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13 <pre>
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14 <a name="package-MolecularDescriptors::TPSADescriptors-"></a> 1 <span class="k">package </span><span class="i">MolecularDescriptors::TPSADescriptors</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: TPSADescriptors.pm,v $</span>
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17 4 <span class="c"># $Date: 2015/02/28 20:49:20 $</span>
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18 5 <span class="c"># $Revision: 1.18 $</span>
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19 6 <span class="c">#</span>
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20 7 <span class="c"># Author: Manish Sud <msud@san.rr.com></span>
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21 8 <span class="c">#</span>
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22 9 <span class="c"># Copyright (C) 2015 Manish Sud. All rights reserved.</span>
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23 10 <span class="c">#</span>
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24 11 <span class="c"># This file is part of MayaChemTools.</span>
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25 12 <span class="c">#</span>
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26 13 <span class="c"># MayaChemTools is free software; you can redistribute it and/or modify it under</span>
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27 14 <span class="c"># the terms of the GNU Lesser General Public License as published by the Free</span>
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28 15 <span class="c"># Software Foundation; either version 3 of the License, or (at your option) any</span>
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29 16 <span class="c"># later version.</span>
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30 17 <span class="c">#</span>
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31 18 <span class="c"># MayaChemTools is distributed in the hope that it will be useful, but without</span>
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32 19 <span class="c"># any warranty; without even the implied warranty of merchantability of fitness</span>
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33 20 <span class="c"># for a particular purpose. See the GNU Lesser General Public License for more</span>
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34 21 <span class="c"># details.</span>
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35 22 <span class="c">#</span>
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36 23 <span class="c"># You should have received a copy of the GNU Lesser General Public License</span>
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37 24 <span class="c"># along with MayaChemTools; if not, see <http://www.gnu.org/licenses/> or</span>
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38 25 <span class="c"># write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,</span>
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39 26 <span class="c"># Boston, MA, 02111-1307, USA.</span>
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40 27 <span class="c">#</span>
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41 28
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42 29 <span class="k">use</span> <span class="w">strict</span><span class="sc">;</span>
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43 30 <span class="k">use</span> <span class="w">Carp</span><span class="sc">;</span>
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44 31 <span class="k">use</span> <span class="w">Exporter</span><span class="sc">;</span>
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45 32 <span class="k">use</span> <span class="w">Scalar::Util</span> <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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46 33 <span class="k">use</span> <span class="w">TextUtil</span> <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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47 34 <span class="k">use</span> <span class="w">MathUtil</span> <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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48 35 <span class="k">use</span> <span class="w">Atom</span><span class="sc">;</span>
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49 36 <span class="k">use</span> <span class="w">Molecule</span><span class="sc">;</span>
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50 37 <span class="k">use</span> <span class="w">MolecularDescriptors::MolecularDescriptors</span><span class="sc">;</span>
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51 38 <span class="k">use</span> <span class="w">AtomTypes::TPSAAtomTypes</span><span class="sc">;</span>
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52 39
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53 40 <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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54 41
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55 42 <span class="i">@ISA</span> = <span class="q">qw(MolecularDescriptors::MolecularDescriptors Exporter)</span><span class="sc">;</span>
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56 43 <span class="i">@EXPORT</span> = <span class="q">qw()</span><span class="sc">;</span>
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57 44 <span class="i">@EXPORT_OK</span> = <span class="q">qw(GetDescriptorNames)</span><span class="sc">;</span>
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58 45
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59 46 <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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60 47
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61 48 <span class="c"># Setup class variables...</span>
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62 49 <span class="k">my</span><span class="s">(</span><span class="i">$ClassName</span><span class="cm">,</span> <span class="i">@DescriptorNames</span><span class="s">)</span><span class="sc">;</span>
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63 50 <span class="i">_InitializeClass</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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64 51
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65 52 <span class="c"># Overload Perl functions...</span>
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66 53 <span class="k">use</span> <span class="w">overload</span> <span class="q">'""'</span> <span class="cm">=></span> <span class="q">'StringifyTPSADescriptors'</span><span class="sc">;</span>
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67 54
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68 55 <span class="c"># Class constructor...</span>
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69 <a name="new-"></a> 56 <span class="k">sub </span><span class="m">new</span> <span class="s">{</span>
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70 57 <span class="k">my</span><span class="s">(</span><span class="i">$Class</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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71 58
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72 59 <span class="c"># Initialize object...</span>
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73 60 <span class="k">my</span> <span class="i">$This</span> = <span class="i">$Class</span><span class="i">->SUPER::new</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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74 61 <span class="k">bless</span> <span class="i">$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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75 62 <span class="i">$This</span><span class="i">->_InitializeTPSADescriptors</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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76 63
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77 64 <span class="i">$This</span><span class="i">->_InitializeTPSADescriptorsProperties</span><span class="s">(</span><span class="i">%NamesAndValues</span><span class="s">)</span><span class="sc">;</span>
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78 65
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79 66 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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80 67 <span class="s">}</span>
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81 68
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82 69 <span class="c"># Initialize class ...</span>
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83 <a name="_InitializeClass-"></a> 70 <span class="k">sub </span><span class="m">_InitializeClass</span> <span class="s">{</span>
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84 71 <span class="c">#Class name...</span>
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85 72 <span class="i">$ClassName</span> = <span class="w">__PACKAGE__</span><span class="sc">;</span>
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86 73
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87 74 <span class="c"># Descriptor names...</span>
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88 75 <span class="i">@DescriptorNames</span> = <span class="s">(</span><span class="q">'TPSA'</span><span class="s">)</span><span class="sc">;</span>
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89 76
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90 77 <span class="s">}</span>
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91 78
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92 79 <span class="c"># Get descriptor names as an array.</span>
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93 80 <span class="c">#</span>
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94 81 <span class="c"># This functionality can be either invoked as a class function or an</span>
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95 82 <span class="c"># object method.</span>
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96 83 <span class="c">#</span>
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97 <a name="GetDescriptorNames-"></a> 84 <span class="k">sub </span><span class="m">GetDescriptorNames</span> <span class="s">{</span>
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98 85 <span class="k">return</span> <span class="i">@DescriptorNames</span><span class="sc">;</span>
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99 86 <span class="s">}</span>
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100 87
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101 88 <span class="c"># Initialize object data...</span>
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102 89 <span class="c">#</span>
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103 <a name="_InitializeTPSADescriptors-"></a> 90 <span class="k">sub </span><span class="m">_InitializeTPSADescriptors</span> <span class="s">{</span>
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104 91 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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105 92
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106 93 <span class="c"># Type of MolecularDescriptor...</span>
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107 94 <span class="i">$This</span>->{<span class="w">Type</span>} = <span class="q">'TPSA'</span><span class="sc">;</span>
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108 95
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109 96 <span class="c"># By default, TPSA atom contributions from Phosphorus and Sulfur atoms</span>
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110 97 <span class="c"># are not included during TPSA calculations. [ Ref 91 ]</span>
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111 98 <span class="c">#</span>
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112 99 <span class="i">$This</span>->{<span class="w">IgnorePhosphorus</span>} = <span class="n">1</span><span class="sc">;</span>
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113 100 <span class="i">$This</span>->{<span class="w">IgnoreSulfur</span>} = <span class="n">1</span><span class="sc">;</span>
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114 101
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115 102 <span class="c"># TPSA atom types assigned to appropriate atoms...</span>
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116 103 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">AtomTypes</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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117 104
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118 105 <span class="c"># Intialize descriptor names and values...</span>
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119 106 <span class="i">$This</span><span class="i">->_InitializeDescriptorNamesAndValues</span><span class="s">(</span><span class="i">@DescriptorNames</span><span class="s">)</span><span class="sc">;</span>
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120 107
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121 108 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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122 109 <span class="s">}</span>
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123 110
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124 111 <span class="c"># Initialize object properties...</span>
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125 112 <span class="c">#</span>
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126 <a name="_InitializeTPSADescriptorsProperties-"></a> 113 <span class="k">sub </span><span class="m">_InitializeTPSADescriptorsProperties</span> <span class="s">{</span>
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127 114 <span class="k">my</span><span class="s">(</span><span class="i">$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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128 115
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129 116 <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">$MethodName</span><span class="s">)</span><span class="sc">;</span>
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130 117 <span class="k">while</span> <span class="s">(</span><span class="s">(</span><span class="i">$Name</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="k">each</span> <span class="i">%NamesAndValues</span><span class="s">)</span> <span class="s">{</span>
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131 118 <span class="i">$MethodName</span> = <span class="q">"Set${Name}"</span><span class="sc">;</span>
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132 119 <span class="i">$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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133 120 <span class="s">}</span>
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134 121
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135 122 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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136 123 <span class="s">}</span>
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137 124
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138 125 <span class="c"># Calculate Topological Polar Surface Area (TPSA) value [ Ref 90-91 ] for molecule...</span>
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139 126 <span class="c">#</span>
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140 127 <span class="c"># Methodology:</span>
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141 128 <span class="c"># . Assign TPSA atom types [ Ref 90-91 ] to Nitrogen and Oxygen</span>
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142 129 <span class="c"># atoms with optional assignment to Phosphorus and Sulfur atoms.</span>
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143 130 <span class="c"># . Calculate TPSA value adding contribution of appropriate atom types.</span>
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144 131 <span class="c">#</span>
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145 <a name="GenerateDescriptors-"></a> 132 <span class="k">sub </span><span class="m">GenerateDescriptors</span> <span class="s">{</span>
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146 133 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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147 134
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148 135 <span class="c"># Initialize descriptor values...</span>
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149 136 <span class="i">$This</span><span class="i">->_InitializeDescriptorValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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150 137
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151 138 <span class="c"># Check availability of molecule...</span>
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152 139 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="s">)</span> <span class="s">{</span>
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153 140 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->GenerateDescriptors: $This->{Type} molecular descriptors generation didn't succeed: Molecule data is not available: Molecule object hasn't been set..."</span><span class="sc">;</span>
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154 141 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
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155 142 <span class="s">}</span>
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156 143
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157 144 <span class="c"># Cache appropriate molecule data...</span>
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158 145 <span class="i">$This</span><span class="i">->_SetupMoleculeDataCache</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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159 146
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160 147 <span class="c"># Assign TPSA atom types...</span>
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161 148 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->_AssignAtomTypes</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
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162 149 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->GenerateDescriptors: $This->{Type} molecular descriptors generation didn't succeed: Couldn't assign valid TPSA atom types to appropriate atoms..."</span><span class="sc">;</span>
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163 150 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
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164 151 <span class="s">}</span>
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165 152
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166 153 <span class="c"># Calculate descriptor values...</span>
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167 154 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->_CalculateDescriptorValues</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
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168 155 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->GenerateDescriptors: $This->{Type} molecular descriptors generation didn't succeed: Couldn't calculate TPSA values corresponding to assigned TPSA atom types..."</span><span class="sc">;</span>
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169 156 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
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170 157 <span class="s">}</span>
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171 158
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172 159 <span class="c"># Set final descriptor values...</span>
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173 160 <span class="i">$This</span><span class="i">->_SetFinalDescriptorValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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174 161
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175 162 <span class="c"># Clear cached molecule data...</span>
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176 163 <span class="i">$This</span><span class="i">->_ClearMoleculeDataCache</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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177 164
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178 165 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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179 166 <span class="s">}</span>
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180 167
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181 168 <span class="c"># Assign TPSA atom types..</span>
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182 169 <span class="c">#</span>
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183 <a name="_AssignAtomTypes-"></a> 170 <span class="k">sub </span><span class="m">_AssignAtomTypes</span> <span class="s">{</span>
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184 171 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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185 172 <span class="k">my</span><span class="s">(</span><span class="i">$TPSAAtomTypes</span><span class="cm">,</span> <span class="i">$Atom</span><span class="cm">,</span> <span class="i">$AtomID</span><span class="s">)</span><span class="sc">;</span>
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186 173
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187 174 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">AtomTypes</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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188 175
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189 176 <span class="c"># Assign atom types...</span>
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190 177 <span class="i">$TPSAAtomTypes</span> = <span class="i">new</span> <span class="i">AtomTypes::TPSAAtomTypes</span><span class="s">(</span><span class="q">'Molecule'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="cm">,</span> <span class="q">'IgnorePhosphorus'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">IgnorePhosphorus</span>}<span class="cm">,</span> <span class="q">'IgnoreSulfur'</span> <span class="cm">=></span> <span class="i">$This</span>->{<span class="w">IgnoreSulfur</span>}<span class="s">)</span><span class="sc">;</span>
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191 178 <span class="i">$TPSAAtomTypes</span><span class="i">->AssignAtomTypes</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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192 179
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193 180 <span class="c"># Make sure TPSA atom types assignment is successful...</span>
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194 181 <span class="k">if</span> <span class="s">(</span>!<span class="i">$TPSAAtomTypes</span><span class="i">->IsAtomTypesAssignmentSuccessful</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
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195 182 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
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196 183 <span class="s">}</span>
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197 184
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198 185 <span class="c"># Collect assigned atom types...</span>
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199 186 <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$This</span>->{<span class="w">Atoms</span>}}<span class="s">)</span> <span class="s">{</span>
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200 187 <span class="i">$AtomID</span> = <span class="i">$Atom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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201 188 <span class="i">$This</span>->{<span class="w">AtomTypes</span>}{<span class="i">$AtomID</span>} = <span class="i">$TPSAAtomTypes</span><span class="i">->GetAtomType</span><span class="s">(</span><span class="i">$Atom</span><span class="s">)</span><span class="sc">;</span>
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202 189 <span class="s">}</span>
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203 190
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204 191 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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205 192 <span class="s">}</span>
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206 193
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207 194 <span class="c"># Calculate TPSA value...</span>
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208 195 <span class="c">#</span>
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209 <a name="_CalculateDescriptorValues-"></a> 196 <span class="k">sub </span><span class="m">_CalculateDescriptorValues</span> <span class="s">{</span>
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210 197 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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211 198 <span class="k">my</span><span class="s">(</span><span class="i">$Atom</span><span class="cm">,</span> <span class="i">$AtomID</span><span class="cm">,</span> <span class="i">$TPSA</span><span class="cm">,</span> <span class="i">$TPSAContribution</span><span class="cm">,</span> <span class="i">$TPSADataRef</span><span class="cm">,</span> <span class="i">$AtomType</span><span class="s">)</span><span class="sc">;</span>
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212 199
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213 200 <span class="i">$TPSA</span> = <span class="n">0</span><span class="sc">;</span>
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214 201
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215 202 <span class="c"># Get TPSA atom types data...</span>
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216 203 <span class="i">$TPSADataRef</span> = <span class="i">AtomTypes::TPSAAtomTypes::GetTPSAAtomTypesData</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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217 204
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218 205 <span class="j">ATOM:</span> <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$This</span>->{<span class="w">Atoms</span>}}<span class="s">)</span> <span class="s">{</span>
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219 206 <span class="i">$AtomID</span> = <span class="i">$Atom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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220 207 <span class="i">$AtomType</span> = <span class="i">$This</span>->{<span class="w">AtomTypes</span>}{<span class="i">$AtomID</span>}<span class="sc">;</span>
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221 208
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222 209 <span class="c"># Ignore inappropriate atoms...</span>
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223 210 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomType</span> =~ <span class="q">/^None$/i</span><span class="s">)</span> <span class="s">{</span>
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224 211 <span class="k">next</span> <span class="j">ATOM</span><span class="sc">;</span>
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225 212 <span class="s">}</span>
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226 213
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227 214 <span class="i">$TPSAContribution</span> = <span class="n">0.0</span><span class="sc">;</span>
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228 215
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229 216 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomType</span> =~ <span class="q">/^(N|O)$/i</span><span class="s">)</span> <span class="s">{</span>
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230 217 <span class="c"># TPSA contributions for Nitrogen and Oxygen atoms not explicity defined using atom</span>
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231 218 <span class="c"># environments in Table 1 [ Ref 90 ]</span>
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232 219 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomType</span> =~ <span class="q">/^N$/i</span><span class="s">)</span> <span class="s">{</span>
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233 220 <span class="c"># N = 30.5 - X*8.2 + H*1.5 or 0.0 for negative value</span>
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234 221 <span class="i">$TPSAContribution</span> = <span class="n">30.5</span> - <span class="i">$Atom</span><span class="i">->GetAtomicInvariantValue</span><span class="s">(</span><span class="q">'X'</span><span class="s">)</span> * <span class="n">8.2</span> + <span class="i">$Atom</span><span class="i">->GetAtomicInvariantValue</span><span class="s">(</span><span class="q">'H'</span><span class="s">)</span> * <span class="n">1.5</span><span class="sc">;</span>
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235 222 <span class="s">}</span>
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236 223 <span class="k">elsif</span> <span class="s">(</span><span class="i">$AtomType</span> =~ <span class="q">/^O$/i</span><span class="s">)</span> <span class="s">{</span>
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237 224 <span class="c"># O = 28.5 - X*8.6 + H*1.5 or 0.0 for negative value</span>
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238 225 <span class="i">$TPSAContribution</span> = <span class="n">28.5</span> - <span class="i">$Atom</span><span class="i">->GetAtomicInvariantValue</span><span class="s">(</span><span class="q">'X'</span><span class="s">)</span> * <span class="n">8.6</span> + <span class="i">$Atom</span><span class="i">->GetAtomicInvariantValue</span><span class="s">(</span><span class="q">'H'</span><span class="s">)</span> * <span class="n">1.5</span><span class="sc">;</span>
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239 226 <span class="s">}</span>
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240 227 <span class="k">if</span> <span class="s">(</span><span class="i">$TPSAContribution</span> < <span class="n">0.0</span><span class="s">)</span> <span class="s">{</span>
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241 228 <span class="i">$TPSAContribution</span> = <span class="n">0.0</span><span class="sc">;</span>
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242 229 <span class="s">}</span>
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243 230 <span class="s">}</span>
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244 231 <span class="k">elsif</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$TPSADataRef</span>->{<span class="w">DataCol3</span>}{<span class="i">$AtomType</span>}<span class="s">)</span> <span class="s">{</span>
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245 232 <span class="c"># Data for TPSA contribution is in column number 3...</span>
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246 233 <span class="i">$TPSAContribution</span> = <span class="i">$TPSADataRef</span>->{<span class="w">DataCol3</span>}{<span class="i">$AtomType</span>}<span class="sc">;</span>
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247 234 <span class="s">}</span>
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248 235 <span class="k">else</span> <span class="s">{</span>
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249 236 <span class="c"># No TPSA data for assigned atom type...</span>
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250 237 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
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251 238 <span class="s">}</span>
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252 239 <span class="i">$TPSA</span> += <span class="i">$TPSAContribution</span><span class="sc">;</span>
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253 240 <span class="s">}</span>
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254 241
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255 242 <span class="c"># Track the calculated values...</span>
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256 243 <span class="i">$This</span>->{<span class="w">TPSA</span>} = <span class="i">MathUtil::round</span><span class="s">(</span><span class="i">$TPSA</span><span class="cm">,</span> <span class="n">2</span><span class="s">)</span><span class="sc">;</span>
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257 244
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258 245 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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259 246 <span class="s">}</span>
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260 247
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261 248 <span class="c"># Setup final descriptor values...</span>
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262 249 <span class="c">#</span>
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263 <a name="_SetFinalDescriptorValues-"></a> 250 <span class="k">sub </span><span class="m">_SetFinalDescriptorValues</span> <span class="s">{</span>
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264 251 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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265 252
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266 253 <span class="i">$This</span>->{<span class="w">DescriptorsGenerated</span>} = <span class="n">1</span><span class="sc">;</span>
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267 254
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268 255 <span class="i">$This</span><span class="i">->SetDescriptorValues</span><span class="s">(</span><span class="i">$This</span>->{<span class="w">TPSA</span>}<span class="s">)</span><span class="sc">;</span>
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269 256
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270 257 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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271 258 <span class="s">}</span>
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272 259
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273 260 <span class="c"># Cache appropriate molecule data...</span>
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274 261 <span class="c">#</span>
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275 <a name="_SetupMoleculeDataCache-"></a> 262 <span class="k">sub </span><span class="m">_SetupMoleculeDataCache</span> <span class="s">{</span>
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276 263 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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277 264
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278 265 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">Atoms</span>}} = <span class="i">$This</span><span class="i">->GetMolecule</span><span class="s">(</span><span class="s">)</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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279 266
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280 267 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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281 268 <span class="s">}</span>
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282 269
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283 270 <span class="c"># Clear cached molecule data...</span>
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284 271 <span class="c">#</span>
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285 <a name="_ClearMoleculeDataCache-"></a> 272 <span class="k">sub </span><span class="m">_ClearMoleculeDataCache</span> <span class="s">{</span>
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286 273 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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287 274
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288 275 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">Atoms</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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289 276
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290 277 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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291 278 <span class="s">}</span>
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292 279
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293 280 <span class="c"># Return a string containg data for TPSADescriptors object...</span>
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294 281 <span class="c">#</span>
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295 <a name="StringifyTPSADescriptors-"></a> 282 <span class="k">sub </span><span class="m">StringifyTPSADescriptors</span> <span class="s">{</span>
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296 283 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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297 284 <span class="k">my</span><span class="s">(</span><span class="i">$TPSADescriptorsString</span><span class="s">)</span><span class="sc">;</span>
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298 285
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299 286 <span class="c"># Type of MolecularDescriptors...</span>
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300 287 <span class="i">$TPSADescriptorsString</span> = <span class="q">"MolecularDescriptorType: $This->{Type}; IgnorePhosphorus: "</span> . <span class="s">(</span><span class="i">$This</span>->{<span class="w">IgnorePhosphorus</span>} ? <span class="q">"Yes"</span> <span class="co">:</span> <span class="q">"No"</span><span class="s">)</span> . <span class="q">"; IgnoreSulfur: "</span> . <span class="s">(</span><span class="i">$This</span>->{<span class="w">IgnoreSulfur</span>} ? <span class="q">"Yes"</span> <span class="co">:</span> <span class="q">"No"</span><span class="s">)</span><span class="sc">;</span>
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301 288
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|
302 289 <span class="c"># Setup molecular descriptor information...</span>
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303 290 <span class="i">$TPSADescriptorsString</span> .= <span class="q">"; "</span> . <span class="i">$This</span><span class="i">->_StringifyDescriptorNamesAndValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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304 291
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305 292 <span class="k">return</span> <span class="i">$TPSADescriptorsString</span><span class="sc">;</span>
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|
306 293 <span class="s">}</span>
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307 294
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308 295 <span class="c"># Is it a TPSADescriptors object?</span>
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309 <a name="_IsTPSADescriptors-"></a> 296 <span class="k">sub </span><span class="m">_IsTPSADescriptors</span> <span class="s">{</span>
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310 297 <span class="k">my</span><span class="s">(</span><span class="i">$Object</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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311 298
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312 299 <span class="k">return</span> <span class="s">(</span><span class="i">Scalar::Util::blessed</span><span class="s">(</span><span class="i">$Object</span><span class="s">)</span> && <span class="i">$Object</span><span class="i">->isa</span><span class="s">(</span><span class="i">$ClassName</span><span class="s">)</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
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313 300 <span class="s">}</span>
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314 301
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315 <a name="EOF-"></a></pre>
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316 <p> </p>
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317 <br />
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318 <center>
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319 <img src="../../../images/h2o2.png">
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320 </center>
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321 </body>
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322 </html>
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