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3 <title>MayaChemTools:Code:AtomicDescriptors::EStateValuesDescriptors.pm</title>
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13 <pre>
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14 <a name="package-AtomicDescriptors::EStateValuesDescriptors-"></a> 1 <span class="k">package </span><span class="i">AtomicDescriptors::EStateValuesDescriptors</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: EStateValuesDescriptors.pm,v $</span>
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17 4 <span class="c"># $Date: 2015/02/28 20:47:49 $</span>
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18 5 <span class="c"># $Revision: 1.16 $</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">Matrix</span><span class="sc">;</span>
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47 34 <span class="k">use</span> <span class="w">Constants</span><span class="sc">;</span>
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48 35 <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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49 36 <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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50 37 <span class="k">use</span> <span class="w">StatisticsUtil</span> <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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51 38 <span class="k">use</span> <span class="w">Atom</span><span class="sc">;</span>
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52 39 <span class="k">use</span> <span class="w">Molecule</span><span class="sc">;</span>
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53 40 <span class="k">use</span> <span class="w">AtomicDescriptors::AtomicDescriptors</span><span class="sc">;</span>
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54 41
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55 42 <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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56 43
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57 44 <span class="i">@ISA</span> = <span class="q">qw(AtomicDescriptors::AtomicDescriptors Exporter)</span><span class="sc">;</span>
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58 45 <span class="i">@EXPORT</span> = <span class="q">qw()</span><span class="sc">;</span>
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59 46 <span class="i">@EXPORT_OK</span> = <span class="q">qw()</span><span class="sc">;</span>
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60 47
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61 48 <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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62 49
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63 50 <span class="c"># Setup class variables...</span>
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64 51 <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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65 52 <span class="i">_InitializeClass</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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66 53
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67 54 <span class="c"># Overload Perl functions...</span>
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68 55 <span class="k">use</span> <span class="w">overload</span> <span class="q">'""'</span> <span class="cm">=></span> <span class="q">'StringifyEStateValuesDescriptors'</span><span class="sc">;</span>
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69 56
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70 57 <span class="c"># Class constructor...</span>
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71 <a name="new-"></a> 58 <span class="k">sub </span><span class="m">new</span> <span class="s">{</span>
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72 59 <span class="k">my</span><span class="s">(</span><span class="i">$Class</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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73 60
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74 61 <span class="c"># Initialize object...</span>
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75 62 <span class="k">my</span> <span class="i">$This</span> = <span class="i">$Class</span><span class="i">->SUPER::new</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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76 63 <span class="k">bless</span> <span class="i">$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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77 64 <span class="i">$This</span><span class="i">->_InitializeEStateValuesDescriptors</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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78 65
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79 66 <span class="i">$This</span><span class="i">->_InitializeEStateValuesDescriptorsProperties</span><span class="s">(</span><span class="i">%NamesAndValues</span><span class="s">)</span><span class="sc">;</span>
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80 67
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81 68 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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82 69 <span class="s">}</span>
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83 70
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84 71 <span class="c"># Initialize class ...</span>
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85 <a name="_InitializeClass-"></a> 72 <span class="k">sub </span><span class="m">_InitializeClass</span> <span class="s">{</span>
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86 73 <span class="c">#Class name...</span>
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87 74 <span class="i">$ClassName</span> = <span class="w">__PACKAGE__</span><span class="sc">;</span>
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88 75 <span class="s">}</span>
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89 76
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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="_InitializeEStateValuesDescriptors-"></a> 80 <span class="k">sub </span><span class="m">_InitializeEStateValuesDescriptors</span> <span class="s">{</span>
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94 81 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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95 82
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96 83 <span class="c"># Type of AtomicDescriptor...</span>
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97 84 <span class="i">$This</span>->{<span class="w">Type</span>} = <span class="q">'EStateValue'</span><span class="sc">;</span>
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98 85
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99 86 <span class="c"># Intrinsic state values calculated for non-hydrogen atom...</span>
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100 87 <span class="c">#</span>
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101 88 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">IStateValues</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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102 89
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103 90 <span class="c"># Calculatetion of E-state values for types for hydrogens is not supported...</span>
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104 91 <span class="i">$This</span>->{<span class="w">IgnoreHydrogens</span>} = <span class="n">1</span><span class="sc">;</span>
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105 92
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106 93 <span class="c"># Perturbation to intrinsic state values of atoms corresponding to all non-hydrogen</span>
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107 94 <span class="c"># atom pairs...</span>
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108 95 <span class="c">#</span>
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109 96 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">DeltaIStateMatrix</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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110 97
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111 98 <span class="c"># E-state values calculated for non-hydrogen atoms...</span>
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112 99 <span class="c">#</span>
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113 100 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">EStateValues</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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114 101
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115 102 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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116 103 <span class="s">}</span>
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117 104
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118 105 <span class="c"># Initialize object properties...</span>
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119 106 <span class="c">#</span>
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120 <a name="_InitializeEStateValuesDescriptorsProperties-"></a> 107 <span class="k">sub </span><span class="m">_InitializeEStateValuesDescriptorsProperties</span> <span class="s">{</span>
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121 108 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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122 109
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123 110 <span class="k">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">$MethodName</span><span class="s">)</span><span class="sc">;</span>
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124 111 <span class="k">while</span> <span class="s">(</span><span class="s">(</span><span class="i">$Name</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="k">each</span> <span class="i">%NamesAndValues</span><span class="s">)</span> <span class="s">{</span>
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125 112 <span class="i">$MethodName</span> = <span class="q">"Set${Name}"</span><span class="sc">;</span>
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126 113 <span class="i">$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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127 114 <span class="s">}</span>
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128 115
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129 116 <span class="c"># Make sure molecule object was specified...</span>
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130 117 <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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131 118 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->New: Object can't be instantiated without specifying molecule..."</span><span class="sc">;</span>
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132 119 <span class="s">}</span>
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133 120
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134 121 <span class="c"># Intialize atomic descriptor values...</span>
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135 122 <span class="i">$This</span><span class="i">->_InitializeDescriptorValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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136 123
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137 124 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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138 125 <span class="s">}</span>
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139 126
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140 127 <span class="c"># Disable change of ignore hydrogens...</span>
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141 128 <span class="c">#</span>
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142 <a name="SetIgnoreHydrogens-"></a> 129 <span class="k">sub </span><span class="m">SetIgnoreHydrogens</span> <span class="s">{</span>
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143 130 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$IgnoreHydrogens</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="w">carp</span> <span class="q">"Warning: ${ClassName}->SetIgnoreHydrogens: Ignore hydrogens value can't be changed: It's not supported..."</span><span class="sc">;</span>
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146 133
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147 134 <span class="k">return</span> <span class="i">$This</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"># Generate electrotopological state (E-state) values [ Ref 75-78 ] for all atoms</span>
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151 138 <span class="c"># in the molecule...</span>
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152 139 <span class="c">#</span>
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153 140 <span class="c"># Calculation of E-state values for non-hydrogen atoms:</span>
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154 141 <span class="c">#</span>
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155 142 <span class="c"># Let:</span>
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156 143 <span class="c">#</span>
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157 144 <span class="c"># N = Principal quantum number or period number corresponding to element symbol</span>
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158 145 <span class="c">#</span>
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159 146 <span class="c"># Sigma = Number of sigma electrons involves in bonds to hydrogen and non-hydrogen atoms</span>
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160 147 <span class="c"># attached to atom</span>
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161 148 <span class="c"># = Number of sigma bonds to hydrogen and non-hydrogen atoms attached to atom</span>
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162 149 <span class="c"># PI = Number of PI electrons involved in bonds to non-hydrogen atoms attached to atom</span>
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163 150 <span class="c"># = Number of PI bonds to non-hydrogen atoms attached to atom</span>
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164 151 <span class="c">#</span>
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165 152 <span class="c"># LP = Number of lone pair electrons on atom</span>
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166 153 <span class="c">#</span>
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167 154 <span class="c"># Zv = Number of electrons in valence shell of atom</span>
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168 155 <span class="c">#</span>
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169 156 <span class="c"># X = Number of non-hydrogen atom neighbors or heavy atoms attached to atom</span>
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170 157 <span class="c"># H = Number of implicit and explicit hydrogens for atom</span>
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171 158 <span class="c">#</span>
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172 159 <span class="c"># Delta = Number of sigma electrons involved to bonds to non-hydrogen atoms</span>
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173 160 <span class="c"># DeltaV = ValenceDelta = Number of valence shell electrons not involved in bonding to hydrogen atoms</span>
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174 161 <span class="c">#</span>
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175 162 <span class="c"># Ii = Intrinsic state value for atom i</span>
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176 163 <span class="c">#</span>
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177 164 <span class="c"># DeltaIi = Sum of perturbations to intrinsic state value Ii of atom i by all other atoms besides atom i</span>
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178 165 <span class="c">#</span>
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179 166 <span class="c"># DeltaIij = Perturbation to intrinsic state value Ii of atom i by atom j</span>
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180 167 <span class="c">#</span>
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181 168 <span class="c"># Dij = Graph/bond distance between atom i and j</span>
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182 169 <span class="c"># Rij = Dij + 1</span>
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183 170 <span class="c">#</span>
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184 171 <span class="c"># Si = E-state value for atom i</span>
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185 172 <span class="c">#</span>
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186 173 <span class="c">#</span>
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187 174 <span class="c"># Then:</span>
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188 175 <span class="c">#</span>
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189 176 <span class="c"># Delta = Sigma - H = X</span>
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190 177 <span class="c">#</span>
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191 178 <span class="c"># DeltaV = Zv - H</span>
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192 179 <span class="c"># = Sigma + PI + LP - H</span>
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193 180 <span class="c">#</span>
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194 181 <span class="c"># Ii = ( ( ( 2 / N ) ** 2 ) * DeltaV + 1 ) / Delta</span>
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195 182 <span class="c">#</span>
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196 183 <span class="c"># Si = Ii + DeltaIi</span>
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197 184 <span class="c">#</span>
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198 185 <span class="c"># DeltaIij = (Ii - Ij) / (Rij ** 2) for j not equal to i</span>
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199 186 <span class="c">#</span>
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200 187 <span class="c"># DeltaIji = - DeltaIij</span>
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201 188 <span class="c">#</span>
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202 189 <span class="c"># DeltaIi = SUM ( (Ii - Ij) / (Rij ** 2) ) for j = 1 to num of atoms skipping atom i</span>
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203 190 <span class="c">#</span>
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204 191 <span class="c"># Methodology:</span>
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205 192 <span class="c"># . Calculate intrinsic state values for atoms.</span>
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206 193 <span class="c"># . Generate a distance matrix.</span>
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207 194 <span class="c"># . Use distance matrix to calculate DeltaIij matrix with each row i containing</span>
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208 195 <span class="c"># DeltaIij values corresponding to perturbation to intrinsic state value of atom</span>
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209 196 <span class="c"># i by atom j.</span>
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210 197 <span class="c"># . Calculate E-state values using DeltaIij matrix.</span>
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211 198 <span class="c"># . Assign E-state values to atoms.</span>
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212 199 <span class="c">#</span>
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213 200 <span class="c"># Notes:</span>
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214 201 <span class="c"># . The current release of MayaChemTools doesn't support calculation of Hydrogen</span>
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215 202 <span class="c"># E-state values.</span>
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216 203 <span class="c">#</span>
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217 <a name="GenerateDescriptors-"></a> 204 <span class="k">sub </span><span class="m">GenerateDescriptors</span> <span class="s">{</span>
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218 205 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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219 206
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220 207 <span class="c"># Cache appropriate molecule data...</span>
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221 208 <span class="i">$This</span><span class="i">->_SetupMoleculeDataCache</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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222 209
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223 210 <span class="c"># Generate distance matrix...</span>
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224 211 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->_SetupDistanceMatrix</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
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225 212 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->GenerateDescriptors: E-state values description generation didn't succeed: Couldn't generate a distance matrix..."</span><span class="sc">;</span>
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226 213 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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227 214 <span class="s">}</span>
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228 215
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229 216 <span class="c"># Calculate EState values..</span>
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|
|
230 217 <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>
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|
|
231 218 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->GenerateDescriptors: E-state values description generation didn't succeed: Couldn't calculate IState values for all atoms..."</span><span class="sc">;</span>
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|
|
232 219 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
233 220 <span class="s">}</span>
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|
|
234 221
|
|
|
235 222 <span class="c"># Set final descriptor values...</span>
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|
|
236 223 <span class="i">$This</span><span class="i">->_SetFinalValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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|
|
237 224
|
|
|
238 225 <span class="c"># Clear cached molecule data...</span>
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|
|
239 226 <span class="i">$This</span><span class="i">->_ClearMoleculeDataCache</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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|
240 227
|
|
|
241 228 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
242 229 <span class="s">}</span>
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|
243 230
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|
|
244 231 <span class="c"># Calculate E-state values for non-hydrogen atoms...</span>
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|
|
245 232 <span class="c">#</span>
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|
246 <a name="_CalculateEStateValuesDescriptors-"></a> 233 <span class="k">sub </span><span class="m">_CalculateEStateValuesDescriptors</span> <span class="s">{</span>
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247 234 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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|
|
248 235 <span class="k">my</span><span class="s">(</span><span class="i">$DeltaIStateMatrix</span><span class="cm">,</span> <span class="i">$NumOfRows</span><span class="cm">,</span> <span class="i">$NumOfCols</span><span class="cm">,</span> <span class="i">$RowIndex</span><span class="cm">,</span> <span class="i">$AtomID</span><span class="cm">,</span> <span class="i">$EStateValue</span><span class="cm">,</span> <span class="i">$IStateValue</span><span class="cm">,</span> <span class="i">$DeltaIStateValue</span><span class="cm">,</span> <span class="i">@DeltaIStateMatrixRowValues</span><span class="s">)</span><span class="sc">;</span>
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249 236
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|
250 237 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">EStateValues</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
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251 238
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|
252 239 <span class="c"># Calculate intrinsic state values for non-hydrogen atoms...</span>
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|
|
253 240 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->_CalculateIStateValues</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
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|
|
254 241 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
|
|
|
255 242 <span class="s">}</span>
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256 243
|
|
|
257 244 <span class="c"># Calculate delta intrinsic state matrix for non-hydrogen atoms...</span>
|
|
|
258 245 <span class="i">$This</span><span class="i">->_CalculateDeltaIStateMatrix</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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259 246
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|
|
260 247 <span class="c"># Get DeltaIState matrix information...</span>
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|
|
261 248 <span class="i">$DeltaIStateMatrix</span> = <span class="i">$This</span>->{<span class="w">DeltaIStateMatrix</span>}<span class="sc">;</span>
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|
|
262 249 <span class="s">(</span><span class="i">$NumOfRows</span><span class="cm">,</span> <span class="i">$NumOfCols</span><span class="s">)</span> = <span class="i">$DeltaIStateMatrix</span><span class="i">->GetSize</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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|
263 250
|
|
|
264 251 <span class="c"># Calculate EState values...</span>
|
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|
265 252 <span class="j">ROWINDEX:</span> <span class="k">for</span> <span class="i">$RowIndex</span> <span class="s">(</span><span class="n">0</span> .. <span class="s">(</span><span class="i">$NumOfRows</span> - <span class="n">1</span><span class="s">)</span> <span class="s">)</span> <span class="s">{</span>
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|
|
266 253 <span class="i">$AtomID</span> = <span class="i">$This</span>->{<span class="w">AtomIndexToID</span>}{<span class="i">$RowIndex</span>}<span class="sc">;</span>
|
|
|
267 254 <span class="k">if</span> <span class="s">(</span> !<span class="s">(</span><span class="k">exists</span><span class="s">(</span><span class="i">$This</span>->{<span class="w">IStateValues</span>}{<span class="i">$AtomID</span>}<span class="s">)</span><span class="s">)</span> <span class="s">)</span> <span class="s">{</span>
|
|
|
268 255 <span class="k">next</span> <span class="j">ROWINDEX</span><span class="sc">;</span>
|
|
|
269 256 <span class="s">}</span>
|
|
|
270 257 <span class="i">$IStateValue</span> = <span class="i">$This</span>->{<span class="w">IStateValues</span>}{<span class="i">$AtomID</span>}<span class="sc">;</span>
|
|
|
271 258
|
|
|
272 259 <span class="i">@DeltaIStateMatrixRowValues</span> = <span class="i">$DeltaIStateMatrix</span><span class="i">->GetRowValues</span><span class="s">(</span><span class="i">$RowIndex</span><span class="s">)</span><span class="sc">;</span>
|
|
|
273 260 <span class="i">$DeltaIStateValue</span> = <span class="i">StatisticsUtil::Sum</span><span class="s">(</span>\<span class="i">@DeltaIStateMatrixRowValues</span><span class="s">)</span><span class="sc">;</span>
|
|
|
274 261
|
|
|
275 262 <span class="i">$EStateValue</span> = <span class="i">$IStateValue</span> + <span class="i">$DeltaIStateValue</span><span class="sc">;</span>
|
|
|
276 263
|
|
|
277 264 <span class="i">$This</span>->{<span class="w">EStateValues</span>}{<span class="i">$AtomID</span>} = <span class="i">$EStateValue</span><span class="sc">;</span>
|
|
|
278 265 <span class="s">}</span>
|
|
|
279 266 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
280 267 <span class="s">}</span>
|
|
|
281 268
|
|
|
282 269 <span class="c"># Calculate intrinsic state values for non-hydrogen atoms...</span>
|
|
|
283 270 <span class="c">#</span>
|
|
|
284 <a name="_CalculateIStateValues-"></a> 271 <span class="k">sub </span><span class="m">_CalculateIStateValues</span> <span class="s">{</span>
|
|
|
285 272 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
286 273 <span class="k">my</span><span class="s">(</span><span class="i">$Atom</span><span class="cm">,</span> <span class="i">$AtomID</span><span class="s">)</span><span class="sc">;</span>
|
|
|
287 274
|
|
|
288 275 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">IStateValues</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
289 276
|
|
|
290 277 <span class="j">ATOM:</span> <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$This</span>->{<span class="w">Atoms</span>}}<span class="s">)</span> <span class="s">{</span>
|
|
|
291 278 <span class="c"># Irrespective of IgoreHydrogens value, just ignore hydrogens...</span>
|
|
|
292 279 <span class="k">if</span> <span class="s">(</span><span class="i">$Atom</span><span class="i">->IsHydrogen</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
293 280 <span class="k">next</span> <span class="j">ATOM</span><span class="sc">;</span>
|
|
|
294 281 <span class="s">}</span>
|
|
|
295 282 <span class="i">$AtomID</span> = <span class="i">$Atom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
296 283 <span class="i">$This</span>->{<span class="w">IStateValues</span>}{<span class="i">$AtomID</span>} = <span class="i">$This</span><span class="i">->_CalculateIStateValue</span><span class="s">(</span><span class="i">$Atom</span><span class="s">)</span><span class="sc">;</span>
|
|
|
297 284 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span><span class="s">(</span><span class="i">$This</span>->{<span class="w">IStateValues</span>}{<span class="i">$AtomID</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
298 285 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
|
|
|
299 286 <span class="s">}</span>
|
|
|
300 287 <span class="s">}</span>
|
|
|
301 288 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
302 289 <span class="s">}</span>
|
|
|
303 290
|
|
|
304 291 <span class="c"># Calculation intrinsic state value for non-hydrogen...</span>
|
|
|
305 292 <span class="c">#</span>
|
|
|
306 <a name="_CalculateIStateValue-"></a> 293 <span class="k">sub </span><span class="m">_CalculateIStateValue</span> <span class="s">{</span>
|
|
|
307 294 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Atom</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
308 295 <span class="k">my</span><span class="s">(</span><span class="i">$IStateValue</span><span class="cm">,</span> <span class="i">$Delta</span><span class="cm">,</span> <span class="i">$DeltaV</span><span class="cm">,</span> <span class="i">$PeriodNumber</span><span class="s">)</span><span class="sc">;</span>
|
|
|
309 296
|
|
|
310 297 <span class="i">$PeriodNumber</span> = <span class="i">$Atom</span><span class="i">->GetPeriodNumber</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
311 298 <span class="s">(</span><span class="i">$Delta</span><span class="cm">,</span> <span class="i">$DeltaV</span><span class="s">)</span> = <span class="i">$This</span><span class="i">->_GetDeltaValues</span><span class="s">(</span><span class="i">$Atom</span><span class="s">)</span><span class="sc">;</span>
|
|
|
312 299
|
|
|
313 300 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$Delta</span><span class="s">)</span> && <span class="k">defined</span><span class="s">(</span><span class="i">$PeriodNumber</span><span class="s">)</span> && <span class="k">defined</span><span class="s">(</span><span class="i">$DeltaV</span><span class="s">)</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
314 301 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
|
|
|
315 302 <span class="s">}</span>
|
|
|
316 303
|
|
|
317 304 <span class="i">$IStateValue</span> = <span class="s">(</span><span class="i">$PeriodNumber</span> && <span class="i">$Delta</span><span class="s">)</span> ? <span class="s">(</span><span class="s">(</span><span class="s">(</span><span class="n">2</span>/<span class="i">$PeriodNumber</span><span class="s">)</span>**<span class="n">2</span><span class="s">)</span>*<span class="i">$DeltaV</span> + <span class="n">1</span><span class="s">)</span>/<span class="i">$Delta</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
318 305
|
|
|
319 306 <span class="k">return</span> <span class="i">$IStateValue</span><span class="sc">;</span>
|
|
|
320 307 <span class="s">}</span>
|
|
|
321 308
|
|
|
322 309 <span class="c"># Get Delta and DeltaV values for atom...</span>
|
|
|
323 310 <span class="c">#</span>
|
|
|
324 <a name="_GetDeltaValues-"></a> 311 <span class="k">sub </span><span class="m">_GetDeltaValues</span> <span class="s">{</span>
|
|
|
325 312 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Atom</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
326 313 <span class="k">my</span><span class="s">(</span><span class="i">$Delta</span><span class="cm">,</span> <span class="i">$DeltaV</span><span class="cm">,</span> <span class="i">$ValenceElectrons</span><span class="cm">,</span> <span class="i">$NumOfHydrogens</span><span class="s">)</span><span class="sc">;</span>
|
|
|
327 314
|
|
|
328 315 <span class="s">(</span><span class="i">$Delta</span><span class="cm">,</span> <span class="i">$DeltaV</span><span class="s">)</span> = <span class="s">(</span><span class="k">undef</span><span class="cm">,</span> <span class="k">undef</span><span class="s">)</span><span class="sc">;</span>
|
|
|
329 316
|
|
|
330 317 <span class="i">$ValenceElectrons</span> = <span class="i">$Atom</span><span class="i">->GetValenceElectrons</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
331 318 <span class="i">$NumOfHydrogens</span> = <span class="i">$Atom</span><span class="i">->GetAtomicInvariantValue</span><span class="s">(</span><span class="q">'H'</span><span class="s">)</span><span class="sc">;</span>
|
|
|
332 319
|
|
|
333 320 <span class="i">$Delta</span> = <span class="i">$Atom</span><span class="i">->GetAtomicInvariantValue</span><span class="s">(</span><span class="q">'X'</span><span class="s">)</span><span class="sc">;</span>
|
|
|
334 321 <span class="k">if</span> <span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$ValenceElectrons</span><span class="s">)</span> && <span class="k">defined</span><span class="s">(</span><span class="i">$NumOfHydrogens</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
335 322 <span class="i">$DeltaV</span> = <span class="i">$ValenceElectrons</span> - <span class="i">$NumOfHydrogens</span><span class="sc">;</span>
|
|
|
336 323 <span class="s">}</span>
|
|
|
337 324
|
|
|
338 325 <span class="k">return</span> <span class="s">(</span><span class="i">$Delta</span><span class="cm">,</span> <span class="i">$DeltaV</span><span class="s">)</span><span class="sc">;</span>
|
|
|
339 326 <span class="s">}</span>
|
|
|
340 327
|
|
|
341 328 <span class="c"># Calculate DeltaIState matrix for atoms with each row i containing DeltaIij values</span>
|
|
|
342 329 <span class="c"># corresponding atom atoms i and j.</span>
|
|
|
343 330 <span class="c">#</span>
|
|
|
344 331 <span class="c"># Notes:</span>
|
|
|
345 332 <span class="c"># . Matrix elements corresponding to hydrogen atoms or unconnected</span>
|
|
|
346 333 <span class="c"># are assigned zero value.</span>
|
|
|
347 334 <span class="c">#</span>
|
|
|
348 <a name="_CalculateDeltaIStateMatrix-"></a> 335 <span class="k">sub </span><span class="m">_CalculateDeltaIStateMatrix</span> <span class="s">{</span>
|
|
|
349 336 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
350 337 <span class="k">my</span><span class="s">(</span><span class="i">$DistanceMatrix</span><span class="cm">,</span> <span class="i">$NumOfRows</span><span class="cm">,</span> <span class="i">$NumOfCols</span><span class="cm">,</span> <span class="i">$RowIndex</span><span class="cm">,</span> <span class="i">$ColIndex</span><span class="cm">,</span> <span class="i">$AtomID1</span><span class="cm">,</span> <span class="i">$AtomID2</span><span class="cm">,</span> <span class="i">$DeltaIStateMatrix</span><span class="cm">,</span> <span class="i">$IStateValue1</span><span class="cm">,</span> <span class="i">$IStateValue2</span><span class="cm">,</span> <span class="i">$GraphDistance</span><span class="cm">,</span> <span class="i">$DeltaIState12</span><span class="cm">,</span> <span class="i">$DeltaIState21</span><span class="cm">,</span> <span class="i">$SkipIndexCheck</span><span class="s">)</span><span class="sc">;</span>
|
|
|
351 338
|
|
|
352 339 <span class="c"># Get distance matrix information...</span>
|
|
|
353 340 <span class="i">$DistanceMatrix</span> = <span class="i">$This</span>->{<span class="w">DistanceMatrix</span>}<span class="sc">;</span>
|
|
|
354 341 <span class="s">(</span><span class="i">$NumOfRows</span><span class="cm">,</span> <span class="i">$NumOfCols</span><span class="s">)</span> = <span class="i">$DistanceMatrix</span><span class="i">->GetSize</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
355 342
|
|
|
356 343 <span class="c"># Initialize DeltaIState matrix...</span>
|
|
|
357 344 <span class="i">$This</span>->{<span class="w">DeltaIStateMatrix</span>} = <span class="i">new</span> <span class="i">Matrix</span><span class="s">(</span><span class="i">$NumOfRows</span><span class="cm">,</span> <span class="i">$NumOfCols</span><span class="s">)</span><span class="sc">;</span>
|
|
|
358 345 <span class="i">$DeltaIStateMatrix</span> = <span class="i">$This</span>->{<span class="w">DeltaIStateMatrix</span>}<span class="sc">;</span>
|
|
|
359 346
|
|
|
360 347 <span class="i">$SkipIndexCheck</span> = <span class="n">1</span><span class="sc">;</span>
|
|
|
361 348
|
|
|
362 349 <span class="c"># Calculate DeltaIState matrix values...</span>
|
|
|
363 350 <span class="j">ROWINDEX:</span> <span class="k">for</span> <span class="i">$RowIndex</span> <span class="s">(</span><span class="n">0</span> .. <span class="s">(</span><span class="i">$NumOfRows</span> - <span class="n">1</span><span class="s">)</span> <span class="s">)</span> <span class="s">{</span>
|
|
|
364 351 <span class="i">$AtomID1</span> = <span class="i">$This</span>->{<span class="w">AtomIndexToID</span>}{<span class="i">$RowIndex</span>}<span class="sc">;</span>
|
|
|
365 352 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span><span class="s">(</span><span class="i">$This</span>->{<span class="w">IStateValues</span>}{<span class="i">$AtomID1</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
366 353 <span class="k">next</span> <span class="j">ROWINDEX</span><span class="sc">;</span>
|
|
|
367 354 <span class="s">}</span>
|
|
|
368 355 <span class="i">$IStateValue1</span> = <span class="i">$This</span>->{<span class="w">IStateValues</span>}{<span class="i">$AtomID1</span>}<span class="sc">;</span>
|
|
|
369 356
|
|
|
370 357 <span class="j">COLINDEX:</span> <span class="k">for</span> <span class="i">$ColIndex</span> <span class="s">(</span><span class="s">(</span><span class="i">$RowIndex</span> + <span class="n">1</span><span class="s">)</span> .. <span class="s">(</span><span class="i">$NumOfCols</span> - <span class="n">1</span><span class="s">)</span> <span class="s">)</span> <span class="s">{</span>
|
|
|
371 358 <span class="i">$AtomID2</span> = <span class="i">$This</span>->{<span class="w">AtomIndexToID</span>}{<span class="i">$ColIndex</span>}<span class="sc">;</span>
|
|
|
372 359 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span><span class="s">(</span><span class="i">$This</span>->{<span class="w">IStateValues</span>}{<span class="i">$AtomID2</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
373 360 <span class="k">next</span> <span class="j">COLINDEX</span><span class="sc">;</span>
|
|
|
374 361 <span class="s">}</span>
|
|
|
375 362 <span class="i">$IStateValue2</span> = <span class="i">$This</span>->{<span class="w">IStateValues</span>}{<span class="i">$AtomID2</span>}<span class="sc">;</span>
|
|
|
376 363
|
|
|
377 364 <span class="c"># Make sure it's a connected atom...</span>
|
|
|
378 365 <span class="i">$GraphDistance</span> = <span class="i">$DistanceMatrix</span><span class="i">->GetValue</span><span class="s">(</span><span class="i">$RowIndex</span><span class="cm">,</span> <span class="i">$ColIndex</span><span class="cm">,</span> <span class="i">$SkipIndexCheck</span><span class="s">)</span><span class="sc">;</span>
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379 366 <span class="k">if</span> <span class="s">(</span><span class="i">$GraphDistance</span> >= <span class="w">BigNumber</span><span class="s">)</span> <span class="s">{</span>
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380 367 <span class="k">next</span> <span class="j">COLINDEX</span><span class="sc">;</span>
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381 368 <span class="s">}</span>
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382 369
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383 370 <span class="i">$DeltaIState12</span> = <span class="s">(</span><span class="i">$IStateValue1</span> - <span class="i">$IStateValue2</span><span class="s">)</span>/<span class="s">(</span><span class="s">(</span><span class="i">$GraphDistance</span> + <span class="n">1</span><span class="s">)</span>**<span class="n">2</span><span class="s">)</span><span class="sc">;</span>
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384 371 <span class="i">$DeltaIState21</span> = -<span class="i">$DeltaIState12</span><span class="sc">;</span>
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385 372
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386 373 <span class="c"># Set DeltaIState values...</span>
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387 374 <span class="i">$DeltaIStateMatrix</span><span class="i">->SetValue</span><span class="s">(</span><span class="i">$RowIndex</span><span class="cm">,</span> <span class="i">$ColIndex</span><span class="cm">,</span> <span class="i">$DeltaIState12</span><span class="cm">,</span> <span class="i">$SkipIndexCheck</span><span class="s">)</span><span class="sc">;</span>
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388 375 <span class="i">$DeltaIStateMatrix</span><span class="i">->SetValue</span><span class="s">(</span><span class="i">$ColIndex</span><span class="cm">,</span> <span class="i">$RowIndex</span><span class="cm">,</span> <span class="i">$DeltaIState21</span><span class="cm">,</span> <span class="i">$SkipIndexCheck</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="s">}</span>
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391 378 <span class="s">}</span>
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392 379
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393 380 <span class="c"># Setup distance matrix...</span>
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394 381 <span class="c">#</span>
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395 <a name="_SetupDistanceMatrix-"></a> 382 <span class="k">sub </span><span class="m">_SetupDistanceMatrix</span> <span class="s">{</span>
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396 383 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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397 384
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398 385 <span class="i">$This</span>->{<span class="w">DistanceMatrix</span>} = <span class="i">$This</span><span class="i">->GetMolecule</span><span class="s">(</span><span class="s">)</span><span class="i">->GetDistanceMatrix</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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399 386
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400 387 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span><span class="s">(</span><span class="i">$This</span>->{<span class="w">DistanceMatrix</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
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401 388 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
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402 389 <span class="s">}</span>
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403 390
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404 391 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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405 392 <span class="s">}</span>
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406 393
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407 394 <span class="c"># Setup final descriptor values...</span>
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408 395 <span class="c">#</span>
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409 <a name="_SetFinalValues-"></a> 396 <span class="k">sub </span><span class="m">_SetFinalValues</span> <span class="s">{</span>
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410 397 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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411 398 <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">$EStateValue</span><span class="s">)</span><span class="sc">;</span>
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412 399
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413 400 <span class="j">ATOM:</span> <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$This</span>->{<span class="w">Atoms</span>}}<span class="s">)</span> <span class="s">{</span>
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414 401 <span class="i">$AtomID</span> = <span class="i">$Atom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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415 402 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$This</span>->{<span class="w">EStateValues</span>}{<span class="i">$AtomID</span>}<span class="s">)</span> <span class="s">{</span>
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416 403 <span class="k">next</span> <span class="j">ATOM</span><span class="sc">;</span>
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|
417 404 <span class="s">}</span>
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|
418 405 <span class="i">$EStateValue</span> = <span class="i">$This</span>->{<span class="w">EStateValues</span>}{<span class="i">$AtomID</span>}<span class="sc">;</span>
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419 406 <span class="i">$This</span><span class="i">->SetDescriptorValue</span><span class="s">(</span><span class="i">$Atom</span><span class="cm">,</span> <span class="i">$EStateValue</span><span class="s">)</span><span class="sc">;</span>
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420 407 <span class="s">}</span>
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421 408
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|
422 409 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
423 410 <span class="s">}</span>
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424 411
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|
425 412 <span class="c"># Cache appropriate molecule data...</span>
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|
426 413 <span class="c">#</span>
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|
427 <a name="_SetupMoleculeDataCache-"></a> 414 <span class="k">sub </span><span class="m">_SetupMoleculeDataCache</span> <span class="s">{</span>
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428 415 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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|
429 416
|
|
|
430 417 <span class="c"># Get all atoms including hydrogens to correctly map atom indicies to atom IDs for</span>
|
|
|
431 418 <span class="c"># usage of distance matrix.</span>
|
|
|
432 419 <span class="c">#</span>
|
|
|
433 420 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">Atoms</span>}} = <span class="i">$This</span><span class="i">->GetMolecule</span><span class="s">(</span><span class="s">)</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
434 421
|
|
|
435 422 <span class="c"># Get all atom IDs...</span>
|
|
|
436 423 <span class="k">my</span><span class="s">(</span><span class="i">@AtomIDs</span><span class="s">)</span><span class="sc">;</span>
|
|
|
437 424 <span class="i">@AtomIDs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
438 425 <span class="i">@AtomIDs</span> = <span class="k">map</span> <span class="s">{</span> <span class="i">$_</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span> <span class="s">}</span> <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">Atoms</span>}}<span class="sc">;</span>
|
|
|
439 426
|
|
|
440 427 <span class="c"># Set AtomIndex to AtomID hash...</span>
|
|
|
441 428 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">AtomIndexToID</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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|
|
442 429 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomIndexToID</span>}}{ <span class="s">(</span><span class="n">0</span> .. <span class="i">$#AtomIDs</span><span class="s">)</span> } = <span class="i">@AtomIDs</span><span class="sc">;</span>
|
|
|
443 430
|
|
|
444 431 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
445 432 <span class="s">}</span>
|
|
|
446 433
|
|
|
447 434 <span class="c"># Clear cached molecule data...</span>
|
|
|
448 435 <span class="c">#</span>
|
|
|
449 <a name="_ClearMoleculeDataCache-"></a> 436 <span class="k">sub </span><span class="m">_ClearMoleculeDataCache</span> <span class="s">{</span>
|
|
|
450 437 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
451 438
|
|
|
452 439 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">Atoms</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
453 440
|
|
|
454 441 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
455 442 <span class="s">}</span>
|
|
|
456 443
|
|
|
457 444 <span class="c"># Return a string containg data for EStateValuesDescriptors object...</span>
|
|
|
458 445 <span class="c">#</span>
|
|
|
459 <a name="StringifyEStateValuesDescriptors-"></a> 446 <span class="k">sub </span><span class="m">StringifyEStateValuesDescriptors</span> <span class="s">{</span>
|
|
|
460 447 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
461 448 <span class="k">my</span><span class="s">(</span><span class="i">$EStateValuesDescriptorsString</span><span class="s">)</span><span class="sc">;</span>
|
|
|
462 449
|
|
|
463 450 <span class="c"># Type of AtomicValues...</span>
|
|
|
464 451 <span class="i">$EStateValuesDescriptorsString</span> = <span class="q">"AtomicDescriptorType: $This->{Type}; IgnoreHydrogens: "</span> . <span class="s">(</span><span class="i">$This</span>->{<span class="w">IgnoreHydrogens</span>} ? <span class="q">"Yes"</span> <span class="co">:</span> <span class="q">"No"</span><span class="s">)</span><span class="sc">;</span>
|
|
|
465 452
|
|
|
466 453 <span class="c"># Setup atomic descriptor information...</span>
|
|
|
467 454 <span class="k">my</span><span class="s">(</span><span class="i">$AtomID</span><span class="cm">,</span> <span class="i">$DescriptorValue</span><span class="cm">,</span> <span class="i">@DescriptorValuesInfo</span><span class="cm">,</span> <span class="i">%DescriptorValues</span><span class="s">)</span><span class="sc">;</span>
|
|
|
468 455
|
|
|
469 456 <span class="i">@DescriptorValuesInfo</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
470 457 <span class="i">%DescriptorValues</span> = <span class="i">$This</span><span class="i">->GetDescriptorValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
471 458
|
|
|
472 459 <span class="k">for</span> <span class="i">$AtomID</span> <span class="s">(</span><span class="k">sort</span> <span class="s">{</span> <span class="i">$a</span> <=> <span class="i">$b</span> <span class="s">}</span> <span class="k">keys</span> <span class="i">%DescriptorValues</span><span class="s">)</span> <span class="s">{</span>
|
|
|
473 460 <span class="i">$DescriptorValue</span> = <span class="i">$DescriptorValues</span>{<span class="i">$AtomID</span>}<span class="sc">;</span>
|
|
|
474 461 <span class="i">$DescriptorValue</span> = <span class="s">(</span><span class="i">TextUtil::IsEmpty</span><span class="s">(</span><span class="i">$DescriptorValue</span><span class="s">)</span> || <span class="i">$DescriptorValue</span> =~ <span class="q">/^None$/i</span><span class="s">)</span> ? <span class="q">'None'</span> <span class="co">:</span> <span class="i">MathUtil::round</span><span class="s">(</span><span class="i">$DescriptorValue</span><span class="cm">,</span> <span class="n">3</span><span class="s">)</span> + <span class="n">0</span><span class="sc">;</span>
|
|
|
475 462 <span class="k">push</span> <span class="i">@DescriptorValuesInfo</span><span class="cm">,</span> <span class="q">"$AtomID:$DescriptorValue"</span><span class="sc">;</span>
|
|
|
476 463 <span class="s">}</span>
|
|
|
477 464 <span class="i">$EStateValuesDescriptorsString</span> .= <span class="q">"; AtomIDs:EStateValuesDescriptors: <"</span> . <span class="i">TextUtil::JoinWords</span><span class="s">(</span>\<span class="i">@DescriptorValuesInfo</span><span class="cm">,</span> <span class="q">", "</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span> . <span class="q">">"</span><span class="sc">;</span>
|
|
|
478 465
|
|
|
479 466 <span class="k">return</span> <span class="i">$EStateValuesDescriptorsString</span><span class="sc">;</span>
|
|
|
480 467 <span class="s">}</span>
|
|
|
481 468
|
|
|
482 469 <span class="c"># Is it a EStateValuesDescriptors object?</span>
|
|
|
483 <a name="_IsEStateValuesDescriptors-"></a> 470 <span class="k">sub </span><span class="m">_IsEStateValuesDescriptors</span> <span class="s">{</span>
|
|
|
484 471 <span class="k">my</span><span class="s">(</span><span class="i">$Object</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
485 472
|
|
|
486 473 <span class="k">return</span> <span class="s">(</span><span class="i">Scalar::Util::blessed</span><span class="s">(</span><span class="i">$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>
|
|
|
487 474 <span class="s">}</span>
|
|
|
488 475
|
|
|
489 <a name="EOF-"></a></pre>
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490 <p> </p>
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491 <br />
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492 <center>
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493 <img src="../../../images/h2o2.png">
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494 </center>
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495 </body>
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496 </html>
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