span><span class="s">(</span>\<span class="i">@ValueIDs</span><span class="s">)</span><span class="sc">;</span>
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parents:
diff changeset
1169 1156 <span class="i">$This</span>-&gt;{<span class="w">FingerprintsVector</span>}<span class="i">-&gt;AddValues</span><span class="s">(</span>\<span class="i">@Values</span><span class="s">)</span><span class="sc">;</span>
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parents:
diff changeset
1170 1157
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diff changeset
1171 1158 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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deepakjadmin
parents:
diff changeset
1172 1159 <span class="s">}</span>
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deepakjadmin
parents:
diff changeset
1173 1160
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parents:
diff changeset
1174 1161 <span class="c"># Cache appropriate molecule data...</span>
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parents:
diff changeset
1175 1162 <span class="c">#</span>
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parents:
diff changeset
1176 <a name="_SetupMoleculeDataCache-"></a>1163 <span class="k">sub </span><span class="m">_SetupMoleculeDataCache</span> <span class="s">{</span>
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diff changeset
1177 1164 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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diff changeset
1178 1165
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diff changeset
1179 1166 <span class="c"># Get all atoms...</span>
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parents:
diff changeset
1180 1167 <span class="i">@</span>{<span class="i">$This</span>-&gt;{<span class="w">Atoms</span>}} = <span class="i">$This</span><span class="i">-&gt;GetMolecule</span><span class="s">(</span><span class="s">)</span><span class="i">-&gt;GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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diff changeset
1181 1168
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diff changeset
1182 1169 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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parents:
diff changeset
1183 1170 <span class="s">}</span>
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diff changeset
1184 1171
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diff changeset
1185 1172 <span class="c"># Clear cached molecule data...</span>
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parents:
diff changeset
1186 1173 <span class="c">#</span>
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parents:
diff changeset
1187 <a name="_ClearMoleculeDataCache-"></a>1174 <span class="k">sub </span><span class="m">_ClearMoleculeDataCache</span> <span class="s">{</span>
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parents:
diff changeset
1188 1175 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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diff changeset
1189 1176
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diff changeset
1190 1177 <span class="c"># Clear atoms...</span>
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diff changeset
1191 1178 <span class="i">@</span>{<span class="i">$This</span>-&gt;{<span class="w">Atoms</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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1192 1179
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diff changeset
1193 1180 <span class="c"># Clear path atoms..</span>
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diff changeset
1194 1181 <span class="i">$This</span>-&gt;{<span class="w">AtomPathsRef</span>} = <span class="q">&#39;&#39;</span><span class="sc">;</span>
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diff changeset
1195 1182
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diff changeset
1196 1183 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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diff changeset
1197 1184 <span class="s">}</span>
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diff changeset
1198 1185
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diff changeset
1199 1186 <span class="c"># Set atomic invariants to use atom identifiers...</span>
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diff changeset
1200 1187 <span class="c">#</span>
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diff changeset
1201 <a name="SetAtomicInvariantsToUse-"></a>1188 <span class="k">sub </span><span class="m">SetAtomicInvariantsToUse</span> <span class="s">{</span>
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diff changeset
1202 1189 <span class="k">my</span><span class="s">(</span><span class="i">$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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diff changeset
1203 1190 <span class="k">my</span><span class="s">(</span><span class="i">$FirstValue</span><span class="cm">,</span> <span class="i">$TypeOfFirstValue</span><span class="cm">,</span> <span class="i">$AtomicInvariant</span><span class="cm">,</span> <span class="i">$SpecifiedAtomicInvariant</span><span class="cm">,</span> <span class="i">$AtomicInvariantValue</span><span class="cm">,</span> <span class="i">@SpecifiedAtomicInvariants</span><span class="cm">,</span> <span class="i">@AtomicInvariantsToUse</span><span class="s">)</span><span class="sc">;</span>
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diff changeset
1204 1191
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diff changeset
1205 1192 <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
1206 1193 <span class="w">carp</span> <span class="q">&quot;Warning: ${ClassName}-&gt;SetAtomicInvariantsToUse: No values specified...&quot;</span><span class="sc">;</span>
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parents:
diff changeset
1207 1194 <span class="k">return</span><span class="sc">;</span>
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parents:
diff changeset
1208 1195 <span class="s">}</span>
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diff changeset
1209 1196
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diff changeset
1210 1197 <span class="i">$FirstValue</span> = <span class="i">$Values</span>[<span class="n">0</span>]<span class="sc">;</span>
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diff changeset
1211 1198 <span class="i">$TypeOfFirstValue</span> = <span class="k">ref</span> <span class="i">$FirstValue</span><span class="sc">;</span>
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diff changeset
1212 1199
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diff changeset
1213 1200 <span class="i">@SpecifiedAtomicInvariants</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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diff changeset
1214 1201 <span class="i">@AtomicInvariantsToUse</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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diff changeset
1215 1202
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diff changeset
1216 1203 <span class="k">if</span> <span class="s">(</span><span class="i">$TypeOfFirstValue</span> =~ <span class="q">/^ARRAY/</span><span class="s">)</span> <span class="s">{</span>
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diff changeset
1217 1204 <span class="k">push</span> <span class="i">@SpecifiedAtomicInvariants</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$FirstValue</span>}<span class="sc">;</span>
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parents:
diff changeset
1218 1205 <span class="s">}</span>
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diff changeset
1219 1206 <span class="k">else</span> <span class="s">{</span>
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parents:
diff changeset
1220 1207 <span class="k">push</span> <span class="i">@SpecifiedAtomicInvariants</span><span class="cm">,</span> <span class="i">@Values</span><span class="sc">;</span>
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diff changeset
1221 1208 <span class="s">}</span>
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diff changeset
1222 1209
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diff changeset
1223 1210 <span class="c"># Make sure specified AtomicInvariants are valid...</span>
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diff changeset
1224 1211 <span class="k">for</span> <span class="i">$SpecifiedAtomicInvariant</span> <span class="s">(</span><span class="i">@SpecifiedAtomicInvariants</span><span class="s">)</span> <span class="s">{</span>
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diff changeset
1225 1212 <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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1226 1213 <span class="w">croak</span> <span class="q">&quot;Error: ${ClassName}-&gt;SetAtomicInvariantsToUse: Specified atomic invariant, $SpecifiedAtomicInvariant, is not supported...\n &quot;</span><span class="sc">;</span>
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diff changeset
1227 1214 <span class="s">}</span>
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diff changeset
1228 1215 <span class="i">$AtomicInvariant</span> = <span class="i">$SpecifiedAtomicInvariant</span><span class="sc">;</span>
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1229 1216 <span class="k">push</span> <span class="i">@AtomicInvariantsToUse</span><span class="cm">,</span> <span class="i">$AtomicInvariant</span><span class="sc">;</span>
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diff changeset
1230 1217 <span class="s">}</span>
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diff changeset
1231 1218
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diff changeset
1232 1219 <span class="c"># Set atomic invariants to use...</span>
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diff changeset
1233 1220 <span class="i">@</span>{<span class="i">$This</span>-&gt;{<span class="w">AtomicInvariantsToUse</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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1234 1221 <span class="k">push</span> <span class="i">@</span>{<span class="i">$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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1235 1222
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diff changeset
1236 1223 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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diff changeset
1237 1224 <span class="s">}</span>
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1238 1225
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diff changeset
1239 1226 <span class="c"># Set functional classes to use for atom identifiers...</span>
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diff changeset
1240 1227 <span class="c">#</span>
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diff changeset
1241 <a name="SetFunctionalClassesToUse-"></a>1228 <span class="k">sub </span><span class="m">SetFunctionalClassesToUse</span> <span class="s">{</span>
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1242 1229 <span class="k">my</span><span class="s">(</span><span class="i">$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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1243 1230 <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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1244 1231
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1245 1232 <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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1246 1233 <span class="w">carp</span> <span class="q">&quot;Warning: ${ClassName}-&gt;SetFunctionalClassesToUse: No values specified...&quot;</span><span class="sc">;</span>
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1247 1234 <span class="k">return</span><span class="sc">;</span>
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diff changeset
1248 1235 <span class="s">}</span>
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1249 1236
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1250 1237 <span class="k">if</span> <span class="s">(</span><span class="i">$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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1251 1238 <span class="w">carp</span> <span class="q">&quot;Warning: ${ClassName}-&gt;SetFunctionalClassesToUse: FunctionalClassesToUse can&#39;t be set for InitialAtomIdentifierType of $This-&gt;{AtomIdentifierType}...&quot;</span><span class="sc">;</span>
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diff changeset
1252 1239 <span class="k">return</span><span class="sc">;</span>
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diff changeset
1253 1240 <span class="s">}</span>
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diff changeset
1254 1241
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1255 1242 <span class="i">$FirstValue</span> = <span class="i">$Values</span>[<span class="n">0</span>]<span class="sc">;</span>
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1256 1243 <span class="i">$TypeOfFirstValue</span> = <span class="k">ref</span> <span class="i">$FirstValue</span><span class="sc">;</span>
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1257 1244
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1258 1245 <span class="i">@SpecifiedFunctionalClasses</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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1259 1246 <span class="i">@FunctionalClassesToUse</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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1260 1247
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diff changeset
1261 1248 <span class="k">if</span> <span class="s">(</span><span class="i">$TypeOfFirstValue</span> =~ <span class="q">/^ARRAY/</span><span class="s">)</span> <span class="s">{</span>
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1262 1249 <span class="k">push</span> <span class="i">@SpecifiedFunctionalClasses</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$FirstValue</span>}<span class="sc">;</span>
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diff changeset
1263 1250 <span class="s">}</span>
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diff changeset
1264 1251 <span class="k">else</span> <span class="s">{</span>
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diff changeset
1265 1252 <span class="k">push</span> <span class="i">@SpecifiedFunctionalClasses</span><span class="cm">,</span> <span class="i">@Values</span><span class="sc">;</span>
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diff changeset
1266 1253 <span class="s">}</span>
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diff changeset
1267 1254
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diff changeset
1268 1255 <span class="c"># Make sure specified FunctionalClasses are valid...</span>
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diff changeset
1269 1256 <span class="k">for</span> <span class="i">$SpecifiedFunctionalClass</span> <span class="s">(</span><span class="i">@SpecifiedFunctionalClasses</span><span class="s">)</span> <span class="s">{</span>
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1270 1257 <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>
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1271 1258 <span class="w">croak</span> <span class="q">&quot;Error: ${ClassName}-&gt;SetFunctionalClassesToUse: Specified functional class, $SpecifiedFunctionalClass, is not supported...\n &quot;</span><span class="sc">;</span>
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diff changeset
1272 1259 <span class="s">}</span>
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diff changeset
1273 1260 <span class="k">push</span> <span class="i">@FunctionalClassesToUse</span><span class="cm">,</span> <span class="i">$SpecifiedFunctionalClass</span><span class="sc">;</span>
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diff changeset
1274 1261 <span class="s">}</span>
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diff changeset
1275 1262
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diff changeset
1276 1263 <span class="c"># Set functional classes to use...</span>
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diff changeset
1277 1264 <span class="i">@</span>{<span class="i">$This</span>-&gt;{<span class="w">FunctionalClassesToUse</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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1278 1265 <span class="k">push</span> <span class="i">@</span>{<span class="i">$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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diff changeset
1279 1266
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diff changeset
1280 1267 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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diff changeset
1281 1268 <span class="s">}</span>
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diff changeset
1282 1269
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diff changeset
1283 1270 <span class="c"># Initialize atom indentifier type information...</span>
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diff changeset
1284 1271 <span class="c">#</span>
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diff changeset
1285 1272 <span class="c"># Current supported values:</span>
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diff changeset
1286 1273 <span class="c">#</span>
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diff changeset
1287 1274 <span class="c"># AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, FunctionalClassAtomTypes,</span>
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diff changeset
1288 1275 <span class="c"># MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes</span>
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diff changeset
1289 1276 <span class="c">#</span>
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diff changeset
1290 <a name="_InitializeAtomIdentifierTypeInformation-"></a>1277 <span class="k">sub </span><span class="m">_InitializeAtomIdentifierTypeInformation</span> <span class="s">{</span>
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diff changeset
1291 1278 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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diff changeset
1292 1279
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diff changeset
1293 1280 <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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1294 1281 <span class="i">$This</span><span class="i">-&gt;_InitializeAtomicInvariantsAtomTypesInformation</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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diff changeset
1295 1282 <span class="s">}</span>
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diff changeset
1296 1283 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^FunctionalClassAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span>
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diff changeset
1297 1284 <span class="i">$This</span><span class="i">-&gt;_InitializeFunctionalClassAtomTypesInformation</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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diff changeset
1298 1285 <span class="s">}</span>
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diff changeset
1299 1286 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^(DREIDINGAtomTypes|EStateAtomTypes|MMFF94AtomTypes|SLogPAtomTypes|SYBYLAtomTypes|TPSAAtomTypes|UFFAtomTypes)$/i</span><span class="s">)</span> <span class="s">{</span>
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diff changeset
1300 1287 <span class="c"># Nothing to do for now...</span>
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diff changeset
1301 1288 <span class="s">}</span>
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diff changeset
1302 1289 <span class="k">else</span> <span class="s">{</span>
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diff changeset
1303 1290 <span class="w">croak</span> <span class="q">&quot;Error: ${ClassName}-&gt;_InitializeAtomIdentifierTypeInformation: Unknown atom indentifier type $This-&gt;{AtomIdentifierType}...&quot;</span><span class="sc">;</span>
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diff changeset
1304 1291 <span class="s">}</span>
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diff changeset
1305 1292
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diff changeset
1306 1293 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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diff changeset
1307 1294 <span class="s">}</span>
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diff changeset
1308 1295
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diff changeset
1309 1296 <span class="c"># Initialize atomic invariants atom types to use for generating atom identifiers...</span>
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diff changeset
1310 1297 <span class="c">#</span>
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diff changeset
1311 1298 <span class="c"># Let:</span>
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diff changeset
1312 1299 <span class="c"># AS = Atom symbol corresponding to element symbol</span>
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diff changeset
1313 1300 <span class="c">#</span>
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diff changeset
1314 1301 <span class="c"># X&lt;n&gt; = Number of non-hydrogen atom neighbors or heavy atoms attached to atom</span>
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diff changeset
1315 1302 <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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diff changeset
1316 1303 <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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diff changeset
1317 1304 <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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diff changeset
1318 1305 <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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diff changeset
1319 1306 <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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diff changeset
1320 1307 <span class="c"># H&lt;n&gt; = Number of implicit and explicit hydrogens for atom</span>
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diff changeset
1321 1308 <span class="c"># Ar = Aromatic annotation indicating whether atom is aromatic</span>
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diff changeset
1322 1309 <span class="c"># RA = Ring atom annotation indicating whether atom is a ring</span>
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diff changeset
1323 1310 <span class="c"># FC&lt;+n/-n&gt; = Formal charge assigned to atom</span>
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diff changeset
1324 1311 <span class="c"># MN&lt;n&gt; = Mass number indicating isotope other than most abundant isotope</span>
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diff changeset
1325 1312 <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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diff changeset
1326 1313 <span class="c">#</span>
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diff changeset
1327 1314 <span class="c"># Then:</span>
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diff changeset
1328 1315 <span class="c">#</span>
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diff changeset
1329 1316 <span class="c"># Atom type generated by AtomTypes::AtomicInvariantsAtomTypes class corresponds to:</span>
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diff changeset
1330 1317 <span class="c">#</span>
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1331 1318 <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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diff changeset
1332 1319 <span class="c">#</span>
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1333 1320 <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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diff changeset
1334 1321 <span class="c"># optional. Default atomic invariants used for AtomID are: AS, X&lt;n&gt;, BO&lt;n&gt;, H&lt;n&gt;, FC&lt;+n/-n&gt;.</span>
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diff changeset
1335 1322 <span class="c"># AtomID specification doesn&#39;t include atomic invariants with zero or undefined values.</span>
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diff changeset
1336 1323 <span class="c">#</span>
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diff changeset
1337 <a name="_InitializeAtomicInvariantsAtomTypesInformation-"></a>1324 <span class="k">sub </span><span class="m">_InitializeAtomicInvariantsAtomTypesInformation</span> <span class="s">{</span>
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diff changeset
1338 1325 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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diff changeset
1339 1326
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diff changeset
1340 1327 <span class="c"># Default atomic invariants to use for generating atom neighborhood atom IDs: AS, X, BO, H, FC</span>
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diff changeset
1341 1328 <span class="c">#</span>
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1342 1329 <span class="i">@</span>{<span class="i">$This</span>-&gt;{<span class="w">AtomicInvariantsToUse</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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1343 1330 <span class="i">@</span>{<span class="i">$This</span>-&gt;{<span class="w">AtomicInvariantsToUse</span>}} = <span class="s">(</span><span class="q">&#39;AS&#39;</span><span class="cm">,</span> <span class="q">&#39;X&#39;</span><span class="cm">,</span> <span class="q">&#39;BO&#39;</span><span class="cm">,</span> <span class="q">&#39;H&#39;</span><span class="cm">,</span> <span class="q">&#39;FC&#39;</span><span class="s">)</span><span class="sc">;</span>
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1344 1331
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1345 1332 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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diff changeset
1346 1333 <span class="s">}</span>
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1347 1334
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1348 1335 <span class="c"># Initialize functional class atom types, generated by AtomTypes::FunctionalClassAtomTypes</span>
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1349 1336 <span class="c"># class, to use for generating atom identifiers...</span>
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1350 1337 <span class="c">#</span>
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1351 1338 <span class="c"># Let:</span>
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1352 1339 <span class="c"># HBD: HydrogenBondDonor</span>
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1353 1340 <span class="c"># HBA: HydrogenBondAcceptor</span>
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1354 1341 <span class="c"># PI : PositivelyIonizable</span>
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diff changeset
1355 1342 <span class="c"># NI : NegativelyIonizable</span>
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1356 1343 <span class="c"># Ar : Aromatic</span>
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1357 1344 <span class="c"># Hal : Halogen</span>
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1358 1345 <span class="c"># H : Hydrophobic</span>
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1359 1346 <span class="c"># RA : RingAtom</span>
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1360 1347 <span class="c"># CA : ChainAtom</span>
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1361 1348 <span class="c">#</span>
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1362 1349 <span class="c"># Then:</span>
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1363 1350 <span class="c">#</span>
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1364 1351 <span class="c"># Functiononal class atom type specification for an atom corresponds to:</span>
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parents:
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1365 1352 <span class="c">#</span>
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1366 1353 <span class="c"># Ar.CA.H.HBA.HBD.Hal.NI.PI.RA</span>
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1367 1354 <span class="c">#</span>
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1368 1355 <span class="c"># Default functional classes used are: HBD, HBA, PI, NI, Ar, Hal</span>
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1369 1356 <span class="c">#</span>
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1370 1357 <span class="c"># FunctionalAtomTypes are assigned using the following definitions [ Ref 60-61, Ref 65-66 ]:</span>
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1371 1358 <span class="c">#</span>
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1372 1359 <span class="c"># HydrogenBondDonor: NH, NH2, OH</span>
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1373 1360 <span class="c"># HydrogenBondAcceptor: N[!H], O</span>
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1374 1361 <span class="c"># PositivelyIonizable: +, NH2</span>
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1375 1362 <span class="c"># NegativelyIonizable: -, C(=O)OH, S(=O)OH, P(=O)OH</span>
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1376 1363 <span class="c">#</span>
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1377 <a name="_InitializeFunctionalClassAtomTypesInformation-"></a>1364 <span class="k">sub </span><span class="m">_InitializeFunctionalClassAtomTypesInformation</span> <span class="s">{</span>
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1378 1365 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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1379 1366
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1380 1367 <span class="c"># Default functional class atom typess to use for generating atom identifiers</span>
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1381 1368 <span class="c"># are: HBD, HBA, PI, NI, Ar, Hal</span>
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1382 1369 <span class="c">#</span>
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1383 1370 <span class="i">@</span>{<span class="i">$This</span>-&gt;{<span class="w">FunctionalClassesToUse</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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1384 1371 <span class="i">@</span>{<span class="i">$This</span>-&gt;{<span class="w">FunctionalClassesToUse</span>}} = <span class="s">(</span><span class="q">&#39;HBD&#39;</span><span class="cm">,</span> <span class="q">&#39;HBA&#39;</span><span class="cm">,</span> <span class="q">&#39;PI&#39;</span><span class="cm">,</span> <span class="q">&#39;NI&#39;</span><span class="cm">,</span> <span class="q">&#39;Ar&#39;</span><span class="cm">,</span> <span class="q">&#39;Hal&#39;</span><span class="s">)</span><span class="sc">;</span>
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1385 1372
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1386 1373 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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1387 1374 <span class="s">}</span>
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1388 1375
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1389 1376 <span class="c"># Return a string containg data for PathLengthFingerprints object...</span>
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1390 1377 <span class="c">#</span>
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1391 <a name="StringifyPathLengthFingerprints-"></a>1378 <span class="k">sub </span><span class="m">StringifyPathLengthFingerprints</span> <span class="s">{</span>
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1392 1379 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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1393 1380 <span class="k">my</span><span class="s">(</span><span class="i">$PathLengthsFingerprintsString</span><span class="s">)</span><span class="sc">;</span>
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1394 1381
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1395 1382 <span class="c"># Type of fingerprint...</span>
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1396 1383 <span class="i">$PathLengthsFingerprintsString</span> = <span class="q">&quot;Fingerprint type: $This-&gt;{Type}; AtomIdentifierType: $This-&gt;{AtomIdentifierType}&quot;</span><span class="sc">;</span>
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1397 1384
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1398 1385 <span class="c"># Path length...</span>
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1399 1386 <span class="i">$PathLengthsFingerprintsString</span> .= <span class="q">&quot;; MinPathLength: $This-&gt;{MinLength}; MaxPathLength: $This-&gt;{MaxLength}&quot;</span><span class="sc">;</span>
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1400 1387
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1401 1388 <span class="c"># Fingerprint generation control...</span>
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1402 1389 <span class="k">my</span><span class="s">(</span><span class="i">$AllowSharedBonds</span><span class="cm">,</span> <span class="i">$AllowRings</span><span class="cm">,</span> <span class="i">$UseBondSymbols</span><span class="cm">,</span> <span class="i">$UseUniquePaths</span><span class="s">)</span><span class="sc">;</span>
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1403 1390
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1404 1391 <span class="i">$AllowSharedBonds</span> = <span class="i">$This</span>-&gt;{<span class="w">AllowSharedBonds</span>} ? <span class="q">&quot;Yes&quot;</span> <span class="co">:</span> <span class="q">&quot;No&quot;</span><span class="sc">;</span>
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1405 1392 <span class="i">$AllowRings</span> = <span class="i">$This</span>-&gt;{<span class="w">AllowRings</span>} ? <span class="q">&quot;Yes&quot;</span> <span class="co">:</span> <span class="q">&quot;No&quot;</span><span class="sc">;</span>
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1406 1393 <span class="i">$UseBondSymbols</span> = <span class="i">$This</span>-&gt;{<span class="w">UseBondSymbols</span>} ? <span class="q">&quot;Yes&quot;</span> <span class="co">:</span> <span class="q">&quot;No&quot;</span><span class="sc">;</span>
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1407 1394 <span class="i">$UseUniquePaths</span> = <span class="i">$This</span>-&gt;{<span class="w">UseBondSymbols</span>} ? <span class="q">&quot;Yes&quot;</span> <span class="co">:</span> <span class="q">&quot;No&quot;</span><span class="sc">;</span>
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1408 1395
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1409 1396 <span class="i">$PathLengthsFingerprintsString</span> .= <span class="q">&quot;; UseUniquePaths: $UseUniquePaths; AllowSharedBonds: $AllowSharedBonds; AllowRings: $AllowRings; UseBondSymbols: $UseBondSymbols&quot;</span><span class="sc">;</span>
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1410 1397
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1411 1398 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^AtomicInvariantsAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span>
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1412 1399 <span class="k">my</span><span class="s">(</span><span class="i">$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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1413 1400
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1414 1401 <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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1415 1402 <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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1416 1403
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1417 1404 <span class="k">for</span> <span class="i">$AtomicInvariant</span> <span class="s">(</span><span class="i">@AtomicInvariantsOrder</span><span class="s">)</span> <span class="s">{</span>
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1418 1405 <span class="k">push</span> <span class="i">@AtomicInvariants</span><span class="cm">,</span> <span class="q">&quot;$AtomicInvariant: $AvailableAtomicInvariants{$AtomicInvariant}&quot;</span><span class="sc">;</span>
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1419 1406 <span class="s">}</span>
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1420 1407
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1421 1408 <span class="i">$PathLengthsFingerprintsString</span> .= <span class="q">&quot;; AtomicInvariantsToUse: &lt;&quot;</span> . <span class="i">TextUtil::JoinWords</span><span class="s">(</span>\<span class="i">@</span>{<span class="i">$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>
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1422 1409 <span class="i">$PathLengthsFingerprintsString</span> .= <span class="q">&quot;; AtomicInvariantsOrder: &lt;&quot;</span> . <span class="i">TextUtil::JoinWords</span><span class="s">(</span>\<span class="i">@AtomicInvariantsOrder</span><span class="cm">,</span> <span class="q">&quot;, &quot;</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span> . <span class="q">&quot;&gt;&quot;</span><span class="sc">;</span>
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1423 1410 <span class="i">$PathLengthsFingerprintsString</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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1424 1411 <span class="s">}</span>
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1425 1412 <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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1426 1413 <span class="k">my</span><span class="s">(</span><span class="i">$FunctionalClass</span><span class="cm">,</span> <span class="i">@FunctionalClasses</span><span class="cm">,</span> <span class="i">@FunctionalClassesOrder</span><span class="cm">,</span> <span class="i">%AvailableFunctionalClasses</span><span class="s">)</span><span class="sc">;</span>
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1427 1414
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1428 1415 <span class="i">@FunctionalClassesOrder</span> = <span class="i">AtomTypes::FunctionalClassAtomTypes::GetFunctionalClassesOrder</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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1429 1416 <span class="i">%AvailableFunctionalClasses</span> = <span class="i">AtomTypes::FunctionalClassAtomTypes::GetAvailableFunctionalClasses</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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1430 1417
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1431 1418 <span class="k">for</span> <span class="i">$FunctionalClass</span> <span class="s">(</span><span class="i">@FunctionalClassesOrder</span><span class="s">)</span> <span class="s">{</span>
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1432 1419 <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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1433 1420 <span class="s">}</span>
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1434 1421
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1435 1422 <span class="i">$PathLengthsFingerprintsString</span> .= <span class="q">&quot;; FunctionalClassesToUse: &lt;&quot;</span> . <span class="i">TextUtil::JoinWords</span><span class="s">(</span>\<span class="i">@</span>{<span class="i">$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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1436 1423 <span class="i">$PathLengthsFingerprintsString</span> .= <span class="q">&quot;; FunctionalClassesOrder: &lt;&quot;</span> . <span class="i">TextUtil::JoinWords</span><span class="s">(</span>\<span class="i">@FunctionalClassesOrder</span><span class="cm">,</span> <span class="q">&quot;, &quot;</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span> . <span class="q">&quot;&gt;&quot;</span><span class="sc">;</span>
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1437 1424 <span class="i">$PathLengthsFingerprintsString</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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1438 1425 <span class="s">}</span>
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1439 1426
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1440 1427 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">Type</span>} =~ <span class="q">/^PathLengthBits$/i</span><span class="s">)</span> <span class="s">{</span>
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1441 1428 <span class="c"># Size...</span>
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diff changeset
1442 1429 <span class="i">$PathLengthsFingerprintsString</span> .= <span class="q">&quot;; Size: $This-&gt;{Size}; MinSize: $This-&gt;{MinSize}; MaxSize: $This-&gt;{MaxSize}&quot;</span><span class="sc">;</span>
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1443 1430
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diff changeset
1444 1431 <span class="c"># NumOfBitsToSetPerPath...</span>
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diff changeset
1445 1432 <span class="i">$PathLengthsFingerprintsString</span> .= <span class="q">&quot;; NumOfBitsToSetPerPath: $This-&gt;{NumOfBitsToSetPerPath}&quot;</span><span class="sc">;</span>
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1446 1433
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diff changeset
1447 1434 <span class="c"># Fingerprint bit density and num of bits set...</span>
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1448 1435 <span class="k">my</span><span class="s">(</span><span class="i">$NumOfSetBits</span><span class="cm">,</span> <span class="i">$BitDensity</span><span class="s">)</span><span class="sc">;</span>
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1449 1436 <span class="i">$NumOfSetBits</span> = <span class="i">$This</span>-&gt;{<span class="w">FingerprintsBitVector</span>}<span class="i">-&gt;GetNumOfSetBits</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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1450 1437 <span class="i">$BitDensity</span> = <span class="i">$This</span>-&gt;{<span class="w">FingerprintsBitVector</span>}<span class="i">-&gt;GetFingerprintsBitDensity</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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diff changeset
1451 1438 <span class="i">$PathLengthsFingerprintsString</span> .= <span class="q">&quot;; NumOfOnBits: $NumOfSetBits; BitDensity: $BitDensity&quot;</span><span class="sc">;</span>
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diff changeset
1452 1439
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diff changeset
1453 1440 <span class="i">$PathLengthsFingerprintsString</span> .= <span class="q">&quot;; FingerprintsBitVector: &lt; $This-&gt;{FingerprintsBitVector} &gt;&quot;</span><span class="sc">;</span>
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diff changeset
1454 1441 <span class="s">}</span>
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1455 1442 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>-&gt;{<span class="w">Type</span>} =~ <span class="q">/^PathLengthCount$/i</span><span class="s">)</span> <span class="s">{</span>
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diff changeset
1456 1443 <span class="i">$PathLengthsFingerprintsString</span> .= <span class="q">&quot;; FingerprintsVector: &lt; $This-&gt;{FingerprintsVector} &gt;&quot;</span><span class="sc">;</span>
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deepakjadmin
parents:
diff changeset
1457 1444 <span class="s">}</span>
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deepakjadmin
parents:
diff changeset
1458 1445
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deepakjadmin
parents:
diff changeset
1459 1446 <span class="k">return</span> <span class="i">$PathLengthsFingerprintsString</span><span class="sc">;</span>
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deepakjadmin
parents:
diff changeset
1460 1447 <span class="s">}</span>
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deepakjadmin
parents:
diff changeset
1461 1448
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deepakjadmin
parents:
diff changeset
1462 <a name="EOF-"></a></pre>
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deepakjadmin
parents:
diff changeset
1463 <p>&nbsp;</p>
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deepakjadmin
parents:
diff changeset
1464 <br />
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deepakjadmin
parents:
diff changeset
1465 <center>
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deepakjadmin
parents:
diff changeset
1466 <img src="../../../images/h2o2.png">
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deepakjadmin
parents:
diff changeset
1467 </center>
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deepakjadmin
parents:
diff changeset
1468 </body>
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deepakjadmin
parents:
diff changeset
1469 </html>