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13 <pre>
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14 <a name="package-MolecularDescriptors::MolecularDescriptorsGenerator-"></a> 1 <span class="k">package </span><span class="i">MolecularDescriptors::MolecularDescriptorsGenerator</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: MolecularDescriptorsGenerator.pm,v $</span>
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17 4 <span class="c"># $Date: 2015/02/28 20:49:20 $</span>
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18 5 <span class="c"># $Revision: 1.13 $</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 <span class="k">use</span> <span class="w">FileUtil</span> <span class="s">(</span><span class="s">)</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(ObjectProperty 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(GetAvailableDescriptorClassNames GetAvailableClassAndDescriptorNames GetAvailableDescriptorNames GetAvailableDescriptorNamesForDescriptorClass GetAvailableClassNameForDescriptorName GetRuleOf5DescriptorNames GetRuleOf3DescriptorNames IsDescriptorClassNameAvailable IsDescriptorNameAvailable)</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">%DescriptorsDataMap</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">'StringifyMolecularDescriptorsGenerator'</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="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">->_InitializeMolecularDescriptorsGenerator</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">$This</span><span class="i">->_InitializeMolecularDescriptorsGeneratorProperties</span><span class="s">(</span><span class="i">%NamesAndValues</span><span class="s">)</span><span class="sc">;</span>
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77 64
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78 65 <span class="k">return</span> <span class="i">$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">$ClassName</span> = <span class="w">__PACKAGE__</span><span class="sc">;</span>
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85 72
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86 73 <span class="c"># Load available molecular descriptor classes...</span>
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87 74 <span class="i">_LoadMolecularDescriptorsData</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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88 75
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89 76 <span class="s">}</span>
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90 77
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91 78 <span class="c"># Initialize object data...</span>
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92 79 <span class="c">#</span>
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93 <a name="_InitializeMolecularDescriptorsGenerator-"></a> 80 <span class="k">sub </span><span class="m">_InitializeMolecularDescriptorsGenerator</span> <span class="s">{</span>
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94 81 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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95 82
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96 83 <span class="c"># Type of desciptors to generate...</span>
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97 84 <span class="c">#</span>
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98 85 <span class="c"># The current release of MayaChemTools supports generation of four sets of</span>
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99 86 <span class="c"># descriptors: All available descriptors, rule of 5 or 3 descriptors or a specified</span>
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100 87 <span class="c"># set of descriptors.</span>
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101 88 <span class="c">#</span>
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102 89 <span class="c"># Possible values: All, RuleOf5, RuleOf3 or Specify</span>
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103 90 <span class="c">#</span>
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104 91 <span class="c"># RuleOf5 [ Ref 91 ] descriptor names: MolecularWeight, HydrogenBondDonors, HydrogenBondAcceptors,</span>
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105 92 <span class="c"># SLogP. RuleOf5 states: MolecularWeight <= 500, HydrogenBondDonors <= 5, HydrogenBondAcceptors <= 10,</span>
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106 93 <span class="c"># and logP <= 5.</span>
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107 94 <span class="c">#</span>
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108 95 <span class="c"># RuleOf3 [ Ref 92 ] descriptor names: MolecularWeight, RotatableBonds, HydrogenBondDonors,</span>
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109 96 <span class="c"># HydrogenBondAcceptors, SLogP, TPSA. RuleOf3 states: MolecularWeight <= 300, RotatableBonds <= 3,</span>
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110 97 <span class="c"># HydrogenBondDonors <= 3, HydrogenBondAcceptors <= 3, logP <= 3, and TPSA <= 60.</span>
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111 98 <span class="c">#</span>
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112 99 <span class="c"># For Specify value of Mode, a set of descritor names must be specified using</span>
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113 100 <span class="c"># DescriptorNames parameter.</span>
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114 101 <span class="c">#</span>
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115 102 <span class="c"># Default: All</span>
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116 103 <span class="c">#</span>
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117 104 <span class="i">$This</span>->{<span class="w">Mode</span>} = <span class="q">''</span><span class="sc">;</span>
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118 105
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119 106 <span class="c"># Descriptor names used to generate descriptor values during a specified descriptor</span>
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120 107 <span class="c"># generation mode...</span>
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121 108 <span class="c">#</span>
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122 109 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DescriptorNames</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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123 110
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124 111 <span class="c"># Descriptor calculation control parameters for specified descriptor class names...</span>
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125 112 <span class="c">#</span>
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126 113 <span class="c"># These parameters are passed on to appropriate descriptor classes during</span>
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127 114 <span class="c"># instantiations of descriptor class objects.</span>
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128 115 <span class="c">#</span>
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129 116 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">DescriptorClassParameters</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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130 117
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131 118 <span class="i">$This</span>->{<span class="w">DescriptorClassesInstantiated</span>} = <span class="n">0</span><span class="sc">;</span>
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132 119
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133 120 <span class="c"># Descriptor class names and objects corresponding to specified descriptor names...</span>
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134 121 <span class="c">#</span>
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135 122 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DescriptorClassNames</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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136 123 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">DescriptorClassObjects</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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137 124
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138 125 <span class="c"># Descriptor values generated for specified descriptor names...</span>
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139 126 <span class="c">#</span>
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140 127 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DescriptorValues</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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141 128
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142 129 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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143 130 <span class="s">}</span>
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144 131
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145 132 <span class="c"># Initialize object properties...</span>
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146 133 <span class="c">#</span>
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147 <a name="_InitializeMolecularDescriptorsGeneratorProperties-"></a> 134 <span class="k">sub </span><span class="m">_InitializeMolecularDescriptorsGeneratorProperties</span> <span class="s">{</span>
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148 135 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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149 136
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150 137 <span class="k">my</span><span class="s">(</span><span class="i">$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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151 138 <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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152 139 <span class="i">$MethodName</span> = <span class="q">"Set${Name}"</span><span class="sc">;</span>
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153 140 <span class="i">$This</span><span class="i">->$MethodName</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="sc">;</span>
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154 141 <span class="s">}</span>
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155 142
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156 143 <span class="c"># Set default value for Mode...</span>
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157 144 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span>->{<span class="w">Mode</span>}<span class="s">)</span> <span class="s">{</span>
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158 145 <span class="i">$This</span>->{<span class="w">Mode</span>} = <span class="q">'All'</span><span class="sc">;</span>
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159 146 <span class="s">}</span>
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160 147
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161 148 <span class="i">$This</span><span class="i">->_CheckAndInitializeDescriptorNames</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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162 149
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163 150 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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164 151 <span class="s">}</span>
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165 152
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166 153 <span class="c"># Set descriptors generation mode......</span>
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167 154 <span class="c">#</span>
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168 <a name="SetMode-"></a> 155 <span class="k">sub </span><span class="m">SetMode</span> <span class="s">{</span>
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169 156 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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170 157
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171 158 <span class="c"># All - all available descriptors</span>
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172 159 <span class="c"># Specify - Specified set of descriptors</span>
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173 160
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174 161 <span class="k">if</span> <span class="s">(</span><span class="i">$Value</span> !~ <span class="q">/^(All|RuleOf5|RuleOf3|Specify)$/i</span><span class="s">)</span> <span class="s">{</span>
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175 162 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetMode: Mode value, $Value, is not valid; Supported values: All, RuleOf5, RuleOf3 or Specify..."</span><span class="sc">;</span>
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176 163 <span class="s">}</span>
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177 164
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178 165 <span class="i">$This</span>->{<span class="w">Mode</span>} = <span class="i">$Value</span><span class="sc">;</span>
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179 166
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180 167 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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181 168 <span class="s">}</span>
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182 169
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183 170 <span class="c"># Set descriptor names to use for generating descriptor values using an array</span>
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184 171 <span class="c"># or reference to an array...</span>
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185 172 <span class="c">#</span>
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186 <a name="SetDescriptorNames-"></a> 173 <span class="k">sub </span><span class="m">SetDescriptorNames</span> <span class="s">{</span>
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187 174 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">@Values</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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188 175
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189 176 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">Mode</span>} =~ <span class="q">/^All$/i</span><span class="s">)</span> <span class="s">{</span>
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190 177 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetDescriptorNames: Descriptor names cann't be specified during \"All\" value of descsriptors generation \"Mode\"..."</span><span class="sc">;</span>
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191 178 <span class="s">}</span>
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192 179
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193 180 <span class="k">if</span> <span class="s">(</span>!<span class="i">@Values</span><span class="s">)</span> <span class="s">{</span>
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194 181 <span class="k">return</span><span class="sc">;</span>
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195 182 <span class="s">}</span>
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196 183
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197 184 <span class="k">my</span><span class="s">(</span><span class="i">$FirstValue</span><span class="cm">,</span> <span class="i">$TypeOfFirstValue</span><span class="s">)</span><span class="sc">;</span>
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198 185
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199 186 <span class="i">$FirstValue</span> = <span class="i">$Values</span>[<span class="n">0</span>]<span class="sc">;</span>
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200 187 <span class="i">$TypeOfFirstValue</span> = <span class="k">ref</span> <span class="i">$FirstValue</span><span class="sc">;</span>
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201 188
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202 189 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DescriptorNames</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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203 190
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204 191 <span class="k">if</span> <span class="s">(</span><span class="i">$TypeOfFirstValue</span> =~ <span class="q">/^ARRAY/</span><span class="s">)</span> <span class="s">{</span>
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205 192 <span class="c"># Initialize using array refernce...</span>
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206 193 <span class="k">push</span> <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DescriptorNames</span>}}<span class="cm">,</span> <span class="i">@</span>{<span class="i">$FirstValue</span>}<span class="sc">;</span>
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207 194 <span class="s">}</span>
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208 195 <span class="k">else</span> <span class="s">{</span>
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209 196 <span class="c"># It's a list of values...</span>
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210 197 <span class="k">push</span> <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DescriptorNames</span>}}<span class="cm">,</span> <span class="i">@Values</span><span class="sc">;</span>
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211 198 <span class="s">}</span>
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212 199
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213 200 <span class="c"># Make sure specified descriptor names are valid...</span>
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214 201 <span class="i">$This</span><span class="i">->_ValidateDescriptorNames</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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215 202
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216 203 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
217 204 <span class="s">}</span>
|
|
|
218 205
|
|
|
219 206 <span class="c"># Get descriptor names as an array...</span>
|
|
|
220 207 <span class="c">#</span>
|
|
|
221 <a name="GetDescriptorNames-"></a> 208 <span class="k">sub </span><span class="m">GetDescriptorNames</span> <span class="s">{</span>
|
|
|
222 209 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
223 210
|
|
|
224 211 <span class="k">return</span> <span class="k">wantarray</span> ? <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DescriptorNames</span>}} <span class="co">:</span> <span class="k">scalar</span> <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DescriptorNames</span>}}<span class="sc">;</span>
|
|
|
225 212 <span class="s">}</span>
|
|
|
226 213
|
|
|
227 214 <span class="c"># Get all descriptor values as an array...</span>
|
|
|
228 215 <span class="c">#</span>
|
|
|
229 <a name="GetDescriptorValues-"></a> 216 <span class="k">sub </span><span class="m">GetDescriptorValues</span> <span class="s">{</span>
|
|
|
230 217 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
231 218
|
|
|
232 219 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">DescriptorsGenerated</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
233 220 <span class="k">return</span> <span class="k">wantarray</span> ? <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DescriptorValues</span>}} <span class="co">:</span> <span class="k">scalar</span> <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DescriptorValues</span>}}<span class="sc">;</span>
|
|
|
234 221 <span class="s">}</span>
|
|
|
235 222 <span class="k">else</span> <span class="s">{</span>
|
|
|
236 223 <span class="k">my</span><span class="s">(</span><span class="i">@DescriptorValues</span><span class="s">)</span><span class="sc">;</span>
|
|
|
237 224
|
|
|
238 225 <span class="i">@DescriptorValues</span> = <span class="s">(</span><span class="q">'None'</span><span class="s">)</span> x <span class="k">scalar</span> <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DescriptorNames</span>}}<span class="sc">;</span>
|
|
|
239 226
|
|
|
240 227 <span class="k">return</span> <span class="k">wantarray</span> ? <span class="i">@DescriptorValues</span> <span class="co">:</span> <span class="k">scalar</span> <span class="i">@DescriptorValues</span><span class="sc">;</span>
|
|
|
241 228 <span class="s">}</span>
|
|
|
242 229 <span class="s">}</span>
|
|
|
243 230
|
|
|
244 231 <span class="c"># Get descriptor value for a specified descriptor name...</span>
|
|
|
245 232 <span class="c">#</span>
|
|
|
246 <a name="GetDescriptorValueByName-"></a> 233 <span class="k">sub </span><span class="m">GetDescriptorValueByName</span> <span class="s">{</span>
|
|
|
247 234 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Name</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
248 235 <span class="k">my</span><span class="s">(</span><span class="i">%NamesAndValues</span><span class="s">)</span><span class="sc">;</span>
|
|
|
249 236
|
|
|
250 237 <span class="i">%NamesAndValues</span> = <span class="i">$This</span><span class="i">->GetDescriptorNamesAndValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
251 238
|
|
|
252 239 <span class="k">return</span> <span class="k">exists</span> <span class="i">$NamesAndValues</span>{<span class="i">$Name</span>} ? <span class="i">$NamesAndValues</span>{<span class="i">$Name</span>} <span class="co">:</span> <span class="q">'None'</span><span class="sc">;</span>
|
|
|
253 240
|
|
|
254 241 <span class="s">}</span>
|
|
|
255 242
|
|
|
256 243 <span class="c"># Get calculated molecular descriptor names sand values as a hash with names</span>
|
|
|
257 244 <span class="c"># and values as key/value pairs...</span>
|
|
|
258 245 <span class="c">#</span>
|
|
|
259 <a name="GetDescriptorNamesAndValues-"></a> 246 <span class="k">sub </span><span class="m">GetDescriptorNamesAndValues</span> <span class="s">{</span>
|
|
|
260 247 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
261 248 <span class="k">my</span><span class="s">(</span><span class="i">%NamesAndValues</span><span class="s">)</span><span class="sc">;</span>
|
|
|
262 249
|
|
|
263 250 <span class="i">%NamesAndValues</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
264 251 <span class="i">@NamesAndValues</span>{ <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DescriptorNames</span>}} } = <span class="i">$This</span><span class="i">->GetDescriptorValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
265 252
|
|
|
266 253 <span class="k">return</span> <span class="i">%NamesAndValues</span><span class="sc">;</span>
|
|
|
267 254 <span class="s">}</span>
|
|
|
268 255
|
|
|
269 256 <span class="c"># Set up descriptor calculation control parameters for a specified descriptor class name...</span>
|
|
|
270 257 <span class="c">#</span>
|
|
|
271 258 <span class="c"># The specified parameter names and values are simply passed on to specified descriptor</span>
|
|
|
272 259 <span class="c"># class during instantiation of descriptor class object without any performing any validation</span>
|
|
|
273 260 <span class="c"># of parameter names and associated values. It's up to the appropriate descriptor class methods</span>
|
|
|
274 261 <span class="c"># to validate these parameters and values.</span>
|
|
|
275 262 <span class="c">#</span>
|
|
|
276 263 <span class="c"># In addition to specified parameter names and values, the parameter hash must also contain</span>
|
|
|
277 264 <span class="c"># descriptor class name as key and value pair with DescriptorClassName as key with class</span>
|
|
|
278 265 <span class="c"># name as value.</span>
|
|
|
279 266 <span class="c">#</span>
|
|
|
280 <a name="SetDescriptorClassParameters-"></a> 267 <span class="k">sub </span><span class="m">SetDescriptorClassParameters</span> <span class="s">{</span>
|
|
|
281 268 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
282 269 <span class="k">my</span><span class="s">(</span><span class="i">$DescriptorClassName</span><span class="cm">,</span> <span class="i">$Name</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span><span class="sc">;</span>
|
|
|
283 270
|
|
|
284 271 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$NamesAndValues</span>{<span class="w">DescriptorClassName</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
285 272 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->_SetDescriptorNameParameters: Can't set descriptor class name paramaters: DescriptorClassName is not specified..."</span><span class="sc">;</span>
|
|
|
286 273 <span class="s">}</span>
|
|
|
287 274
|
|
|
288 275 <span class="i">$DescriptorClassName</span> = <span class="i">$NamesAndValues</span>{<span class="w">DescriptorClassName</span>}<span class="sc">;</span>
|
|
|
289 276 <span class="k">if</span> <span class="s">(</span>!<span class="i">IsDescriptorClassNameAvailable</span><span class="s">(</span><span class="i">$DescriptorClassName</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
290 277 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->_SetDescriptorClassParameters: Can't set descriptor class name paramaters: Specified descriptor class name, $DescriptorClassName, is not available..."</span><span class="sc">;</span>
|
|
|
291 278 <span class="k">return</span> <span class="i">$This</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="k">exists</span> <span class="i">$This</span>->{<span class="w">DescriptorClassParameters</span>}{<span class="i">$DescriptorClassName</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
295 282 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->SetDescriptorClassParameters: Class name parameters for $DescriptorClassName have already been specified: Replacing previous values..."</span><span class="sc">;</span>
|
|
|
296 283 <span class="s">}</span>
|
|
|
297 284
|
|
|
298 285 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">DescriptorClassParameters</span>}{<span class="i">$DescriptorClassName</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
299 286 <span class="j">NAME:</span> <span class="k">while</span> <span class="s">(</span><span class="s">(</span><span class="i">$Name</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="k">each</span> <span class="i">%NamesAndValues</span><span class="s">)</span> <span class="s">{</span>
|
|
|
300 287 <span class="k">if</span> <span class="s">(</span><span class="i">$Name</span> =~ <span class="q">/^DescriptorClassName$/</span><span class="s">)</span> <span class="s">{</span>
|
|
|
301 288 <span class="k">next</span> <span class="j">NAME</span><span class="sc">;</span>
|
|
|
302 289 <span class="s">}</span>
|
|
|
303 290 <span class="i">$This</span>->{<span class="w">DescriptorClassParameters</span>}{<span class="i">$DescriptorClassName</span>}{<span class="i">$Name</span>} = <span class="i">$Value</span><span class="sc">;</span>
|
|
|
304 291 <span class="s">}</span>
|
|
|
305 292
|
|
|
306 293 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
307 294 <span class="s">}</span>
|
|
|
308 295
|
|
|
309 296 <span class="c"># Get descriptor name parameters as a reference to hash of hashes with hash</span>
|
|
|
310 297 <span class="c"># keys corresponding to class name and class parameter name with hash value</span>
|
|
|
311 298 <span class="c"># as class parameter value...</span>
|
|
|
312 299 <span class="c">#</span>
|
|
|
313 <a name="GetDescriptorClassParameters-"></a> 300 <span class="k">sub </span><span class="m">GetDescriptorClassParameters</span> <span class="s">{</span>
|
|
|
314 301 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
315 302
|
|
|
316 303 <span class="k">return</span> \<span class="i">%</span>{<span class="i">$This</span>->{<span class="w">DescriptorClassParameters</span>}}<span class="sc">;</span>
|
|
|
317 304 <span class="s">}</span>
|
|
|
318 305
|
|
|
319 306 <span class="c"># Get available descriptor class names as an array.</span>
|
|
|
320 307 <span class="c">#</span>
|
|
|
321 308 <span class="c"># This functionality can be either invoked as a class function or an</span>
|
|
|
322 309 <span class="c"># object method.</span>
|
|
|
323 310 <span class="c">#</span>
|
|
|
324 <a name="GetAvailableDescriptorClassNames-"></a> 311 <span class="k">sub </span><span class="m">GetAvailableDescriptorClassNames</span> <span class="s">{</span>
|
|
|
325 312
|
|
|
326 313 <span class="k">return</span> <span class="k">wantarray</span> ? <span class="i">@</span>{<span class="i">$DescriptorsDataMap</span>{<span class="w">ClassNames</span>}} <span class="co">:</span> <span class="k">scalar</span> <span class="i">@</span>{<span class="i">$DescriptorsDataMap</span>{<span class="w">ClassNames</span>}}<span class="sc">;</span>
|
|
|
327 314 <span class="s">}</span>
|
|
|
328 315
|
|
|
329 316 <span class="c"># Get available descriptors class and descriptors names as a hash containing key/value</span>
|
|
|
330 317 <span class="c"># pairs corresponding to class name and an array of descriptor names available for the</span>
|
|
|
331 318 <span class="c"># class.</span>
|
|
|
332 319 <span class="c">#</span>
|
|
|
333 320 <span class="c"># This functionality can be either invoked as a class function or an</span>
|
|
|
334 321 <span class="c"># object method.</span>
|
|
|
335 322 <span class="c">#</span>
|
|
|
336 <a name="GetAvailableClassAndDescriptorNames-"></a> 323 <span class="k">sub </span><span class="m">GetAvailableClassAndDescriptorNames</span> <span class="s">{</span>
|
|
|
337 324 <span class="k">my</span><span class="s">(</span><span class="i">$DescriptorClassName</span><span class="cm">,</span> <span class="i">@DescriptorNames</span><span class="cm">,</span> <span class="i">%ClassAndDescriptorNames</span><span class="s">)</span><span class="sc">;</span>
|
|
|
338 325
|
|
|
339 326 <span class="i">%ClassAndDescriptorNames</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
340 327 <span class="k">for</span> <span class="i">$DescriptorClassName</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$DescriptorsDataMap</span>{<span class="w">ClassNames</span>}}<span class="s">)</span> <span class="s">{</span>
|
|
|
341 328 <span class="i">@</span>{<span class="i">$ClassAndDescriptorNames</span>{<span class="i">$DescriptorClassName</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
342 329 <span class="k">push</span> <span class="i">@</span>{<span class="i">$ClassAndDescriptorNames</span>{<span class="i">$DescriptorClassName</span>}}<span class="cm">,</span> <span class="i">@</span>{<span class="i">$DescriptorsDataMap</span>{<span class="w">ClassToDescriptorNames</span>}{<span class="i">$DescriptorClassName</span>}}<span class="sc">;</span>
|
|
|
343 330 <span class="s">}</span>
|
|
|
344 331
|
|
|
345 332 <span class="k">return</span> <span class="i">%ClassAndDescriptorNames</span><span class="sc">;</span>
|
|
|
346 333 <span class="s">}</span>
|
|
|
347 334
|
|
|
348 335 <span class="c"># Get available descriptor names as an array.</span>
|
|
|
349 336 <span class="c">#</span>
|
|
|
350 337 <span class="c"># This functionality can be either invoked as a class function or an</span>
|
|
|
351 338 <span class="c"># object method.</span>
|
|
|
352 339 <span class="c">#</span>
|
|
|
353 <a name="GetAvailableDescriptorNames-"></a> 340 <span class="k">sub </span><span class="m">GetAvailableDescriptorNames</span> <span class="s">{</span>
|
|
|
354 341 <span class="k">my</span><span class="s">(</span><span class="i">@DescriptorNames</span><span class="s">)</span><span class="sc">;</span>
|
|
|
355 342
|
|
|
356 343 <span class="i">@DescriptorNames</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
357 344 <span class="k">push</span> <span class="i">@DescriptorNames</span><span class="cm">,</span> <span class="k">map</span> <span class="s">{</span> <span class="i">@</span>{<span class="i">$DescriptorsDataMap</span>{<span class="w">ClassToDescriptorNames</span>}{<span class="i">$_</span>}} <span class="s">}</span> <span class="i">@</span>{<span class="i">$DescriptorsDataMap</span>{<span class="w">ClassNames</span>}}<span class="sc">;</span>
|
|
|
358 345
|
|
|
359 346 <span class="k">return</span> <span class="k">wantarray</span> ? <span class="i">@DescriptorNames</span> <span class="co">:</span> <span class="k">scalar</span> <span class="i">@DescriptorNames</span><span class="sc">;</span>
|
|
|
360 347 <span class="s">}</span>
|
|
|
361 348
|
|
|
362 349 <span class="c"># Is it a valid descriptors class name?</span>
|
|
|
363 350 <span class="c">#</span>
|
|
|
364 351 <span class="c"># This functionality can be either invoked as a class function or an</span>
|
|
|
365 352 <span class="c"># object method.</span>
|
|
|
366 353 <span class="c">#</span>
|
|
|
367 <a name="IsDescriptorClassNameAvailable-"></a> 354 <span class="k">sub </span><span class="m">IsDescriptorClassNameAvailable</span> <span class="s">{</span>
|
|
|
368 355 <span class="k">my</span><span class="s">(</span><span class="i">$FirstParameter</span><span class="cm">,</span> <span class="i">$SecondParameter</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
369 356 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$DescriptorClassName</span><span class="s">)</span><span class="sc">;</span>
|
|
|
370 357
|
|
|
371 358 <span class="k">if</span> <span class="s">(</span><span class="s">(</span><span class="i">@_</span> == <span class="n">2</span><span class="s">)</span> && <span class="s">(</span><span class="i">_IsMolecularDescriptorsGenerator</span><span class="s">(</span><span class="i">$FirstParameter</span><span class="s">)</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
372 359 <span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$DescriptorClassName</span><span class="s">)</span> = <span class="s">(</span><span class="i">$FirstParameter</span><span class="cm">,</span> <span class="i">$SecondParameter</span><span class="s">)</span><span class="sc">;</span>
|
|
|
373 360 <span class="s">}</span>
|
|
|
374 361 <span class="k">else</span> <span class="s">{</span>
|
|
|
375 362 <span class="s">(</span><span class="i">$DescriptorClassName</span><span class="s">)</span> = <span class="s">(</span><span class="i">$FirstParameter</span><span class="s">)</span><span class="sc">;</span>
|
|
|
376 363 <span class="s">}</span>
|
|
|
377 364
|
|
|
378 365 <span class="k">return</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$DescriptorsDataMap</span>{<span class="w">ClassToDescriptorNames</span>}{<span class="i">$DescriptorClassName</span>}<span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
379 366 <span class="s">}</span>
|
|
|
380 367
|
|
|
381 368 <span class="c"># Is it a valid descriptor name?</span>
|
|
|
382 369 <span class="c">#</span>
|
|
|
383 370 <span class="c"># This functionality can be either invoked as a class function or an</span>
|
|
|
384 371 <span class="c"># object method.</span>
|
|
|
385 372 <span class="c">#</span>
|
|
|
386 <a name="IsDescriptorNameAvailable-"></a> 373 <span class="k">sub </span><span class="m">IsDescriptorNameAvailable</span> <span class="s">{</span>
|
|
|
387 374 <span class="k">my</span><span class="s">(</span><span class="i">$FirstParameter</span><span class="cm">,</span> <span class="i">$SecondParameter</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
388 375 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$DescriptorName</span><span class="s">)</span><span class="sc">;</span>
|
|
|
389 376
|
|
|
390 377 <span class="k">if</span> <span class="s">(</span><span class="s">(</span><span class="i">@_</span> == <span class="n">2</span><span class="s">)</span> && <span class="s">(</span><span class="i">_IsMolecularDescriptorsGenerator</span><span class="s">(</span><span class="i">$FirstParameter</span><span class="s">)</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
391 378 <span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$DescriptorName</span><span class="s">)</span> = <span class="s">(</span><span class="i">$FirstParameter</span><span class="cm">,</span> <span class="i">$SecondParameter</span><span class="s">)</span><span class="sc">;</span>
|
|
|
392 379 <span class="s">}</span>
|
|
|
393 380 <span class="k">else</span> <span class="s">{</span>
|
|
|
394 381 <span class="s">(</span><span class="i">$DescriptorName</span><span class="s">)</span> = <span class="s">(</span><span class="i">$FirstParameter</span><span class="s">)</span><span class="sc">;</span>
|
|
|
395 382 <span class="s">}</span>
|
|
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396 383
|
|
|
397 384 <span class="k">return</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$DescriptorsDataMap</span>{<span class="w">DescriptorToClassName</span>}{<span class="i">$DescriptorName</span>}<span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
398 385 <span class="s">}</span>
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399 386
|
|
|
400 387 <span class="c"># Get available descriptors names for a descriptor class as an array.</span>
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|
401 388 <span class="c">#</span>
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|
402 389 <span class="c"># This functionality can be either invoked as a class function or an</span>
|
|
|
403 390 <span class="c"># object method.</span>
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|
|
404 391 <span class="c">#</span>
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|
405 <a name="GetAvailableDescriptorNamesForDescriptorClass-"></a> 392 <span class="k">sub </span><span class="m">GetAvailableDescriptorNamesForDescriptorClass</span> <span class="s">{</span>
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406 393 <span class="k">my</span><span class="s">(</span><span class="i">$FirstParameter</span><span class="cm">,</span> <span class="i">$SecondParameter</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
407 394 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$DescriptorClassName</span><span class="cm">,</span> <span class="i">@DescriptorNames</span><span class="s">)</span><span class="sc">;</span>
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408 395
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|
|
409 396 <span class="k">if</span> <span class="s">(</span><span class="s">(</span><span class="i">@_</span> == <span class="n">2</span><span class="s">)</span> && <span class="s">(</span><span class="i">_IsMolecularDescriptorsGenerator</span><span class="s">(</span><span class="i">$FirstParameter</span><span class="s">)</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
410 397 <span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$DescriptorClassName</span><span class="s">)</span> = <span class="s">(</span><span class="i">$FirstParameter</span><span class="cm">,</span> <span class="i">$SecondParameter</span><span class="s">)</span><span class="sc">;</span>
|
|
|
411 398 <span class="s">}</span>
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|
412 399 <span class="k">else</span> <span class="s">{</span>
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|
|
413 400 <span class="s">(</span><span class="i">$DescriptorClassName</span><span class="s">)</span> = <span class="s">(</span><span class="i">$FirstParameter</span><span class="s">)</span><span class="sc">;</span>
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|
|
414 401 <span class="s">}</span>
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415 402
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416 403 <span class="i">@DescriptorNames</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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|
417 404 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$DescriptorsDataMap</span>{<span class="w">ClassToDescriptorNames</span>}{<span class="i">$DescriptorClassName</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
418 405 <span class="k">push</span> <span class="i">@DescriptorNames</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$DescriptorsDataMap</span>{<span class="w">ClassToDescriptorNames</span>}{<span class="i">$DescriptorClassName</span>}}<span class="sc">;</span>
|
|
|
419 406 <span class="s">}</span>
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420 407
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|
|
421 408 <span class="k">return</span> <span class="k">wantarray</span> ? <span class="i">@DescriptorNames</span> <span class="co">:</span> <span class="k">scalar</span> <span class="i">@DescriptorNames</span><span class="sc">;</span>
|
|
|
422 409 <span class="s">}</span>
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423 410
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|
424 411 <span class="c"># Get available descriptors class name for a descriptor name.</span>
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|
|
425 412 <span class="c">#</span>
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|
426 413 <span class="c"># This functionality can be either invoked as a class function or an</span>
|
|
|
427 414 <span class="c"># object method.</span>
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|
428 415 <span class="c">#</span>
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|
429 <a name="GetAvailableClassNameForDescriptorName-"></a> 416 <span class="k">sub </span><span class="m">GetAvailableClassNameForDescriptorName</span> <span class="s">{</span>
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430 417 <span class="k">my</span><span class="s">(</span><span class="i">$FirstParameter</span><span class="cm">,</span> <span class="i">$SecondParameter</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
431 418 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$DescriptorClassName</span><span class="cm">,</span> <span class="i">$DescriptorName</span><span class="s">)</span><span class="sc">;</span>
|
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|
432 419
|
|
|
433 420 <span class="k">if</span> <span class="s">(</span><span class="s">(</span><span class="i">@_</span> == <span class="n">2</span><span class="s">)</span> && <span class="s">(</span><span class="i">_IsMolecularDescriptorsGenerator</span><span class="s">(</span><span class="i">$FirstParameter</span><span class="s">)</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
434 421 <span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$DescriptorName</span><span class="s">)</span> = <span class="s">(</span><span class="i">$FirstParameter</span><span class="cm">,</span> <span class="i">$SecondParameter</span><span class="s">)</span><span class="sc">;</span>
|
|
|
435 422 <span class="s">}</span>
|
|
|
436 423 <span class="k">else</span> <span class="s">{</span>
|
|
|
437 424 <span class="s">(</span><span class="i">$DescriptorName</span><span class="s">)</span> = <span class="s">(</span><span class="i">$FirstParameter</span><span class="s">)</span><span class="sc">;</span>
|
|
|
438 425 <span class="s">}</span>
|
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|
439 426
|
|
|
440 427 <span class="i">$DescriptorClassName</span> = <span class="q">''</span><span class="sc">;</span>
|
|
|
441 428 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$DescriptorsDataMap</span>{<span class="w">DescriptorToClassName</span>}{<span class="i">$DescriptorName</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
442 429 <span class="i">$DescriptorClassName</span> = <span class="i">$DescriptorsDataMap</span>{<span class="w">DescriptorToClassName</span>}{<span class="i">$DescriptorName</span>}<span class="sc">;</span>
|
|
|
443 430 <span class="s">}</span>
|
|
|
444 431
|
|
|
445 432 <span class="k">return</span> <span class="i">$DescriptorClassName</span><span class="sc">;</span>
|
|
|
446 433 <span class="s">}</span>
|
|
|
447 434
|
|
|
448 435 <span class="c"># Get RuleOf5 descriptor names as an array.</span>
|
|
|
449 436 <span class="c">#</span>
|
|
|
450 437 <span class="c"># This functionality can be either invoked as a class function or an</span>
|
|
|
451 438 <span class="c"># object method.</span>
|
|
|
452 439 <span class="c">#</span>
|
|
|
453 <a name="GetRuleOf5DescriptorNames-"></a> 440 <span class="k">sub </span><span class="m">GetRuleOf5DescriptorNames</span> <span class="s">{</span>
|
|
|
454 441 <span class="k">my</span><span class="s">(</span><span class="i">@DescriptorNames</span><span class="s">)</span><span class="sc">;</span>
|
|
|
455 442
|
|
|
456 443 <span class="i">@DescriptorNames</span> = <span class="q">qw(MolecularWeight HydrogenBondDonors HydrogenBondAcceptors SLogP)</span><span class="sc">;</span>
|
|
|
457 444
|
|
|
458 445 <span class="k">return</span> <span class="k">wantarray</span> ? <span class="i">@DescriptorNames</span> <span class="co">:</span> <span class="k">scalar</span> <span class="i">@DescriptorNames</span><span class="sc">;</span>
|
|
|
459 446 <span class="s">}</span>
|
|
|
460 447
|
|
|
461 448 <span class="c"># Get RuleOf3 descriptor names as an array.</span>
|
|
|
462 449 <span class="c">#</span>
|
|
|
463 450 <span class="c"># This functionality can be either invoked as a class function or an</span>
|
|
|
464 451 <span class="c"># object method.</span>
|
|
|
465 452 <span class="c">#</span>
|
|
|
466 <a name="GetRuleOf3DescriptorNames-"></a> 453 <span class="k">sub </span><span class="m">GetRuleOf3DescriptorNames</span> <span class="s">{</span>
|
|
|
467 454 <span class="k">my</span><span class="s">(</span><span class="i">@DescriptorNames</span><span class="s">)</span><span class="sc">;</span>
|
|
|
468 455
|
|
|
469 456 <span class="i">@DescriptorNames</span> = <span class="q">qw(MolecularWeight RotatableBonds HydrogenBondDonors HydrogenBondAcceptors SLogP TPSA)</span><span class="sc">;</span>
|
|
|
470 457
|
|
|
471 458 <span class="k">return</span> <span class="k">wantarray</span> ? <span class="i">@DescriptorNames</span> <span class="co">:</span> <span class="k">scalar</span> <span class="i">@DescriptorNames</span><span class="sc">;</span>
|
|
|
472 459 <span class="s">}</span>
|
|
|
473 460
|
|
|
474 461
|
|
|
475 462 <span class="c"># Set molecule object...</span>
|
|
|
476 463 <span class="c">#</span>
|
|
|
477 <a name="SetMolecule-"></a> 464 <span class="k">sub </span><span class="m">SetMolecule</span> <span class="s">{</span>
|
|
|
478 465 <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>
|
|
|
479 466
|
|
|
480 467 <span class="i">$This</span>->{<span class="w">Molecule</span>} = <span class="i">$Molecule</span><span class="sc">;</span>
|
|
|
481 468
|
|
|
482 469 <span class="c"># Weaken the reference to disable increment of reference count...</span>
|
|
|
483 470 <span class="i">Scalar::Util::weaken</span><span class="s">(</span><span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="s">)</span><span class="sc">;</span>
|
|
|
484 471
|
|
|
485 472 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
486 473 <span class="s">}</span>
|
|
|
487 474
|
|
|
488 475 <span class="c"># Generate specified molecular descriptors...</span>
|
|
|
489 476 <span class="c">#</span>
|
|
|
490 477 <span class="c"># After instantiating descriptor class objects at first invocation and initialializing</span>
|
|
|
491 478 <span class="c"># descriptor values during subsequent invocations, GenerateDescriptors method</span>
|
|
|
492 479 <span class="c"># provided by each descriptor class is used to calculate descriptor values for</span>
|
|
|
493 480 <span class="c"># specified descriptors.</span>
|
|
|
494 481 <span class="c">#</span>
|
|
|
495 <a name="GenerateDescriptors-"></a> 482 <span class="k">sub </span><span class="m">GenerateDescriptors</span> <span class="s">{</span>
|
|
|
496 483 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
497 484 <span class="k">my</span><span class="s">(</span><span class="i">$DescriptorClassName</span><span class="cm">,</span> <span class="i">$DescriptorClassObject</span><span class="s">)</span><span class="sc">;</span>
|
|
|
498 485
|
|
|
499 486 <span class="c"># Initialize descriptor values...</span>
|
|
|
500 487 <span class="i">$This</span><span class="i">->_InitializeDescriptorValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
501 488
|
|
|
502 489 <span class="c"># Instantiate decriptor classed corresponding to specified descriptors...</span>
|
|
|
503 490 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span>->{<span class="w">DescriptorClassesInstantiated</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
504 491 <span class="i">$This</span><span class="i">->_InstantiateDescriptorClasses</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
505 492 <span class="s">}</span>
|
|
|
506 493
|
|
|
507 494 <span class="c"># Check availability of molecule...</span>
|
|
|
508 495 <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>
|
|
|
509 496 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->GenerateDescriptors: $This->{Type} molecular descriptors generation didn't succeed: Molecule data is not available: Molecule object hasn't been set..."</span><span class="sc">;</span>
|
|
|
510 497 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
|
|
|
511 498 <span class="s">}</span>
|
|
|
512 499
|
|
|
513 500 <span class="c"># Calculate descriptor values...</span>
|
|
|
514 501 <span class="k">for</span> <span class="i">$DescriptorClassName</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DescriptorClassNames</span>}}<span class="s">)</span> <span class="s">{</span>
|
|
|
515 502 <span class="i">$DescriptorClassObject</span> = <span class="i">$This</span>->{<span class="w">DescriptorClassObjects</span>}{<span class="i">$DescriptorClassName</span>}<span class="sc">;</span>
|
|
|
516 503
|
|
|
517 504 <span class="i">$DescriptorClassObject</span><span class="i">->SetMolecule</span><span class="s">(</span><span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="s">)</span><span class="sc">;</span>
|
|
|
518 505 <span class="i">$DescriptorClassObject</span><span class="i">->GenerateDescriptors</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
519 506
|
|
|
520 507 <span class="k">if</span> <span class="s">(</span>!<span class="i">$DescriptorClassObject</span><span class="i">->IsDescriptorsGenerationSuccessful</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
521 508 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
|
|
|
522 509 <span class="s">}</span>
|
|
|
523 510 <span class="s">}</span>
|
|
|
524 511
|
|
|
525 512 <span class="c"># Set final descriptor values...</span>
|
|
|
526 513 <span class="i">$This</span><span class="i">->_SetFinalDescriptorValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
527 514
|
|
|
528 515 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
529 516 <span class="s">}</span>
|
|
|
530 517
|
|
|
531 518 <span class="c"># Initialize descriptor values...</span>
|
|
|
532 519 <span class="c">#</span>
|
|
|
533 <a name="_InitializeDescriptorValues-"></a> 520 <span class="k">sub </span><span class="m">_InitializeDescriptorValues</span> <span class="s">{</span>
|
|
|
534 521 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
535 522
|
|
|
536 523 <span class="i">$This</span>->{<span class="w">DescriptorsGenerated</span>} = <span class="n">0</span><span class="sc">;</span>
|
|
|
537 524
|
|
|
538 525 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DescriptorValues</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
539 526
|
|
|
540 527 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
541 528 <span class="s">}</span>
|
|
|
542 529
|
|
|
543 530 <span class="c"># Setup final descriptor values...</span>
|
|
|
544 531 <span class="c">#</span>
|
|
|
545 <a name="_SetFinalDescriptorValues-"></a> 532 <span class="k">sub </span><span class="m">_SetFinalDescriptorValues</span> <span class="s">{</span>
|
|
|
546 533 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
547 534 <span class="k">my</span><span class="s">(</span><span class="i">$DescriptorName</span><span class="cm">,</span> <span class="i">$DescriptorClassName</span><span class="cm">,</span> <span class="i">$DescriptorClassObject</span><span class="s">)</span><span class="sc">;</span>
|
|
|
548 535
|
|
|
549 536 <span class="i">$This</span>->{<span class="w">DescriptorsGenerated</span>} = <span class="n">1</span><span class="sc">;</span>
|
|
|
550 537
|
|
|
551 538 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DescriptorValues</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
552 539
|
|
|
553 540 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">Mode</span>} =~ <span class="q">/^All$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
554 541 <span class="c"># Set descriptor values for all available descriptors...</span>
|
|
|
555 542 <span class="k">for</span> <span class="i">$DescriptorClassName</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DescriptorClassNames</span>}}<span class="s">)</span> <span class="s">{</span>
|
|
|
556 543 <span class="i">$DescriptorClassObject</span> = <span class="i">$This</span>->{<span class="w">DescriptorClassObjects</span>}{<span class="i">$DescriptorClassName</span>}<span class="sc">;</span>
|
|
|
557 544
|
|
|
558 545 <span class="k">push</span> <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DescriptorValues</span>}}<span class="cm">,</span> <span class="i">$DescriptorClassObject</span><span class="i">->GetDescriptorValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
559 546 <span class="s">}</span>
|
|
|
560 547 <span class="s">}</span>
|
|
|
561 548 <span class="k">else</span> <span class="s">{</span>
|
|
|
562 549 <span class="c"># Set descriptor values for a subset of available descriptors...</span>
|
|
|
563 550 <span class="k">for</span> <span class="i">$DescriptorName</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DescriptorNames</span>}}<span class="s">)</span> <span class="s">{</span>
|
|
|
564 551 <span class="i">$DescriptorClassName</span> = <span class="i">$DescriptorsDataMap</span>{<span class="w">DescriptorToClassName</span>}{<span class="i">$DescriptorName</span>}<span class="sc">;</span>
|
|
|
565 552 <span class="i">$DescriptorClassObject</span> = <span class="i">$This</span>->{<span class="w">DescriptorClassObjects</span>}{<span class="i">$DescriptorClassName</span>}<span class="sc">;</span>
|
|
|
566 553
|
|
|
567 554 <span class="k">push</span> <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DescriptorValues</span>}}<span class="cm">,</span> <span class="i">$DescriptorClassObject</span><span class="i">->GetDescriptorValueByName</span><span class="s">(</span><span class="i">$DescriptorName</span><span class="s">)</span><span class="sc">;</span>
|
|
|
568 555 <span class="s">}</span>
|
|
|
569 556 <span class="s">}</span>
|
|
|
570 557
|
|
|
571 558 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
572 559 <span class="s">}</span>
|
|
|
573 560
|
|
|
574 561 <span class="c"># Is descriptors generation successful?</span>
|
|
|
575 562 <span class="c">#</span>
|
|
|
576 563 <span class="c"># Notes:</span>
|
|
|
577 564 <span class="c"># . After successful generation of descriptor values by each descriptor class</span>
|
|
|
578 565 <span class="c"># corresponding to specified descriptor names, DescriptorsCalculated to 1;</span>
|
|
|
579 566 <span class="c"># otherwise, it's set to 0.</span>
|
|
|
580 567 <span class="c">#</span>
|
|
|
581 <a name="IsDescriptorsGenerationSuccessful-"></a> 568 <span class="k">sub </span><span class="m">IsDescriptorsGenerationSuccessful</span> <span class="s">{</span>
|
|
|
582 569 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
583 570
|
|
|
584 571 <span class="k">return</span> <span class="i">$This</span>->{<span class="w">DescriptorsGenerated</span>} ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
585 572 <span class="s">}</span>
|
|
|
586 573
|
|
|
587 574 <span class="c"># Check and set default descriptor names for generating descriptor values...</span>
|
|
|
588 575 <span class="c">#</span>
|
|
|
589 <a name="_CheckAndInitializeDescriptorNames-"></a> 576 <span class="k">sub </span><span class="m">_CheckAndInitializeDescriptorNames</span> <span class="s">{</span>
|
|
|
590 577 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
591 578
|
|
|
592 579 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">Mode</span>} =~ <span class="q">/^(All|RuleOf5|RuleOf3)$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
593 580 <span class="k">if</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DescriptorNames</span>}}<span class="s">)</span> <span class="s">{</span>
|
|
|
594 581 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->_CheckAndInitializeDescriptorNames: Descriptor names can't be specified during \"All, RuleOf5 or RuleOf3\" values of descsriptors generation \"Mode\"..."</span><span class="sc">;</span>
|
|
|
595 582 <span class="s">}</span>
|
|
|
596 583 <span class="s">}</span>
|
|
|
597 584
|
|
|
598 585 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">Mode</span>} =~ <span class="q">/^All$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
599 586 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DescriptorNames</span>}} = <span class="i">GetAvailableDescriptorNames</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
600 587 <span class="s">}</span>
|
|
|
601 588 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">Mode</span>} =~ <span class="q">/^RuleOf5$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
602 589 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DescriptorNames</span>}} = <span class="i">GetRuleOf5DescriptorNames</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
603 590 <span class="s">}</span>
|
|
|
604 591 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">Mode</span>} =~ <span class="q">/^RuleOf3$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
605 592 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DescriptorNames</span>}} = <span class="i">GetRuleOf3DescriptorNames</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
606 593 <span class="s">}</span>
|
|
|
607 594 <span class="k">elsif</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">Mode</span>} =~ <span class="q">/^Specify$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
608 595 <span class="k">if</span> <span class="s">(</span>!<span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DescriptorNames</span>}}<span class="s">)</span> <span class="s">{</span>
|
|
|
609 596 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->_CheckAndInitializeDescriptorNames: DescriptorNames must be specified during Specify value for Mode..."</span><span class="sc">;</span>
|
|
|
610 597 <span class="s">}</span>
|
|
|
611 598 <span class="s">}</span>
|
|
|
612 599 <span class="k">else</span> <span class="s">{</span>
|
|
|
613 600 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->_CheckAndInitializeDescriptorNames: Mode value, $This->{Mode}, is not valid..."</span><span class="sc">;</span>
|
|
|
614 601 <span class="s">}</span>
|
|
|
615 602 <span class="s">}</span>
|
|
|
616 603
|
|
|
617 604 <span class="c"># Instantiate descriptor classes corresponding to specified descriptor names...</span>
|
|
|
618 605 <span class="c">#</span>
|
|
|
619 <a name="_InstantiateDescriptorClasses-"></a> 606 <span class="k">sub </span><span class="m">_InstantiateDescriptorClasses</span> <span class="s">{</span>
|
|
|
620 607 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
621 608 <span class="k">my</span><span class="s">(</span><span class="i">$DescriptorClassName</span><span class="cm">,</span> <span class="i">$DescriptorName</span><span class="cm">,</span> <span class="i">$DescriptorClassPath</span><span class="s">)</span><span class="sc">;</span>
|
|
|
622 609
|
|
|
623 610 <span class="i">$This</span>->{<span class="w">DescriptorClassesInstantiated</span>} = <span class="n">1</span><span class="sc">;</span>
|
|
|
624 611
|
|
|
625 612 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DescriptorClassNames</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
626 613 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">DescriptorClassObjects</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
627 614
|
|
|
628 615 <span class="j">NAME:</span> <span class="k">for</span> <span class="i">$DescriptorName</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DescriptorNames</span>}}<span class="s">)</span> <span class="s">{</span>
|
|
|
629 616 <span class="i">$DescriptorClassName</span> = <span class="i">$DescriptorsDataMap</span>{<span class="w">DescriptorToClassName</span>}{<span class="i">$DescriptorName</span>}<span class="sc">;</span>
|
|
|
630 617
|
|
|
631 618 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$This</span>->{<span class="w">DescriptorClassObjects</span>}{<span class="i">$DescriptorClassName</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
632 619 <span class="k">next</span> <span class="j">NAME</span><span class="sc">;</span>
|
|
|
633 620 <span class="s">}</span>
|
|
|
634 621 <span class="k">push</span> <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DescriptorClassNames</span>}}<span class="cm">,</span> <span class="i">$DescriptorClassName</span><span class="sc">;</span>
|
|
|
635 622
|
|
|
636 623 <span class="i">$DescriptorClassPath</span> = <span class="i">$DescriptorsDataMap</span>{<span class="w">ClassNameToClassPath</span>}{<span class="i">$DescriptorClassName</span>}<span class="sc">;</span>
|
|
|
637 624
|
|
|
638 625 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$This</span>->{<span class="w">DescriptorClassParameters</span>}{<span class="i">$DescriptorClassName</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
639 626 <span class="i">$This</span>->{<span class="w">DescriptorClassObjects</span>}{<span class="i">$DescriptorClassName</span>} = <span class="i">$DescriptorClassPath</span><span class="i">->new</span><span class="s">(</span><span class="i">%</span>{<span class="i">$This</span>->{<span class="w">DescriptorClassParameters</span>}{<span class="i">$DescriptorClassName</span>}}<span class="s">)</span><span class="sc">;</span>
|
|
|
640 627 <span class="s">}</span>
|
|
|
641 628 <span class="k">else</span> <span class="s">{</span>
|
|
|
642 629 <span class="i">$This</span>->{<span class="w">DescriptorClassObjects</span>}{<span class="i">$DescriptorClassName</span>} = <span class="i">$DescriptorClassPath</span><span class="i">->new</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
643 630 <span class="s">}</span>
|
|
|
644 631 <span class="s">}</span>
|
|
|
645 632
|
|
|
646 633 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
647 634 <span class="s">}</span>
|
|
|
648 635
|
|
|
649 636 <span class="c"># Return a string containg data for MolecularDescriptorsGenerator object...</span>
|
|
|
650 637 <span class="c">#</span>
|
|
|
651 <a name="StringifyMolecularDescriptorsGenerator-"></a> 638 <span class="k">sub </span><span class="m">StringifyMolecularDescriptorsGenerator</span> <span class="s">{</span>
|
|
|
652 639 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
653 640 <span class="k">my</span><span class="s">(</span><span class="i">$TheString</span><span class="cm">,</span> <span class="i">$NamesAndValuesString</span><span class="cm">,</span> <span class="i">$Name</span><span class="cm">,</span> <span class="i">$Value</span><span class="cm">,</span> <span class="i">@NamesAndValuesInfo</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span><span class="sc">;</span>
|
|
|
654 641
|
|
|
655 642 <span class="c"># Type of MolecularDescriptors...</span>
|
|
|
656 643 <span class="i">$TheString</span> = <span class="q">"MolecularDescriptorsGenerator: Mode - $This->{Mode}; SpecifiedDescriptorNames - < @{$This->{DescriptorNames}} >; AvailableMolecularDescriptorClassNames - < @{$DescriptorsDataMap{ClassNames}} >"</span><span class="sc">;</span>
|
|
|
657 644
|
|
|
658 645 <span class="i">@NamesAndValuesInfo</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
659 646 <span class="i">%NamesAndValues</span> = <span class="i">$This</span><span class="i">->GetDescriptorNamesAndValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
660 647
|
|
|
661 648 <span class="k">for</span> <span class="i">$Name</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DescriptorNames</span>}}<span class="s">)</span> <span class="s">{</span>
|
|
|
662 649 <span class="i">$Value</span> = <span class="i">$NamesAndValues</span>{<span class="i">$Name</span>}<span class="sc">;</span>
|
|
|
663 650 <span class="i">$Value</span> = <span class="s">(</span><span class="i">TextUtil::IsEmpty</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span> || <span class="i">$Value</span> =~ <span class="q">/^None$/i</span><span class="s">)</span> ? <span class="q">'None'</span> <span class="co">:</span> <span class="i">$Value</span><span class="sc">;</span>
|
|
|
664 651 <span class="k">push</span> <span class="i">@NamesAndValuesInfo</span><span class="cm">,</span> <span class="q">"$Name - $Value"</span><span class="sc">;</span>
|
|
|
665 652 <span class="s">}</span>
|
|
|
666 653 <span class="k">if</span> <span class="s">(</span><span class="i">@NamesAndValuesInfo</span><span class="s">)</span> <span class="s">{</span>
|
|
|
667 654 <span class="i">$TheString</span> .= <span class="q">"Names - Values: <"</span> . <span class="i">TextUtil::JoinWords</span><span class="s">(</span>\<span class="i">@NamesAndValuesInfo</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>
|
|
|
668 655 <span class="s">}</span>
|
|
|
669 656 <span class="k">else</span> <span class="s">{</span>
|
|
|
670 657 <span class="i">$TheString</span> .= <span class="q">"Names - Values: < None>"</span><span class="sc">;</span>
|
|
|
671 658 <span class="s">}</span>
|
|
|
672 659
|
|
|
673 660 <span class="k">return</span> <span class="i">$TheString</span><span class="sc">;</span>
|
|
|
674 661 <span class="s">}</span>
|
|
|
675 662
|
|
|
676 663 <span class="c"># Is it a MolecularDescriptorsGenerator object?</span>
|
|
|
677 <a name="_IsMolecularDescriptorsGenerator-"></a> 664 <span class="k">sub </span><span class="m">_IsMolecularDescriptorsGenerator</span> <span class="s">{</span>
|
|
|
678 665 <span class="k">my</span><span class="s">(</span><span class="i">$Object</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
679 666
|
|
|
680 667 <span class="k">return</span> <span class="s">(</span><span class="i">Scalar::Util::blessed</span><span class="s">(</span><span class="i">$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>
|
|
|
681 668 <span class="s">}</span>
|
|
|
682 669
|
|
|
683 670 <span class="c"># Validate descriptor names for generating descriptor values...</span>
|
|
|
684 671 <span class="c">#</span>
|
|
|
685 <a name="_ValidateDescriptorNames-"></a> 672 <span class="k">sub </span><span class="m">_ValidateDescriptorNames</span> <span class="s">{</span>
|
|
|
686 673 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
687 674 <span class="k">my</span><span class="s">(</span><span class="i">$DescriptorName</span><span class="s">)</span><span class="sc">;</span>
|
|
|
688 675
|
|
|
689 676 <span class="k">for</span> <span class="i">$DescriptorName</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$This</span>->{<span class="w">DescriptorNames</span>}}<span class="s">)</span> <span class="s">{</span>
|
|
|
690 677 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$DescriptorsDataMap</span>{<span class="w">DescriptorToClassName</span>}{<span class="i">$DescriptorName</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
691 678 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->_SetAndValidateDescriptorNames: Specified descriptor name, $DescriptorName, is not valid..."</span><span class="sc">;</span>
|
|
|
692 679 <span class="s">}</span>
|
|
|
693 680 <span class="s">}</span>
|
|
|
694 681
|
|
|
695 682 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
696 683 <span class="s">}</span>
|
|
|
697 684
|
|
|
698 685 <span class="c">#</span>
|
|
|
699 686 <span class="c"># Load available molecular descriptors data...</span>
|
|
|
700 687 <span class="c">#</span>
|
|
|
701 688 <span class="c"># All available molecular descriptors classes are automatically detected in</span>
|
|
|
702 689 <span class="c"># MolecularDescriptors directory under <MayaChemTools>/lib directory and</span>
|
|
|
703 690 <span class="c"># information about available descriptor names is retrieved from each descriptor</span>
|
|
|
704 691 <span class="c"># class using function GetDescriptorNames. The following %DescriptorsDataMap</span>
|
|
|
705 692 <span class="c"># is setup containing all available molecular descriptors data:</span>
|
|
|
706 693 <span class="c">#</span>
|
|
|
707 694 <span class="c"># @{$DescriptorsDataMap{ClassNames}}</span>
|
|
|
708 695 <span class="c"># %{$DescriptorsDataMap{ClassNameToPath}}</span>
|
|
|
709 696 <span class="c"># %{$DescriptorsDataMap{ClassToDescriptorNames}}</span>
|
|
|
710 697 <span class="c"># %{$DescriptorsDataMap{DescriptorToClassName}}</span>
|
|
|
711 698 <span class="c">#</span>
|
|
|
712 699 <span class="c"># GenerateDescriptors method is invoked fo each specified descriptor class</span>
|
|
|
713 700 <span class="c"># object to calculate descriptor values for specified descriptors. After successful</span>
|
|
|
714 701 <span class="c"># calculation of descriptors, GetDescriptorValues or GetDescriptorValueByName</span>
|
|
|
715 702 <span class="c"># methods provided by descriptor objects are used to retrieve calculated</span>
|
|
|
716 703 <span class="c"># descriptor values.</span>
|
|
|
717 704 <span class="c">#</span>
|
|
|
718 <a name="_LoadMolecularDescriptorsData-"></a> 705 <span class="k">sub </span><span class="m">_LoadMolecularDescriptorsData</span> <span class="s">{</span>
|
|
|
719 706
|
|
|
720 707 <span class="i">%DescriptorsDataMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
721 708
|
|
|
722 709 <span class="i">_RetrieveAndLoadDescriptorClasses</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
723 710 <span class="i">_SetupDescriptorsDataMap</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
724 711 <span class="s">}</span>
|
|
|
725 712
|
|
|
726 713 <span class="c">#</span>
|
|
|
727 714 <span class="c"># Retrieve available molecular descriptors classes from MolecularDescriptors directory under</span>
|
|
|
728 715 <span class="c"># <MayaChemTools>/lib directory...</span>
|
|
|
729 716 <span class="c">#</span>
|
|
|
730 <a name="_RetrieveAndLoadDescriptorClasses-"></a> 717 <span class="k">sub </span><span class="m">_RetrieveAndLoadDescriptorClasses</span> <span class="s">{</span>
|
|
|
731 718 <span class="k">my</span><span class="s">(</span><span class="i">$DescriptorsDirName</span><span class="cm">,</span> <span class="i">$MayaChemToolsLibDir</span><span class="cm">,</span> <span class="i">$DescriptorsDirPath</span><span class="cm">,</span> <span class="i">$IncludeDirName</span><span class="cm">,</span> <span class="i">$DescriptorClassName</span><span class="cm">,</span> <span class="i">$DescriptorClassPath</span><span class="cm">,</span> <span class="i">$DescriptorsClassFileName</span><span class="cm">,</span> <span class="i">@FileNames</span><span class="cm">,</span> <span class="i">@DescriptorsClassFileNames</span><span class="s">)</span><span class="sc">;</span>
|
|
|
732 719
|
|
|
733 720 <span class="i">@</span>{<span class="i">$DescriptorsDataMap</span>{<span class="w">ClassNames</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
734 721 <span class="i">%</span>{<span class="i">$DescriptorsDataMap</span>{<span class="w">ClassNameToPath</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
735 722
|
|
|
736 723 <span class="i">$DescriptorsDirName</span> = <span class="q">"MolecularDescriptors"</span><span class="sc">;</span>
|
|
|
737 724 <span class="i">$MayaChemToolsLibDir</span> = <span class="i">FileUtil::GetMayaChemToolsLibDirName</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
738 725
|
|
|
739 726 <span class="i">$DescriptorsDirPath</span> = <span class="q">"$MayaChemToolsLibDir/$DescriptorsDirName"</span><span class="sc">;</span>
|
|
|
740 727
|
|
|
741 728 <span class="k">if</span> <span class="s">(</span>! <span class="k">-d</span> <span class="q">"$DescriptorsDirPath"</span><span class="s">)</span> <span class="s">{</span>
|
|
|
742 729 <span class="w">croak</span> <span class="q">"Error: ${ClassName}::_RetrieveAndLoadDescriptorClasses: MayaChemTools package molecular descriptors directory, $DescriptorsDirPath, is missing: Possible installation problems..."</span><span class="sc">;</span>
|
|
|
743 730 <span class="s">}</span>
|
|
|
744 731
|
|
|
745 732 <span class="i">@FileNames</span> = <span class="s">(</span><span class="q">"$DescriptorsDirPath/*"</span><span class="s">)</span><span class="sc">;</span>
|
|
|
746 733 <span class="i">$IncludeDirName</span> = <span class="n">0</span><span class="sc">;</span>
|
|
|
747 734 <span class="i">@DescriptorsClassFileNames</span> = <span class="i">FileUtil::ExpandFileNames</span><span class="s">(</span>\<span class="i">@FileNames</span><span class="cm">,</span> <span class="q">"pm"</span><span class="cm">,</span> <span class="i">$IncludeDirName</span><span class="s">)</span><span class="sc">;</span>
|
|
|
748 735
|
|
|
749 736 <span class="k">if</span> <span class="s">(</span>!<span class="i">@DescriptorsClassFileNames</span><span class="s">)</span> <span class="s">{</span>
|
|
|
750 737 <span class="w">croak</span> <span class="q">"Error: ${ClassName}::_RetrieveAndLoadDescriptorClasses: MayaChemTools package molecular descriptors directory, $DescriptorsDirPath, doesn't contain any molecular descriptor class: Possible installation problems..."</span><span class="sc">;</span>
|
|
|
751 738 <span class="s">}</span>
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|
|
752 739
|
|
|
753 740 <span class="j">FILENAME:</span> <span class="k">for</span> <span class="i">$DescriptorsClassFileName</span> <span class="s">(</span><span class="k">sort</span> <span class="i">@DescriptorsClassFileNames</span><span class="s">)</span> <span class="s">{</span>
|
|
|
754 741 <span class="k">if</span> <span class="s">(</span><span class="i">$DescriptorsClassFileName</span> !~ <span class="q">/\.pm/</span><span class="s">)</span> <span class="s">{</span>
|
|
|
755 742 <span class="w">croak</span> <span class="q">"Error: ${ClassName}::_RetrieveAndLoadDescriptorClasses: MayaChemTools package molecular descriptors directory, $DescriptorsDirPath, contains invalid class file name $DescriptorsClassFileName: Possible installation problems..."</span><span class="sc">;</span>
|
|
|
756 743 <span class="s">}</span>
|
|
|
757 744
|
|
|
758 745 <span class="c"># Ignore base class and descriptors generator class...</span>
|
|
|
759 746 <span class="k">if</span> <span class="s">(</span><span class="i">$DescriptorsClassFileName</span> =~ <span class="q">/^(MolecularDescriptorsGenerator\.pm|MolecularDescriptors\.pm)$/</span><span class="s">)</span> <span class="s">{</span>
|
|
|
760 747 <span class="k">next</span> <span class="j">FILENAME</span><span class="sc">;</span>
|
|
|
761 748 <span class="s">}</span>
|
|
|
762 749
|
|
|
763 750 <span class="s">(</span><span class="i">$DescriptorClassName</span><span class="s">)</span> = <span class="k">split</span> <span class="q">/\./</span><span class="cm">,</span> <span class="i">$DescriptorsClassFileName</span><span class="sc">;</span>
|
|
|
764 751 <span class="i">$DescriptorClassPath</span> = <span class="q">"${DescriptorsDirName}::${DescriptorClassName}"</span><span class="sc">;</span>
|
|
|
765 752
|
|
|
766 753 <span class="c"># Load descriptors class...</span>
|
|
|
767 754 <span class="k">eval</span> <span class="q">"use $DescriptorClassPath"</span><span class="sc">;</span>
|
|
|
768 755
|
|
|
769 756 <span class="k">if</span> <span class="s">(</span><span class="i">$@</span><span class="s">)</span> <span class="s">{</span>
|
|
|
770 757 <span class="w">croak</span> <span class="q">"Error: ${ClassName}::_RetrieveAndLoadDescriptorClasses: use $DescriptorClassPath failed: $@ ..."</span><span class="sc">;</span>
|
|
|
771 758 <span class="s">}</span>
|
|
|
772 759
|
|
|
773 760 <span class="k">push</span> <span class="i">@</span>{<span class="i">$DescriptorsDataMap</span>{<span class="w">ClassNames</span>}}<span class="cm">,</span> <span class="i">$DescriptorClassName</span><span class="sc">;</span>
|
|
|
774 761
|
|
|
775 762 <span class="i">$DescriptorsDataMap</span>{<span class="w">ClassNameToClassPath</span>}{<span class="i">$DescriptorClassName</span>} = <span class="i">$DescriptorClassPath</span><span class="sc">;</span>
|
|
|
776 763 <span class="s">}</span>
|
|
|
777 764 <span class="s">}</span>
|
|
|
778 765
|
|
|
779 766 <span class="c">#</span>
|
|
|
780 767 <span class="c"># Setup descriptors data map using loaded descriptor classes...</span>
|
|
|
781 768 <span class="c">#</span>
|
|
|
782 <a name="_SetupDescriptorsDataMap-"></a> 769 <span class="k">sub </span><span class="m">_SetupDescriptorsDataMap</span> <span class="s">{</span>
|
|
|
783 770 <span class="k">my</span><span class="s">(</span><span class="i">$DescriptorClassName</span><span class="cm">,</span> <span class="i">$DescriptorName</span><span class="cm">,</span> <span class="i">$DescriptorClassPath</span><span class="cm">,</span> <span class="i">@DescriptorNames</span><span class="s">)</span><span class="sc">;</span>
|
|
|
784 771
|
|
|
785 772 <span class="c"># Class to decriptor names map...</span>
|
|
|
786 773 <span class="i">%</span>{<span class="i">$DescriptorsDataMap</span>{<span class="w">ClassToDescriptorNames</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
787 774
|
|
|
788 775 <span class="c"># Descriptor to class name map...</span>
|
|
|
789 776 <span class="i">%</span>{<span class="i">$DescriptorsDataMap</span>{<span class="w">DescriptorToClassName</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
790 777
|
|
|
791 778 <span class="k">for</span> <span class="i">$DescriptorClassName</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$DescriptorsDataMap</span>{<span class="w">ClassNames</span>}}<span class="s">)</span> <span class="s">{</span>
|
|
|
792 779 <span class="i">$DescriptorClassPath</span> = <span class="i">$DescriptorsDataMap</span>{<span class="w">ClassNameToClassPath</span>}{<span class="i">$DescriptorClassName</span>}<span class="sc">;</span>
|
|
|
793 780
|
|
|
794 781 <span class="i">@DescriptorNames</span> = <span class="i">$DescriptorClassPath</span><span class="i">->GetDescriptorNames</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
795 782
|
|
|
796 783 <span class="k">if</span> <span class="s">(</span>!<span class="i">@DescriptorNames</span><span class="s">)</span> <span class="s">{</span>
|
|
|
797 784 <span class="w">croak</span> <span class="q">"Error: ${ClassName}::_SetupDescriptorsDataMap: Molecular descriptor class $DescriptorClassName doesn't provide any descriptor names..."</span><span class="sc">;</span>
|
|
|
798 785 <span class="s">}</span>
|
|
|
799 786
|
|
|
800 787 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$DescriptorsDataMap</span>{<span class="w">ClassToDescriptorNames</span>}{<span class="i">$DescriptorClassName</span>} <span class="s">)</span> <span class="s">{</span>
|
|
|
801 788 <span class="w">croak</span> <span class="q">"Error: ${ClassName}::_SetupDescriptorsDataMap: Molecular descriptor class $DescriptorClassName has already been processed..."</span><span class="sc">;</span>
|
|
|
802 789 <span class="s">}</span>
|
|
|
803 790
|
|
|
804 791 <span class="i">@</span>{<span class="i">$DescriptorsDataMap</span>{<span class="w">ClassToDescriptorNames</span>}{<span class="i">$DescriptorClassName</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
805 792 <span class="i">@</span>{<span class="i">$DescriptorsDataMap</span>{<span class="w">ClassToDescriptorNames</span>}{<span class="i">$DescriptorClassName</span>}} = <span class="i">@DescriptorNames</span><span class="sc">;</span>
|
|
|
806 793
|
|
|
807 794 <span class="k">for</span> <span class="i">$DescriptorName</span> <span class="s">(</span><span class="i">@DescriptorNames</span><span class="s">)</span> <span class="s">{</span>
|
|
|
808 795 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$DescriptorsDataMap</span>{<span class="w">DescriptorToClassName</span>}{<span class="i">$DescriptorName</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
809 796 <span class="w">croak</span> <span class="q">"Error: ${ClassName}::_SetupDescriptorsDataMap: Molecular descriptor name, $DescriptorName, in class name, $DescriptorClassName, has already been provided by class name $DescriptorsDataMap{DescriptorToClassName}{$DescriptorName}..."</span><span class="sc">;</span>
|
|
|
810 797 <span class="s">}</span>
|
|
|
811 798
|
|
|
812 799 <span class="i">$DescriptorsDataMap</span>{<span class="w">DescriptorToClassName</span>}{<span class="i">$DescriptorName</span>} = <span class="i">$DescriptorClassName</span><span class="sc">;</span>
|
|
|
813 800 <span class="s">}</span>
|
|
|
814 801 <span class="s">}</span>
|
|
|
815 802 <span class="s">}</span>
|
|
|
816 803
|
|
|
817 <a name="EOF-"></a></pre>
|
|
|
818 <p> </p>
|
|
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819 <br />
|
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|
820 <center>
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821 <img src="../../../images/h2o2.png">
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822 </center>
|
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823 </body>
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824 </html>
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