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13 <pre>
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14 <a name="package-MolecularDescriptors::RotatableBondsDescriptors-"></a> 1 <span class="k">package </span><span class="i">MolecularDescriptors::RotatableBondsDescriptors</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: RotatableBondsDescriptors.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">Atom</span><span class="sc">;</span>
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48 35 <span class="k">use</span> <span class="w">Molecule</span><span class="sc">;</span>
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49 36 <span class="k">use</span> <span class="w">MolecularDescriptors::MolecularDescriptors</span><span class="sc">;</span>
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50 37
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51 38 <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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52 39
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53 40 <span class="i">@ISA</span> = <span class="q">qw(MolecularDescriptors::MolecularDescriptors Exporter)</span><span class="sc">;</span>
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54 41 <span class="i">@EXPORT</span> = <span class="q">qw()</span><span class="sc">;</span>
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55 42 <span class="i">@EXPORT_OK</span> = <span class="q">qw(GetDescriptorNames)</span><span class="sc">;</span>
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56 43
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57 44 <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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58 45
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59 46 <span class="c"># Setup class variables...</span>
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60 47 <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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61 48 <span class="i">_InitializeClass</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"># Overload Perl functions...</span>
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64 51 <span class="k">use</span> <span class="w">overload</span> <span class="q">'""'</span> <span class="cm">=></span> <span class="q">'StringifyRotatableBondsDescriptors'</span><span class="sc">;</span>
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65 52
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66 53 <span class="c"># Class constructor...</span>
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67 <a name="new-"></a> 54 <span class="k">sub </span><span class="m">new</span> <span class="s">{</span>
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68 55 <span class="k">my</span><span class="s">(</span><span class="i">$Class</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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69 56
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70 57 <span class="c"># Initialize object...</span>
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71 58 <span class="k">my</span> <span class="i">$This</span> = <span class="i">$Class</span><span class="i">->SUPER::new</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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72 59 <span class="k">bless</span> <span class="i">$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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73 60 <span class="i">$This</span><span class="i">->_InitializeRotatableBondsDescriptors</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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74 61
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75 62 <span class="i">$This</span><span class="i">->_InitializeRotatableBondsDescriptorsProperties</span><span class="s">(</span><span class="i">%NamesAndValues</span><span class="s">)</span><span class="sc">;</span>
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76 63
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77 64 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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78 65 <span class="s">}</span>
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79 66
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80 67 <span class="c"># Initialize class ...</span>
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81 <a name="_InitializeClass-"></a> 68 <span class="k">sub </span><span class="m">_InitializeClass</span> <span class="s">{</span>
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82 69 <span class="c">#Class name...</span>
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83 70 <span class="i">$ClassName</span> = <span class="w">__PACKAGE__</span><span class="sc">;</span>
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84 71
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85 72 <span class="c"># Descriptor names...</span>
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86 73 <span class="i">@DescriptorNames</span> = <span class="s">(</span><span class="q">'RotatableBonds'</span><span class="s">)</span><span class="sc">;</span>
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87 74
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88 75 <span class="s">}</span>
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89 76
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90 77 <span class="c"># Get descriptor names as an array.</span>
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91 78 <span class="c">#</span>
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92 79 <span class="c"># This functionality can be either invoked as a class function or an</span>
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93 80 <span class="c"># object method.</span>
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94 81 <span class="c">#</span>
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95 <a name="GetDescriptorNames-"></a> 82 <span class="k">sub </span><span class="m">GetDescriptorNames</span> <span class="s">{</span>
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96 83 <span class="k">return</span> <span class="i">@DescriptorNames</span><span class="sc">;</span>
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97 84 <span class="s">}</span>
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98 85
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99 86 <span class="c"># Initialize object data...</span>
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100 87 <span class="c">#</span>
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101 <a name="_InitializeRotatableBondsDescriptors-"></a> 88 <span class="k">sub </span><span class="m">_InitializeRotatableBondsDescriptors</span> <span class="s">{</span>
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102 89 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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103 90
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104 91 <span class="c"># Type of MolecularDescriptor...</span>
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105 92 <span class="i">$This</span>->{<span class="w">Type</span>} = <span class="q">'RotatableBonds'</span><span class="sc">;</span>
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106 93
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107 94 <span class="c"># MayaChemTools rotatable bonds default definition corresponds to modifed</span>
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108 95 <span class="c"># version of rotatable bonds definition used by Veber et al. [ Ref 92 ]</span>
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109 96 <span class="c">#</span>
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110 97 <span class="i">$This</span>->{<span class="w">IgnoreTerminalBonds</span>} = <span class="n">1</span><span class="sc">;</span>
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111 98 <span class="i">$This</span>->{<span class="w">IgnoreBondsToTripleBonds</span>} = <span class="n">1</span><span class="sc">;</span>
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112 99 <span class="i">$This</span>->{<span class="w">IgnoreAmideBonds</span>} = <span class="n">1</span><span class="sc">;</span>
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113 100 <span class="i">$This</span>->{<span class="w">IgnoreThioamideBonds</span>} = <span class="n">1</span><span class="sc">;</span>
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114 101 <span class="i">$This</span>->{<span class="w">IgnoreSulfonamideBonds</span>} = <span class="n">1</span><span class="sc">;</span>
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115 102
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116 103 <span class="c"># Intialize descriptor names and values...</span>
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117 104 <span class="i">$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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118 105
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119 106 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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120 107 <span class="s">}</span>
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121 108
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122 109 <span class="c"># Initialize object properties...</span>
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123 110 <span class="c">#</span>
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124 <a name="_InitializeRotatableBondsDescriptorsProperties-"></a> 111 <span class="k">sub </span><span class="m">_InitializeRotatableBondsDescriptorsProperties</span> <span class="s">{</span>
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125 112 <span class="k">my</span><span class="s">(</span><span class="i">$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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126 113
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127 114 <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">$MethodName</span><span class="s">)</span><span class="sc">;</span>
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128 115 <span class="k">while</span> <span class="s">(</span><span class="s">(</span><span class="i">$Name</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="k">each</span> <span class="i">%NamesAndValues</span><span class="s">)</span> <span class="s">{</span>
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129 116 <span class="i">$MethodName</span> = <span class="q">"Set${Name}"</span><span class="sc">;</span>
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130 117 <span class="i">$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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131 118 <span class="s">}</span>
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132 119
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133 120 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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134 121 <span class="s">}</span>
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135 122
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136 123 <span class="c"># Calculate number of rotatable bonds in a molecule...</span>
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137 124 <span class="c">#</span>
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138 125 <span class="c"># A rotatable bond is defined as any single bond which is not in a ring</span>
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139 126 <span class="c"># and involves only non-hydrogen atoms. By default, the following types</span>
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140 127 <span class="c"># of single bonds are not considered rotatable bonds:</span>
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141 128 <span class="c">#</span>
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142 129 <span class="c"># . Terminal bonds</span>
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143 130 <span class="c"># . Bonds attached to triple bonds</span>
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144 131 <span class="c"># . Amide C-N bonds</span>
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145 132 <span class="c"># . Thioamide C-N bond bonds</span>
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146 133 <span class="c"># . Sulfonamide S-N bonds</span>
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147 134 <span class="c">#</span>
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148 135 <span class="c"># MayaChemTools rotatable bonds default definition corresponds to modifed</span>
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149 136 <span class="c"># version of rotatable bonds definition used by Veber et al. [ Ref 92 ]</span>
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150 137 <span class="c">#</span>
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151 <a name="GenerateDescriptors-"></a> 138 <span class="k">sub </span><span class="m">GenerateDescriptors</span> <span class="s">{</span>
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152 139 <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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153 140
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154 141 <span class="c"># Initialize descriptor values...</span>
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155 142 <span class="i">$This</span><span class="i">->_InitializeDescriptorValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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156 143
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157 144 <span class="c"># Check availability of molecule...</span>
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158 145 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="s">)</span> <span class="s">{</span>
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159 146 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->GenerateDescriptors: $This->{Type} molecular descriptors generation didn't succeed: Molecule data is not available: Molecule object hasn't been set..."</span><span class="sc">;</span>
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160 147 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
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161 148 <span class="s">}</span>
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162 149
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163 150 <span class="c"># Calculate descriptor values...</span>
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164 151 <span class="k">if</span> <span class="s">(</span>!<span class="i">$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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165 152 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->GenerateDescriptors: $This->{Type} molecular descriptors generation didn't succeed: Couldn't calculate RotatableBonds values..."</span><span class="sc">;</span>
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166 153 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
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167 154 <span class="s">}</span>
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168 155
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169 156 <span class="c"># Set final descriptor values...</span>
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170 157 <span class="i">$This</span><span class="i">->_SetFinalDescriptorValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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171 158
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172 159 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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173 160 <span class="s">}</span>
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174 161
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175 162 <span class="c"># Calculate RotatableBonds value...</span>
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176 163 <span class="c">#</span>
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177 <a name="_CalculateDescriptorValues-"></a> 164 <span class="k">sub </span><span class="m">_CalculateDescriptorValues</span> <span class="s">{</span>
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178 165 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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179 166 <span class="k">my</span><span class="s">(</span><span class="i">$Bond</span><span class="cm">,</span> <span class="i">$RotatableBonds</span><span class="cm">,</span> <span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">)</span><span class="sc">;</span>
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180 167
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181 168 <span class="i">$RotatableBonds</span> = <span class="n">0</span><span class="sc">;</span>
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182 169
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183 170 <span class="j">BOND:</span> <span class="k">for</span> <span class="i">$Bond</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="i">->GetBonds</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
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184 171 <span class="c"># Is it a non-ring ring bond?</span>
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185 172 <span class="k">if</span> <span class="s">(</span>!<span class="i">$Bond</span><span class="i">->IsSingle</span><span class="s">(</span><span class="s">)</span> || <span class="i">$Bond</span><span class="i">->IsInRing</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
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186 173 <span class="k">next</span> <span class="j">BOND</span><span class="sc">;</span>
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187 174 <span class="s">}</span>
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188 175
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189 176 <span class="s">(</span><span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">)</span> = <span class="i">$Bond</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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190 177
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191 178 <span class="c"># Does bond contain any Hydrogen atoms?</span>
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192 179 <span class="k">if</span> <span class="s">(</span><span class="i">$Atom1</span><span class="i">->IsHydrogen</span><span class="s">(</span><span class="s">)</span> || <span class="i">$Atom2</span><span class="i">->IsHydrogen</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
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193 180 <span class="k">next</span> <span class="j">BOND</span><span class="sc">;</span>
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194 181 <span class="s">}</span>
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195 182
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196 183 <span class="c"># Check for terminal bonds...</span>
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197 184 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">IgnoreTerminalBonds</span>} && <span class="i">$This</span><span class="i">->_IsTerminalBond</span><span class="s">(</span><span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
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198 185 <span class="k">next</span> <span class="j">BOND</span><span class="sc">;</span>
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199 186 <span class="s">}</span>
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200 187
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201 188 <span class="c"># Check for bonds attached to triple bonds...</span>
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202 189 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">IgnoreBondsToTripleBonds</span>} && <span class="i">$This</span><span class="i">->_IsAttachedToTripleBond</span><span class="s">(</span><span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
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203 190 <span class="k">next</span> <span class="j">BOND</span><span class="sc">;</span>
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204 191 <span class="s">}</span>
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205 192
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206 193 <span class="c"># Check for amide bonds...</span>
|
|
|
207 194 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">IgnoreAmideBonds</span>} && <span class="i">$This</span><span class="i">->_IsAmideBond</span><span class="s">(</span><span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
208 195 <span class="k">next</span> <span class="j">BOND</span><span class="sc">;</span>
|
|
|
209 196 <span class="s">}</span>
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210 197
|
|
|
211 198 <span class="c"># Check for amide bonds...</span>
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|
212 199 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">IgnoreThioamideBonds</span>} && <span class="i">$This</span><span class="i">->_IsThioamideBond</span><span class="s">(</span><span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
213 200 <span class="k">next</span> <span class="j">BOND</span><span class="sc">;</span>
|
|
|
214 201 <span class="s">}</span>
|
|
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215 202
|
|
|
216 203 <span class="c"># Check for sulfonamide bonds...</span>
|
|
|
217 204 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">IgnoreSulfonamideBonds</span>} && <span class="i">$This</span><span class="i">->_IsSulfonamideBond</span><span class="s">(</span><span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
218 205 <span class="k">next</span> <span class="j">BOND</span><span class="sc">;</span>
|
|
|
219 206 <span class="s">}</span>
|
|
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220 207
|
|
|
221 208 <span class="i">$RotatableBonds</span> += <span class="n">1</span><span class="sc">;</span>
|
|
|
222 209 <span class="s">}</span>
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223 210
|
|
|
224 211 <span class="c"># Track the calculated values...</span>
|
|
|
225 212 <span class="i">$This</span>->{<span class="w">RotatableBonds</span>} = <span class="i">$RotatableBonds</span><span class="sc">;</span>
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226 213
|
|
|
227 214 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
228 215 <span class="s">}</span>
|
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229 216
|
|
|
230 217 <span class="c"># Is it a terminal bond?</span>
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231 218 <span class="c">#</span>
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232 <a name="_IsTerminalBond-"></a> 219 <span class="k">sub </span><span class="m">_IsTerminalBond</span> <span class="s">{</span>
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233 220 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
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234 221
|
|
|
235 222 <span class="k">return</span> <span class="s">(</span><span class="i">$Atom1</span><span class="i">->GetAtomicInvariantValue</span><span class="s">(</span><span class="q">'X'</span><span class="s">)</span> <= <span class="n">1</span> || <span class="i">$Atom2</span><span class="i">->GetAtomicInvariantValue</span><span class="s">(</span><span class="q">'X'</span><span class="s">)</span> <= <span class="n">1</span> <span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
236 223 <span class="s">}</span>
|
|
|
237 224
|
|
|
238 225 <span class="c"># Is it attached to a terminal bond?</span>
|
|
|
239 226 <span class="c">#</span>
|
|
|
240 <a name="_IsAttachedToTripleBond-"></a> 227 <span class="k">sub </span><span class="m">_IsAttachedToTripleBond</span> <span class="s">{</span>
|
|
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241 228 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
242 229
|
|
|
243 230 <span class="k">return</span> <span class="s">(</span><span class="i">$Atom1</span><span class="i">->GetAtomicInvariantValue</span><span class="s">(</span><span class="q">'LBO'</span><span class="s">)</span> == <span class="n">3</span> || <span class="i">$Atom2</span><span class="i">->GetAtomicInvariantValue</span><span class="s">(</span><span class="q">'LBO'</span><span class="s">)</span> == <span class="n">3</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
244 231 <span class="s">}</span>
|
|
|
245 232
|
|
|
246 233 <span class="c"># Is it an amide bond?</span>
|
|
|
247 234 <span class="c">#</span>
|
|
|
248 235 <span class="c"># Amide: R-C(=O)-N(-R)(-R")</span>
|
|
|
249 236 <span class="c">#</span>
|
|
|
250 <a name="_IsAmideBond-"></a> 237 <span class="k">sub </span><span class="m">_IsAmideBond</span> <span class="s">{</span>
|
|
|
251 238 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
252 239 <span class="k">my</span><span class="s">(</span><span class="i">$CarbonAtom</span><span class="cm">,</span> <span class="i">$NitrogenAtom</span><span class="s">)</span><span class="sc">;</span>
|
|
|
253 240
|
|
|
254 241 <span class="s">(</span><span class="i">$CarbonAtom</span><span class="cm">,</span> <span class="i">$NitrogenAtom</span><span class="s">)</span> = <span class="s">(</span><span class="k">undef</span><span class="cm">,</span> <span class="k">undef</span><span class="s">)</span><span class="sc">;</span>
|
|
|
255 242
|
|
|
256 243 <span class="k">if</span> <span class="s">(</span><span class="i">$Atom1</span><span class="i">->IsCarbon</span><span class="s">(</span><span class="s">)</span> && <span class="i">$Atom2</span><span class="i">->IsNitrogen</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
257 244 <span class="s">(</span><span class="i">$CarbonAtom</span><span class="cm">,</span> <span class="i">$NitrogenAtom</span><span class="s">)</span> = <span class="s">(</span><span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">)</span><span class="sc">;</span>
|
|
|
258 245 <span class="s">}</span>
|
|
|
259 246 <span class="k">elsif</span> <span class="s">(</span><span class="i">$Atom2</span><span class="i">->IsCarbon</span><span class="s">(</span><span class="s">)</span> && <span class="i">$Atom1</span><span class="i">->IsNitrogen</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
260 247 <span class="s">(</span><span class="i">$CarbonAtom</span><span class="cm">,</span> <span class="i">$NitrogenAtom</span><span class="s">)</span> = <span class="s">(</span><span class="i">$Atom2</span><span class="cm">,</span> <span class="i">$Atom1</span><span class="s">)</span><span class="sc">;</span>
|
|
|
261 248 <span class="s">}</span>
|
|
|
262 249
|
|
|
263 250 <span class="k">if</span> <span class="s">(</span>!<span class="i">$CarbonAtom</span><span class="s">)</span> <span class="s">{</span>
|
|
|
264 251 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
265 252 <span class="s">}</span>
|
|
|
266 253
|
|
|
267 254 <span class="k">return</span> <span class="i">$CarbonAtom</span><span class="i">->DoesAtomNeighborhoodMatch</span><span class="s">(</span><span class="q">'C.T3.DB1'</span><span class="cm">,</span> <span class="s">[</span><span class="q">'O'</span><span class="cm">,</span> <span class="q">'N'</span><span class="cm">,</span> <span class="q">'C,H'</span><span class="s">]</span><span class="cm">,</span> <span class="s">[</span><span class="q">'='</span><span class="cm">,</span> <span class="q">'-'</span><span class="cm">,</span> <span class="q">'-'</span><span class="s">]</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
268 255 <span class="s">}</span>
|
|
|
269 256
|
|
|
270 257 <span class="c"># Is it a thioamide bond?</span>
|
|
|
271 258 <span class="c">#</span>
|
|
|
272 259 <span class="c"># Thioamide: R-C(=S)-N(-R)(-R")</span>
|
|
|
273 260 <span class="c">#</span>
|
|
|
274 <a name="_IsThioamideBond-"></a> 261 <span class="k">sub </span><span class="m">_IsThioamideBond</span> <span class="s">{</span>
|
|
|
275 262 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
276 263 <span class="k">my</span><span class="s">(</span><span class="i">$CarbonAtom</span><span class="cm">,</span> <span class="i">$NitrogenAtom</span><span class="s">)</span><span class="sc">;</span>
|
|
|
277 264
|
|
|
278 265 <span class="s">(</span><span class="i">$CarbonAtom</span><span class="cm">,</span> <span class="i">$NitrogenAtom</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>
|
|
|
279 266
|
|
|
280 267 <span class="k">if</span> <span class="s">(</span><span class="i">$Atom1</span><span class="i">->IsCarbon</span><span class="s">(</span><span class="s">)</span> && <span class="i">$Atom2</span><span class="i">->IsNitrogen</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
281 268 <span class="s">(</span><span class="i">$CarbonAtom</span><span class="cm">,</span> <span class="i">$NitrogenAtom</span><span class="s">)</span> = <span class="s">(</span><span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">)</span><span class="sc">;</span>
|
|
|
282 269 <span class="s">}</span>
|
|
|
283 270 <span class="k">elsif</span> <span class="s">(</span><span class="i">$Atom2</span><span class="i">->IsCarbon</span><span class="s">(</span><span class="s">)</span> && <span class="i">$Atom1</span><span class="i">->IsNitrogen</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
284 271 <span class="s">(</span><span class="i">$CarbonAtom</span><span class="cm">,</span> <span class="i">$NitrogenAtom</span><span class="s">)</span> = <span class="s">(</span><span class="i">$Atom2</span><span class="cm">,</span> <span class="i">$Atom1</span><span class="s">)</span><span class="sc">;</span>
|
|
|
285 272 <span class="s">}</span>
|
|
|
286 273
|
|
|
287 274 <span class="k">if</span> <span class="s">(</span>!<span class="i">$CarbonAtom</span><span class="s">)</span> <span class="s">{</span>
|
|
|
288 275 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
289 276 <span class="s">}</span>
|
|
|
290 277
|
|
|
291 278 <span class="k">return</span> <span class="i">$CarbonAtom</span><span class="i">->DoesAtomNeighborhoodMatch</span><span class="s">(</span><span class="q">'C.T3.DB1'</span><span class="cm">,</span> <span class="s">[</span><span class="q">'S'</span><span class="cm">,</span> <span class="q">'N'</span><span class="cm">,</span> <span class="q">'C,H'</span><span class="s">]</span><span class="cm">,</span> <span class="s">[</span><span class="q">'='</span><span class="cm">,</span> <span class="q">'-'</span><span class="cm">,</span> <span class="q">'-'</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>
|
|
|
292 279 <span class="s">}</span>
|
|
|
293 280
|
|
|
294 281 <span class="c"># Is it a sulfonamide bond?</span>
|
|
|
295 282 <span class="c">#</span>
|
|
|
296 283 <span class="c"># Sulfonamide: R-S(=O)(=O)-N(-R)(-R")</span>
|
|
|
297 284 <span class="c">#</span>
|
|
|
298 <a name="_IsSulfonamideBond-"></a> 285 <span class="k">sub </span><span class="m">_IsSulfonamideBond</span> <span class="s">{</span>
|
|
|
299 286 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
300 287 <span class="k">my</span><span class="s">(</span><span class="i">$SulfurAtom</span><span class="cm">,</span> <span class="i">$NitrogenAtom</span><span class="s">)</span><span class="sc">;</span>
|
|
|
301 288
|
|
|
302 289 <span class="s">(</span><span class="i">$SulfurAtom</span><span class="cm">,</span> <span class="i">$NitrogenAtom</span><span class="s">)</span> = <span class="s">(</span><span class="k">undef</span><span class="cm">,</span> <span class="k">undef</span><span class="s">)</span><span class="sc">;</span>
|
|
|
303 290
|
|
|
304 291 <span class="k">if</span> <span class="s">(</span><span class="i">$Atom1</span><span class="i">->IsSulfur</span><span class="s">(</span><span class="s">)</span> && <span class="i">$Atom2</span><span class="i">->IsNitrogen</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
305 292 <span class="s">(</span><span class="i">$SulfurAtom</span><span class="cm">,</span> <span class="i">$NitrogenAtom</span><span class="s">)</span> = <span class="s">(</span><span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">)</span><span class="sc">;</span>
|
|
|
306 293 <span class="s">}</span>
|
|
|
307 294 <span class="k">elsif</span> <span class="s">(</span><span class="i">$Atom2</span><span class="i">->IsSulfur</span><span class="s">(</span><span class="s">)</span> && <span class="i">$Atom1</span><span class="i">->IsNitrogen</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
308 295 <span class="s">(</span><span class="i">$SulfurAtom</span><span class="cm">,</span> <span class="i">$NitrogenAtom</span><span class="s">)</span> = <span class="s">(</span><span class="i">$Atom2</span><span class="cm">,</span> <span class="i">$Atom1</span><span class="s">)</span><span class="sc">;</span>
|
|
|
309 296 <span class="s">}</span>
|
|
|
310 297
|
|
|
311 298 <span class="k">if</span> <span class="s">(</span>!<span class="i">$SulfurAtom</span><span class="s">)</span> <span class="s">{</span>
|
|
|
312 299 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
313 300 <span class="s">}</span>
|
|
|
314 301
|
|
|
315 302 <span class="k">return</span> <span class="i">$SulfurAtom</span><span class="i">->DoesAtomNeighborhoodMatch</span><span class="s">(</span><span class="q">'S.T4.DB2'</span><span class="cm">,</span> <span class="s">[</span><span class="q">'O'</span><span class="cm">,</span> <span class="q">'O'</span><span class="cm">,</span> <span class="q">'N'</span><span class="cm">,</span> <span class="q">'!O'</span><span class="s">]</span><span class="cm">,</span> <span class="s">[</span><span class="q">'='</span><span class="cm">,</span> <span class="q">'='</span><span class="cm">,</span> <span class="q">'-'</span><span class="cm">,</span> <span class="q">'-'</span><span class="s">]</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
316 303 <span class="s">}</span>
|
|
|
317 304
|
|
|
318 305 <span class="c"># Setup final descriptor values...</span>
|
|
|
319 306 <span class="c">#</span>
|
|
|
320 <a name="_SetFinalDescriptorValues-"></a> 307 <span class="k">sub </span><span class="m">_SetFinalDescriptorValues</span> <span class="s">{</span>
|
|
|
321 308 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
322 309
|
|
|
323 310 <span class="i">$This</span>->{<span class="w">DescriptorsGenerated</span>} = <span class="n">1</span><span class="sc">;</span>
|
|
|
324 311
|
|
|
325 312 <span class="i">$This</span><span class="i">->SetDescriptorValues</span><span class="s">(</span><span class="i">$This</span>->{<span class="w">RotatableBonds</span>}<span class="s">)</span><span class="sc">;</span>
|
|
|
326 313
|
|
|
327 314 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
328 315 <span class="s">}</span>
|
|
|
329 316
|
|
|
330 317 <span class="c"># Return a string containg data for RotatableBondsDescriptors object...</span>
|
|
|
331 318 <span class="c">#</span>
|
|
|
332 <a name="StringifyRotatableBondsDescriptors-"></a> 319 <span class="k">sub </span><span class="m">StringifyRotatableBondsDescriptors</span> <span class="s">{</span>
|
|
|
333 320 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
334 321 <span class="k">my</span><span class="s">(</span><span class="i">$RotatableBondsDescriptorsString</span><span class="s">)</span><span class="sc">;</span>
|
|
|
335 322
|
|
|
336 323 <span class="c"># Type of MolecularDescriptors...</span>
|
|
|
337 324 <span class="i">$RotatableBondsDescriptorsString</span> = <span class="q">"MolecularDescriptorType: $This->{Type}; IgnoreTerminalBonds: "</span> . <span class="s">(</span><span class="i">$This</span>->{<span class="w">IgnoreTerminalBonds</span>} ? <span class="q">"Yes"</span> <span class="co">:</span> <span class="q">"No"</span><span class="s">)</span> . <span class="q">"; IgnoreBondsToTripleBonds: "</span> . <span class="s">(</span><span class="i">$This</span>->{<span class="w">IgnoreBondsToTripleBonds</span>} ? <span class="q">"Yes"</span> <span class="co">:</span> <span class="q">"No"</span><span class="s">)</span> . <span class="q">"; IgnoreAmideBonds: "</span> . <span class="s">(</span><span class="i">$This</span>->{<span class="w">IgnoreAmideBonds</span>} ? <span class="q">"Yes"</span> <span class="co">:</span> <span class="q">"No"</span><span class="s">)</span> . <span class="q">"; IgnoreThioamideBonds: "</span> . <span class="s">(</span><span class="i">$This</span>->{<span class="w">IgnoreThioamideBonds</span>} ? <span class="q">"Yes"</span> <span class="co">:</span> <span class="q">"No"</span><span class="s">)</span> . <span class="q">"; IgnoreSulfonamideBonds: "</span> . <span class="s">(</span><span class="i">$This</span>->{<span class="w">IgnoreSulfonamideBonds</span>} ? <span class="q">"Yes"</span> <span class="co">:</span> <span class="q">"No"</span><span class="s">)</span><span class="sc">;</span>
|
|
|
338 325
|
|
|
339 326 <span class="c"># Setup molecular descriptor information...</span>
|
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340 327 <span class="i">$RotatableBondsDescriptorsString</span> .= <span class="q">"; "</span> . <span class="i">$This</span><span class="i">->_StringifyDescriptorNamesAndValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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341 328
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342 329 <span class="k">return</span> <span class="i">$RotatableBondsDescriptorsString</span><span class="sc">;</span>
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343 330 <span class="s">}</span>
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344 331
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345 332 <span class="c"># Is it a RotatableBondsDescriptors object?</span>
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346 <a name="_IsRotatableBondsDescriptors-"></a> 333 <span class="k">sub </span><span class="m">_IsRotatableBondsDescriptors</span> <span class="s">{</span>
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347 334 <span class="k">my</span><span class="s">(</span><span class="i">$Object</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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348 335
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349 336 <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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350 337 <span class="s">}</span>
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351 338
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352 <a name="EOF-"></a></pre>
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353 <p> </p>
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354 <br />
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355 <center>
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356 <img src="../../../images/h2o2.png">
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357 </center>
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358 </body>
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359 </html>
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