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13 <pre>
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14 <a name="package-Fingerprints::EStateIndiciesFingerprints-"></a> 1 <span class="k">package </span><span class="i">Fingerprints::EStateIndiciesFingerprints</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: EStateIndiciesFingerprints.pm,v $</span>
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17 4 <span class="c"># $Date: 2015/02/28 20:48:54 $</span>
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18 5 <span class="c"># $Revision: 1.19 $</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">Text::ParseWords</span><span class="sc">;</span>
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46 33 <span class="k">use</span> <span class="w">TextUtil</span> <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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47 34 <span class="k">use</span> <span class="w">FileUtil</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">MathUtil</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">Fingerprints::Fingerprints</span><span class="sc">;</span>
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50 37 <span class="k">use</span> <span class="w">Molecule</span><span class="sc">;</span>
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51 38 <span class="k">use</span> <span class="w">AtomTypes::EStateAtomTypes</span><span class="sc">;</span>
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52 39 <span class="k">use</span> <span class="w">AtomicDescriptors::EStateValuesDescriptors</span><span class="sc">;</span>
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53 40
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54 41 <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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55 42
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56 43 <span class="i">@ISA</span> = <span class="q">qw(Fingerprints::Fingerprints Exporter)</span><span class="sc">;</span>
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57 44 <span class="i">@EXPORT</span> = <span class="q">qw()</span><span class="sc">;</span>
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58 45 <span class="i">@EXPORT_OK</span> = <span class="q">qw()</span><span class="sc">;</span>
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59 46
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60 47 <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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61 48
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62 49 <span class="c"># Setup class variables...</span>
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63 50 <span class="k">my</span><span class="s">(</span><span class="i">$ClassName</span><span class="s">)</span><span class="sc">;</span>
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64 51 <span class="i">_InitializeClass</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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65 52
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66 53 <span class="c"># Overload Perl functions...</span>
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67 54 <span class="k">use</span> <span class="w">overload</span> <span class="q">'""'</span> <span class="cm">=></span> <span class="q">'StringifyEStateIndiciesFingerprints'</span><span class="sc">;</span>
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68 55
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69 56 <span class="c"># Class constructor...</span>
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70 <a name="new-"></a> 57 <span class="k">sub </span><span class="m">new</span> <span class="s">{</span>
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71 58 <span class="k">my</span><span class="s">(</span><span class="i">$Class</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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72 59
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73 60 <span class="c"># Initialize object...</span>
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74 61 <span class="k">my</span> <span class="i">$This</span> = <span class="i">$Class</span><span class="i">->SUPER::new</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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75 62 <span class="k">bless</span> <span class="i">$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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76 63 <span class="i">$This</span><span class="i">->_InitializeEStateIndiciesFingerprints</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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77 64
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78 65 <span class="i">$This</span><span class="i">->_InitializeEStateIndiciesFingerprintsProperties</span><span class="s">(</span><span class="i">%NamesAndValues</span><span class="s">)</span><span class="sc">;</span>
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79 66
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80 67 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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81 68 <span class="s">}</span>
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82 69
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83 70 <span class="c"># Initialize object data...</span>
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84 71 <span class="c">#</span>
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85 <a name="_InitializeEStateIndiciesFingerprints-"></a> 72 <span class="k">sub </span><span class="m">_InitializeEStateIndiciesFingerprints</span> <span class="s">{</span>
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86 73 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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87 74
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88 75 <span class="c"># EStateIndicies is a vector containing sum of E-state values for E-state atom types</span>
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89 76 <span class="c">#</span>
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90 77 <span class="i">$This</span>->{<span class="w">Type</span>} = <span class="q">'EStateIndicies'</span><span class="sc">;</span>
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91 78
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92 79 <span class="c"># EStateAtomTypesSetToUse for EStateIndicies:</span>
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93 80 <span class="c">#</span>
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94 81 <span class="c"># ArbitrarySize - Corrresponds to only E-state atom types detected in molecule</span>
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95 82 <span class="c"># FixedSize - Corresponds to fixed number of E-state atom types previously defined [ Ref 77 ]</span>
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96 83 <span class="c">#</span>
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97 84 <span class="c"># The default EStateAtomTypesSetToUse value for EStateIndicies fingerprints type: ArbitrarySize.</span>
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98 85 <span class="c"># Possible values: ArbitrarySize or FixedSize.</span>
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99 86 <span class="c">#</span>
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100 87 <span class="i">$This</span>->{<span class="w">EStateAtomTypesSetToUse</span>} = <span class="q">''</span><span class="sc">;</span>
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101 88
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102 89 <span class="c"># Assigned E-state atom types...</span>
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103 90 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">EStateAtomTypes</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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104 91
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105 92 <span class="c"># Vector values precision for real values during E-state indicies...</span>
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106 93 <span class="i">$This</span>->{<span class="w">ValuesPrecision</span>} = <span class="n">3</span><span class="sc">;</span>
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107 94
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108 95 <span class="c"># Calculated E-state values and indicies for generating E-state indicies fingerprints...</span>
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109 96 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">EStateValues</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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110 97 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">EStateIndicies</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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111 98 <span class="s">}</span>
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112 99
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113 100 <span class="c"># Initialize class ...</span>
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114 <a name="_InitializeClass-"></a> 101 <span class="k">sub </span><span class="m">_InitializeClass</span> <span class="s">{</span>
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115 102 <span class="c">#Class name...</span>
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116 103 <span class="i">$ClassName</span> = <span class="w">__PACKAGE__</span><span class="sc">;</span>
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117 104
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118 105 <span class="s">}</span>
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119 106
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120 107 <span class="c"># Initialize object properties....</span>
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121 <a name="_InitializeEStateIndiciesFingerprintsProperties-"></a> 108 <span class="k">sub </span><span class="m">_InitializeEStateIndiciesFingerprintsProperties</span> <span class="s">{</span>
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122 109 <span class="k">my</span><span class="s">(</span><span class="i">$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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123 110
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124 111 <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">$MethodName</span><span class="s">)</span><span class="sc">;</span>
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125 112 <span class="k">while</span> <span class="s">(</span><span class="s">(</span><span class="i">$Name</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="k">each</span> <span class="i">%NamesAndValues</span><span class="s">)</span> <span class="s">{</span>
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126 113 <span class="i">$MethodName</span> = <span class="q">"Set${Name}"</span><span class="sc">;</span>
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127 114 <span class="i">$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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128 115 <span class="s">}</span>
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129 116
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130 117 <span class="c"># Make sure molecule object was specified...</span>
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131 118 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$NamesAndValues</span>{<span class="w">Molecule</span>}<span class="s">)</span> <span class="s">{</span>
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132 119 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->New: Object can't be instantiated without specifying molecule..."</span><span class="sc">;</span>
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133 120 <span class="s">}</span>
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134 121
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135 122 <span class="i">$This</span><span class="i">->_InitializeEstateIndicies</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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136 123
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137 124 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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138 125 <span class="s">}</span>
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139 126
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140 127 <span class="c"># Initialize E-state indicies...</span>
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141 128 <span class="c">#</span>
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142 <a name="_InitializeEstateIndicies-"></a> 129 <span class="k">sub </span><span class="m">_InitializeEstateIndicies</span> <span class="s">{</span>
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143 130 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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144 131
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145 132 <span class="c"># Set default EStateAtomTypesSetToUse...</span>
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146 133 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span>->{<span class="w">EStateAtomTypesSetToUse</span>}<span class="s">)</span> <span class="s">{</span>
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147 134 <span class="i">$This</span>->{<span class="w">EStateAtomTypesSetToUse</span>} = <span class="q">'ArbitrarySize'</span><span class="sc">;</span>
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148 135 <span class="s">}</span>
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149 136
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150 137 <span class="c"># Vector type...</span>
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151 138 <span class="i">$This</span>->{<span class="w">VectorType</span>} = <span class="q">'FingerprintsVector'</span><span class="sc">;</span>
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152 139
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153 140 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">EStateAtomTypesSetToUse</span>} =~ <span class="q">/^FixedSize$/i</span><span class="s">)</span> <span class="s">{</span>
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154 141 <span class="i">$This</span>->{<span class="w">FingerprintsVectorType</span>} = <span class="q">'OrderedNumericalValues'</span><span class="sc">;</span>
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155 142 <span class="s">}</span>
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156 143 <span class="k">else</span> <span class="s">{</span>
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157 144 <span class="i">$This</span>->{<span class="w">FingerprintsVectorType</span>} = <span class="q">'NumericalValues'</span><span class="sc">;</span>
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158 145 <span class="s">}</span>
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159 146
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160 147 <span class="i">$This</span><span class="i">->_InitializeFingerprintsVector</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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161 148
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162 149 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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163 150 <span class="s">}</span>
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164 151
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165 152 <span class="c"># Disable set size method...</span>
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166 153 <span class="c">#</span>
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167 <a name="SetSize-"></a> 154 <span class="k">sub </span><span class="m">SetSize</span> <span class="s">{</span>
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168 155 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Type</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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169 156
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170 157 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetSize: Can't change size: It's not allowed..."</span><span class="sc">;</span>
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171 158 <span class="s">}</span>
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172 159
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173 160 <span class="c"># Set E-state atom types set to use...</span>
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174 161 <span class="c">#</span>
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175 <a name="SetEStateAtomTypesSetToUse-"></a> 162 <span class="k">sub </span><span class="m">SetEStateAtomTypesSetToUse</span> <span class="s">{</span>
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176 163 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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177 164
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178 165 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">EStateAtomTypesSetToUse</span>}<span class="s">)</span> <span class="s">{</span>
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179 166 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetEStateAtomTypesSetToUse: Can't change size: It's already set..."</span><span class="sc">;</span>
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180 167 <span class="s">}</span>
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181 168
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182 169 <span class="k">if</span> <span class="s">(</span><span class="i">$Value</span> !~ <span class="q">/^(ArbitrarySize|FixedSize)/i</span><span class="s">)</span> <span class="s">{</span>
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183 170 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetEStateAtomTypesSetToUse: Unknown EStateAtomTypesSetToUse value: $Value; Supported values: ArbitrarySize or FixedSize"</span><span class="sc">;</span>
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184 171 <span class="s">}</span>
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185 172
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186 173 <span class="i">$This</span>->{<span class="w">EStateAtomTypesSetToUse</span>} = <span class="i">$Value</span><span class="sc">;</span>
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187 174
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188 175 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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189 176 <span class="s">}</span>
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190 177
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191 178 <span class="c"># Set vector values precision for real values for E-state indicies...</span>
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192 179 <span class="c">#</span>
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193 <a name="SetValuesPrecision-"></a> 180 <span class="k">sub </span><span class="m">SetValuesPrecision</span> <span class="s">{</span>
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194 181 <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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195 182
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196 183 <span class="k">if</span> <span class="s">(</span>!<span class="i">TextUtil::IsPositiveInteger</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
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197 184 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetValuesPrecision: ValuesPrecision value, $Value, is not valid: It must be a positive integer..."</span><span class="sc">;</span>
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198 185 <span class="s">}</span>
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199 186 <span class="i">$This</span>->{<span class="w">ValuesPrecision</span>} = <span class="i">$Value</span><span class="sc">;</span>
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200 187
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201 188 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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202 189 <span class="s">}</span>
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203 190
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204 191 <span class="c"># Generate fingerprints description...</span>
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205 192 <span class="c">#</span>
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206 <a name="GetDescription-"></a> 193 <span class="k">sub </span><span class="m">GetDescription</span> <span class="s">{</span>
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207 194 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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208 195
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209 196 <span class="c"># Is description explicity set?</span>
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|
210 197 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$This</span>->{<span class="w">Description</span>}<span class="s">)</span> <span class="s">{</span>
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211 198 <span class="k">return</span> <span class="i">$This</span>->{<span class="w">Description</span>}<span class="sc">;</span>
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|
212 199 <span class="s">}</span>
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213 200
|
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|
214 201 <span class="c"># Generate fingerprints description...</span>
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215 202
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216 203 <span class="k">return</span> <span class="q">"$This->{Type}:$This->{EStateAtomTypesSetToUse}"</span><span class="sc">;</span>
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|
217 204 <span class="s">}</span>
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218 205
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219 206 <span class="c"># Generate electrotopological state indicies (E-state) [ Ref 75-78 ] fingerprints for</span>
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220 207 <span class="c"># non-hydrogen atoms in a molecule...</span>
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221 208 <span class="c">#</span>
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222 209 <span class="c"># EStateIndicies fingerprints constitute a vector containing sum of E-state values</span>
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223 210 <span class="c"># for E-state atom types. Two types of E-state atom types set size are allowed:</span>
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224 211 <span class="c">#</span>
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|
225 212 <span class="c"># ArbitrarySize - Corrresponds to only E-state atom types detected in molecule</span>
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226 213 <span class="c"># FixedSize - Corresponds to fixed number of E-state atom types previously defined</span>
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227 214 <span class="c">#</span>
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228 215 <span class="c"># Module AtomTypes::EStateAtomTypes.pm is used to assign E-state atom types to</span>
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229 216 <span class="c"># non-hydrogen atoms in the molecule which is able to assign atom types to any valid</span>
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230 217 <span class="c"># atom group. However, for FixedSize value of EStateAtomTypesSetToUse, only a fixed</span>
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231 218 <span class="c"># set of E-state atom types corresponding to specific atom groups [ Appendix III in</span>
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232 219 <span class="c"># Ref 77 ] are used for fingerprints.</span>
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233 220 <span class="c">#</span>
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234 221 <span class="c"># The fixed size E-state atom type set size used during generation of fingerprints corresponding</span>
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235 222 <span class="c"># FixedSize value of EStateAtomTypesSetToUse contains 87 E-state non-hydrogen atom types</span>
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|
236 223 <span class="c"># in EStateAtomTypes.csv data file distributed with MayaChemTools.</span>
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237 224 <span class="c">#</span>
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238 225 <span class="c"># Combination of Type and EStateAtomTypesSetToUse allow generation of 2 different types of</span>
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239 226 <span class="c"># E-state indicies fingerprints:</span>
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|
240 227 <span class="c">#</span>
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241 228 <span class="c"># Type EStateAtomTypesSetToUse</span>
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242 229 <span class="c">#</span>
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243 230 <span class="c"># EStateIndicies ArbitrarySize [ default fingerprints ]</span>
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244 231 <span class="c"># EStateIndicies FixedSize</span>
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245 232 <span class="c">#</span>
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246 233 <span class="c"># The default is generate EStateIndicies type fingeprints corresponding to ArbitrarySize as</span>
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247 234 <span class="c"># EStateAtomTypesSetToUse value.</span>
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248 235 <span class="c">#</span>
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249 236 <span class="c">#</span>
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250 <a name="GenerateFingerprints-"></a> 237 <span class="k">sub </span><span class="m">GenerateFingerprints</span> <span class="s">{</span>
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251 238 <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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252 239
|
|
|
253 240 <span class="c"># Cache appropriate molecule data...</span>
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|
254 241 <span class="i">$This</span><span class="i">->_SetupMoleculeDataCache</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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255 242
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|
|
256 243 <span class="c"># Assign E-state atom types...</span>
|
|
|
257 244 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->_AssignEStateAtomTypes</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
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|
|
258 245 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->GenerateFingerprints: $This->{Type} fingerprints generation didn't succeed: Couldn't assign valid E-state atom types to all atoms..."</span><span class="sc">;</span>
|
|
|
259 246 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
260 247 <span class="s">}</span>
|
|
|
261 248
|
|
|
262 249 <span class="c"># Calculate E-state indicies...</span>
|
|
|
263 250 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->_CalculateEStateIndicies</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
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|
|
264 251 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->GenerateFingerprints: $This->{Type} fingerprints generation didn't succeed: Couldn't calculate E-state values for all atoms..."</span><span class="sc">;</span>
|
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|
265 252 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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|
|
266 253 <span class="s">}</span>
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|
267 254
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|
|
268 255 <span class="c"># Set final fingerprints...</span>
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|
|
269 256 <span class="i">$This</span><span class="i">->_SetFinalFingerprints</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
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270 257
|
|
|
271 258 <span class="c"># Clear cached molecule data...</span>
|
|
|
272 259 <span class="i">$This</span><span class="i">->_ClearMoleculeDataCache</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
273 260
|
|
|
274 261 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
275 262 <span class="s">}</span>
|
|
|
276 263
|
|
|
277 264 <span class="c"># Assign E-state atom types...</span>
|
|
|
278 265 <span class="c">#</span>
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|
|
279 <a name="_AssignEStateAtomTypes-"></a> 266 <span class="k">sub </span><span class="m">_AssignEStateAtomTypes</span> <span class="s">{</span>
|
|
|
280 267 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
281 268 <span class="k">my</span><span class="s">(</span><span class="i">$EStateAtomTypes</span><span class="cm">,</span> <span class="i">$Atom</span><span class="cm">,</span> <span class="i">$AtomID</span><span class="cm">,</span> <span class="i">$AtomType</span><span class="s">)</span><span class="sc">;</span>
|
|
|
282 269
|
|
|
283 270 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">EStateAtomTypes</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
284 271
|
|
|
285 272 <span class="c"># Assign E-state atom types...</span>
|
|
|
286 273 <span class="i">$EStateAtomTypes</span> = <span class="i">new</span> <span class="i">AtomTypes::EStateAtomTypes</span><span class="s">(</span><span class="q">'Molecule'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="cm">,</span> <span class="q">'IgnoreHydrogens'</span> <span class="cm">=></span> <span class="n">1</span><span class="s">)</span><span class="sc">;</span>
|
|
|
287 274 <span class="i">$EStateAtomTypes</span><span class="i">->AssignAtomTypes</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
288 275
|
|
|
289 276 <span class="c"># Make sure atom types assignment is successful...</span>
|
|
|
290 277 <span class="k">if</span> <span class="s">(</span>!<span class="i">$EStateAtomTypes</span><span class="i">->IsAtomTypesAssignmentSuccessful</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
291 278 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
|
|
|
292 279 <span class="s">}</span>
|
|
|
293 280
|
|
|
294 281 <span class="c"># Collect assigned atom types...</span>
|
|
|
295 282 <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$This</span>->{<span class="w">Atoms</span>}}<span class="s">)</span> <span class="s">{</span>
|
|
|
296 283 <span class="i">$AtomID</span> = <span class="i">$Atom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
297 284
|
|
|
298 285 <span class="i">$AtomType</span> = <span class="i">$EStateAtomTypes</span><span class="i">->GetAtomType</span><span class="s">(</span><span class="i">$Atom</span><span class="s">)</span><span class="sc">;</span>
|
|
|
299 286 <span class="i">$This</span>->{<span class="w">EStateAtomTypes</span>}{<span class="i">$AtomID</span>} = <span class="i">$AtomType</span><span class="sc">;</span>
|
|
|
300 287 <span class="s">}</span>
|
|
|
301 288 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
302 289 <span class="s">}</span>
|
|
|
303 290
|
|
|
304 291 <span class="c"># Calculate E-state indicies by summing up E-state values for specific</span>
|
|
|
305 292 <span class="c"># E-state atom types...</span>
|
|
|
306 293 <span class="c">#</span>
|
|
|
307 <a name="_CalculateEStateIndicies-"></a> 294 <span class="k">sub </span><span class="m">_CalculateEStateIndicies</span> <span class="s">{</span>
|
|
|
308 295 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
309 296 <span class="k">my</span><span class="s">(</span><span class="i">$Atom</span><span class="cm">,</span> <span class="i">$AtomID</span><span class="cm">,</span> <span class="i">$AtomType</span><span class="cm">,</span> <span class="i">$EStateValue</span><span class="s">)</span><span class="sc">;</span>
|
|
|
310 297
|
|
|
311 298 <span class="c"># Calculate E-state values to generate E-state indicies...</span>
|
|
|
312 299 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->_CalculateEStateValuesDescriptors</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
313 300 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
|
|
|
314 301 <span class="s">}</span>
|
|
|
315 302
|
|
|
316 303 <span class="c"># Calculate E-state indicies...</span>
|
|
|
317 304 <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$This</span>->{<span class="w">Atoms</span>}}<span class="s">)</span> <span class="s">{</span>
|
|
|
318 305 <span class="i">$AtomID</span> = <span class="i">$Atom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
319 306
|
|
|
320 307 <span class="i">$AtomType</span> = <span class="i">$This</span>->{<span class="w">EStateAtomTypes</span>}{<span class="i">$AtomID</span>}<span class="sc">;</span>
|
|
|
321 308 <span class="i">$EStateValue</span> = <span class="i">$This</span>->{<span class="w">EStateValues</span>}{<span class="i">$AtomID</span>}<span class="sc">;</span>
|
|
|
322 309
|
|
|
323 310 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$This</span>->{<span class="w">EStateIndicies</span>}{<span class="i">$AtomType</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
324 311 <span class="i">$This</span>->{<span class="w">EStateIndicies</span>}{<span class="i">$AtomType</span>} = <span class="n">0</span><span class="sc">;</span>
|
|
|
325 312 <span class="s">}</span>
|
|
|
326 313
|
|
|
327 314 <span class="i">$This</span>->{<span class="w">EStateIndicies</span>}{<span class="i">$AtomType</span>} += <span class="i">$EStateValue</span><span class="sc">;</span>
|
|
|
328 315 <span class="s">}</span>
|
|
|
329 316 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
330 317 <span class="s">}</span>
|
|
|
331 318
|
|
|
332 319 <span class="c"># Calculate E-state values for E-state indicies...</span>
|
|
|
333 320 <span class="c">#</span>
|
|
|
334 <a name="_CalculateEStateValuesDescriptors-"></a> 321 <span class="k">sub </span><span class="m">_CalculateEStateValuesDescriptors</span> <span class="s">{</span>
|
|
|
335 322 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
336 323 <span class="k">my</span><span class="s">(</span><span class="i">$EStateValuesDescriptors</span><span class="cm">,</span> <span class="i">$Atom</span><span class="cm">,</span> <span class="i">$AtomID</span><span class="cm">,</span> <span class="i">$EStateValue</span><span class="s">)</span><span class="sc">;</span>
|
|
|
337 324
|
|
|
338 325 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">EStateValues</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
339 326
|
|
|
340 327 <span class="c"># Calculate and assign E-state values...</span>
|
|
|
341 328 <span class="i">$EStateValuesDescriptors</span> = <span class="i">new</span> <span class="i">AtomicDescriptors::EStateValuesDescriptors</span><span class="s">(</span><span class="q">'Molecule'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="s">)</span><span class="sc">;</span>
|
|
|
342 329 <span class="i">$EStateValuesDescriptors</span><span class="i">->GenerateDescriptors</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
343 330
|
|
|
344 331 <span class="c"># Make sure E-state values calculation is successful...</span>
|
|
|
345 332 <span class="k">if</span> <span class="s">(</span>!<span class="i">$EStateValuesDescriptors</span><span class="i">->IsDescriptorsGenerationSuccessful</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
346 333 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
|
|
|
347 334 <span class="s">}</span>
|
|
|
348 335
|
|
|
349 336 <span class="c"># Collect assigned E-state values...</span>
|
|
|
350 337 <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$This</span>->{<span class="w">Atoms</span>}}<span class="s">)</span> <span class="s">{</span>
|
|
|
351 338 <span class="i">$AtomID</span> = <span class="i">$Atom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
352 339 <span class="i">$EStateValue</span> = <span class="i">$EStateValuesDescriptors</span><span class="i">->GetDescriptorValue</span><span class="s">(</span><span class="i">$Atom</span><span class="s">)</span><span class="sc">;</span>
|
|
|
353 340 <span class="i">$This</span>->{<span class="w">EStateValues</span>}{<span class="i">$AtomID</span>} = <span class="i">$EStateValue</span><span class="sc">;</span>
|
|
|
354 341 <span class="s">}</span>
|
|
|
355 342 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
356 343 <span class="s">}</span>
|
|
|
357 344
|
|
|
358 345 <span class="c"># Set final final fingerpritns for E-state indicies...</span>
|
|
|
359 346 <span class="c">#</span>
|
|
|
360 <a name="_SetFinalFingerprints-"></a> 347 <span class="k">sub </span><span class="m">_SetFinalFingerprints</span> <span class="s">{</span>
|
|
|
361 348 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
362 349 <span class="k">my</span><span class="s">(</span><span class="i">$AtomType</span><span class="cm">,</span> <span class="i">$ValuesPrecision</span><span class="cm">,</span> <span class="i">$EStateAtomTypesDataRef</span><span class="cm">,</span> <span class="i">@Values</span><span class="cm">,</span> <span class="i">@IDs</span><span class="s">)</span><span class="sc">;</span>
|
|
|
363 350
|
|
|
364 351 <span class="c"># Mark successful generation of fingerprints...</span>
|
|
|
365 352 <span class="i">$This</span>->{<span class="w">FingerprintsGenerated</span>} = <span class="n">1</span><span class="sc">;</span>
|
|
|
366 353
|
|
|
367 354 <span class="i">@Values</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
368 355 <span class="i">@IDs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
369 356
|
|
|
370 357 <span class="i">$ValuesPrecision</span> = <span class="i">$This</span>->{<span class="w">ValuesPrecision</span>}<span class="sc">;</span>
|
|
|
371 358
|
|
|
372 359 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">EStateAtomTypesSetToUse</span>} =~ <span class="q">/^FixedSize$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
373 360 <span class="c"># Use fixed size E-state atom types set for non-hydrogen atoms...</span>
|
|
|
374 361 <span class="k">for</span> <span class="i">$AtomType</span> <span class="s">(</span><span class="i">@</span>{<span class="i">AtomTypes::EStateAtomTypes::GetAllPossibleEStateNonHydrogenAtomTypes</span><span class="s">(</span><span class="s">)</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
375 362 <span class="k">push</span> <span class="i">@IDs</span><span class="cm">,</span> <span class="q">"S${AtomType}"</span><span class="sc">;</span>
|
|
|
376 363 <span class="k">push</span> <span class="i">@Values</span><span class="cm">,</span> <span class="k">exists</span><span class="s">(</span><span class="i">$This</span>->{<span class="w">EStateIndicies</span>}{<span class="i">$AtomType</span>}<span class="s">)</span> ? <span class="i">MathUtil::round</span><span class="s">(</span><span class="i">$This</span>->{<span class="w">EStateIndicies</span>}{<span class="i">$AtomType</span>}<span class="cm">,</span> <span class="i">$ValuesPrecision</span><span class="s">)</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
377 364 <span class="s">}</span>
|
|
|
378 365 <span class="s">}</span>
|
|
|
379 366 <span class="k">else</span> <span class="s">{</span>
|
|
|
380 367 <span class="k">for</span> <span class="i">$AtomType</span> <span class="s">(</span><span class="k">sort</span> <span class="k">keys</span> <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">EStateIndicies</span>}}<span class="s">)</span> <span class="s">{</span>
|
|
|
381 368 <span class="k">push</span> <span class="i">@IDs</span><span class="cm">,</span> <span class="q">"S${AtomType}"</span><span class="sc">;</span>
|
|
|
382 369 <span class="k">push</span> <span class="i">@Values</span><span class="cm">,</span> <span class="i">MathUtil::round</span><span class="s">(</span><span class="i">$This</span>->{<span class="w">EStateIndicies</span>}{<span class="i">$AtomType</span>}<span class="cm">,</span> <span class="i">$ValuesPrecision</span><span class="s">)</span><span class="sc">;</span>
|
|
|
383 370 <span class="s">}</span>
|
|
|
384 371 <span class="s">}</span>
|
|
|
385 372
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386 373 <span class="c"># Add IDs and values to fingerprint vector...</span>
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387 374 <span class="k">if</span> <span class="s">(</span><span class="i">@IDs</span><span class="s">)</span> <span class="s">{</span>
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388 375 <span class="i">$This</span>->{<span class="w">FingerprintsVector</span>}<span class="i">->AddValueIDs</span><span class="s">(</span>\<span class="i">@IDs</span><span class="s">)</span><span class="sc">;</span>
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389 376 <span class="s">}</span>
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390 377 <span class="i">$This</span>->{<span class="w">FingerprintsVector</span>}<span class="i">->AddValues</span><span class="s">(</span>\<span class="i">@Values</span><span class="s">)</span><span class="sc">;</span>
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391 378
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392 379 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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393 380 <span class="s">}</span>
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394 381
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395 382 <span class="c"># Cache appropriate molecule data...</span>
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396 383 <span class="c">#</span>
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397 <a name="_SetupMoleculeDataCache-"></a> 384 <span class="k">sub </span><span class="m">_SetupMoleculeDataCache</span> <span class="s">{</span>
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398 385 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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399 386
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400 387 <span class="c"># Get all non-hydrogen atoms...</span>
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401 388 <span class="k">my</span><span class="s">(</span><span class="i">$NegateAtomCheckMethod</span><span class="s">)</span><span class="sc">;</span>
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402 389 <span class="i">$NegateAtomCheckMethod</span> = <span class="n">1</span><span class="sc">;</span>
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403 390 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">Atoms</span>}} = <span class="i">$This</span><span class="i">->GetMolecule</span><span class="s">(</span><span class="s">)</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="q">"IsHydrogen"</span><span class="cm">,</span> <span class="i">$NegateAtomCheckMethod</span><span class="s">)</span><span class="sc">;</span>
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404 391
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405 392 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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406 393 <span class="s">}</span>
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407 394
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408 395 <span class="c"># Clear cached molecule data...</span>
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409 396 <span class="c">#</span>
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410 <a name="_ClearMoleculeDataCache-"></a> 397 <span class="k">sub </span><span class="m">_ClearMoleculeDataCache</span> <span class="s">{</span>
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411 398 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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412 399
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413 400 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">Atoms</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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414 401
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415 402 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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416 403 <span class="s">}</span>
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417 404
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418 405 <span class="c"># Return a string containg data for EStateIndiciesFingerprints object...</span>
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419 <a name="StringifyEStateIndiciesFingerprints-"></a> 406 <span class="k">sub </span><span class="m">StringifyEStateIndiciesFingerprints</span> <span class="s">{</span>
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420 407 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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421 408 <span class="k">my</span><span class="s">(</span><span class="i">$EStateIndiciesFingerprintsString</span><span class="s">)</span><span class="sc">;</span>
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422 409
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423 410 <span class="c"># Type of Keys...</span>
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424 411 <span class="i">$EStateIndiciesFingerprintsString</span> = <span class="q">"Type: $This->{Type}; EStateAtomTypesSetToUse: $This->{EStateAtomTypesSetToUse}"</span><span class="sc">;</span>
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425 412
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426 413 <span class="c"># Fingerprint vector...</span>
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427 414 <span class="i">$EStateIndiciesFingerprintsString</span> .= <span class="q">"; FingerprintsVector: < $This->{FingerprintsVector} >"</span><span class="sc">;</span>
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428 415
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429 416 <span class="k">return</span> <span class="i">$EStateIndiciesFingerprintsString</span><span class="sc">;</span>
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430 417 <span class="s">}</span>
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431 418
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432 <a name="EOF-"></a></pre>
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433 <p> </p>
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434 <br />
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435 <center>
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436 <img src="../../../images/h2o2.png">
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437 </center>
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438 </body>
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439 </html>
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