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13 <pre>
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14 <a name="package-MolecularDescriptors::Fsp3CarbonsDescriptors-"></a> 1 <span class="k">package </span><span class="i">MolecularDescriptors::Fsp3CarbonsDescriptors</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: Fsp3CarbonsDescriptors.pm,v $</span>
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17 4 <span class="c"># $Date: 2015/02/28 20:49:19 $</span>
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18 5 <span class="c"># $Revision: 1.12 $</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">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">MathUtil</span> <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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48 35 <span class="k">use</span> <span class="w">Atom</span><span class="sc">;</span>
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49 36 <span class="k">use</span> <span class="w">Molecule</span><span class="sc">;</span>
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50 37 <span class="k">use</span> <span class="w">MolecularDescriptors::MolecularDescriptors</span><span class="sc">;</span>
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51 38
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52 39 <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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53 40
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54 41 <span class="i">@ISA</span> = <span class="q">qw(MolecularDescriptors::MolecularDescriptors Exporter)</span><span class="sc">;</span>
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55 42 <span class="i">@EXPORT</span> = <span class="q">qw()</span><span class="sc">;</span>
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56 43 <span class="i">@EXPORT_OK</span> = <span class="q">qw(GetDescriptorNames)</span><span class="sc">;</span>
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57 44
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58 45 <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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59 46
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60 47 <span class="c"># Setup class variables...</span>
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61 48 <span class="k">my</span><span class="s">(</span><span class="i">$ClassName</span><span class="cm">,</span> <span class="i">@DescriptorNames</span><span class="s">)</span><span class="sc">;</span>
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62 49 <span class="i">_InitializeClass</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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63 50
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64 51 <span class="c"># Overload Perl functions...</span>
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65 52 <span class="k">use</span> <span class="w">overload</span> <span class="q">'""'</span> <span class="cm">=></span> <span class="q">'StringifyFsp3CarbonsDescriptors'</span><span class="sc">;</span>
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66 53
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67 54 <span class="c"># Class constructor...</span>
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68 <a name="new-"></a> 55 <span class="k">sub </span><span class="m">new</span> <span class="s">{</span>
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69 56 <span class="k">my</span><span class="s">(</span><span class="i">$Class</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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70 57
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71 58 <span class="c"># Initialize object...</span>
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72 59 <span class="k">my</span> <span class="i">$This</span> = <span class="i">$Class</span><span class="i">->SUPER::new</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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73 60 <span class="k">bless</span> <span class="i">$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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74 61 <span class="i">$This</span><span class="i">->_InitializeFsp3CarbonsDescriptors</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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75 62
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76 63 <span class="i">$This</span><span class="i">->_InitializeFsp3CarbonsDescriptorsProperties</span><span class="s">(</span><span class="i">%NamesAndValues</span><span class="s">)</span><span class="sc">;</span>
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77 64
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78 65 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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79 66 <span class="s">}</span>
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80 67
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81 68 <span class="c"># Initialize class ...</span>
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82 <a name="_InitializeClass-"></a> 69 <span class="k">sub </span><span class="m">_InitializeClass</span> <span class="s">{</span>
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83 70 <span class="c">#Class name...</span>
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84 71 <span class="i">$ClassName</span> = <span class="w">__PACKAGE__</span><span class="sc">;</span>
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85 72
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86 73 <span class="c"># Descriptor names...</span>
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87 74 <span class="i">@DescriptorNames</span> = <span class="s">(</span><span class="q">'Fsp3Carbons'</span><span class="cm">,</span> <span class="q">'Sp3Carbons'</span><span class="s">)</span><span class="sc">;</span>
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88 75
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89 76 <span class="s">}</span>
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90 77
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91 78 <span class="c"># Get descriptor names as an array.</span>
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92 79 <span class="c">#</span>
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93 80 <span class="c"># This functionality can be either invoked as a class function or an</span>
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94 81 <span class="c"># object method.</span>
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95 82 <span class="c">#</span>
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96 <a name="GetDescriptorNames-"></a> 83 <span class="k">sub </span><span class="m">GetDescriptorNames</span> <span class="s">{</span>
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97 84 <span class="k">return</span> <span class="i">@DescriptorNames</span><span class="sc">;</span>
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98 85 <span class="s">}</span>
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99 86
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100 87 <span class="c"># Initialize object data...</span>
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101 88 <span class="c">#</span>
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102 <a name="_InitializeFsp3CarbonsDescriptors-"></a> 89 <span class="k">sub </span><span class="m">_InitializeFsp3CarbonsDescriptors</span> <span class="s">{</span>
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103 90 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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104 91
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105 92 <span class="c"># Type of MolecularDescriptor...</span>
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106 93 <span class="i">$This</span>->{<span class="w">Type</span>} = <span class="q">'Fsp3Carbons'</span><span class="sc">;</span>
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107 94
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108 95 <span class="c"># Intialize descriptor names and values...</span>
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109 96 <span class="i">$This</span><span class="i">->_InitializeDescriptorNamesAndValues</span><span class="s">(</span><span class="i">@DescriptorNames</span><span class="s">)</span><span class="sc">;</span>
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110 97
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111 98 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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112 99 <span class="s">}</span>
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113 100
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114 101 <span class="c"># Initialize object properties...</span>
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115 102 <span class="c">#</span>
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116 <a name="_InitializeFsp3CarbonsDescriptorsProperties-"></a> 103 <span class="k">sub </span><span class="m">_InitializeFsp3CarbonsDescriptorsProperties</span> <span class="s">{</span>
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117 104 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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118 105
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119 106 <span class="k">my</span><span class="s">(</span><span class="i">$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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120 107 <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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121 108 <span class="i">$MethodName</span> = <span class="q">"Set${Name}"</span><span class="sc">;</span>
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122 109 <span class="i">$This</span><span class="i">->$MethodName</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="sc">;</span>
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123 110 <span class="s">}</span>
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124 111
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125 112 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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126 113 <span class="s">}</span>
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127 114
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128 115 <span class="c"># Calculate fraction of SP3 carbons (Fsp3Carbons) [ Ref 115-116, Ref 119 ] in a molecule...</span>
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129 116 <span class="c">#</span>
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130 117 <span class="c"># It is defined as follows:</span>
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131 118 <span class="c">#</span>
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132 119 <span class="c"># Fsp3 = Number of SP3 carbons/Total number of carbons</span>
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133 120 <span class="c">#</span>
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134 <a name="GenerateDescriptors-"></a> 121 <span class="k">sub </span><span class="m">GenerateDescriptors</span> <span class="s">{</span>
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135 122 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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136 123
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137 124 <span class="c"># Initialize descriptor values...</span>
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138 125 <span class="i">$This</span><span class="i">->_InitializeDescriptorValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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139 126
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140 127 <span class="c"># Check availability of molecule...</span>
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141 128 <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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142 129 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->GenerateDescriptors: $This->{Type} molecular descriptors generation didn't succeed: Molecule data is not available: Molecule object hasn't been set..."</span><span class="sc">;</span>
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143 130 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
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144 131 <span class="s">}</span>
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145 132
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146 133 <span class="c"># Calculate descriptor values...</span>
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147 134 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->_CalculateDescriptorValues</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
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148 135 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->GenerateDescriptors: $This->{Type} molecular descriptors generation didn't succeed: Couldn't calculate Fsp3Carbons values corresponding to assigned Fsp3Carbons atom types..."</span><span class="sc">;</span>
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149 136 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
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150 137 <span class="s">}</span>
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151 138
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152 139 <span class="c"># Set final descriptor values...</span>
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153 140 <span class="i">$This</span><span class="i">->_SetFinalDescriptorValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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154 141
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155 142 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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156 143 <span class="s">}</span>
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157 144
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158 145 <span class="c"># Calculate Fsp3Carbons value...</span>
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159 146 <span class="c">#</span>
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160 <a name="_CalculateDescriptorValues-"></a> 147 <span class="k">sub </span><span class="m">_CalculateDescriptorValues</span> <span class="s">{</span>
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161 148 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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162 149 <span class="k">my</span><span class="s">(</span><span class="i">$Atom</span><span class="cm">,</span> <span class="i">$AtomID</span><span class="cm">,</span> <span class="i">$TotalCarbons</span><span class="cm">,</span> <span class="i">$NumOfSp3Carbons</span><span class="cm">,</span> <span class="i">$Fsp3Carbons</span><span class="s">)</span><span class="sc">;</span>
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163 150
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164 151 <span class="i">$TotalCarbons</span> = <span class="n">0</span><span class="sc">;</span>
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165 152 <span class="i">$NumOfSp3Carbons</span> = <span class="n">0</span><span class="sc">;</span>
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166 153
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167 154 <span class="j">ATOM:</span> <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
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168 155 <span class="k">if</span> <span class="s">(</span>!<span class="i">$Atom</span><span class="i">->IsCarbon</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
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169 156 <span class="k">next</span> <span class="j">ATOM</span><span class="sc">;</span>
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170 157 <span class="s">}</span>
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171 158 <span class="i">$TotalCarbons</span> += <span class="n">1</span><span class="sc">;</span>
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172 159
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173 160 <span class="k">if</span> <span class="s">(</span><span class="i">$Atom</span><span class="i">->DoesAtomNeighborhoodMatch</span><span class="s">(</span><span class="q">'C.T4.TSB4'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
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174 161 <span class="i">$NumOfSp3Carbons</span> += <span class="n">1</span><span class="sc">;</span>
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175 162 <span class="s">}</span>
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176 163 <span class="s">}</span>
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177 164
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178 165 <span class="i">$Fsp3Carbons</span> = <span class="i">$NumOfSp3Carbons</span> ? <span class="i">$NumOfSp3Carbons</span>/<span class="i">$TotalCarbons</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
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179 166
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180 167 <span class="c"># Track values...</span>
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181 168 <span class="i">$This</span>->{<span class="w">Fsp3Carbons</span>} = <span class="i">MathUtil::round</span><span class="s">(</span><span class="i">$Fsp3Carbons</span><span class="cm">,</span> <span class="n">2</span><span class="s">)</span><span class="sc">;</span>
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182 169 <span class="i">$This</span>->{<span class="w">Sp3Carbons</span>} = <span class="i">$NumOfSp3Carbons</span><span class="sc">;</span>
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183 170
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184 171 <span class="k">return</span> <span class="i">$This</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="c"># Setup final descriptor values...</span>
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188 175 <span class="c">#</span>
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189 <a name="_SetFinalDescriptorValues-"></a> 176 <span class="k">sub </span><span class="m">_SetFinalDescriptorValues</span> <span class="s">{</span>
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190 177 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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191 178
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192 179 <span class="i">$This</span>->{<span class="w">DescriptorsGenerated</span>} = <span class="n">1</span><span class="sc">;</span>
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193 180
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194 181 <span class="i">$This</span><span class="i">->SetDescriptorValues</span><span class="s">(</span><span class="i">$This</span>->{<span class="w">Fsp3Carbons</span>}<span class="cm">,</span> <span class="i">$This</span>->{<span class="w">Sp3Carbons</span>}<span class="s">)</span><span class="sc">;</span>
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195 182
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196 183 <span class="k">return</span> <span class="i">$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"># Return a string containg data for Fsp3CarbonsDescriptors object...</span>
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200 187 <span class="c">#</span>
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201 <a name="StringifyFsp3CarbonsDescriptors-"></a> 188 <span class="k">sub </span><span class="m">StringifyFsp3CarbonsDescriptors</span> <span class="s">{</span>
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202 189 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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203 190 <span class="k">my</span><span class="s">(</span><span class="i">$Fsp3CarbonsDescriptorsString</span><span class="s">)</span><span class="sc">;</span>
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204 191
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205 192 <span class="i">$Fsp3CarbonsDescriptorsString</span> = <span class="q">"MolecularDescriptorType: $This->{Type}; "</span> . <span class="i">$This</span><span class="i">->_StringifyDescriptorNamesAndValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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206 193
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207 194 <span class="k">return</span> <span class="i">$Fsp3CarbonsDescriptorsString</span><span class="sc">;</span>
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208 195 <span class="s">}</span>
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209 196
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210 197 <span class="c"># Is it a Fsp3CarbonsDescriptors object?</span>
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211 <a name="_IsFsp3CarbonsDescriptors-"></a> 198 <span class="k">sub </span><span class="m">_IsFsp3CarbonsDescriptors</span> <span class="s">{</span>
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212 199 <span class="k">my</span><span class="s">(</span><span class="i">$Object</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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213 200
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214 201 <span class="k">return</span> <span class="s">(</span><span class="i">Scalar::Util::blessed</span><span class="s">(</span><span class="i">$Object</span><span class="s">)</span> && <span class="i">$Object</span><span class="i">->isa</span><span class="s">(</span><span class="i">$ClassName</span><span class="s">)</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
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215 202 <span class="s">}</span>
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216 203
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217 <a name="EOF-"></a></pre>
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218 <p> </p>
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219 <br />
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220 <center>
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221 <img src="../../../images/h2o2.png">
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222 </center>
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223 </body>
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224 </html>
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