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13 <pre>
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14 <a name="package-Fingerprints::TopologicalAtomPairsFingerprints-"></a> 1 <span class="k">package </span><span class="i">Fingerprints::TopologicalAtomPairsFingerprints</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: TopologicalAtomPairsFingerprints.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: 1.30 $</span>
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19 6 <span class="c">#</span>
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20 7 <span class="c"># Author: Manish Sud <msud@san.rr.com></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 <http://www.gnu.org/licenses/> 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">Fingerprints::Fingerprints</span><span class="sc">;</span>
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46 33 <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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47 34 <span class="k">use</span> <span class="w">Molecule</span><span class="sc">;</span>
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48 35 <span class="k">use</span> <span class="w">AtomTypes::AtomicInvariantsAtomTypes</span><span class="sc">;</span>
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49 36 <span class="k">use</span> <span class="w">AtomTypes::DREIDINGAtomTypes</span><span class="sc">;</span>
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50 37 <span class="k">use</span> <span class="w">AtomTypes::EStateAtomTypes</span><span class="sc">;</span>
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51 38 <span class="k">use</span> <span class="w">AtomTypes::FunctionalClassAtomTypes</span><span class="sc">;</span>
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52 39 <span class="k">use</span> <span class="w">AtomTypes::MMFF94AtomTypes</span><span class="sc">;</span>
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53 40 <span class="k">use</span> <span class="w">AtomTypes::SLogPAtomTypes</span><span class="sc">;</span>
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54 41 <span class="k">use</span> <span class="w">AtomTypes::SYBYLAtomTypes</span><span class="sc">;</span>
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55 42 <span class="k">use</span> <span class="w">AtomTypes::TPSAAtomTypes</span><span class="sc">;</span>
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56 43 <span class="k">use</span> <span class="w">AtomTypes::UFFAtomTypes</span><span class="sc">;</span>
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57 44
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58 45 <span class="k">use</span> <span class="w">vars</span> <span class="q">qw(@ISA @EXPORT @EXPORT_OK %EXPORT_TAGS)</span><span class="sc">;</span>
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59 46
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60 47 <span class="i">@ISA</span> = <span class="q">qw(Fingerprints::Fingerprints Exporter)</span><span class="sc">;</span>
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61 48 <span class="i">@EXPORT</span> = <span class="q">qw()</span><span class="sc">;</span>
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62 49 <span class="i">@EXPORT_OK</span> = <span class="q">qw()</span><span class="sc">;</span>
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63 50
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64 51 <span class="i">%EXPORT_TAGS</span> = <span class="s">(</span><span class="w">all</span> <span class="cm">=></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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65 52
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66 53 <span class="c"># Setup class variables...</span>
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67 54 <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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68 55 <span class="i">_InitializeClass</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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69 56
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70 57 <span class="c"># Overload Perl functions...</span>
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71 58 <span class="k">use</span> <span class="w">overload</span> <span class="q">'""'</span> <span class="cm">=></span> <span class="q">'StringifyTopologicalAtomPairsFingerprints'</span><span class="sc">;</span>
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72 59
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73 60 <span class="c"># Class constructor...</span>
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74 <a name="new-"></a> 61 <span class="k">sub </span><span class="m">new</span> <span class="s">{</span>
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75 62 <span class="k">my</span><span class="s">(</span><span class="i">$Class</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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76 63
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77 64 <span class="c"># Initialize object...</span>
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78 65 <span class="k">my</span> <span class="i">$This</span> = <span class="i">$Class</span><span class="i">->SUPER::new</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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79 66 <span class="k">bless</span> <span class="i">$This</span><span class="cm">,</span> <span class="k">ref</span><span class="s">(</span><span class="i">$Class</span><span class="s">)</span> || <span class="i">$Class</span><span class="sc">;</span>
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80 67 <span class="i">$This</span><span class="i">->_InitializeTopologicalAtomPairsFingerprints</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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81 68
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82 69 <span class="i">$This</span><span class="i">->_InitializeTopologicalAtomPairsFingerprintsProperties</span><span class="s">(</span><span class="i">%NamesAndValues</span><span class="s">)</span><span class="sc">;</span>
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83 70
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84 71 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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85 72 <span class="s">}</span>
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86 73
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87 74 <span class="c"># Initialize object data...</span>
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88 75 <span class="c">#</span>
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89 <a name="_InitializeTopologicalAtomPairsFingerprints-"></a> 76 <span class="k">sub </span><span class="m">_InitializeTopologicalAtomPairsFingerprints</span> <span class="s">{</span>
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90 77 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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91 78
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92 79 <span class="c"># Type of fingerprint...</span>
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93 80 <span class="i">$This</span>->{<span class="w">Type</span>} = <span class="q">'TopologicalAtomPairs'</span><span class="sc">;</span>
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94 81
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95 82 <span class="c"># Type of vector...</span>
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96 83 <span class="i">$This</span>->{<span class="w">VectorType</span>} = <span class="q">'FingerprintsVector'</span><span class="sc">;</span>
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97 84
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98 85 <span class="c"># Type of FingerprintsVector...</span>
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99 86 <span class="i">$This</span>->{<span class="w">FingerprintsVectorType</span>} = <span class="q">'NumericalValues'</span><span class="sc">;</span>
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100 87
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101 88 <span class="c"># Minimum and maximum bond distance between atom paris...</span>
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102 89 <span class="i">$This</span>->{<span class="w">MinDistance</span>} = <span class="n">1</span><span class="sc">;</span>
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103 90 <span class="i">$This</span>->{<span class="w">MaxDistance</span>} = <span class="n">10</span><span class="sc">;</span>
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104 91
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105 92 <span class="c"># Atom identifier type to use for atom IDs in atom pairs...</span>
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106 93 <span class="c">#</span>
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107 94 <span class="c"># Currently supported values are: AtomicInvariantsAtomTypes, DREIDINGAtomTypes,</span>
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108 95 <span class="c"># EStateAtomTypes, FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes,</span>
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109 96 <span class="c"># SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes</span>
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110 97 <span class="c">#</span>
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111 98 <span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} = <span class="q">''</span><span class="sc">;</span>
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112 99
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113 100 <span class="c"># Atom types assigned to each heavy atom...</span>
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114 101 <span class="c">#</span>
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115 102 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">AssignedAtomTypes</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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116 103
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117 104 <span class="c"># All atom pairs between minimum and maximum distance...</span>
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118 105 <span class="c">#</span>
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119 106 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomPairsIDs</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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120 107 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">AtomPairsCount</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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121 108 <span class="s">}</span>
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122 109
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123 110 <span class="c"># Initialize class ...</span>
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124 <a name="_InitializeClass-"></a> 111 <span class="k">sub </span><span class="m">_InitializeClass</span> <span class="s">{</span>
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125 112 <span class="c">#Class name...</span>
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126 113 <span class="i">$ClassName</span> = <span class="w">__PACKAGE__</span><span class="sc">;</span>
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127 114 <span class="s">}</span>
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128 115
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129 116 <span class="c"># Initialize object properties....</span>
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130 <a name="_InitializeTopologicalAtomPairsFingerprintsProperties-"></a> 117 <span class="k">sub </span><span class="m">_InitializeTopologicalAtomPairsFingerprintsProperties</span> <span class="s">{</span>
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131 118 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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132 119
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133 120 <span class="k">my</span><span class="s">(</span><span class="i">$Name</span><span class="cm">,</span> <span class="i">$Value</span><span class="cm">,</span> <span class="i">$MethodName</span><span class="s">)</span><span class="sc">;</span>
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134 121 <span class="k">while</span> <span class="s">(</span><span class="s">(</span><span class="i">$Name</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="k">each</span> <span class="i">%NamesAndValues</span><span class="s">)</span> <span class="s">{</span>
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135 122 <span class="i">$MethodName</span> = <span class="q">"Set${Name}"</span><span class="sc">;</span>
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136 123 <span class="i">$This</span><span class="i">->$MethodName</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="sc">;</span>
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137 124 <span class="s">}</span>
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138 125
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139 126 <span class="c"># Make sure molecule object was specified...</span>
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140 127 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$NamesAndValues</span>{<span class="w">Molecule</span>}<span class="s">)</span> <span class="s">{</span>
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141 128 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->New: Object can't be instantiated without specifying molecule..."</span><span class="sc">;</span>
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142 129 <span class="s">}</span>
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143 130 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$NamesAndValues</span>{<span class="w">AtomIdentifierType</span>}<span class="s">)</span> <span class="s">{</span>
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144 131 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->New: Object can't be instantiated without specifying AtomIdentifierType..."</span><span class="sc">;</span>
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145 132 <span class="s">}</span>
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146 133
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147 134 <span class="i">$This</span><span class="i">->_InitializeFingerprintsVector</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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148 135
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149 136 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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150 137 <span class="s">}</span>
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151 138
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152 139 <span class="c"># Set minimum distance for atom pairs...</span>
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153 140 <span class="c">#</span>
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154 <a name="SetMinDistance-"></a> 141 <span class="k">sub </span><span class="m">SetMinDistance</span> <span class="s">{</span>
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155 142 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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156 143
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157 144 <span class="k">if</span> <span class="s">(</span>!<span class="i">TextUtil::IsPositiveInteger</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
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158 145 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetMinDistance: MinDistance value, $Value, is not valid: It must be a positive integer..."</span><span class="sc">;</span>
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159 146 <span class="s">}</span>
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160 147 <span class="i">$This</span>->{<span class="w">MinDistance</span>} = <span class="i">$Value</span><span class="sc">;</span>
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161 148
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162 149 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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163 150 <span class="s">}</span>
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164 151
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165 152 <span class="c"># Set maximum distance for atom pairs...</span>
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166 153 <span class="c">#</span>
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167 <a name="SetMaxDistance-"></a> 154 <span class="k">sub </span><span class="m">SetMaxDistance</span> <span class="s">{</span>
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168 155 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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169 156
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170 157 <span class="k">if</span> <span class="s">(</span>!<span class="i">TextUtil::IsPositiveInteger</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
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171 158 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetMaxDistance: MaxDistance value, $Value, is not valid: It must be a positive integer..."</span><span class="sc">;</span>
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172 159 <span class="s">}</span>
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173 160 <span class="i">$This</span>->{<span class="w">MaxDistance</span>} = <span class="i">$Value</span><span class="sc">;</span>
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174 161
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175 162 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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176 163 <span class="s">}</span>
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177 164
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178 165 <span class="c"># Set atom identifier type..</span>
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179 166 <span class="c">#</span>
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180 <a name="SetAtomIdentifierType-"></a> 167 <span class="k">sub </span><span class="m">SetAtomIdentifierType</span> <span class="s">{</span>
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181 168 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$IdentifierType</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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182 169
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183 170 <span class="k">if</span> <span class="s">(</span><span class="i">$IdentifierType</span> !~ <span class="q">/^(AtomicInvariantsAtomTypes|DREIDINGAtomTypes|EStateAtomTypes|FunctionalClassAtomTypes|MMFF94AtomTypes|SLogPAtomTypes|SYBYLAtomTypes|TPSAAtomTypes|UFFAtomTypes)$/i</span><span class="s">)</span> <span class="s">{</span>
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184 171 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetAtomIdentifierType: Specified value, $IdentifierType, for AtomIdentifierType is not vaild. Supported types in current release of MayaChemTools: AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes, and UFFAtomTypes."</span><span class="sc">;</span>
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185 172 <span class="s">}</span>
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186 173
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187 174 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>}<span class="s">)</span> <span class="s">{</span>
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188 175 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SeAtomIdentifierType: Can't change intial atom identifier type: It's already set..."</span><span class="sc">;</span>
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189 176 <span class="s">}</span>
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190 177
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191 178 <span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} = <span class="i">$IdentifierType</span><span class="sc">;</span>
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192 179
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193 180 <span class="c"># Initialize atom identifier type information...</span>
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194 181 <span class="i">$This</span><span class="i">->_InitializeAtomIdentifierTypeInformation</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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195 182
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196 183 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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197 184 <span class="s">}</span>
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198 185
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199 186 <span class="c"># Generate fingerprints description...</span>
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200 187 <span class="c">#</span>
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201 <a name="GetDescription-"></a> 188 <span class="k">sub </span><span class="m">GetDescription</span> <span class="s">{</span>
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202 189 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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203 190
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|
204 191 <span class="c"># Is description explicity set?</span>
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|
205 192 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$This</span>->{<span class="w">Description</span>}<span class="s">)</span> <span class="s">{</span>
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|
|
206 193 <span class="k">return</span> <span class="i">$This</span>->{<span class="w">Description</span>}<span class="sc">;</span>
|
|
|
207 194 <span class="s">}</span>
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208 195
|
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|
209 196 <span class="c"># Generate fingerprints description...</span>
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210 197
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|
211 198 <span class="k">return</span> <span class="q">"$This->{Type}:$This->{AtomIdentifierType}:MinDistance$This->{MinDistance}:MaxDistance$This->{MaxDistance}"</span><span class="sc">;</span>
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|
|
212 199 <span class="s">}</span>
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213 200
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|
214 201 <span class="c"># Generate topological atom pairs [ Ref 57, Ref 59, Ref 72 ] fingerprints...</span>
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|
215 202 <span class="c">#</span>
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|
|
216 203 <span class="c"># Methodology:</span>
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|
|
217 204 <span class="c"># . Generate a distance matrix.</span>
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|
|
218 205 <span class="c"># . Assign atom types to all the atoms.</span>
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|
219 206 <span class="c"># . Using distance matrix and atom types, count occurrence of</span>
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|
220 207 <span class="c"># unique atom pairs within specified distance range - It corresponds to the</span>
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|
221 208 <span class="c"># correlation-vector for the atom pairs.</span>
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|
222 209 <span class="c">#</span>
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|
223 210 <span class="c"># Notes:</span>
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|
224 211 <span class="c"># . Hydrogen atoms are ignored during the fingerprint generation.</span>
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|
225 212 <span class="c">#</span>
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|
226 <a name="GenerateFingerprints-"></a> 213 <span class="k">sub </span><span class="m">GenerateFingerprints</span> <span class="s">{</span>
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227 214 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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228 215
|
|
|
229 216 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MinDistance</span>} > <span class="i">$This</span>->{<span class="w">MaxDistance</span>}<span class="s">)</span> <span class="s">{</span>
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|
|
230 217 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->GenerateTopologicalAtomPairsFingerprints: No fingerpritns generated: MinDistance, $This->{MinDistance}, must be <= MaxDistance, $This->{MaxDistance}..."</span><span class="sc">;</span>
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|
231 218 <span class="s">}</span>
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232 219
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233 220 <span class="c"># Cache appropriate molecule data...</span>
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|
234 221 <span class="i">$This</span><span class="i">->_SetupMoleculeDataCache</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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235 222
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236 223 <span class="c"># Generate distance matrix...</span>
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|
|
237 224 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->_SetupDistanceMatrix</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
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|
238 225 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->GenerateFingerprints: $This->{AtomIdentifierType} fingerprints generation didn't succeed: Couldn't generate distance matrix..."</span><span class="sc">;</span>
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|
239 226 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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|
|
240 227 <span class="s">}</span>
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241 228
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|
242 229 <span class="c"># Assign atom types to all heavy atoms...</span>
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|
243 230 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->_AssignAtomTypes</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
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|
244 231 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->GenerateFingerprints: $This->{AtomIdentifierType} fingerprints generation didn't succeed: Couldn't assign valid $This->{AtomIdentifierType} to all atoms..."</span><span class="sc">;</span>
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|
245 232 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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|
|
246 233 <span class="s">}</span>
|
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|
247 234
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|
248 235 <span class="c"># Intialize values of toplogical atom pairs...</span>
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|
|
249 236 <span class="i">$This</span><span class="i">->_InitializeToplogicalAtomPairs</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
250 237
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|
|
251 238 <span class="c"># Count atom pairs...</span>
|
|
|
252 239 <span class="i">$This</span><span class="i">->_GenerateAndCountAtomPairs</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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|
253 240
|
|
|
254 241 <span class="c"># Set final fingerprints...</span>
|
|
|
255 242 <span class="i">$This</span><span class="i">->_SetFinalFingerprints</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
256 243
|
|
|
257 244 <span class="c"># Clear cached molecule data...</span>
|
|
|
258 245 <span class="i">$This</span><span class="i">->_ClearMoleculeDataCache</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
259 246
|
|
|
260 247 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
261 248 <span class="s">}</span>
|
|
|
262 249
|
|
|
263 250 <span class="c"># Setup distance matrix...</span>
|
|
|
264 251 <span class="c">#</span>
|
|
|
265 <a name="_SetupDistanceMatrix-"></a> 252 <span class="k">sub </span><span class="m">_SetupDistanceMatrix</span> <span class="s">{</span>
|
|
|
266 253 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
267 254
|
|
|
268 255 <span class="i">$This</span>->{<span class="w">DistanceMatrix</span>} = <span class="i">$This</span><span class="i">->GetMolecule</span><span class="s">(</span><span class="s">)</span><span class="i">->GetDistanceMatrix</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
269 256
|
|
|
270 257 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span>->{<span class="w">DistanceMatrix</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
271 258 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
|
|
|
272 259 <span class="s">}</span>
|
|
|
273 260
|
|
|
274 261 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
275 262 <span class="s">}</span>
|
|
|
276 263
|
|
|
277 264 <span class="c"># Assign appropriate atom types to all heavy atoms...</span>
|
|
|
278 265 <span class="c">#</span>
|
|
|
279 <a name="_AssignAtomTypes-"></a> 266 <span class="k">sub </span><span class="m">_AssignAtomTypes</span> <span class="s">{</span>
|
|
|
280 267 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
281 268 <span class="k">my</span><span class="s">(</span><span class="i">$SpecifiedAtomTypes</span><span class="cm">,</span> <span class="i">$Atom</span><span class="cm">,</span> <span class="i">$AtomID</span><span class="cm">,</span> <span class="i">$IgnoreHydrogens</span><span class="s">)</span><span class="sc">;</span>
|
|
|
282 269
|
|
|
283 270 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">AssignedAtomTypes</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
284 271 <span class="i">$IgnoreHydrogens</span> = <span class="n">1</span><span class="sc">;</span>
|
|
|
285 272
|
|
|
286 273 <span class="i">$SpecifiedAtomTypes</span> = <span class="k">undef</span><span class="sc">;</span>
|
|
|
287 274
|
|
|
288 275 <span class="j">IDENTIFIERTYPE:</span> <span class="s">{</span>
|
|
|
289 276 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^AtomicInvariantsAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
290 277 <span class="i">$SpecifiedAtomTypes</span> = <span class="i">new</span> <span class="i">AtomTypes::AtomicInvariantsAtomTypes</span><span class="s">(</span><span class="q">'Molecule'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="cm">,</span> <span class="q">'IgnoreHydrogens'</span> <span class="cm">=></span> <span class="i">$IgnoreHydrogens</span><span class="cm">,</span> <span class="q">'AtomicInvariantsToUse'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">AtomicInvariantsToUse</span>}<span class="s">)</span><span class="sc">;</span>
|
|
|
291 278 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span>
|
|
|
292 279 <span class="s">}</span>
|
|
|
293 280
|
|
|
294 281 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^DREIDINGAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
295 282 <span class="i">$SpecifiedAtomTypes</span> = <span class="i">new</span> <span class="i">AtomTypes::DREIDINGAtomTypes</span><span class="s">(</span><span class="q">'Molecule'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="cm">,</span> <span class="q">'IgnoreHydrogens'</span> <span class="cm">=></span> <span class="i">$IgnoreHydrogens</span><span class="s">)</span><span class="sc">;</span>
|
|
|
296 283 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span>
|
|
|
297 284 <span class="s">}</span>
|
|
|
298 285
|
|
|
299 286 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^EStateAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
300 287 <span class="i">$SpecifiedAtomTypes</span> = <span class="i">new</span> <span class="i">AtomTypes::EStateAtomTypes</span><span class="s">(</span><span class="q">'Molecule'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="cm">,</span> <span class="q">'IgnoreHydrogens'</span> <span class="cm">=></span> <span class="i">$IgnoreHydrogens</span><span class="s">)</span><span class="sc">;</span>
|
|
|
301 288 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span>
|
|
|
302 289 <span class="s">}</span>
|
|
|
303 290
|
|
|
304 291 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^FunctionalClassAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
305 292 <span class="i">$SpecifiedAtomTypes</span> = <span class="i">new</span> <span class="i">AtomTypes::FunctionalClassAtomTypes</span><span class="s">(</span><span class="q">'Molecule'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="cm">,</span> <span class="q">'IgnoreHydrogens'</span> <span class="cm">=></span> <span class="i">$IgnoreHydrogens</span><span class="cm">,</span> <span class="q">'FunctionalClassesToUse'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">FunctionalClassesToUse</span>}<span class="s">)</span><span class="sc">;</span>
|
|
|
306 293 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span>
|
|
|
307 294 <span class="s">}</span>
|
|
|
308 295
|
|
|
309 296 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^MMFF94AtomTypes$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
310 297 <span class="i">$SpecifiedAtomTypes</span> = <span class="i">new</span> <span class="i">AtomTypes::MMFF94AtomTypes</span><span class="s">(</span><span class="q">'Molecule'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="cm">,</span> <span class="q">'IgnoreHydrogens'</span> <span class="cm">=></span> <span class="i">$IgnoreHydrogens</span><span class="s">)</span><span class="sc">;</span>
|
|
|
311 298 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span>
|
|
|
312 299 <span class="s">}</span>
|
|
|
313 300
|
|
|
314 301 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^SLogPAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
315 302 <span class="i">$SpecifiedAtomTypes</span> = <span class="i">new</span> <span class="i">AtomTypes::SLogPAtomTypes</span><span class="s">(</span><span class="q">'Molecule'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="cm">,</span> <span class="q">'IgnoreHydrogens'</span> <span class="cm">=></span> <span class="i">$IgnoreHydrogens</span><span class="s">)</span><span class="sc">;</span>
|
|
|
316 303 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span>
|
|
|
317 304 <span class="s">}</span>
|
|
|
318 305 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^SYBYLAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
319 306 <span class="i">$SpecifiedAtomTypes</span> = <span class="i">new</span> <span class="i">AtomTypes::SYBYLAtomTypes</span><span class="s">(</span><span class="q">'Molecule'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="cm">,</span> <span class="q">'IgnoreHydrogens'</span> <span class="cm">=></span> <span class="i">$IgnoreHydrogens</span><span class="s">)</span><span class="sc">;</span>
|
|
|
320 307 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span>
|
|
|
321 308 <span class="s">}</span>
|
|
|
322 309
|
|
|
323 310 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^TPSAAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
324 311 <span class="i">$SpecifiedAtomTypes</span> = <span class="i">new</span> <span class="i">AtomTypes::TPSAAtomTypes</span><span class="s">(</span><span class="q">'Molecule'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="cm">,</span> <span class="q">'IgnorePhosphorus'</span> <span class="cm">=></span> <span class="n">0</span><span class="cm">,</span> <span class="q">'IgnoreSulfur'</span> <span class="cm">=></span> <span class="n">0</span><span class="s">)</span><span class="sc">;</span>
|
|
|
325 312 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span>
|
|
|
326 313 <span class="s">}</span>
|
|
|
327 314
|
|
|
328 315 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^UFFAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
329 316 <span class="i">$SpecifiedAtomTypes</span> = <span class="i">new</span> <span class="i">AtomTypes::UFFAtomTypes</span><span class="s">(</span><span class="q">'Molecule'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="cm">,</span> <span class="q">'IgnoreHydrogens'</span> <span class="cm">=></span> <span class="i">$IgnoreHydrogens</span><span class="s">)</span><span class="sc">;</span>
|
|
|
330 317 <span class="k">last</span> <span class="j">IDENTIFIERTYPE</span><span class="sc">;</span>
|
|
|
331 318 <span class="s">}</span>
|
|
|
332 319
|
|
|
333 320 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->_AssignAtomTypes: Unknown atom indentifier type $This->{AtomIdentifierType}..."</span><span class="sc">;</span>
|
|
|
334 321 <span class="s">}</span>
|
|
|
335 322
|
|
|
336 323 <span class="c"># Assign atom types...</span>
|
|
|
337 324 <span class="i">$SpecifiedAtomTypes</span><span class="i">->AssignAtomTypes</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
338 325
|
|
|
339 326 <span class="c"># Make sure atom types assignment is successful...</span>
|
|
|
340 327 <span class="k">if</span> <span class="s">(</span>!<span class="i">$SpecifiedAtomTypes</span><span class="i">->IsAtomTypesAssignmentSuccessful</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
341 328 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
|
|
|
342 329 <span class="s">}</span>
|
|
|
343 330
|
|
|
344 331 <span class="c"># Collect assigned atom types...</span>
|
|
|
345 332 <span class="j">ATOM:</span> <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$This</span>->{<span class="w">Atoms</span>}}<span class="s">)</span> <span class="s">{</span>
|
|
|
346 333 <span class="k">if</span> <span class="s">(</span><span class="i">$Atom</span><span class="i">->IsHydrogen</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
347 334 <span class="k">next</span> <span class="j">ATOM</span><span class="sc">;</span>
|
|
|
348 335 <span class="s">}</span>
|
|
|
349 336 <span class="i">$AtomID</span> = <span class="i">$Atom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
350 337 <span class="i">$This</span>->{<span class="w">AssignedAtomTypes</span>}{<span class="i">$AtomID</span>} = <span class="i">$SpecifiedAtomTypes</span><span class="i">->GetAtomType</span><span class="s">(</span><span class="i">$Atom</span><span class="s">)</span><span class="sc">;</span>
|
|
|
351 338 <span class="s">}</span>
|
|
|
352 339
|
|
|
353 340 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
354 341 <span class="s">}</span>
|
|
|
355 342
|
|
|
356 343 <span class="c"># Initialize topological atom pairs between specified distance range...</span>
|
|
|
357 344 <span class="c">#</span>
|
|
|
358 <a name="_InitializeToplogicalAtomPairs-"></a> 345 <span class="k">sub </span><span class="m">_InitializeToplogicalAtomPairs</span> <span class="s">{</span>
|
|
|
359 346 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
360 347 <span class="k">my</span><span class="s">(</span><span class="i">$Distance</span><span class="s">)</span><span class="sc">;</span>
|
|
|
361 348
|
|
|
362 349 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomPairsIDs</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
363 350 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">AtomPairsCount</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
364 351
|
|
|
365 352 <span class="k">for</span> <span class="i">$Distance</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MinDistance</span>} .. <span class="i">$This</span>->{<span class="w">MaxDistance</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
366 353 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">AtomPairsCount</span>}{<span class="i">$Distance</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
367 354 <span class="s">}</span>
|
|
|
368 355
|
|
|
369 356 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
370 357 <span class="s">}</span>
|
|
|
371 358
|
|
|
372 359 <span class="c"># Count atom pairs between mininum and maximum distance at each</span>
|
|
|
373 360 <span class="c"># distance using distance matrix and atom types assiged to each heavy</span>
|
|
|
374 361 <span class="c"># atom.</span>
|
|
|
375 362 <span class="c">#</span>
|
|
|
376 363 <span class="c"># Notes:</span>
|
|
|
377 364 <span class="c"># . The row and column indices of distance matrix correspond to atom indices.</span>
|
|
|
378 365 <span class="c"># . Distance value of BigNumber implies the atom is not connected to any other atom.</span>
|
|
|
379 366 <span class="c"># . Due to symmetric nature of distance matrix, only upper or lower triangular matrix</span>
|
|
|
380 367 <span class="c"># needs to be processed during identification and count of atom pairs.</span>
|
|
|
381 368 <span class="c">#</span>
|
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|
382 <a name="_GenerateAndCountAtomPairs-"></a> 369 <span class="k">sub </span><span class="m">_GenerateAndCountAtomPairs</span> <span class="s">{</span>
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|
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383 370 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
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384 371
|
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|
385 372 <span class="k">my</span><span class="s">(</span><span class="i">$NumOfRows</span><span class="cm">,</span> <span class="i">$NumOfCols</span><span class="cm">,</span> <span class="i">$RowIndex</span><span class="cm">,</span> <span class="i">$ColIndex</span><span class="cm">,</span> <span class="i">$DistanceMatrix</span><span class="cm">,</span> <span class="i">$Distance</span><span class="cm">,</span> <span class="i">$AtomID1</span><span class="cm">,</span> <span class="i">$AtomID2</span><span class="cm">,</span> <span class="i">$AtomType1</span><span class="cm">,</span> <span class="i">$AtomType2</span><span class="cm">,</span> <span class="i">$SkipIndexCheck</span><span class="cm">,</span> <span class="i">$CountIncrement</span><span class="s">)</span><span class="sc">;</span>
|
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386 373
|
|
|
387 374 <span class="i">$DistanceMatrix</span> = <span class="i">$This</span>->{<span class="w">DistanceMatrix</span>}<span class="sc">;</span>
|
|
|
388 375 <span class="s">(</span><span class="i">$NumOfRows</span><span class="cm">,</span> <span class="i">$NumOfCols</span><span class="s">)</span> = <span class="i">$DistanceMatrix</span><span class="i">->GetSize</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
389 376 <span class="i">$SkipIndexCheck</span> = <span class="n">0</span><span class="sc">;</span>
|
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390 377
|
|
|
391 378 <span class="j">ROWINDEX:</span> <span class="k">for</span> <span class="i">$RowIndex</span> <span class="s">(</span><span class="n">0</span> .. <span class="s">(</span><span class="i">$NumOfRows</span> - <span class="n">1</span><span class="s">)</span> <span class="s">)</span> <span class="s">{</span>
|
|
|
392 379 <span class="i">$AtomID1</span> = <span class="i">$This</span>->{<span class="w">AtomIndexToID</span>}{<span class="i">$RowIndex</span>}<span class="sc">;</span>
|
|
|
393 380 <span class="k">if</span> <span class="s">(</span> !<span class="s">(</span><span class="k">exists</span><span class="s">(</span><span class="i">$This</span>->{<span class="w">AssignedAtomTypes</span>}{<span class="i">$AtomID1</span>}<span class="s">)</span><span class="s">)</span> <span class="s">)</span> <span class="s">{</span>
|
|
|
394 381 <span class="k">next</span> <span class="j">ROWINDEX</span><span class="sc">;</span>
|
|
|
395 382 <span class="s">}</span>
|
|
|
396 383 <span class="i">$AtomType1</span> = <span class="i">$This</span>->{<span class="w">AssignedAtomTypes</span>}{<span class="i">$AtomID1</span>}<span class="sc">;</span>
|
|
|
397 384
|
|
|
398 385 <span class="j">COLINDEX:</span> <span class="k">for</span> <span class="i">$ColIndex</span> <span class="s">(</span><span class="s">(</span><span class="i">$RowIndex</span> + <span class="n">1</span><span class="s">)</span> .. <span class="s">(</span><span class="i">$NumOfCols</span> - <span class="n">1</span><span class="s">)</span> <span class="s">)</span> <span class="s">{</span>
|
|
|
399 386 <span class="i">$AtomID2</span> = <span class="i">$This</span>->{<span class="w">AtomIndexToID</span>}{<span class="i">$ColIndex</span>}<span class="sc">;</span>
|
|
|
400 387 <span class="k">if</span> <span class="s">(</span> !<span class="s">(</span><span class="k">exists</span><span class="s">(</span><span class="i">$This</span>->{<span class="w">AssignedAtomTypes</span>}{<span class="i">$AtomID2</span>}<span class="s">)</span><span class="s">)</span> <span class="s">)</span> <span class="s">{</span>
|
|
|
401 388 <span class="k">next</span> <span class="j">COLINDEX</span><span class="sc">;</span>
|
|
|
402 389 <span class="s">}</span>
|
|
|
403 390 <span class="i">$Distance</span> = <span class="i">$DistanceMatrix</span><span class="i">->GetValue</span><span class="s">(</span><span class="i">$RowIndex</span><span class="cm">,</span> <span class="i">$ColIndex</span><span class="cm">,</span> <span class="i">$SkipIndexCheck</span><span class="s">)</span><span class="sc">;</span>
|
|
|
404 391 <span class="k">if</span> <span class="s">(</span><span class="i">$Distance</span> < <span class="i">$This</span>->{<span class="w">MinDistance</span>} || <span class="i">$Distance</span> > <span class="i">$This</span>->{<span class="w">MaxDistance</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
405 392 <span class="k">next</span> <span class="j">COLINDEX</span><span class="sc">;</span>
|
|
|
406 393 <span class="s">}</span>
|
|
|
407 394 <span class="i">$AtomType2</span> = <span class="i">$This</span>->{<span class="w">AssignedAtomTypes</span>}{<span class="i">$AtomID2</span>}<span class="sc">;</span>
|
|
|
408 395
|
|
|
409 396 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomType1</span> <span class="k">le</span> <span class="i">$AtomType2</span><span class="s">)</span> <span class="s">{</span>
|
|
|
410 397 <span class="i">$This</span><span class="i">->_SetAtomPairsCount</span><span class="s">(</span><span class="i">$Distance</span><span class="cm">,</span> <span class="i">$AtomType1</span><span class="cm">,</span> <span class="i">$AtomType2</span><span class="s">)</span><span class="sc">;</span>
|
|
|
411 398 <span class="s">}</span>
|
|
|
412 399 <span class="k">else</span> <span class="s">{</span>
|
|
|
413 400 <span class="i">$This</span><span class="i">->_SetAtomPairsCount</span><span class="s">(</span><span class="i">$Distance</span><span class="cm">,</span> <span class="i">$AtomType2</span><span class="cm">,</span> <span class="i">$AtomType1</span><span class="s">)</span><span class="sc">;</span>
|
|
|
414 401 <span class="s">}</span>
|
|
|
415 402 <span class="s">}</span>
|
|
|
416 403 <span class="s">}</span>
|
|
|
417 404 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
418 405 <span class="s">}</span>
|
|
|
419 406
|
|
|
420 407 <span class="c"># Set atom paris count for a specific atom ID pair at a specific distance...</span>
|
|
|
421 408 <span class="c">#</span>
|
|
|
422 <a name="_SetAtomPairsCount-"></a> 409 <span class="k">sub </span><span class="m">_SetAtomPairsCount</span> <span class="s">{</span>
|
|
|
423 410 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Distance</span><span class="cm">,</span> <span class="i">$AtomType1</span><span class="cm">,</span> <span class="i">$AtomType2</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
424 411
|
|
|
425 412 <span class="k">if</span> <span class="s">(</span>! <span class="k">exists</span> <span class="i">$This</span>->{<span class="w">AtomPairsCount</span>}{<span class="i">$Distance</span>}{<span class="i">$AtomType1</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
426 413 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">AtomPairsCount</span>}{<span class="i">$Distance</span>}{<span class="i">$AtomType1</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
427 414 <span class="i">$This</span>->{<span class="w">AtomPairsCount</span>}{<span class="i">$Distance</span>}{<span class="i">$AtomType1</span>}{<span class="i">$AtomType2</span>} = <span class="n">1</span><span class="sc">;</span>
|
|
|
428 415 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
429 416 <span class="s">}</span>
|
|
|
430 417
|
|
|
431 418 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$This</span>->{<span class="w">AtomPairsCount</span>}{<span class="i">$Distance</span>}{<span class="i">$AtomType1</span>}{<span class="i">$AtomType2</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
432 419 <span class="i">$This</span>->{<span class="w">AtomPairsCount</span>}{<span class="i">$Distance</span>}{<span class="i">$AtomType1</span>}{<span class="i">$AtomType2</span>} += <span class="n">1</span><span class="sc">;</span>
|
|
|
433 420 <span class="s">}</span>
|
|
|
434 421 <span class="k">else</span> <span class="s">{</span>
|
|
|
435 422 <span class="i">$This</span>->{<span class="w">AtomPairsCount</span>}{<span class="i">$Distance</span>}{<span class="i">$AtomType1</span>}{<span class="i">$AtomType2</span>} = <span class="n">1</span><span class="sc">;</span>
|
|
|
436 423 <span class="s">}</span>
|
|
|
437 424
|
|
|
438 425 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
439 426 <span class="s">}</span>
|
|
|
440 427
|
|
|
441 428 <span class="c"># Set final fingerpritns vector...</span>
|
|
|
442 429 <span class="c">#</span>
|
|
|
443 <a name="_SetFinalFingerprints-"></a> 430 <span class="k">sub </span><span class="m">_SetFinalFingerprints</span> <span class="s">{</span>
|
|
|
444 431 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
445 432 <span class="k">my</span><span class="s">(</span><span class="i">$Distance</span><span class="cm">,</span> <span class="i">$AtomType1</span><span class="cm">,</span> <span class="i">$AtomType2</span><span class="cm">,</span> <span class="i">$Value</span><span class="cm">,</span> <span class="i">@Values</span><span class="s">)</span><span class="sc">;</span>
|
|
|
446 433
|
|
|
447 434 <span class="c"># Mark successful generation of fingerprints...</span>
|
|
|
448 435 <span class="i">$This</span>->{<span class="w">FingerprintsGenerated</span>} = <span class="n">1</span><span class="sc">;</span>
|
|
|
449 436
|
|
|
450 437 <span class="i">@Values</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
451 438 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomPairsIDs</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
452 439
|
|
|
453 440 <span class="k">for</span> <span class="i">$Distance</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">MinDistance</span>} .. <span class="i">$This</span>->{<span class="w">MaxDistance</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
454 441 <span class="k">for</span> <span class="i">$AtomType1</span> <span class="s">(</span><span class="k">sort</span> <span class="k">keys</span> <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">AtomPairsCount</span>}{<span class="i">$Distance</span>}} <span class="s">)</span> <span class="s">{</span>
|
|
|
455 442 <span class="k">for</span> <span class="i">$AtomType2</span> <span class="s">(</span><span class="k">sort</span> <span class="k">keys</span> <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">AtomPairsCount</span>}{<span class="i">$Distance</span>}{<span class="i">$AtomType1</span>}} <span class="s">)</span> <span class="s">{</span>
|
|
|
456 443 <span class="k">push</span> <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomPairsIDs</span>}}<span class="cm">,</span> <span class="q">"${AtomType1}-D${Distance}-${AtomType2}"</span><span class="sc">;</span>
|
|
|
457 444 <span class="i">$Value</span> = <span class="i">$This</span>->{<span class="w">AtomPairsCount</span>}{<span class="i">$Distance</span>}{<span class="i">$AtomType1</span>}{<span class="i">$AtomType2</span>}<span class="sc">;</span>
|
|
|
458 445 <span class="k">push</span> <span class="i">@Values</span><span class="cm">,</span> <span class="i">$Value</span><span class="sc">;</span>
|
|
|
459 446 <span class="s">}</span>
|
|
|
460 447 <span class="s">}</span>
|
|
|
461 448 <span class="s">}</span>
|
|
|
462 449
|
|
|
463 450 <span class="c"># Add AtomPairsIDs and values to fingerprint vector...</span>
|
|
|
464 451 <span class="i">$This</span>->{<span class="w">FingerprintsVector</span>}<span class="i">->AddValueIDs</span><span class="s">(</span>\<span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomPairsIDs</span>}}<span class="s">)</span><span class="sc">;</span>
|
|
|
465 452 <span class="i">$This</span>->{<span class="w">FingerprintsVector</span>}<span class="i">->AddValues</span><span class="s">(</span>\<span class="i">@Values</span><span class="s">)</span><span class="sc">;</span>
|
|
|
466 453
|
|
|
467 454 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
468 455 <span class="s">}</span>
|
|
|
469 456
|
|
|
470 457 <span class="c"># Get atom pair IDs corresponding to atom pairs count values in fingerprint</span>
|
|
|
471 458 <span class="c"># vector as an array or reference to an array...</span>
|
|
|
472 459 <span class="c">#</span>
|
|
|
473 460 <span class="c"># AtomPairIDs list differes in molecules and is generated during finalization</span>
|
|
|
474 461 <span class="c"># of fingerprints to make sure the fingerprint vector containing count values</span>
|
|
|
475 462 <span class="c"># matches the atom pairs array.</span>
|
|
|
476 463 <span class="c">#</span>
|
|
|
477 <a name="GetAtomPairIDs-"></a> 464 <span class="k">sub </span><span class="m">GetAtomPairIDs</span> <span class="s">{</span>
|
|
|
478 465 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
479 466
|
|
|
480 467 <span class="k">return</span> <span class="k">wantarray</span> ? <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomPairsIDs</span>}} <span class="co">:</span> \<span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomPairsIDs</span>}}<span class="sc">;</span>
|
|
|
481 468 <span class="s">}</span>
|
|
|
482 469
|
|
|
483 470 <span class="c"># Cache appropriate molecule data...</span>
|
|
|
484 471 <span class="c">#</span>
|
|
|
485 <a name="_SetupMoleculeDataCache-"></a> 472 <span class="k">sub </span><span class="m">_SetupMoleculeDataCache</span> <span class="s">{</span>
|
|
|
486 473 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
487 474
|
|
|
488 475 <span class="c"># Get all atoms including hydrogens to correctly map atom indices to atom IDs for</span>
|
|
|
489 476 <span class="c"># usage of distance matrix. The hydrogen atoms are ignored during processing...</span>
|
|
|
490 477 <span class="c">#</span>
|
|
|
491 478 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">Atoms</span>}} = <span class="i">$This</span><span class="i">->GetMolecule</span><span class="s">(</span><span class="s">)</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
492 479
|
|
|
493 480 <span class="c"># Get all atom IDs...</span>
|
|
|
494 481 <span class="k">my</span><span class="s">(</span><span class="i">@AtomIDs</span><span class="s">)</span><span class="sc">;</span>
|
|
|
495 482 <span class="i">@AtomIDs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
496 483 <span class="i">@AtomIDs</span> = <span class="k">map</span> <span class="s">{</span> <span class="i">$_</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span> <span class="s">}</span> <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">Atoms</span>}}<span class="sc">;</span>
|
|
|
497 484
|
|
|
498 485 <span class="c"># Set AtomIndex to AtomID hash...</span>
|
|
|
499 486 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">AtomIndexToID</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
500 487 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomIndexToID</span>}}{ <span class="s">(</span><span class="n">0</span> .. <span class="i">$#AtomIDs</span><span class="s">)</span> } = <span class="i">@AtomIDs</span><span class="sc">;</span>
|
|
|
501 488
|
|
|
502 489 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
503 490 <span class="s">}</span>
|
|
|
504 491
|
|
|
505 492 <span class="c"># Clear cached molecule data...</span>
|
|
|
506 493 <span class="c">#</span>
|
|
|
507 <a name="_ClearMoleculeDataCache-"></a> 494 <span class="k">sub </span><span class="m">_ClearMoleculeDataCache</span> <span class="s">{</span>
|
|
|
508 495 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
509 496
|
|
|
510 497 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">Atoms</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
511 498
|
|
|
512 499 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
513 500 <span class="s">}</span>
|
|
|
514 501
|
|
|
515 502 <span class="c"># Set atomic invariants to use for atom identifiers...</span>
|
|
|
516 503 <span class="c">#</span>
|
|
|
517 <a name="SetAtomicInvariantsToUse-"></a> 504 <span class="k">sub </span><span class="m">SetAtomicInvariantsToUse</span> <span class="s">{</span>
|
|
|
518 505 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">@Values</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
519 506 <span class="k">my</span><span class="s">(</span><span class="i">$FirstValue</span><span class="cm">,</span> <span class="i">$TypeOfFirstValue</span><span class="cm">,</span> <span class="i">$AtomicInvariant</span><span class="cm">,</span> <span class="i">$SpecifiedAtomicInvariant</span><span class="cm">,</span> <span class="i">$AtomicInvariantValue</span><span class="cm">,</span> <span class="i">@SpecifiedAtomicInvariants</span><span class="cm">,</span> <span class="i">@AtomicInvariantsToUse</span><span class="s">)</span><span class="sc">;</span>
|
|
|
520 507
|
|
|
521 508 <span class="k">if</span> <span class="s">(</span>!<span class="i">@Values</span><span class="s">)</span> <span class="s">{</span>
|
|
|
522 509 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->SetAtomicInvariantsToUse: No values specified..."</span><span class="sc">;</span>
|
|
|
523 510 <span class="k">return</span><span class="sc">;</span>
|
|
|
524 511 <span class="s">}</span>
|
|
|
525 512
|
|
|
526 513 <span class="i">$FirstValue</span> = <span class="i">$Values</span>[<span class="n">0</span>]<span class="sc">;</span>
|
|
|
527 514 <span class="i">$TypeOfFirstValue</span> = <span class="k">ref</span> <span class="i">$FirstValue</span><span class="sc">;</span>
|
|
|
528 515
|
|
|
529 516 <span class="i">@SpecifiedAtomicInvariants</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
530 517 <span class="i">@AtomicInvariantsToUse</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
531 518
|
|
|
532 519 <span class="k">if</span> <span class="s">(</span><span class="i">$TypeOfFirstValue</span> =~ <span class="q">/^ARRAY/</span><span class="s">)</span> <span class="s">{</span>
|
|
|
533 520 <span class="k">push</span> <span class="i">@SpecifiedAtomicInvariants</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$FirstValue</span>}<span class="sc">;</span>
|
|
|
534 521 <span class="s">}</span>
|
|
|
535 522 <span class="k">else</span> <span class="s">{</span>
|
|
|
536 523 <span class="k">push</span> <span class="i">@SpecifiedAtomicInvariants</span><span class="cm">,</span> <span class="i">@Values</span><span class="sc">;</span>
|
|
|
537 524 <span class="s">}</span>
|
|
|
538 525
|
|
|
539 526 <span class="c"># Make sure specified AtomicInvariants are valid...</span>
|
|
|
540 527 <span class="k">for</span> <span class="i">$SpecifiedAtomicInvariant</span> <span class="s">(</span><span class="i">@SpecifiedAtomicInvariants</span><span class="s">)</span> <span class="s">{</span>
|
|
|
541 528 <span class="k">if</span> <span class="s">(</span>!<span class="i">AtomTypes::AtomicInvariantsAtomTypes::IsAtomicInvariantAvailable</span><span class="s">(</span><span class="i">$SpecifiedAtomicInvariant</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
542 529 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetAtomicInvariantsToUse: Specified atomic invariant, $SpecifiedAtomicInvariant, is not supported...\n "</span><span class="sc">;</span>
|
|
|
543 530 <span class="s">}</span>
|
|
|
544 531 <span class="i">$AtomicInvariant</span> = <span class="i">$SpecifiedAtomicInvariant</span><span class="sc">;</span>
|
|
|
545 532 <span class="k">push</span> <span class="i">@AtomicInvariantsToUse</span><span class="cm">,</span> <span class="i">$AtomicInvariant</span><span class="sc">;</span>
|
|
|
546 533 <span class="s">}</span>
|
|
|
547 534
|
|
|
548 535 <span class="c"># Set atomic invariants to use...</span>
|
|
|
549 536 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomicInvariantsToUse</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
550 537 <span class="k">push</span> <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomicInvariantsToUse</span>}}<span class="cm">,</span> <span class="i">@AtomicInvariantsToUse</span><span class="sc">;</span>
|
|
|
551 538
|
|
|
552 539 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
553 540 <span class="s">}</span>
|
|
|
554 541
|
|
|
555 542 <span class="c"># Set functional classes to use for atom identifiers...</span>
|
|
|
556 543 <span class="c">#</span>
|
|
|
557 <a name="SetFunctionalClassesToUse-"></a> 544 <span class="k">sub </span><span class="m">SetFunctionalClassesToUse</span> <span class="s">{</span>
|
|
|
558 545 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">@Values</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
559 546 <span class="k">my</span><span class="s">(</span><span class="i">$FirstValue</span><span class="cm">,</span> <span class="i">$TypeOfFirstValue</span><span class="cm">,</span> <span class="i">$FunctionalClass</span><span class="cm">,</span> <span class="i">$SpecifiedFunctionalClass</span><span class="cm">,</span> <span class="i">@SpecifiedFunctionalClasses</span><span class="cm">,</span> <span class="i">@FunctionalClassesToUse</span><span class="s">)</span><span class="sc">;</span>
|
|
|
560 547
|
|
|
561 548 <span class="k">if</span> <span class="s">(</span>!<span class="i">@Values</span><span class="s">)</span> <span class="s">{</span>
|
|
|
562 549 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->SetFunctionalClassesToUse: No values specified..."</span><span class="sc">;</span>
|
|
|
563 550 <span class="k">return</span><span class="sc">;</span>
|
|
|
564 551 <span class="s">}</span>
|
|
|
565 552
|
|
|
566 553 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} !~ <span class="q">/^FunctionalClassAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
567 554 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->SetFunctionalClassesToUse: FunctionalClassesToUse can't be set for InitialAtomIdentifierType of $This->{AtomIdentifierType}..."</span><span class="sc">;</span>
|
|
|
568 555 <span class="k">return</span><span class="sc">;</span>
|
|
|
569 556 <span class="s">}</span>
|
|
|
570 557
|
|
|
571 558 <span class="i">$FirstValue</span> = <span class="i">$Values</span>[<span class="n">0</span>]<span class="sc">;</span>
|
|
|
572 559 <span class="i">$TypeOfFirstValue</span> = <span class="k">ref</span> <span class="i">$FirstValue</span><span class="sc">;</span>
|
|
|
573 560
|
|
|
574 561 <span class="i">@SpecifiedFunctionalClasses</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
575 562 <span class="i">@FunctionalClassesToUse</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
576 563
|
|
|
577 564 <span class="k">if</span> <span class="s">(</span><span class="i">$TypeOfFirstValue</span> =~ <span class="q">/^ARRAY/</span><span class="s">)</span> <span class="s">{</span>
|
|
|
578 565 <span class="k">push</span> <span class="i">@SpecifiedFunctionalClasses</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$FirstValue</span>}<span class="sc">;</span>
|
|
|
579 566 <span class="s">}</span>
|
|
|
580 567 <span class="k">else</span> <span class="s">{</span>
|
|
|
581 568 <span class="k">push</span> <span class="i">@SpecifiedFunctionalClasses</span><span class="cm">,</span> <span class="i">@Values</span><span class="sc">;</span>
|
|
|
582 569 <span class="s">}</span>
|
|
|
583 570
|
|
|
584 571 <span class="c"># Make sure specified FunctionalClasses are valid...</span>
|
|
|
585 572 <span class="k">for</span> <span class="i">$SpecifiedFunctionalClass</span> <span class="s">(</span><span class="i">@SpecifiedFunctionalClasses</span><span class="s">)</span> <span class="s">{</span>
|
|
|
586 573 <span class="k">if</span> <span class="s">(</span>!<span class="i">AtomTypes::FunctionalClassAtomTypes::IsFunctionalClassAvailable</span><span class="s">(</span><span class="i">$SpecifiedFunctionalClass</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
587 574 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetFunctionalClassesToUse: Specified functional class, $SpecifiedFunctionalClass, is not supported...\n "</span><span class="sc">;</span>
|
|
|
588 575 <span class="s">}</span>
|
|
|
589 576 <span class="k">push</span> <span class="i">@FunctionalClassesToUse</span><span class="cm">,</span> <span class="i">$SpecifiedFunctionalClass</span><span class="sc">;</span>
|
|
|
590 577 <span class="s">}</span>
|
|
|
591 578
|
|
|
592 579 <span class="c"># Set functional classes to use...</span>
|
|
|
593 580 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">FunctionalClassesToUse</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
594 581 <span class="k">push</span> <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">FunctionalClassesToUse</span>}}<span class="cm">,</span> <span class="i">@FunctionalClassesToUse</span><span class="sc">;</span>
|
|
|
595 582
|
|
|
596 583 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
597 584 <span class="s">}</span>
|
|
|
598 585
|
|
|
599 586 <span class="c"># Initialize atom indentifier type information...</span>
|
|
|
600 587 <span class="c">#</span>
|
|
|
601 588 <span class="c"># Current supported values:</span>
|
|
|
602 589 <span class="c">#</span>
|
|
|
603 590 <span class="c"># AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, FunctionalClassAtomTypes,</span>
|
|
|
604 591 <span class="c"># MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes</span>
|
|
|
605 592 <span class="c">#</span>
|
|
|
606 <a name="_InitializeAtomIdentifierTypeInformation-"></a> 593 <span class="k">sub </span><span class="m">_InitializeAtomIdentifierTypeInformation</span> <span class="s">{</span>
|
|
|
607 594 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
608 595
|
|
|
609 596 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^AtomicInvariantsAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
610 597 <span class="i">$This</span><span class="i">->_InitializeAtomicInvariantsAtomTypesInformation</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
611 598 <span class="s">}</span>
|
|
|
612 599 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^FunctionalClassAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
613 600 <span class="i">$This</span><span class="i">->_InitializeFunctionalClassAtomTypesInformation</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
614 601 <span class="s">}</span>
|
|
|
615 602 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^(DREIDINGAtomTypes|EStateAtomTypes|MMFF94AtomTypes|SLogPAtomTypes|SYBYLAtomTypes|TPSAAtomTypes|UFFAtomTypes)$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
616 603 <span class="c"># Nothing to do for now...</span>
|
|
|
617 604 <span class="s">}</span>
|
|
|
618 605 <span class="k">else</span> <span class="s">{</span>
|
|
|
619 606 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->_InitializeAtomIdentifierTypeInformation: Unknown atom indentifier type $This->{AtomIdentifierType}..."</span><span class="sc">;</span>
|
|
|
620 607 <span class="s">}</span>
|
|
|
621 608
|
|
|
622 609 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
623 610 <span class="s">}</span>
|
|
|
624 611
|
|
|
625 612 <span class="c"># Initialize atomic invariants atom types to use for generating atom identifiers...</span>
|
|
|
626 613 <span class="c">#</span>
|
|
|
627 614 <span class="c"># Let:</span>
|
|
|
628 615 <span class="c"># AS = Atom symbol corresponding to element symbol</span>
|
|
|
629 616 <span class="c">#</span>
|
|
|
630 617 <span class="c"># X<n> = Number of non-hydrogen atom neighbors or heavy atoms attached to atom</span>
|
|
|
631 618 <span class="c"># BO<n> = Sum of bond orders to non-hydrogen atom neighbors or heavy atoms attached to atom</span>
|
|
|
632 619 <span class="c"># LBO<n> = Largest bond order of non-hydrogen atom neighbors or heavy atoms attached to atom</span>
|
|
|
633 620 <span class="c"># SB<n> = Number of single bonds to non-hydrogen atom neighbors or heavy atoms attached to atom</span>
|
|
|
634 621 <span class="c"># DB<n> = Number of double bonds to non-hydrogen atom neighbors or heavy atoms attached to atom</span>
|
|
|
635 622 <span class="c"># TB<n> = Number of triple bonds to non-hydrogen atom neighbors or heavy atoms attached to atom</span>
|
|
|
636 623 <span class="c"># H<n> = Number of implicit and explicit hydrogens for atom</span>
|
|
|
637 624 <span class="c"># Ar = Aromatic annotation indicating whether atom is aromatic</span>
|
|
|
638 625 <span class="c"># RA = Ring atom annotation indicating whether atom is a ring</span>
|
|
|
639 626 <span class="c"># FC<+n/-n> = Formal charge assigned to atom</span>
|
|
|
640 627 <span class="c"># MN<n> = Mass number indicating isotope other than most abundant isotope</span>
|
|
|
641 628 <span class="c"># SM<n> = Spin multiplicity of atom. Possible values: 1 (singlet), 2 (doublet) or 3 (triplet)</span>
|
|
|
642 629 <span class="c">#</span>
|
|
|
643 630 <span class="c"># AtomTypeIDx = Atomic invariants atom type for atom x</span>
|
|
|
644 631 <span class="c"># AtomTypeIDy = Atomic invariants atom type for atom y</span>
|
|
|
645 632 <span class="c"># Dn = Topological distance between atom x and y</span>
|
|
|
646 633 <span class="c">#</span>
|
|
|
647 634 <span class="c"># Then:</span>
|
|
|
648 635 <span class="c">#</span>
|
|
|
649 636 <span class="c"># Atom pair AtomID generated by AtomTypes::AtomicInvariantsAtomTypes class corresponds to:</span>
|
|
|
650 637 <span class="c">#</span>
|
|
|
651 638 <span class="c"># AS.X<n>.BO<n>.LBO<n>.<SB><n>.<DB><n>.<TB><n>.H<n>.Ar.RA.FC<+n/-n>.MN<n>.SM<n></span>
|
|
|
652 639 <span class="c">#</span>
|
|
|
653 640 <span class="c"># AtomPairID corresponds to:</span>
|
|
|
654 641 <span class="c">#</span>
|
|
|
655 642 <span class="c"># AtomTypeIDx-D<n>-AtomTypeIDy</span>
|
|
|
656 643 <span class="c">#</span>
|
|
|
657 644 <span class="c"># Except for AS which is a required atomic invariant in atom pair AtomIDs, all other atomic invariants are</span>
|
|
|
658 645 <span class="c"># optional. Default atomic invariants used for AtomID are: AS, X<n>, BO<n>, H<n>, FC<+n/-n>.</span>
|
|
|
659 646 <span class="c"># AtomID specification doesn't include atomic invariants with zero or undefined values.</span>
|
|
|
660 647 <span class="c">#</span>
|
|
|
661 648 <span class="c"># Examples of atom pair AtomIDs:</span>
|
|
|
662 649 <span class="c">#</span>
|
|
|
663 650 <span class="c"># O.X1.BO1.H1 - Hydroxyl oxygen in carboxylate with attached hydrogen and no explicit charge</span>
|
|
|
664 651 <span class="c"># O.X1.BO1.FC-1 - Hydroxyl ozygen in carboxylate with explicit negative charge</span>
|
|
|
665 652 <span class="c"># O.X1.BO2 - Carbonyl oxygen in carboxylate with double bond to carbon</span>
|
|
|
666 653 <span class="c"># O.X2.BO2 - Hydroxyl ozygen in carboxylate attached to carbonyl carbon and another heavy atom</span>
|
|
|
667 654 <span class="c">#</span>
|
|
|
668 655 <span class="c"># C.X2.BO3.H1.Ar - Aromatic carbon</span>
|
|
|
669 656 <span class="c">#</span>
|
|
|
670 657 <span class="c"># Examples of AtomPairIDs:</span>
|
|
|
671 658 <span class="c">#</span>
|
|
|
672 659 <span class="c"># C.X2.BO2.H3-D1-O.X1.BO1 - Carbon with two heavy atom neighbors attached to oxygen at bond distance 1(methanol)</span>
|
|
|
673 660 <span class="c">#</span>
|
|
|
674 661 <span class="c"># C.X2.BO3.H1.Ar-D3-C.X2.BO3.H1.Ar - Two aromatic carbons at bond distance 3 where each carbon has</span>
|
|
|
675 662 <span class="c"># two heavy atom neighbors and bond order of 3 (benzene)</span>
|
|
|
676 663 <span class="c">#</span>
|
|
|
677 <a name="_InitializeAtomicInvariantsAtomTypesInformation-"></a> 664 <span class="k">sub </span><span class="m">_InitializeAtomicInvariantsAtomTypesInformation</span> <span class="s">{</span>
|
|
|
678 665 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
679 666
|
|
|
680 667 <span class="c"># Default atomic invariants to use for generating atom neighborhood atom IDs: AS, X, BO, H, FC</span>
|
|
|
681 668 <span class="c">#</span>
|
|
|
682 669 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomicInvariantsToUse</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
683 670 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomicInvariantsToUse</span>}} = <span class="s">(</span><span class="q">'AS'</span><span class="cm">,</span> <span class="q">'X'</span><span class="cm">,</span> <span class="q">'BO'</span><span class="cm">,</span> <span class="q">'H'</span><span class="cm">,</span> <span class="q">'FC'</span><span class="s">)</span><span class="sc">;</span>
|
|
|
684 671
|
|
|
685 672 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
686 673 <span class="s">}</span>
|
|
|
687 674
|
|
|
688 675 <span class="c"># Initialize functional class atom types, generated by AtomTypes::FunctionalClassAtomTypes</span>
|
|
|
689 676 <span class="c"># class, to use for generating atom identifiers...</span>
|
|
|
690 677 <span class="c">#</span>
|
|
|
691 678 <span class="c"># Let:</span>
|
|
|
692 679 <span class="c"># HBD: HydrogenBondDonor</span>
|
|
|
693 680 <span class="c"># HBA: HydrogenBondAcceptor</span>
|
|
|
694 681 <span class="c"># PI : PositivelyIonizable</span>
|
|
|
695 682 <span class="c"># NI : NegativelyIonizable</span>
|
|
|
696 683 <span class="c"># Ar : Aromatic</span>
|
|
|
697 684 <span class="c"># Hal : Halogen</span>
|
|
|
698 685 <span class="c"># H : Hydrophobic</span>
|
|
|
699 686 <span class="c"># RA : RingAtom</span>
|
|
|
700 687 <span class="c"># CA : ChainAtom</span>
|
|
|
701 688 <span class="c">#</span>
|
|
|
702 689 <span class="c"># Then:</span>
|
|
|
703 690 <span class="c">#</span>
|
|
|
704 691 <span class="c"># Functiononal class atom type specification for an atom corresponds to:</span>
|
|
|
705 692 <span class="c">#</span>
|
|
|
706 693 <span class="c"># Ar.CA.H.HBA.HBD.Hal.NI.PI.RA</span>
|
|
|
707 694 <span class="c">#</span>
|
|
|
708 695 <span class="c"># Default functional classes used are: HBD, HBA, PI, NI, Ar, Hal</span>
|
|
|
709 696 <span class="c">#</span>
|
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710 697 <span class="c"># FunctionalAtomTypes are assigned using the following definitions [ Ref 60-61, Ref 65-66 ]:</span>
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711 698 <span class="c">#</span>
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712 699 <span class="c"># HydrogenBondDonor: NH, NH2, OH</span>
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713 700 <span class="c"># HydrogenBondAcceptor: N[!H], O</span>
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714 701 <span class="c"># PositivelyIonizable: +, NH2</span>
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715 702 <span class="c"># NegativelyIonizable: -, C(=O)OH, S(=O)OH, P(=O)OH</span>
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716 703 <span class="c">#</span>
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717 <a name="_InitializeFunctionalClassAtomTypesInformation-"></a> 704 <span class="k">sub </span><span class="m">_InitializeFunctionalClassAtomTypesInformation</span> <span class="s">{</span>
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718 705 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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719 706
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720 707 <span class="c"># Default functional class atom typess to use for generating atom identifiers</span>
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721 708 <span class="c"># are: HBD, HBA, PI, NI, Ar, Hal</span>
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722 709 <span class="c">#</span>
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723 710 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">FunctionalClassesToUse</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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724 711 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">FunctionalClassesToUse</span>}} = <span class="s">(</span><span class="q">'HBD'</span><span class="cm">,</span> <span class="q">'HBA'</span><span class="cm">,</span> <span class="q">'PI'</span><span class="cm">,</span> <span class="q">'NI'</span><span class="cm">,</span> <span class="q">'Ar'</span><span class="cm">,</span> <span class="q">'Hal'</span><span class="s">)</span><span class="sc">;</span>
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725 712
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726 713 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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727 714 <span class="s">}</span>
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728 715
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729 716 <span class="c"># Return a string containg data for TopologicalAtomPairsFingerprints object...</span>
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730 717 <span class="c">#</span>
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731 <a name="StringifyTopologicalAtomPairsFingerprints-"></a> 718 <span class="k">sub </span><span class="m">StringifyTopologicalAtomPairsFingerprints</span> <span class="s">{</span>
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732 719 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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733 720 <span class="k">my</span><span class="s">(</span><span class="i">$FingerprintsString</span><span class="s">)</span><span class="sc">;</span>
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734 721
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735 722 <span class="c"># Type of fingerprint...</span>
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736 723 <span class="i">$FingerprintsString</span> = <span class="q">"Fingerprint type: $This->{Type}; AtomIdentifierType: $This->{AtomIdentifierType}"</span><span class="sc">;</span>
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737 724
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738 725 <span class="c"># Min and max distance...</span>
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739 726 <span class="i">$FingerprintsString</span> .= <span class="q">"; MinDistance: $This->{MinDistance}; MaxDistance: $This->{MaxDistance}"</span><span class="sc">;</span>
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740 727
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741 728 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^AtomicInvariantsAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span>
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742 729 <span class="k">my</span><span class="s">(</span><span class="i">$AtomicInvariant</span><span class="cm">,</span> <span class="i">@AtomicInvariants</span><span class="cm">,</span> <span class="i">@AtomicInvariantsOrder</span><span class="cm">,</span> <span class="i">%AvailableAtomicInvariants</span><span class="s">)</span><span class="sc">;</span>
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743 730
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744 731 <span class="i">@AtomicInvariantsOrder</span> = <span class="i">AtomTypes::AtomicInvariantsAtomTypes::GetAtomicInvariantsOrder</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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745 732 <span class="i">%AvailableAtomicInvariants</span> = <span class="i">AtomTypes::AtomicInvariantsAtomTypes::GetAvailableAtomicInvariants</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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746 733
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747 734 <span class="k">for</span> <span class="i">$AtomicInvariant</span> <span class="s">(</span><span class="i">@AtomicInvariantsOrder</span><span class="s">)</span> <span class="s">{</span>
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748 735 <span class="k">push</span> <span class="i">@AtomicInvariants</span><span class="cm">,</span> <span class="q">"$AtomicInvariant: $AvailableAtomicInvariants{$AtomicInvariant}"</span><span class="sc">;</span>
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749 736 <span class="s">}</span>
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750 737
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751 738 <span class="i">$FingerprintsString</span> .= <span class="q">"; AtomicInvariantsToUse: <"</span> . <span class="i">TextUtil::JoinWords</span><span class="s">(</span>\<span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomicInvariantsToUse</span>}}<span class="cm">,</span> <span class="q">", "</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span> . <span class="q">">"</span><span class="sc">;</span>
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752 739 <span class="i">$FingerprintsString</span> .= <span class="q">"; AtomicInvariantsOrder: <"</span> . <span class="i">TextUtil::JoinWords</span><span class="s">(</span>\<span class="i">@AtomicInvariantsOrder</span><span class="cm">,</span> <span class="q">", "</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span> . <span class="q">">"</span><span class="sc">;</span>
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753 740 <span class="i">$FingerprintsString</span> .= <span class="q">"; AvailableAtomicInvariants: <"</span> . <span class="i">TextUtil::JoinWords</span><span class="s">(</span>\<span class="i">@AtomicInvariants</span><span class="cm">,</span> <span class="q">", "</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span> . <span class="q">">"</span><span class="sc">;</span>
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754 741 <span class="s">}</span>
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755 742 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^FunctionalClassAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span>
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756 743 <span class="k">my</span><span class="s">(</span><span class="i">$FunctionalClass</span><span class="cm">,</span> <span class="i">@FunctionalClasses</span><span class="cm">,</span> <span class="i">@FunctionalClassesOrder</span><span class="cm">,</span> <span class="i">%AvailableFunctionalClasses</span><span class="s">)</span><span class="sc">;</span>
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757 744
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758 745 <span class="i">@FunctionalClassesOrder</span> = <span class="i">AtomTypes::FunctionalClassAtomTypes::GetFunctionalClassesOrder</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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759 746 <span class="i">%AvailableFunctionalClasses</span> = <span class="i">AtomTypes::FunctionalClassAtomTypes::GetAvailableFunctionalClasses</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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760 747
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761 748 <span class="k">for</span> <span class="i">$FunctionalClass</span> <span class="s">(</span><span class="i">@FunctionalClassesOrder</span><span class="s">)</span> <span class="s">{</span>
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762 749 <span class="k">push</span> <span class="i">@FunctionalClasses</span><span class="cm">,</span> <span class="q">"$FunctionalClass: $AvailableFunctionalClasses{$FunctionalClass}"</span><span class="sc">;</span>
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763 750 <span class="s">}</span>
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764 751
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765 752 <span class="i">$FingerprintsString</span> .= <span class="q">"; FunctionalClassesToUse: <"</span> . <span class="i">TextUtil::JoinWords</span><span class="s">(</span>\<span class="i">@</span>{<span class="i">$This</span>->{<span class="w">FunctionalClassesToUse</span>}}<span class="cm">,</span> <span class="q">", "</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span> . <span class="q">">"</span><span class="sc">;</span>
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766 753 <span class="i">$FingerprintsString</span> .= <span class="q">"; FunctionalClassesOrder: <"</span> . <span class="i">TextUtil::JoinWords</span><span class="s">(</span>\<span class="i">@FunctionalClassesOrder</span><span class="cm">,</span> <span class="q">", "</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span> . <span class="q">">"</span><span class="sc">;</span>
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767 754 <span class="i">$FingerprintsString</span> .= <span class="q">"; AvailableFunctionalClasses: <"</span> . <span class="i">TextUtil::JoinWords</span><span class="s">(</span>\<span class="i">@FunctionalClasses</span><span class="cm">,</span> <span class="q">", "</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span> . <span class="q">">"</span><span class="sc">;</span>
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768 755 <span class="s">}</span>
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769 756
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770 757 <span class="c"># Total number of atom pairs...</span>
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771 758 <span class="i">$FingerprintsString</span> .= <span class="q">"; NumOfAtomPairs: "</span> . <span class="i">$This</span>->{<span class="w">FingerprintsVector</span>}<span class="i">->GetNumOfValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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772 759
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773 760 <span class="c"># FingerprintsVector...</span>
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774 761 <span class="i">$FingerprintsString</span> .= <span class="q">"; FingerprintsVector: < $This->{FingerprintsVector} >"</span><span class="sc">;</span>
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775 762
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776 763 <span class="k">return</span> <span class="i">$FingerprintsString</span><span class="sc">;</span>
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777 764 <span class="s">}</span>
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778 765
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779 <a name="EOF-"></a></pre>
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780 <p> </p>
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781 <br />
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782 <center>
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783 <img src="../../../images/h2o2.png">
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784 </center>
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785 </body>
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786 </html>
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