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14 <a name="package-AtomicDescriptors::AtomicDescriptors-"></a> 1 <span class="k">package </span><span class="i">AtomicDescriptors::AtomicDescriptors</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: AtomicDescriptors.pm,v $</span>
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17 4 <span class="c"># $Date: 2015/02/28 20:47:48 $</span>
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18 5 <span class="c"># $Revision: 1.17 $</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">Scalar::Util</span> <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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46 33 <span class="k">use</span> <span class="w">ObjectProperty</span><span class="sc">;</span>
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47 34 <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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48 35
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49 36 <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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50 37
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51 38 <span class="i">@ISA</span> = <span class="q">qw(ObjectProperty Exporter)</span><span class="sc">;</span>
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52 39 <span class="i">@EXPORT</span> = <span class="q">qw()</span><span class="sc">;</span>
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53 40 <span class="i">@EXPORT_OK</span> = <span class="q">qw()</span><span class="sc">;</span>
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54 41
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55 42 <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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56 43
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57 44 <span class="c"># Setup class variables...</span>
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58 45 <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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59 46 <span class="i">_InitializeClass</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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60 47
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61 48 <span class="c"># Class constructor...</span>
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62 <a name="new-"></a> 49 <span class="k">sub </span><span class="m">new</span> <span class="s">{</span>
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63 50 <span class="k">my</span><span class="s">(</span><span class="i">$Class</span><span class="cm">,</span> <span class="i">%PropertyNamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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64 51
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65 52 <span class="c"># Initialize object...</span>
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66 53 <span class="k">my</span> <span class="i">$This</span> = <span class="s">{</span><span class="s">}</span><span class="sc">;</span>
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67 54 <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">$Class</span><span class="sc">;</span>
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68 55 <span class="i">$This</span><span class="i">->_InitializeAtomicDescriptors</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="i">$This</span><span class="i">->_InitializeAtomicDescriptorsProperties</span><span class="s">(</span><span class="i">%PropertyNamesAndValues</span><span class="s">)</span><span class="sc">;</span>
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71 58
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72 59 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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73 60 <span class="s">}</span>
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74 61
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75 62 <span class="c"># Initialize object data...</span>
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76 63 <span class="c">#</span>
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77 <a name="_InitializeAtomicDescriptors-"></a> 64 <span class="k">sub </span><span class="m">_InitializeAtomicDescriptors</span> <span class="s">{</span>
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78 65 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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79 66
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80 67 <span class="c"># Molecule object...</span>
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81 68 <span class="i">$This</span>->{<span class="w">Molecule</span>} = <span class="q">''</span><span class="sc">;</span>
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82 69
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83 70 <span class="c"># Type of atomic descriptors...</span>
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84 71 <span class="i">$This</span>->{<span class="w">Type</span>} = <span class="q">''</span><span class="sc">;</span>
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85 72
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86 73 <span class="c"># By default, atomic decriptor values are also calculated for hydrogens...</span>
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87 74 <span class="i">$This</span>->{<span class="w">IgnoreHydrogens</span>} = <span class="n">0</span><span class="sc">;</span>
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88 75
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89 76 <span class="c"># Calculated atomic descriptor values hash. Instead of assigning the calculated values to Atom</span>
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90 77 <span class="c"># objects, these values are stored in the current object in a hash with atom ID and atomic descriptor</span>
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91 78 <span class="c"># values as key/value pairs.</span>
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92 79 <span class="c">#</span>
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93 80 <span class="c"># Unlike molecular descriptors, no descriptor names are assigned to individual atomic descriptor</span>
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94 81 <span class="c"># values.</span>
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95 82 <span class="c">#</span>
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96 83 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">DescriptorValues</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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97 84 <span class="s">}</span>
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98 85
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99 86 <span class="c"># Initialize class ...</span>
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100 <a name="_InitializeClass-"></a> 87 <span class="k">sub </span><span class="m">_InitializeClass</span> <span class="s">{</span>
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101 88 <span class="c">#Class name...</span>
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102 89 <span class="i">$ClassName</span> = <span class="w">__PACKAGE__</span><span class="sc">;</span>
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103 90 <span class="s">}</span>
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104 91
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105 92 <span class="c"># Initialize object properties....</span>
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106 <a name="_InitializeAtomicDescriptorsProperties-"></a> 93 <span class="k">sub </span><span class="m">_InitializeAtomicDescriptorsProperties</span> <span class="s">{</span>
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107 94 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">%PropertiesNamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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108 95
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109 96 <span class="k">my</span><span class="s">(</span><span class="i">$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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110 97 <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">%PropertiesNamesAndValues</span><span class="s">)</span> <span class="s">{</span>
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111 98 <span class="i">$MethodName</span> = <span class="q">"Set${Name}"</span><span class="sc">;</span>
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112 99 <span class="i">$This</span><span class="i">->$MethodName</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="sc">;</span>
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113 100 <span class="s">}</span>
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114 101
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115 102 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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116 103 <span class="s">}</span>
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117 104
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118 105 <span class="c"># Initialize descriptor values for all atoms in a molecule...</span>
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119 106 <span class="c">#</span>
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120 <a name="_InitializeDescriptorValues-"></a> 107 <span class="k">sub </span><span class="m">_InitializeDescriptorValues</span> <span class="s">{</span>
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121 108 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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122 109
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123 110 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="s">)</span> <span class="s">{</span>
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124 111 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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125 112 <span class="s">}</span>
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126 113
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127 114 <span class="c"># Assign 'None' to all atomic descriptor values...</span>
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128 115 <span class="c">#</span>
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129 116 <span class="k">my</span><span class="s">(</span><span class="i">$Atom</span><span class="cm">,</span> <span class="i">$AtomID</span><span class="s">)</span><span class="sc">;</span>
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130 117
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131 118 <span class="j">ATOM:</span> <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
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132 119 <span class="i">$AtomID</span> = <span class="i">$Atom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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133 120 <span class="i">$This</span>->{<span class="w">DescriptorValues</span>}{<span class="i">$AtomID</span>} = <span class="q">'None'</span><span class="sc">;</span>
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134 121 <span class="s">}</span>
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135 122
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136 123 <span class="k">return</span> <span class="i">$This</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"># Set molecule object and make sure it's not already set...</span>
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140 127 <span class="c">#</span>
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141 <a name="SetMolecule-"></a> 128 <span class="k">sub </span><span class="m">SetMolecule</span> <span class="s">{</span>
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142 129 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Molecule</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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143 130
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144 131 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="s">)</span> <span class="s">{</span>
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145 132 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetMolecule: Can't change molecule object: It's already set..."</span><span class="sc">;</span>
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146 133 <span class="s">}</span>
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147 134 <span class="i">$This</span>->{<span class="w">Molecule</span>} = <span class="i">$Molecule</span><span class="sc">;</span>
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148 135
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149 136 <span class="c"># Weaken the reference to disable increment of reference count...</span>
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150 137 <span class="i">Scalar::Util::weaken</span><span class="s">(</span><span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="s">)</span><span class="sc">;</span>
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151 138
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152 139 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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153 140 <span class="s">}</span>
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154 141
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155 142 <span class="c"># Set type and make sure it's not already set...</span>
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156 143 <span class="c">#</span>
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157 <a name="SetType-"></a> 144 <span class="k">sub </span><span class="m">SetType</span> <span class="s">{</span>
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158 145 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Type</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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159 146
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160 147 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">Type</span>}<span class="s">)</span> <span class="s">{</span>
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161 148 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetType: Can't change AtomicDescriptors type: It's already set..."</span><span class="sc">;</span>
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162 149 <span class="s">}</span>
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163 150 <span class="i">$This</span>->{<span class="w">Type</span>} = <span class="i">$Type</span><span class="sc">;</span>
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164 151
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165 152 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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166 153 <span class="s">}</span>
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167 154
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168 155 <span class="c"># Set specific atomic descriptor value...</span>
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169 156 <span class="c">#</span>
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170 <a name="SetDescriptorValue-"></a> 157 <span class="k">sub </span><span class="m">SetDescriptorValue</span> <span class="s">{</span>
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171 158 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Atom</span><span class="cm">,</span> <span class="i">$AtomicDescriptor</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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172 159 <span class="k">my</span><span class="s">(</span><span class="i">$AtomID</span><span class="s">)</span><span class="sc">;</span>
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173 160
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174 161 <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>
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175 162 <span class="i">$This</span>->{<span class="w">DescriptorValues</span>}{<span class="i">$AtomID</span>} = <span class="i">$AtomicDescriptor</span><span class="sc">;</span>
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176 163
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177 164 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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178 165 <span class="s">}</span>
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179 166
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180 167 <span class="c"># Get specific atomic descriptor value...</span>
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181 168 <span class="c">#</span>
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182 <a name="GetDescriptorValue-"></a> 169 <span class="k">sub </span><span class="m">GetDescriptorValue</span> <span class="s">{</span>
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183 170 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Atom</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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184 171 <span class="k">my</span><span class="s">(</span><span class="i">$AtomID</span><span class="s">)</span><span class="sc">;</span>
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185 172
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186 173 <span class="i">$AtomID</span> = <span class="i">$Atom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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187 174
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188 175 <span class="k">return</span> <span class="k">exists</span> <span class="i">$This</span>->{<span class="w">DescriptorValues</span>}{<span class="i">$AtomID</span>} ? <span class="i">$This</span>->{<span class="w">DescriptorValues</span>}{<span class="i">$AtomID</span>} <span class="co">:</span> <span class="q">'None'</span><span class="sc">;</span>
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189 176 <span class="s">}</span>
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190 177
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191 178 <span class="c"># Get calculated atomic descriptor values as a hash with atom ID and atomic descriptor</span>
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192 179 <span class="c"># values as key/value pairs...</span>
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193 180 <span class="c">#</span>
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194 <a name="GetDescriptorValues-"></a> 181 <span class="k">sub </span><span class="m">GetDescriptorValues</span> <span class="s">{</span>
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195 182 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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196 183
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197 184 <span class="k">return</span> <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">DescriptorValues</span>}}<span class="sc">;</span>
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198 185 <span class="s">}</span>
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199 186
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200 187 <span class="c"># Are all atomic descriptor values successfully calculated?</span>
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201 188 <span class="c">#</span>
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202 189 <span class="c"># Notes:</span>
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203 190 <span class="c"># . Dynamic checking of calculated descriptor values for atoms eliminates the need</span>
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204 191 <span class="c"># to check and synchronize valid descriptor values during SetDescriptorValue.</span>
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205 192 <span class="c">#</span>
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206 <a name="IsDescriptorsGenerationSuccessful-"></a> 193 <span class="k">sub </span><span class="m">IsDescriptorsGenerationSuccessful</span> <span class="s">{</span>
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207 194 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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208 195 <span class="k">my</span><span class="s">(</span><span class="i">$Atom</span><span class="cm">,</span> <span class="i">$DescriptorValue</span><span class="cm">,</span> <span class="i">@Atoms</span><span class="s">)</span><span class="sc">;</span>
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209 196
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210 197 <span class="j">ATOM:</span> <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
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211 198 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">IgnoreHydrogens</span>} && <span class="i">$Atom</span><span class="i">->IsHydrogen</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
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212 199 <span class="k">next</span> <span class="j">ATOM</span><span class="sc">;</span>
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213 200 <span class="s">}</span>
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214 201 <span class="i">$DescriptorValue</span> = <span class="i">$This</span><span class="i">->GetDescriptorValue</span><span class="s">(</span><span class="i">$Atom</span><span class="s">)</span><span class="sc">;</span>
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215 202 <span class="k">if</span> <span class="s">(</span><span class="i">$DescriptorValue</span> =~ <span class="q">/^None$/i</span><span class="s">)</span> <span class="s">{</span>
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216 203 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
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217 204 <span class="s">}</span>
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218 205 <span class="s">}</span>
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219 206
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220 207 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span>
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221 208 <span class="s">}</span>
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222 209
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223 <a name="EOF-"></a></pre>
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224 <p> </p>
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225 <br />
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226 <center>
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227 <img src="../../../images/h2o2.png">
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228 </center>
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229 </body>
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230 </html>
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