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3 <title>MayaChemTools:Code:Molecule.pm</title>
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13 <pre>
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14 <a name="package-Molecule-"></a> 1 <span class="k">package </span><span class="i">Molecule</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: Molecule.pm,v $</span>
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17 4 <span class="c"># $Date: 2015/02/28 20:47:18 $</span>
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18 5 <span class="c"># $Revision: 1.59 $</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">Storable</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">Scalar::Util</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">ObjectProperty</span><span class="sc">;</span>
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48 35 <span class="k">use</span> <span class="w">MathUtil</span><span class="sc">;</span>
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49 36 <span class="k">use</span> <span class="w">PeriodicTable</span><span class="sc">;</span>
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50 37 <span class="k">use</span> <span class="w">Text::ParseWords</span><span class="sc">;</span>
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51 38 <span class="k">use</span> <span class="w">TextUtil</span><span class="sc">;</span>
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52 39 <span class="k">use</span> <span class="w">FileUtil</span><span class="sc">;</span>
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53 40 <span class="k">use</span> <span class="w">Graph</span><span class="sc">;</span>
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54 41 <span class="k">use</span> <span class="w">Atom</span><span class="sc">;</span>
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55 42 <span class="k">use</span> <span class="w">Bond</span><span class="sc">;</span>
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56 43 <span class="k">use</span> <span class="w">MolecularFormula</span><span class="sc">;</span>
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57 44
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58 45 <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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59 46
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60 47 <span class="i">@ISA</span> = <span class="q">qw(Graph ObjectProperty Exporter)</span><span class="sc">;</span>
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61 48 <span class="i">@EXPORT</span> = <span class="q">qw(IsMolecule)</span><span class="sc">;</span>
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62 49 <span class="i">@EXPORT_OK</span> = <span class="q">qw(FormatElementalCompositionInformation GetSupportedAromaticityModels IsSupportedAromaticityModel)</span><span class="sc">;</span>
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63 50
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64 51 <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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65 52
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66 53 <span class="c"># Setup class variables...</span>
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67 54 <span class="k">my</span><span class="s">(</span><span class="i">$ClassName</span><span class="cm">,</span> <span class="i">$ObjectID</span><span class="cm">,</span> <span class="i">%AromaticityModelsDataMap</span><span class="cm">,</span> <span class="i">%CanonicalAromaticityModelNamesMap</span><span class="s">)</span><span class="sc">;</span>
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68 55 <span class="i">_InitializeClass</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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69 56
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70 57 <span class="c"># Overload Perl functions...</span>
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71 58 <span class="k">use</span> <span class="w">overload</span> <span class="q">'""'</span> <span class="cm">=></span> <span class="q">'StringifyMolecule'</span><span class="sc">;</span>
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72 59
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73 60 <span class="c"># Class constructor...</span>
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74 <a name="new-"></a> 61 <span class="k">sub </span><span class="m">new</span> <span class="s">{</span>
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75 62 <span class="k">my</span><span class="s">(</span><span class="i">$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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76 63
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77 64 <span class="c"># Initialize object...</span>
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78 65 <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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79 66 <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">$Class</span><span class="sc">;</span>
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80 67 <span class="i">$This</span><span class="i">->_InitializeMolecule</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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81 68
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82 69 <span class="k">if</span> <span class="s">(</span><span class="k">keys</span> <span class="i">%NamesAndValues</span><span class="s">)</span> <span class="s">{</span> <span class="i">$This</span><span class="i">->_InitializeMoleculeProperties</span><span class="s">(</span><span class="i">%NamesAndValues</span><span class="s">)</span><span class="sc">;</span> <span class="s">}</span>
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83 70
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84 71 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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85 72 <span class="s">}</span>
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86 73
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87 74 <span class="c"># Initialize object data...</span>
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88 <a name="_InitializeMolecule-"></a> 75 <span class="k">sub </span><span class="m">_InitializeMolecule</span> <span class="s">{</span>
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89 76 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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90 77 <span class="k">my</span><span class="s">(</span><span class="i">$ObjectID</span><span class="s">)</span> = <span class="i">_GetNewObjectID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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91 78
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92 79 <span class="c"># All other property names and values along with all Set/Get<PropertyName> methods</span>
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93 80 <span class="c"># are implemented on-demand using ObjectProperty class.</span>
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94 81 <span class="i">$This</span>->{<span class="w">ID</span>} = <span class="i">$ObjectID</span><span class="sc">;</span>
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95 82 <span class="i">$This</span>->{<span class="w">Name</span>} = <span class="q">"Molecule ${ObjectID}"</span><span class="sc">;</span>
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96 83 <span class="s">}</span>
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97 84
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98 85 <span class="c"># Initialize molecule properties...</span>
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99 <a name="_InitializeMoleculeProperties-"></a> 86 <span class="k">sub </span><span class="m">_InitializeMoleculeProperties</span> <span class="s">{</span>
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100 87 <span class="k">my</span><span class="s">(</span><span class="i">$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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101 88
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102 89 <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">$MethodName</span><span class="s">)</span><span class="sc">;</span>
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103 90 <span class="k">while</span> <span class="s">(</span><span class="s">(</span><span class="i">$Name</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="k">each</span> <span class="i">%NamesAndValues</span><span class="s">)</span> <span class="s">{</span>
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104 91 <span class="i">$MethodName</span> = <span class="q">"Set${Name}"</span><span class="sc">;</span>
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105 92 <span class="i">$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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106 93 <span class="s">}</span>
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107 94 <span class="s">}</span>
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108 95
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109 96 <span class="c"># Initialize class ...</span>
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110 <a name="_InitializeClass-"></a> 97 <span class="k">sub </span><span class="m">_InitializeClass</span> <span class="s">{</span>
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111 98 <span class="c">#Class name...</span>
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112 99 <span class="i">$ClassName</span> = <span class="w">__PACKAGE__</span><span class="sc">;</span>
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113 100
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114 101 <span class="c"># ID to keep track of objects...</span>
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115 102 <span class="i">$ObjectID</span> = <span class="n">0</span><span class="sc">;</span>
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116 103
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117 104 <span class="c"># Load molecule class data...</span>
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118 105 <span class="i">_LoadMoleculeClassData</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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119 106 <span class="s">}</span>
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120 107
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121 108 <span class="c"># Setup an explicit SetID method to block setting of ID by AUTOLOAD function...</span>
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122 <a name="SetID-"></a> 109 <span class="k">sub </span><span class="m">SetID</span> <span class="s">{</span>
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123 110 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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124 111
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125 112 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->SetID: Object ID can't be changed: it's used for internal tracking..."</span><span class="sc">;</span>
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126 113
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127 114 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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128 115 <span class="s">}</span>
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129 116
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130 117 <span class="c"># Add an atom...</span>
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131 <a name="AddAtom-"></a> 118 <span class="k">sub </span><span class="m">AddAtom</span> <span class="s">{</span>
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132 119 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Atom</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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133 120
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134 121 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$Atom</span><span class="s">)</span> <span class="s">{</span>
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135 122 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->AddAtom: No atom added: Atom must be specified..."</span><span class="sc">;</span>
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136 123 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
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137 124 <span class="s">}</span>
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138 125 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span><span class="i">->HasAtom</span><span class="s">(</span><span class="i">$Atom</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
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139 126 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->AddAtom: No atom added: Atom already exists..."</span><span class="sc">;</span>
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140 127 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
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141 128 <span class="s">}</span>
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142 129 <span class="k">return</span> <span class="i">$This</span><span class="i">->_AddAtom</span><span class="s">(</span><span class="i">$Atom</span><span class="s">)</span><span class="sc">;</span>
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143 130 <span class="s">}</span>
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144 131
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145 132 <span class="c"># Add an atom...</span>
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146 <a name="_AddAtom-"></a> 133 <span class="k">sub </span><span class="m">_AddAtom</span> <span class="s">{</span>
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147 134 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Atom</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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148 135
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149 136 <span class="c"># Assign atom to this molecule...</span>
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150 137 <span class="i">$Atom</span><span class="i">->_SetMolecule</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span><span class="sc">;</span>
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151 138
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152 139 <span class="c"># Add it to the graph as a vertex...</span>
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153 140 <span class="k">my</span><span class="s">(</span><span class="i">$AtomID</span><span class="s">)</span><span class="sc">;</span>
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154 141 <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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155 142 <span class="i">$This</span><span class="i">->AddVertex</span><span class="s">(</span><span class="i">$AtomID</span><span class="s">)</span><span class="sc">;</span>
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156 143 <span class="i">$This</span><span class="i">->SetVertexProperty</span><span class="s">(</span><span class="q">'Atom'</span><span class="cm">,</span> <span class="i">$Atom</span><span class="cm">,</span> <span class="i">$AtomID</span><span class="s">)</span><span class="sc">;</span>
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157 144
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158 145 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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159 146 <span class="s">}</span>
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160 147
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161 148 <span class="c"># Add atoms...</span>
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162 <a name="AddAtoms-"></a> 149 <span class="k">sub </span><span class="m">AddAtoms</span> <span class="s">{</span>
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163 150 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">@Atoms</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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164 151
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165 152 <span class="k">if</span> <span class="s">(</span>!<span class="i">@Atoms</span><span class="s">)</span> <span class="s">{</span>
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166 153 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->AddAtoms: No atoms added: Atoms list must be specified..."</span><span class="sc">;</span>
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167 154 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
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168 155 <span class="s">}</span>
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169 156 <span class="k">my</span><span class="s">(</span><span class="i">$Atom</span><span class="s">)</span><span class="sc">;</span>
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170 157 <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="i">@Atoms</span><span class="s">)</span> <span class="s">{</span>
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171 158 <span class="i">$This</span><span class="i">->AddAtom</span><span class="s">(</span><span class="i">$Atom</span><span class="s">)</span><span class="sc">;</span>
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172 159 <span class="s">}</span>
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173 160 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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174 161 <span class="s">}</span>
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175 162
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176 163 <span class="c"># Create an atom and add it to molecule...</span>
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177 <a name="NewAtom-"></a> 164 <span class="k">sub </span><span class="m">NewAtom</span> <span class="s">{</span>
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178 165 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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179 166 <span class="k">my</span><span class="s">(</span><span class="i">$Atom</span><span class="s">)</span><span class="sc">;</span>
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180 167
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181 168 <span class="i">$Atom</span> = <span class="i">new</span> <span class="i">Atom</span><span class="s">(</span><span class="i">%NamesAndValues</span><span class="s">)</span><span class="sc">;</span>
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182 169 <span class="i">$This</span><span class="i">->AddAtom</span><span class="s">(</span><span class="i">$Atom</span><span class="s">)</span><span class="sc">;</span>
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183 170
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184 171 <span class="k">return</span> <span class="i">$Atom</span><span class="sc">;</span>
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185 172 <span class="s">}</span>
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186 173
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187 174 <span class="c"># Delete an atom...</span>
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188 <a name="DeleteAtom-"></a> 175 <span class="k">sub </span><span class="m">DeleteAtom</span> <span class="s">{</span>
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189 176 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Atom</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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190 177
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191 178 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$Atom</span><span class="s">)</span> <span class="s">{</span>
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192 179 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->DeleteAtom: No atom deleted: Atom must be specified..."</span><span class="sc">;</span>
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193 180 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
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194 181 <span class="s">}</span>
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195 182 <span class="c"># Does the atom exist in molecule?</span>
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196 183 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasAtom</span><span class="s">(</span><span class="i">$Atom</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
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|
|
197 184 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->DeleteAtom: No atom deleted: Atom doesn't exist..."</span><span class="sc">;</span>
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|
198 185 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
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|
199 186 <span class="s">}</span>
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|
200 187 <span class="k">return</span> <span class="i">$This</span><span class="i">->_DeleteAtom</span><span class="s">(</span><span class="i">$Atom</span><span class="s">)</span><span class="sc">;</span>
|
|
|
201 188 <span class="s">}</span>
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202 189
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203 190 <span class="c"># Delete atom...</span>
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|
204 <a name="_DeleteAtom-"></a> 191 <span class="k">sub </span><span class="m">_DeleteAtom</span> <span class="s">{</span>
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205 192 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Atom</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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|
206 193
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|
|
207 194 <span class="k">my</span><span class="s">(</span><span class="i">$AtomID</span><span class="s">)</span><span class="sc">;</span>
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|
208 195 <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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209 196 <span class="i">$This</span><span class="i">->DeleteVertex</span><span class="s">(</span><span class="i">$AtomID</span><span class="s">)</span><span class="sc">;</span>
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210 197
|
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|
211 198 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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|
212 199 <span class="s">}</span>
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213 200
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|
214 201 <span class="c"># Delete atoms...</span>
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215 <a name="DeleteAtoms-"></a> 202 <span class="k">sub </span><span class="m">DeleteAtoms</span> <span class="s">{</span>
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216 203 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">@Atoms</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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217 204
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218 205 <span class="k">if</span> <span class="s">(</span>!<span class="i">@Atoms</span><span class="s">)</span> <span class="s">{</span>
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219 206 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->DeleteAtoms: No atoms added: Atoms list must be specified..."</span><span class="sc">;</span>
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220 207 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
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221 208 <span class="s">}</span>
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222 209 <span class="k">my</span><span class="s">(</span><span class="i">$Atom</span><span class="s">)</span><span class="sc">;</span>
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223 210 <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="i">@Atoms</span><span class="s">)</span> <span class="s">{</span>
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224 211 <span class="i">$This</span><span class="i">->DeleteAtom</span><span class="s">(</span><span class="i">$Atom</span><span class="s">)</span><span class="sc">;</span>
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225 212 <span class="s">}</span>
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226 213
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|
227 214 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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|
228 215 <span class="s">}</span>
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229 216
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230 217 <span class="c"># Is this atom present?</span>
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231 <a name="HasAtom-"></a> 218 <span class="k">sub </span><span class="m">HasAtom</span> <span class="s">{</span>
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232 219 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Atom</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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233 220
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234 221 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$Atom</span><span class="s">)</span> <span class="s">{</span>
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235 222 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
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236 223 <span class="s">}</span>
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|
237 224 <span class="k">if</span> <span class="s">(</span>!<span class="i">$Atom</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
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238 225 <span class="c"># It's not in molecule...</span>
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|
239 226 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
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|
240 227 <span class="s">}</span>
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|
241 228 <span class="k">my</span><span class="s">(</span><span class="i">$AtomID</span><span class="s">)</span><span class="sc">;</span>
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|
242 229 <span class="i">$AtomID</span> = <span class="i">$Atom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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243 230 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasVertex</span><span class="s">(</span><span class="i">$AtomID</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
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|
244 231 <span class="c"># It's not in molecule...</span>
|
|
|
245 232 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
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|
246 233 <span class="s">}</span>
|
|
|
247 234 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span>
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|
|
248 235 <span class="i">$Molecule</span> = <span class="i">$Atom</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="sc">;</span>
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|
249 236
|
|
|
250 237 <span class="k">return</span> <span class="s">(</span><span class="i">$This</span><span class="i">->HasVertex</span><span class="s">(</span><span class="i">$AtomID</span><span class="s">)</span> && <span class="i">$This</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span> == <span class="i">$Molecule</span><span class="i">->GetID</span><span class="s">(</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>
|
|
|
251 238 <span class="s">}</span>
|
|
|
252 239
|
|
|
253 240 <span class="c"># Return an array of atoms. In scalar context, it returns number of atoms. Additionally,</span>
|
|
|
254 241 <span class="c"># atoms array can be filtered by any user specifiable Atom class method...</span>
|
|
|
255 242 <span class="c">#</span>
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|
|
256 <a name="GetAtoms-"></a> 243 <span class="k">sub </span><span class="m">GetAtoms</span> <span class="s">{</span>
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|
|
257 244 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$AtomCheckMethodName</span><span class="cm">,</span> <span class="i">$NegateMethodResult</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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|
|
258 245 <span class="k">my</span><span class="s">(</span><span class="i">@Atoms</span><span class="cm">,</span> <span class="i">@AtomIDs</span><span class="s">)</span><span class="sc">;</span>
|
|
|
259 246
|
|
|
260 247 <span class="i">@Atoms</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> <span class="i">@AtomIDs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
261 248
|
|
|
262 249 <span class="i">@AtomIDs</span> = <span class="i">$This</span><span class="i">->GetVertices</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
263 250 <span class="k">if</span> <span class="s">(</span>!<span class="i">@AtomIDs</span><span class="s">)</span> <span class="s">{</span>
|
|
|
264 251 <span class="k">return</span> <span class="k">wantarray</span> ? <span class="i">@Atoms</span> <span class="co">:</span> <span class="k">scalar</span> <span class="i">@Atoms</span><span class="sc">;</span>
|
|
|
265 252 <span class="s">}</span>
|
|
|
266 253
|
|
|
267 254 <span class="i">@Atoms</span> = <span class="i">$This</span><span class="i">->GetVerticesProperty</span><span class="s">(</span><span class="q">'Atom'</span><span class="cm">,</span> <span class="i">@AtomIDs</span><span class="s">)</span><span class="sc">;</span>
|
|
|
268 255
|
|
|
269 256 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$AtomCheckMethodName</span><span class="s">)</span> <span class="s">{</span>
|
|
|
270 257 <span class="k">return</span> <span class="k">wantarray</span> ? <span class="i">@Atoms</span> <span class="co">:</span> <span class="k">scalar</span> <span class="i">@Atoms</span><span class="sc">;</span>
|
|
|
271 258 <span class="s">}</span>
|
|
|
272 259 <span class="i">$NegateMethodResult</span> = <span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$NegateMethodResult</span><span class="s">)</span> && <span class="i">$NegateMethodResult</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
273 260
|
|
|
274 261 <span class="c"># Filter out atoms...</span>
|
|
|
275 262 <span class="k">my</span><span class="s">(</span><span class="i">$Atom</span><span class="cm">,</span> <span class="i">$KeepAtom</span><span class="cm">,</span> <span class="i">@FilteredAtoms</span><span class="s">)</span><span class="sc">;</span>
|
|
|
276 263 <span class="i">@FilteredAtoms</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
277 264 <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="i">@Atoms</span><span class="s">)</span> <span class="s">{</span>
|
|
|
278 265 <span class="i">$KeepAtom</span> = <span class="i">$NegateMethodResult</span> ? <span class="s">(</span>!<span class="i">$Atom</span><span class="i">->$AtomCheckMethodName</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="co">:</span> <span class="i">$Atom</span><span class="i">->$AtomCheckMethodName</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
279 266 <span class="k">if</span> <span class="s">(</span><span class="i">$KeepAtom</span><span class="s">)</span> <span class="s">{</span>
|
|
|
280 267 <span class="k">push</span> <span class="i">@FilteredAtoms</span><span class="cm">,</span> <span class="i">$Atom</span><span class="sc">;</span>
|
|
|
281 268 <span class="s">}</span>
|
|
|
282 269 <span class="s">}</span>
|
|
|
283 270 <span class="k">return</span> <span class="k">wantarray</span> ? <span class="i">@FilteredAtoms</span> <span class="co">:</span> <span class="k">scalar</span> <span class="i">@FilteredAtoms</span><span class="sc">;</span>
|
|
|
284 271 <span class="s">}</span>
|
|
|
285 272
|
|
|
286 273 <span class="c"># Return an array of bonds. In scalar context, it returns number of bonds...</span>
|
|
|
287 <a name="GetBonds-"></a> 274 <span class="k">sub </span><span class="m">GetBonds</span> <span class="s">{</span>
|
|
|
288 275 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
289 276 <span class="k">my</span><span class="s">(</span><span class="i">@Bonds</span><span class="cm">,</span> <span class="i">@EdgesAtomsIDs</span><span class="s">)</span><span class="sc">;</span>
|
|
|
290 277
|
|
|
291 278 <span class="i">@Bonds</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> <span class="i">@EdgesAtomsIDs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
292 279
|
|
|
293 280 <span class="i">@EdgesAtomsIDs</span> = <span class="i">$This</span><span class="i">->GetEdges</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
294 281 <span class="k">if</span> <span class="s">(</span><span class="i">@EdgesAtomsIDs</span><span class="s">)</span> <span class="s">{</span>
|
|
|
295 282 <span class="i">@Bonds</span> = <span class="i">$This</span><span class="i">->GetEdgesProperty</span><span class="s">(</span><span class="q">'Bond'</span><span class="cm">,</span> <span class="i">@EdgesAtomsIDs</span><span class="s">)</span><span class="sc">;</span>
|
|
|
296 283 <span class="s">}</span>
|
|
|
297 284 <span class="k">return</span> <span class="k">wantarray</span> ? <span class="i">@Bonds</span> <span class="co">:</span> <span class="k">scalar</span> <span class="i">@Bonds</span><span class="sc">;</span>
|
|
|
298 285 <span class="s">}</span>
|
|
|
299 286
|
|
|
300 287 <span class="c"># Get number of atoms in molecule...</span>
|
|
|
301 <a name="GetNumOfAtoms-"></a> 288 <span class="k">sub </span><span class="m">GetNumOfAtoms</span> <span class="s">{</span>
|
|
|
302 289 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
303 290 <span class="k">my</span><span class="s">(</span><span class="i">$NumOfAtoms</span><span class="s">)</span><span class="sc">;</span>
|
|
|
304 291
|
|
|
305 292 <span class="i">$NumOfAtoms</span> = <span class="i">$This</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
306 293
|
|
|
307 294 <span class="k">return</span> <span class="i">$NumOfAtoms</span><span class="sc">;</span>
|
|
|
308 295 <span class="s">}</span>
|
|
|
309 296
|
|
|
310 297 <span class="c"># Get number of bonds in molecule...</span>
|
|
|
311 <a name="GetNumOfBonds-"></a> 298 <span class="k">sub </span><span class="m">GetNumOfBonds</span> <span class="s">{</span>
|
|
|
312 299 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
313 300 <span class="k">my</span><span class="s">(</span><span class="i">$NumOfBonds</span><span class="s">)</span><span class="sc">;</span>
|
|
|
314 301
|
|
|
315 302 <span class="i">$NumOfBonds</span> = <span class="i">$This</span><span class="i">->GetBonds</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
316 303
|
|
|
317 304 <span class="k">return</span> <span class="i">$NumOfBonds</span><span class="sc">;</span>
|
|
|
318 305 <span class="s">}</span>
|
|
|
319 306
|
|
|
320 307 <span class="c"># Get number of heavy atoms in molecule...</span>
|
|
|
321 <a name="GetNumOfHeavyAtoms-"></a> 308 <span class="k">sub </span><span class="m">GetNumOfHeavyAtoms</span> <span class="s">{</span>
|
|
|
322 309 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
323 310
|
|
|
324 311 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetNumOfNonHydrogenAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
325 312 <span class="s">}</span>
|
|
|
326 313
|
|
|
327 314 <span class="c"># Get number of non-hydrogen atoms in molecule...</span>
|
|
|
328 <a name="GetNumOfNonHydrogenAtoms-"></a> 315 <span class="k">sub </span><span class="m">GetNumOfNonHydrogenAtoms</span> <span class="s">{</span>
|
|
|
329 316 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
330 317 <span class="k">my</span><span class="s">(</span><span class="i">$NumOfNonHydrogenAtoms</span><span class="cm">,</span> <span class="i">$Atom</span><span class="cm">,</span> <span class="i">@Atoms</span><span class="s">)</span><span class="sc">;</span>
|
|
|
331 318
|
|
|
332 319 <span class="i">@Atoms</span> = <span class="i">$This</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
333 320 <span class="i">$NumOfNonHydrogenAtoms</span> = <span class="n">0</span><span class="sc">;</span>
|
|
|
334 321 <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="i">@Atoms</span><span class="s">)</span> <span class="s">{</span>
|
|
|
335 322 <span class="k">if</span> <span class="s">(</span>!<span class="i">$Atom</span><span class="i">->IsHydrogen</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
336 323 <span class="i">$NumOfNonHydrogenAtoms</span>++<span class="sc">;</span>
|
|
|
337 324 <span class="s">}</span>
|
|
|
338 325 <span class="s">}</span>
|
|
|
339 326 <span class="k">return</span> <span class="i">$NumOfNonHydrogenAtoms</span><span class="sc">;</span>
|
|
|
340 327 <span class="s">}</span>
|
|
|
341 328
|
|
|
342 329 <span class="c"># Get number of hydrogen atoms in molecule...</span>
|
|
|
343 <a name="GetNumOfHydrogenAtoms-"></a> 330 <span class="k">sub </span><span class="m">GetNumOfHydrogenAtoms</span> <span class="s">{</span>
|
|
|
344 331 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
345 332 <span class="k">my</span><span class="s">(</span><span class="i">$NumOfHydrogenAtoms</span><span class="cm">,</span> <span class="i">$Atom</span><span class="cm">,</span> <span class="i">@Atoms</span><span class="s">)</span><span class="sc">;</span>
|
|
|
346 333
|
|
|
347 334 <span class="i">@Atoms</span> = <span class="i">$This</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
348 335 <span class="i">$NumOfHydrogenAtoms</span> = <span class="n">0</span><span class="sc">;</span>
|
|
|
349 336 <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="i">@Atoms</span><span class="s">)</span> <span class="s">{</span>
|
|
|
350 337 <span class="k">if</span> <span class="s">(</span><span class="i">$Atom</span><span class="i">->IsHydrogen</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
351 338 <span class="i">$NumOfHydrogenAtoms</span>++<span class="sc">;</span>
|
|
|
352 339 <span class="s">}</span>
|
|
|
353 340 <span class="s">}</span>
|
|
|
354 341 <span class="k">return</span> <span class="i">$NumOfHydrogenAtoms</span><span class="sc">;</span>
|
|
|
355 342 <span class="s">}</span>
|
|
|
356 343
|
|
|
357 344 <span class="c"># Get number of missing hydrogen atoms in molecule...</span>
|
|
|
358 <a name="GetNumOfMissingHydrogenAtoms-"></a> 345 <span class="k">sub </span><span class="m">GetNumOfMissingHydrogenAtoms</span> <span class="s">{</span>
|
|
|
359 346 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
360 347 <span class="k">my</span><span class="s">(</span><span class="i">$NumOfMissingHydrogenAtoms</span><span class="cm">,</span> <span class="i">$Atom</span><span class="cm">,</span> <span class="i">@Atoms</span><span class="s">)</span><span class="sc">;</span>
|
|
|
361 348
|
|
|
362 349 <span class="i">@Atoms</span> = <span class="i">$This</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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|
|
363 350 <span class="i">$NumOfMissingHydrogenAtoms</span> = <span class="n">0</span><span class="sc">;</span>
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|
|
364 351 <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="i">@Atoms</span><span class="s">)</span> <span class="s">{</span>
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|
|
365 352 <span class="k">if</span> <span class="s">(</span>!<span class="i">$Atom</span><span class="i">->IsHydrogen</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
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|
|
366 353 <span class="i">$NumOfMissingHydrogenAtoms</span> += <span class="i">$Atom</span><span class="i">->GetNumOfMissingHydrogens</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
367 354 <span class="s">}</span>
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|
|
368 355 <span class="s">}</span>
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|
|
369 356 <span class="k">return</span> <span class="i">$NumOfMissingHydrogenAtoms</span><span class="sc">;</span>
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|
370 357 <span class="s">}</span>
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371 358
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372 359 <span class="c"># Add bond...</span>
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373 <a name="AddBond-"></a> 360 <span class="k">sub </span><span class="m">AddBond</span> <span class="s">{</span>
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374 361 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Bond</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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375 362 <span class="k">my</span><span class="s">(</span><span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">)</span><span class="sc">;</span>
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|
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376 363
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377 364 <span class="s">(</span><span class="i">$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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|
|
378 365 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$Atom1</span><span class="s">)</span> && <span class="k">defined</span><span class="s">(</span><span class="i">$Atom2</span><span class="s">)</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
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|
|
379 366 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->AddBond: No bond added: Both atoms must be specified..."</span><span class="sc">;</span>
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|
|
380 367 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
|
|
|
381 368 <span class="s">}</span>
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|
|
382 369 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="i">$This</span><span class="i">->HasAtom</span><span class="s">(</span><span class="i">$Atom1</span><span class="s">)</span> && <span class="i">$This</span><span class="i">->HasAtom</span><span class="s">(</span><span class="i">$Atom2</span><span class="s">)</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
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|
|
383 370 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->AddBond: No bond added: Both atoms must be present..."</span><span class="sc">;</span>
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|
|
384 371 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
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|
385 372 <span class="s">}</span>
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|
386 373 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span><span class="i">->HasBond</span><span class="s">(</span><span class="i">$Bond</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
387 374 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->AddBond: No bond added: Bond already exists..."</span><span class="sc">;</span>
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|
|
388 375 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
|
|
|
389 376 <span class="s">}</span>
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|
|
390 377 <span class="k">return</span> <span class="i">$This</span><span class="i">->_AddBond</span><span class="s">(</span><span class="i">$Bond</span><span class="s">)</span><span class="sc">;</span>
|
|
|
391 378 <span class="s">}</span>
|
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392 379
|
|
|
393 380 <span class="c"># Add bond...</span>
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|
394 <a name="_AddBond-"></a> 381 <span class="k">sub </span><span class="m">_AddBond</span> <span class="s">{</span>
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|
395 382 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Bond</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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|
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396 383
|
|
|
397 384 <span class="c"># Assign bond to this molecule...</span>
|
|
|
398 385 <span class="i">$Bond</span><span class="i">->_SetMolecule</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span><span class="sc">;</span>
|
|
|
399 386
|
|
|
400 387 <span class="c"># Add it to the graph as an edge...</span>
|
|
|
401 388 <span class="k">my</span><span class="s">(</span><span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="cm">,</span> <span class="i">$AtomID1</span><span class="cm">,</span> <span class="i">$AtomID2</span><span class="s">)</span><span class="sc">;</span>
|
|
|
402 389 <span class="s">(</span><span class="i">$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>
|
|
|
403 390 <span class="i">$AtomID1</span> = <span class="i">$Atom1</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> <span class="i">$AtomID2</span> = <span class="i">$Atom2</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
404 391 <span class="i">$This</span><span class="i">->AddEdge</span><span class="s">(</span><span class="i">$AtomID1</span><span class="cm">,</span> <span class="i">$AtomID2</span><span class="s">)</span><span class="sc">;</span>
|
|
|
405 392 <span class="i">$This</span><span class="i">->SetEdgeProperty</span><span class="s">(</span><span class="q">'Bond'</span><span class="cm">,</span> <span class="i">$Bond</span><span class="cm">,</span> <span class="i">$AtomID1</span><span class="cm">,</span> <span class="i">$AtomID2</span><span class="s">)</span><span class="sc">;</span>
|
|
|
406 393
|
|
|
407 394 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
408 395 <span class="s">}</span>
|
|
|
409 396
|
|
|
410 397 <span class="c"># Add Bonds...</span>
|
|
|
411 <a name="AddBonds-"></a> 398 <span class="k">sub </span><span class="m">AddBonds</span> <span class="s">{</span>
|
|
|
412 399 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">@Bonds</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
413 400
|
|
|
414 401 <span class="k">if</span> <span class="s">(</span>!<span class="i">@Bonds</span><span class="s">)</span> <span class="s">{</span>
|
|
|
415 402 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->AddBonds: No bonds added: Bonds list must be specified..."</span><span class="sc">;</span>
|
|
|
416 403 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
|
|
|
417 404 <span class="s">}</span>
|
|
|
418 405 <span class="k">my</span><span class="s">(</span><span class="i">$Bond</span><span class="s">)</span><span class="sc">;</span>
|
|
|
419 406 <span class="k">for</span> <span class="i">$Bond</span> <span class="s">(</span><span class="i">@Bonds</span><span class="s">)</span> <span class="s">{</span>
|
|
|
420 407 <span class="i">$This</span><span class="i">->AddBond</span><span class="s">(</span><span class="i">$Bond</span><span class="s">)</span><span class="sc">;</span>
|
|
|
421 408 <span class="s">}</span>
|
|
|
422 409 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
423 410 <span class="s">}</span>
|
|
|
424 411
|
|
|
425 412 <span class="c"># Create a bond and add it to molecule...</span>
|
|
|
426 <a name="NewBond-"></a> 413 <span class="k">sub </span><span class="m">NewBond</span> <span class="s">{</span>
|
|
|
427 414 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
428 415 <span class="k">my</span><span class="s">(</span><span class="i">$Bond</span><span class="s">)</span><span class="sc">;</span>
|
|
|
429 416
|
|
|
430 417 <span class="i">$Bond</span> = <span class="i">new</span> <span class="i">Bond</span><span class="s">(</span><span class="i">%NamesAndValues</span><span class="s">)</span><span class="sc">;</span>
|
|
|
431 418 <span class="i">$This</span><span class="i">->AddBond</span><span class="s">(</span><span class="i">$Bond</span><span class="s">)</span><span class="sc">;</span>
|
|
|
432 419
|
|
|
433 420 <span class="k">return</span> <span class="i">$Bond</span><span class="sc">;</span>
|
|
|
434 421 <span class="s">}</span>
|
|
|
435 422
|
|
|
436 423 <span class="c"># Delete a bond...</span>
|
|
|
437 <a name="DeleteBond-"></a> 424 <span class="k">sub </span><span class="m">DeleteBond</span> <span class="s">{</span>
|
|
|
438 425 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Bond</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
439 426
|
|
|
440 427 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$Bond</span><span class="s">)</span> <span class="s">{</span>
|
|
|
441 428 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->DeleteBond: No bond deleted: Bond must be specified..."</span><span class="sc">;</span>
|
|
|
442 429 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
|
|
|
443 430 <span class="s">}</span>
|
|
|
444 431 <span class="c"># Does the bond exist in molecule?</span>
|
|
|
445 432 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasBond</span><span class="s">(</span><span class="i">$Bond</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
446 433 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->DeleteBond: No bond deleted: Bond doesn't exist..."</span><span class="sc">;</span>
|
|
|
447 434 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
|
|
|
448 435 <span class="s">}</span>
|
|
|
449 436 <span class="k">return</span> <span class="i">$This</span><span class="i">->_DeleteBond</span><span class="s">(</span><span class="i">$Bond</span><span class="s">)</span><span class="sc">;</span>
|
|
|
450 437 <span class="s">}</span>
|
|
|
451 438
|
|
|
452 439 <span class="c"># Delete bond...</span>
|
|
|
453 <a name="_DeleteBond-"></a> 440 <span class="k">sub </span><span class="m">_DeleteBond</span> <span class="s">{</span>
|
|
|
454 441 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Bond</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
455 442
|
|
|
456 443 <span class="k">my</span><span class="s">(</span><span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="cm">,</span> <span class="i">$AtomID1</span><span class="cm">,</span> <span class="i">$AtomID2</span><span class="s">)</span><span class="sc">;</span>
|
|
|
457 444 <span class="s">(</span><span class="i">$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>
|
|
|
458 445 <span class="i">$AtomID1</span> = <span class="i">$Atom1</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> <span class="i">$AtomID2</span> = <span class="i">$Atom2</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
459 446 <span class="i">$This</span><span class="i">->DeleteEdge</span><span class="s">(</span><span class="i">$AtomID1</span><span class="cm">,</span> <span class="i">$AtomID2</span><span class="s">)</span><span class="sc">;</span>
|
|
|
460 447
|
|
|
461 448 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
462 449 <span class="s">}</span>
|
|
|
463 450
|
|
|
464 451 <span class="c"># Delete bonds...</span>
|
|
|
465 <a name="DeleteBonds-"></a> 452 <span class="k">sub </span><span class="m">DeleteBonds</span> <span class="s">{</span>
|
|
|
466 453 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">@Bonds</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
467 454
|
|
|
468 455 <span class="k">if</span> <span class="s">(</span>!<span class="i">@Bonds</span><span class="s">)</span> <span class="s">{</span>
|
|
|
469 456 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->DeleteBonds: No bonds added: Bonds list must be specified..."</span><span class="sc">;</span>
|
|
|
470 457 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
|
|
|
471 458 <span class="s">}</span>
|
|
|
472 459 <span class="k">my</span><span class="s">(</span><span class="i">$Bond</span><span class="s">)</span><span class="sc">;</span>
|
|
|
473 460 <span class="k">for</span> <span class="i">$Bond</span> <span class="s">(</span><span class="i">@Bonds</span><span class="s">)</span> <span class="s">{</span>
|
|
|
474 461 <span class="i">$This</span><span class="i">->DeleteBond</span><span class="s">(</span><span class="i">$Bond</span><span class="s">)</span><span class="sc">;</span>
|
|
|
475 462 <span class="s">}</span>
|
|
|
476 463
|
|
|
477 464 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
478 465 <span class="s">}</span>
|
|
|
479 466
|
|
|
480 467 <span class="c"># Has bond...</span>
|
|
|
481 <a name="HasBond-"></a> 468 <span class="k">sub </span><span class="m">HasBond</span> <span class="s">{</span>
|
|
|
482 469 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Bond</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
483 470 <span class="k">my</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>
|
|
|
484 471
|
|
|
485 472 <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">$Bond</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
486 473 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="i">$This</span><span class="i">->HasAtom</span><span class="s">(</span><span class="i">$Atom1</span><span class="s">)</span> && <span class="i">$This</span><span class="i">->HasAtom</span><span class="s">(</span><span class="i">$Atom2</span><span class="s">)</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
487 474 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
488 475 <span class="s">}</span>
|
|
|
489 476 <span class="k">if</span> <span class="s">(</span>!<span class="i">$Bond</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
490 477 <span class="c"># It's not in molecule...</span>
|
|
|
491 478 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
492 479 <span class="s">}</span>
|
|
|
493 480 <span class="k">my</span><span class="s">(</span><span class="i">$AtomID1</span><span class="cm">,</span> <span class="i">$AtomID2</span><span class="cm">,</span> <span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span>
|
|
|
494 481 <span class="i">$AtomID1</span> = <span class="i">$Atom1</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> <span class="i">$AtomID2</span> = <span class="i">$Atom2</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
495 482 <span class="i">$Molecule</span> = <span class="i">$Bond</span><span class="i">->GetMolecule</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
496 483
|
|
|
497 484 <span class="k">return</span> <span class="s">(</span><span class="i">$This</span><span class="i">->HasEdge</span><span class="s">(</span><span class="i">$AtomID1</span><span class="cm">,</span> <span class="i">$AtomID2</span><span class="s">)</span> && <span class="i">$This</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span> == <span class="i">$Molecule</span><span class="i">->GetID</span><span class="s">(</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>
|
|
|
498 485 <span class="s">}</span>
|
|
|
499 486
|
|
|
500 487 <span class="c"># Get atom neighbors...</span>
|
|
|
501 <a name="_GetAtomNeighbors-"></a> 488 <span class="k">sub </span><span class="m">_GetAtomNeighbors</span> <span class="s">{</span>
|
|
|
502 489 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Atom</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
503 490
|
|
|
504 491 <span class="k">my</span><span class="s">(</span><span class="i">$AtomID</span><span class="cm">,</span> <span class="i">@Atoms</span><span class="cm">,</span> <span class="i">@AtomIDs</span><span class="s">)</span><span class="sc">;</span>
|
|
|
505 492
|
|
|
506 493 <span class="i">@Atoms</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> <span class="i">@AtomIDs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
507 494 <span class="i">$AtomID</span> = <span class="i">$Atom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
508 495 <span class="i">@AtomIDs</span> = <span class="i">$This</span><span class="i">->GetNeighbors</span><span class="s">(</span><span class="i">$AtomID</span><span class="s">)</span><span class="sc">;</span>
|
|
|
509 496 <span class="k">if</span> <span class="s">(</span><span class="i">@AtomIDs</span><span class="s">)</span> <span class="s">{</span>
|
|
|
510 497 <span class="i">@Atoms</span> = <span class="i">$This</span><span class="i">->GetVerticesProperty</span><span class="s">(</span><span class="q">'Atom'</span><span class="cm">,</span> <span class="i">@AtomIDs</span><span class="s">)</span><span class="sc">;</span>
|
|
|
511 498 <span class="s">}</span>
|
|
|
512 499 <span class="k">return</span> <span class="k">wantarray</span> ? <span class="i">@Atoms</span> <span class="co">:</span> <span class="k">scalar</span> <span class="i">@Atoms</span><span class="sc">;</span>
|
|
|
513 500 <span class="s">}</span>
|
|
|
514 501
|
|
|
515 502 <span class="c"># Get atom bonds...</span>
|
|
|
516 <a name="_GetAtomBonds-"></a> 503 <span class="k">sub </span><span class="m">_GetAtomBonds</span> <span class="s">{</span>
|
|
|
517 504 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Atom</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
518 505 <span class="k">my</span><span class="s">(</span><span class="i">$AtomID</span><span class="cm">,</span> <span class="i">@AtomIDs</span><span class="cm">,</span> <span class="i">@Bonds</span><span class="s">)</span><span class="sc">;</span>
|
|
|
519 506
|
|
|
520 507 <span class="i">@Bonds</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> <span class="i">@AtomIDs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
521 508 <span class="i">$AtomID</span> = <span class="i">$Atom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
522 509 <span class="i">@AtomIDs</span> = <span class="i">$This</span><span class="i">->GetEdges</span><span class="s">(</span><span class="i">$AtomID</span><span class="s">)</span><span class="sc">;</span>
|
|
|
523 510 <span class="k">if</span> <span class="s">(</span><span class="i">@AtomIDs</span><span class="s">)</span> <span class="s">{</span>
|
|
|
524 511 <span class="i">@Bonds</span> = <span class="i">$This</span><span class="i">->GetEdgesProperty</span><span class="s">(</span><span class="q">'Bond'</span><span class="cm">,</span> <span class="i">@AtomIDs</span><span class="s">)</span><span class="sc">;</span>
|
|
|
525 512 <span class="s">}</span>
|
|
|
526 513 <span class="k">return</span> <span class="k">wantarray</span> ? <span class="i">@Bonds</span> <span class="co">:</span> <span class="k">scalar</span> <span class="i">@Bonds</span><span class="sc">;</span>
|
|
|
527 514 <span class="s">}</span>
|
|
|
528 515
|
|
|
529 516 <span class="c"># Get bond to specified atom...</span>
|
|
|
530 <a name="_GetBondToAtom-"></a> 517 <span class="k">sub </span><span class="m">_GetBondToAtom</span> <span class="s">{</span>
|
|
|
531 518 <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">$Atom2</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
532 519 <span class="k">my</span><span class="s">(</span><span class="i">$AtomID1</span><span class="cm">,</span> <span class="i">$AtomID2</span><span class="s">)</span><span class="sc">;</span>
|
|
|
533 520
|
|
|
534 521 <span class="i">$AtomID1</span> = <span class="i">$Atom1</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
535 522 <span class="i">$AtomID2</span> = <span class="i">$Atom2</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
536 523
|
|
|
537 524 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetEdgeProperty</span><span class="s">(</span><span class="q">'Bond'</span><span class="cm">,</span> <span class="i">$AtomID1</span><span class="cm">,</span> <span class="i">$AtomID2</span><span class="s">)</span><span class="sc">;</span>
|
|
|
538 525 <span class="s">}</span>
|
|
|
539 526
|
|
|
540 527 <span class="c"># Are two specified atoms bonded?</span>
|
|
|
541 <a name="_IsBondedToAtom-"></a> 528 <span class="k">sub </span><span class="m">_IsBondedToAtom</span> <span class="s">{</span>
|
|
|
542 529 <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">$Atom2</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
543 530 <span class="k">my</span><span class="s">(</span><span class="i">$AtomID1</span><span class="cm">,</span> <span class="i">$AtomID2</span><span class="s">)</span><span class="sc">;</span>
|
|
|
544 531
|
|
|
545 532 <span class="i">$AtomID1</span> = <span class="i">$Atom1</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
546 533 <span class="i">$AtomID2</span> = <span class="i">$Atom2</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
547 534
|
|
|
548 535 <span class="k">return</span> <span class="i">$This</span><span class="i">->HasEdgeProperty</span><span class="s">(</span><span class="q">'Bond'</span><span class="cm">,</span> <span class="i">$AtomID1</span><span class="cm">,</span> <span class="i">$AtomID2</span><span class="s">)</span><span class="sc">;</span>
|
|
|
549 536 <span class="s">}</span>
|
|
|
550 537
|
|
|
551 538 <span class="c"># Add hydrogens to each atoms in molecule and return total number of hydrogens added...</span>
|
|
|
552 <a name="AddHydrogens-"></a> 539 <span class="k">sub </span><span class="m">AddHydrogens</span> <span class="s">{</span>
|
|
|
553 540 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
554 541
|
|
|
555 542 <span class="k">return</span> <span class="i">$This</span><span class="i">->_AddHydrogens</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
556 543 <span class="s">}</span>
|
|
|
557 544
|
|
|
558 545 <span class="c"># Add hydrogens to polar atoms (N, O, P, S) in molecule and return total number of hydrogens added...</span>
|
|
|
559 <a name="AddPolarHydrogens-"></a> 546 <span class="k">sub </span><span class="m">AddPolarHydrogens</span> <span class="s">{</span>
|
|
|
560 547 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
561 548 <span class="k">my</span><span class="s">(</span><span class="i">$PolarHydrogensOnly</span><span class="s">)</span> = <span class="n">1</span><span class="sc">;</span>
|
|
|
562 549
|
|
|
563 550 <span class="k">return</span> <span class="i">$This</span><span class="i">->_AddHydrogens</span><span class="s">(</span><span class="i">$PolarHydrogensOnly</span><span class="s">)</span><span class="sc">;</span>
|
|
|
564 551 <span class="s">}</span>
|
|
|
565 552
|
|
|
566 553 <span class="c"># Add all the hydrogens or hydrogens for polar atoms only...</span>
|
|
|
567 554 <span class="c">#</span>
|
|
|
568 555 <span class="c"># Note:</span>
|
|
|
569 556 <span class="c"># . The current release of MayaChemTools doesn't assign any hydrogen positions.</span>
|
|
|
570 557 <span class="c">#</span>
|
|
|
571 <a name="_AddHydrogens-"></a> 558 <span class="k">sub </span><span class="m">_AddHydrogens</span> <span class="s">{</span>
|
|
|
572 559 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$PolarHydrogensOnly</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
573 560 <span class="k">my</span><span class="s">(</span><span class="i">$Atom</span><span class="cm">,</span> <span class="i">$NumOfHydrogensAdded</span><span class="cm">,</span> <span class="i">$HydrogenPositionsWarning</span><span class="cm">,</span> <span class="i">@Atoms</span><span class="s">)</span><span class="sc">;</span>
|
|
|
574 561
|
|
|
575 562 <span class="k">if</span> <span class="s">(</span>! <span class="k">defined</span> <span class="i">$PolarHydrogensOnly</span><span class="s">)</span> <span class="s">{</span>
|
|
|
576 563 <span class="i">$PolarHydrogensOnly</span> = <span class="n">0</span><span class="sc">;</span>
|
|
|
577 564 <span class="s">}</span>
|
|
|
578 565
|
|
|
579 566 <span class="i">$NumOfHydrogensAdded</span> = <span class="n">0</span><span class="sc">;</span>
|
|
|
580 567 <span class="i">@Atoms</span> = <span class="i">$This</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
581 568 <span class="i">$HydrogenPositionsWarning</span> = <span class="n">0</span><span class="sc">;</span>
|
|
|
582 569
|
|
|
583 570 <span class="j">ATOM:</span> <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="i">@Atoms</span><span class="s">)</span> <span class="s">{</span>
|
|
|
584 571 <span class="k">if</span> <span class="s">(</span><span class="i">$PolarHydrogensOnly</span><span class="s">)</span> <span class="s">{</span>
|
|
|
585 572 <span class="k">if</span> <span class="s">(</span>!<span class="i">$Atom</span><span class="i">->IsPolarAtom</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
586 573 <span class="k">next</span> <span class="j">ATOM</span><span class="sc">;</span>
|
|
|
587 574 <span class="s">}</span>
|
|
|
588 575 <span class="s">}</span>
|
|
|
589 576 <span class="i">$NumOfHydrogensAdded</span> += <span class="i">$Atom</span><span class="i">->AddHydrogens</span><span class="s">(</span><span class="i">$HydrogenPositionsWarning</span><span class="s">)</span><span class="sc">;</span>
|
|
|
590 577 <span class="s">}</span>
|
|
|
591 578 <span class="k">return</span> <span class="i">$NumOfHydrogensAdded</span><span class="sc">;</span>
|
|
|
592 579 <span class="s">}</span>
|
|
|
593 580
|
|
|
594 581 <span class="c"># Delete all hydrogens atoms in molecule and return total number of hydrogens removed...</span>
|
|
|
595 <a name="DeleteHydrogens-"></a> 582 <span class="k">sub </span><span class="m">DeleteHydrogens</span> <span class="s">{</span>
|
|
|
596 583 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
597 584
|
|
|
598 585 <span class="k">return</span> <span class="i">$This</span><span class="i">->_DeleteHydrogens</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
599 586 <span class="s">}</span>
|
|
|
600 587
|
|
|
601 588 <span class="c"># Delete hydrogens to polar atoms (N, O, P, S) in molecule and return total number of hydrogens removed...</span>
|
|
|
602 <a name="DeletePolarHydrogens-"></a> 589 <span class="k">sub </span><span class="m">DeletePolarHydrogens</span> <span class="s">{</span>
|
|
|
603 590 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
604 591 <span class="k">my</span><span class="s">(</span><span class="i">$PolarHydrogensOnly</span><span class="s">)</span> = <span class="n">1</span><span class="sc">;</span>
|
|
|
605 592
|
|
|
606 593 <span class="k">return</span> <span class="i">$This</span><span class="i">->_DeleteHydrogens</span><span class="s">(</span><span class="i">$PolarHydrogensOnly</span><span class="s">)</span><span class="sc">;</span>
|
|
|
607 594 <span class="s">}</span>
|
|
|
608 595
|
|
|
609 596 <span class="c"># Delete all hydrogens atoms in molecule and return total number of hydrogens removed...</span>
|
|
|
610 <a name="_DeleteHydrogens-"></a> 597 <span class="k">sub </span><span class="m">_DeleteHydrogens</span> <span class="s">{</span>
|
|
|
611 598 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$PolarHydrogensOnly</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
612 599 <span class="k">my</span><span class="s">(</span><span class="i">$Atom</span><span class="cm">,</span> <span class="i">$NumOfHydrogensRemoved</span><span class="cm">,</span> <span class="i">@Atoms</span><span class="s">)</span><span class="sc">;</span>
|
|
|
613 600
|
|
|
614 601 <span class="k">if</span> <span class="s">(</span>! <span class="k">defined</span> <span class="i">$PolarHydrogensOnly</span><span class="s">)</span> <span class="s">{</span>
|
|
|
615 602 <span class="i">$PolarHydrogensOnly</span> = <span class="n">0</span><span class="sc">;</span>
|
|
|
616 603 <span class="s">}</span>
|
|
|
617 604
|
|
|
618 605 <span class="i">$NumOfHydrogensRemoved</span> = <span class="n">0</span><span class="sc">;</span>
|
|
|
619 606 <span class="i">@Atoms</span> = <span class="i">$This</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
620 607
|
|
|
621 608 <span class="j">ATOM:</span> <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="i">@Atoms</span><span class="s">)</span> <span class="s">{</span>
|
|
|
622 609 <span class="k">if</span> <span class="s">(</span><span class="i">$PolarHydrogensOnly</span><span class="s">)</span> <span class="s">{</span>
|
|
|
623 610 <span class="k">if</span> <span class="s">(</span>!<span class="i">$Atom</span><span class="i">->IsPolarHydrogen</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
624 611 <span class="k">next</span> <span class="j">ATOM</span><span class="sc">;</span>
|
|
|
625 612 <span class="s">}</span>
|
|
|
626 613 <span class="s">}</span>
|
|
|
627 614 <span class="k">elsif</span> <span class="s">(</span>!<span class="i">$Atom</span><span class="i">->IsHydrogen</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
628 615 <span class="k">next</span> <span class="j">ATOM</span><span class="sc">;</span>
|
|
|
629 616 <span class="s">}</span>
|
|
|
630 617 <span class="i">$This</span><span class="i">->_DeleteAtom</span><span class="s">(</span><span class="i">$Atom</span><span class="s">)</span><span class="sc">;</span>
|
|
|
631 618 <span class="i">$NumOfHydrogensRemoved</span>++<span class="sc">;</span>
|
|
|
632 619 <span class="s">}</span>
|
|
|
633 620 <span class="k">return</span> <span class="i">$NumOfHydrogensRemoved</span><span class="sc">;</span>
|
|
|
634 621 <span class="s">}</span>
|
|
|
635 622
|
|
|
636 623 <span class="c"># Get molecular weight by summing up atomic weights of all the atoms...</span>
|
|
|
637 <a name="GetMolecularWeight-"></a> 624 <span class="k">sub </span><span class="m">GetMolecularWeight</span> <span class="s">{</span>
|
|
|
638 625 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$IncludeMissingHydrogens</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
639 626 <span class="k">my</span><span class="s">(</span><span class="i">$MolecularWeight</span><span class="cm">,</span> <span class="i">$AtomicWeight</span><span class="cm">,</span> <span class="i">@Atoms</span><span class="cm">,</span> <span class="i">$Atom</span><span class="s">)</span><span class="sc">;</span>
|
|
|
640 627
|
|
|
641 628 <span class="i">$IncludeMissingHydrogens</span> = <span class="k">defined</span><span class="s">(</span><span class="i">$IncludeMissingHydrogens</span><span class="s">)</span> ? <span class="i">$IncludeMissingHydrogens</span> <span class="co">:</span> <span class="n">1</span><span class="sc">;</span>
|
|
|
642 629
|
|
|
643 630 <span class="i">$MolecularWeight</span> = <span class="n">0</span><span class="sc">;</span>
|
|
|
644 631 <span class="i">@Atoms</span> = <span class="i">$This</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
645 632 <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="i">@Atoms</span><span class="s">)</span> <span class="s">{</span>
|
|
|
646 633 <span class="i">$AtomicWeight</span> = <span class="i">$Atom</span><span class="i">->GetAtomicWeight</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
647 634 <span class="k">if</span> <span class="s">(</span><span class="k">defined</span> <span class="i">$AtomicWeight</span><span class="s">)</span> <span class="s">{</span>
|
|
|
648 635 <span class="i">$MolecularWeight</span> += <span class="i">$AtomicWeight</span><span class="sc">;</span>
|
|
|
649 636 <span class="s">}</span>
|
|
|
650 637 <span class="s">}</span>
|
|
|
651 638
|
|
|
652 639 <span class="k">if</span> <span class="s">(</span>!<span class="i">$IncludeMissingHydrogens</span><span class="s">)</span> <span class="s">{</span>
|
|
|
653 640 <span class="k">return</span> <span class="i">$MolecularWeight</span><span class="sc">;</span>
|
|
|
654 641 <span class="s">}</span>
|
|
|
655 642
|
|
|
656 643 <span class="c"># Account for missing hydrogen atoms...</span>
|
|
|
657 644 <span class="k">my</span><span class="s">(</span><span class="i">$NumOfMissingHydrogenAtoms</span><span class="s">)</span><span class="sc">;</span>
|
|
|
658 645
|
|
|
659 646 <span class="i">$NumOfMissingHydrogenAtoms</span> = <span class="i">$This</span><span class="i">->GetNumOfMissingHydrogenAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
660 647 <span class="k">if</span> <span class="s">(</span><span class="i">$NumOfMissingHydrogenAtoms</span><span class="s">)</span> <span class="s">{</span>
|
|
|
661 648 <span class="i">$MolecularWeight</span> += <span class="i">$NumOfMissingHydrogenAtoms</span> * <span class="i">PeriodicTable::GetElementAtomicWeight</span><span class="s">(</span><span class="q">'H'</span><span class="s">)</span><span class="sc">;</span>
|
|
|
662 649 <span class="s">}</span>
|
|
|
663 650
|
|
|
664 651 <span class="k">return</span> <span class="i">$MolecularWeight</span><span class="sc">;</span>
|
|
|
665 652 <span class="s">}</span>
|
|
|
666 653
|
|
|
667 654 <span class="c"># Get exact mass by summing up exact masses of all the atoms...</span>
|
|
|
668 <a name="GetExactMass-"></a> 655 <span class="k">sub </span><span class="m">GetExactMass</span> <span class="s">{</span>
|
|
|
669 656 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$IncludeMissingHydrogens</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
670 657 <span class="k">my</span><span class="s">(</span><span class="i">$ExactMass</span><span class="cm">,</span> <span class="i">$AtomicMass</span><span class="cm">,</span> <span class="i">@Atoms</span><span class="cm">,</span> <span class="i">$Atom</span><span class="s">)</span><span class="sc">;</span>
|
|
|
671 658
|
|
|
672 659 <span class="i">$IncludeMissingHydrogens</span> = <span class="k">defined</span><span class="s">(</span><span class="i">$IncludeMissingHydrogens</span><span class="s">)</span> ? <span class="i">$IncludeMissingHydrogens</span> <span class="co">:</span> <span class="n">1</span><span class="sc">;</span>
|
|
|
673 660
|
|
|
674 661 <span class="i">$ExactMass</span> = <span class="n">0</span><span class="sc">;</span>
|
|
|
675 662 <span class="i">@Atoms</span> = <span class="i">$This</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
676 663 <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="i">@Atoms</span><span class="s">)</span> <span class="s">{</span>
|
|
|
677 664 <span class="i">$AtomicMass</span> = <span class="i">$Atom</span><span class="i">->GetExactMass</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
678 665 <span class="k">if</span> <span class="s">(</span><span class="k">defined</span> <span class="i">$AtomicMass</span><span class="s">)</span> <span class="s">{</span>
|
|
|
679 666 <span class="i">$ExactMass</span> += <span class="i">$AtomicMass</span><span class="sc">;</span>
|
|
|
680 667 <span class="s">}</span>
|
|
|
681 668 <span class="s">}</span>
|
|
|
682 669
|
|
|
683 670 <span class="k">if</span> <span class="s">(</span>!<span class="i">$IncludeMissingHydrogens</span><span class="s">)</span> <span class="s">{</span>
|
|
|
684 671 <span class="k">return</span> <span class="i">$ExactMass</span><span class="sc">;</span>
|
|
|
685 672 <span class="s">}</span>
|
|
|
686 673
|
|
|
687 674 <span class="c"># Account for missing hydrogen atoms...</span>
|
|
|
688 675 <span class="k">my</span><span class="s">(</span><span class="i">$NumOfMissingHydrogenAtoms</span><span class="s">)</span><span class="sc">;</span>
|
|
|
689 676
|
|
|
690 677 <span class="i">$NumOfMissingHydrogenAtoms</span> = <span class="i">$This</span><span class="i">->GetNumOfMissingHydrogenAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
691 678 <span class="k">if</span> <span class="s">(</span><span class="i">$NumOfMissingHydrogenAtoms</span><span class="s">)</span> <span class="s">{</span>
|
|
|
692 679 <span class="i">$ExactMass</span> += <span class="i">$NumOfMissingHydrogenAtoms</span> * <span class="i">PeriodicTable::GetElementMostAbundantNaturalIsotopeMass</span><span class="s">(</span><span class="q">'H'</span><span class="s">)</span><span class="sc">;</span>
|
|
|
693 680 <span class="s">}</span>
|
|
|
694 681
|
|
|
695 682 <span class="k">return</span> <span class="i">$ExactMass</span><span class="sc">;</span>
|
|
|
696 683 <span class="s">}</span>
|
|
|
697 684
|
|
|
698 685 <span class="c"># Get net formal charge on the molecule using one of the following two methods:</span>
|
|
|
699 686 <span class="c"># . Using explicitly set FormalCharge property</span>
|
|
|
700 687 <span class="c"># . Adding up formal charge on each atom in the molecule</span>
|
|
|
701 688 <span class="c">#</span>
|
|
|
702 689 <span class="c"># Caveats:</span>
|
|
|
703 690 <span class="c"># . FormalCharge is different from Charge property of the molecule which corresponds to</span>
|
|
|
704 691 <span class="c"># sum of partial atomic charges explicitly set for each atom using a specific methodology.</span>
|
|
|
705 692 <span class="c">#</span>
|
|
|
706 <a name="GetFormalCharge-"></a> 693 <span class="k">sub </span><span class="m">GetFormalCharge</span> <span class="s">{</span>
|
|
|
707 694 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
708 695
|
|
|
709 696 <span class="c"># Is FormalCharge property explicitly set?</span>
|
|
|
710 697 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'FormalCharge'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
711 698 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'FormalCharge'</span><span class="s">)</span><span class="sc">;</span>
|
|
|
712 699 <span class="s">}</span>
|
|
|
713 700 <span class="k">my</span><span class="s">(</span><span class="i">$FormalCharge</span><span class="cm">,</span> <span class="i">$AtomicFormalCharge</span><span class="cm">,</span> <span class="i">@Atoms</span><span class="cm">,</span> <span class="i">$Atom</span><span class="s">)</span><span class="sc">;</span>
|
|
|
714 701
|
|
|
715 702 <span class="i">$FormalCharge</span> = <span class="n">0</span><span class="sc">;</span>
|
|
|
716 703 <span class="i">@Atoms</span> = <span class="i">$This</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
717 704 <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="i">@Atoms</span><span class="s">)</span> <span class="s">{</span>
|
|
|
718 705 <span class="i">$AtomicFormalCharge</span> = <span class="i">$Atom</span><span class="i">->GetFormalCharge</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
719 706 <span class="k">if</span> <span class="s">(</span><span class="k">defined</span> <span class="i">$AtomicFormalCharge</span><span class="s">)</span> <span class="s">{</span>
|
|
|
720 707 <span class="i">$FormalCharge</span> += <span class="i">$AtomicFormalCharge</span><span class="sc">;</span>
|
|
|
721 708 <span class="s">}</span>
|
|
|
722 709 <span class="s">}</span>
|
|
|
723 710 <span class="k">return</span> <span class="i">$FormalCharge</span><span class="sc">;</span>
|
|
|
724 711 <span class="s">}</span>
|
|
|
725 712
|
|
|
726 713 <span class="c"># Get net charge on the molecule using one of the following two methods:</span>
|
|
|
727 714 <span class="c"># . Using explicitly set Charge property</span>
|
|
|
728 715 <span class="c"># . Adding up charge on each atom in the molecule</span>
|
|
|
729 716 <span class="c">#</span>
|
|
|
730 717 <span class="c"># Caveats:</span>
|
|
|
731 718 <span class="c"># . FormalCharge is different from Charge property of the molecule which corresponds to</span>
|
|
|
732 719 <span class="c"># sum of partial atomic charges explicitly set for each atom using a specific methodology.</span>
|
|
|
733 720 <span class="c">#</span>
|
|
|
734 <a name="GetCharge-"></a> 721 <span class="k">sub </span><span class="m">GetCharge</span> <span class="s">{</span>
|
|
|
735 722 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
736 723
|
|
|
737 724 <span class="c"># Is Charge property explicitly set?</span>
|
|
|
738 725 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Charge'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
739 726 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'Charge'</span><span class="s">)</span><span class="sc">;</span>
|
|
|
740 727 <span class="s">}</span>
|
|
|
741 728 <span class="k">my</span><span class="s">(</span><span class="i">$Charge</span><span class="cm">,</span> <span class="i">$AtomicCharge</span><span class="cm">,</span> <span class="i">@Atoms</span><span class="cm">,</span> <span class="i">$Atom</span><span class="s">)</span><span class="sc">;</span>
|
|
|
742 729
|
|
|
743 730 <span class="i">$Charge</span> = <span class="n">0</span><span class="sc">;</span>
|
|
|
744 731 <span class="i">@Atoms</span> = <span class="i">$This</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
745 732 <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="i">@Atoms</span><span class="s">)</span> <span class="s">{</span>
|
|
|
746 733 <span class="i">$AtomicCharge</span> = <span class="i">$Atom</span><span class="i">->GetCharge</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
747 734 <span class="k">if</span> <span class="s">(</span><span class="k">defined</span> <span class="i">$AtomicCharge</span><span class="s">)</span> <span class="s">{</span>
|
|
|
748 735 <span class="i">$Charge</span> += <span class="i">$AtomicCharge</span><span class="sc">;</span>
|
|
|
749 736 <span class="s">}</span>
|
|
|
750 737 <span class="s">}</span>
|
|
|
751 738 <span class="k">return</span> <span class="i">$Charge</span><span class="sc">;</span>
|
|
|
752 739 <span class="s">}</span>
|
|
|
753 740
|
|
|
754 741 <span class="c"># Get total SpinMultiplicity for the molecule using one of the following two methods:</span>
|
|
|
755 742 <span class="c"># . Using explicitly set SpinMultiplicity property</span>
|
|
|
756 743 <span class="c"># . Adding up SpinMultiplicity on each atom in the molecule</span>
|
|
|
757 744 <span class="c">#</span>
|
|
|
758 745 <span class="c">#</span>
|
|
|
759 <a name="GetSpinMultiplicity-"></a> 746 <span class="k">sub </span><span class="m">GetSpinMultiplicity</span> <span class="s">{</span>
|
|
|
760 747 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
761 748
|
|
|
762 749 <span class="c"># Is SpinMultiplicity property explicitly set?</span>
|
|
|
763 750 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'SpinMultiplicity'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
764 751 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'SpinMultiplicity'</span><span class="s">)</span><span class="sc">;</span>
|
|
|
765 752 <span class="s">}</span>
|
|
|
766 753 <span class="k">my</span><span class="s">(</span><span class="i">$AtomicSpinMultiplicity</span><span class="cm">,</span> <span class="i">$SpinMultiplicity</span><span class="cm">,</span> <span class="i">@Atoms</span><span class="cm">,</span> <span class="i">$Atom</span><span class="s">)</span><span class="sc">;</span>
|
|
|
767 754
|
|
|
768 755 <span class="i">$SpinMultiplicity</span> = <span class="n">0</span><span class="sc">;</span>
|
|
|
769 756 <span class="i">@Atoms</span> = <span class="i">$This</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
770 757 <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="i">@Atoms</span><span class="s">)</span> <span class="s">{</span>
|
|
|
771 758 <span class="i">$AtomicSpinMultiplicity</span> = <span class="i">$Atom</span><span class="i">->GetSpinMultiplicity</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
772 759 <span class="k">if</span> <span class="s">(</span><span class="k">defined</span> <span class="i">$AtomicSpinMultiplicity</span><span class="s">)</span> <span class="s">{</span>
|
|
|
773 760 <span class="i">$SpinMultiplicity</span> += <span class="i">$AtomicSpinMultiplicity</span><span class="sc">;</span>
|
|
|
774 761 <span class="s">}</span>
|
|
|
775 762 <span class="s">}</span>
|
|
|
776 763 <span class="k">return</span> <span class="i">$SpinMultiplicity</span><span class="sc">;</span>
|
|
|
777 764 <span class="s">}</span>
|
|
|
778 765
|
|
|
779 766 <span class="c"># Get total FreeRadicalElectrons for the molecule using one of the following two methods:</span>
|
|
|
780 767 <span class="c"># . Using explicitly set FreeRadicalElectrons property</span>
|
|
|
781 768 <span class="c"># . Adding up FreeRadicalElectrons on each atom in the molecule</span>
|
|
|
782 769 <span class="c">#</span>
|
|
|
783 770 <span class="c">#</span>
|
|
|
784 <a name="GetFreeRadicalElectrons-"></a> 771 <span class="k">sub </span><span class="m">GetFreeRadicalElectrons</span> <span class="s">{</span>
|
|
|
785 772 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
786 773
|
|
|
787 774 <span class="c"># Is FreeRadicalElectrons property explicitly set?</span>
|
|
|
788 775 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'FreeRadicalElectrons'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
789 776 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'FreeRadicalElectrons'</span><span class="s">)</span><span class="sc">;</span>
|
|
|
790 777 <span class="s">}</span>
|
|
|
791 778 <span class="k">my</span><span class="s">(</span><span class="i">$AtomicFreeRadicalElectrons</span><span class="cm">,</span> <span class="i">$FreeRadicalElectrons</span><span class="cm">,</span> <span class="i">@Atoms</span><span class="cm">,</span> <span class="i">$Atom</span><span class="s">)</span><span class="sc">;</span>
|
|
|
792 779
|
|
|
793 780 <span class="i">$FreeRadicalElectrons</span> = <span class="n">0</span><span class="sc">;</span>
|
|
|
794 781 <span class="i">@Atoms</span> = <span class="i">$This</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
795 782 <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="i">@Atoms</span><span class="s">)</span> <span class="s">{</span>
|
|
|
796 783 <span class="i">$AtomicFreeRadicalElectrons</span> = <span class="i">$Atom</span><span class="i">->GetFreeRadicalElectrons</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
797 784 <span class="k">if</span> <span class="s">(</span><span class="k">defined</span> <span class="i">$AtomicFreeRadicalElectrons</span><span class="s">)</span> <span class="s">{</span>
|
|
|
798 785 <span class="i">$FreeRadicalElectrons</span> += <span class="i">$AtomicFreeRadicalElectrons</span><span class="sc">;</span>
|
|
|
799 786 <span class="s">}</span>
|
|
|
800 787 <span class="s">}</span>
|
|
|
801 788 <span class="k">return</span> <span class="i">$FreeRadicalElectrons</span><span class="sc">;</span>
|
|
|
802 789 <span class="s">}</span>
|
|
|
803 790
|
|
|
804 791 <span class="c"># Set valence model...</span>
|
|
|
805 792 <span class="c">#</span>
|
|
|
806 <a name="SetValenceModel-"></a> 793 <span class="k">sub </span><span class="m">SetValenceModel</span> <span class="s">{</span>
|
|
|
807 794 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$ValenceModel</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
808 795
|
|
|
809 796 <span class="k">if</span> <span class="s">(</span><span class="i">$ValenceModel</span> !~ <span class="q">/^(MDLValenceModel|DaylightValenceModel|InternalValenceModel|MayaChemToolsValenceModel)$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
810 797 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->SetValenceModel: The current release of MayaChemTools doesn't support the specified valence model $ValenceModel. Supported valence models: MDLValenceModel, DaylightValenceModel, InternalValenceModel or MayaChemToolsValenceModel. Using internal valence model..."</span><span class="sc">;</span>
|
|
|
811 798 <span class="i">$ValenceModel</span> = <span class="q">'InternalValenceModel'</span><span class="sc">;</span>
|
|
|
812 799 <span class="s">}</span>
|
|
|
813 800
|
|
|
814 801 <span class="i">$This</span><span class="i">->SetProperty</span><span class="s">(</span><span class="q">'ValenceModel'</span><span class="cm">,</span> <span class="i">$ValenceModel</span><span class="s">)</span><span class="sc">;</span>
|
|
|
815 802
|
|
|
816 803 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
817 804 <span class="s">}</span>
|
|
|
818 805
|
|
|
819 806 <span class="c"># Get valence model...</span>
|
|
|
820 807 <span class="c">#</span>
|
|
|
821 <a name="GetValenceModel-"></a> 808 <span class="k">sub </span><span class="m">GetValenceModel</span> <span class="s">{</span>
|
|
|
822 809 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
823 810
|
|
|
824 811 <span class="c"># Is ValenceModel property explicitly set?</span>
|
|
|
825 812 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'ValenceModel'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
826 813 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'ValenceModel'</span><span class="s">)</span><span class="sc">;</span>
|
|
|
827 814 <span class="s">}</span>
|
|
|
828 815
|
|
|
829 816 <span class="c"># Used internal valence model as default model...</span>
|
|
|
830 817 <span class="k">return</span> <span class="q">'InternalValenceModel'</span><span class="sc">;</span>
|
|
|
831 818 <span class="s">}</span>
|
|
|
832 819
|
|
|
833 820 <span class="c"># Get molecular formula by collecting information about all atoms in the molecule and</span>
|
|
|
834 821 <span class="c"># composing the formula using Hills ordering system:</span>
|
|
|
835 822 <span class="c"># . C shows up first and H follows assuming C is present</span>
|
|
|
836 823 <span class="c"># . All other standard elements are sorted alphanumerically</span>
|
|
|
837 824 <span class="c"># . All other non-stanard atom symbols are also sorted alphanumerically and follow standard elements</span>
|
|
|
838 825 <span class="c">#</span>
|
|
|
839 826 <span class="c"># Caveats:</span>
|
|
|
840 827 <span class="c"># . By default, missing hydrogens and nonelements are also included</span>
|
|
|
841 828 <span class="c"># . Elements for disconnected fragments are combined into the same formula</span>
|
|
|
842 829 <span class="c">#</span>
|
|
|
843 830 <span class="c"># Handle formula generation for disconnected structures. e.g: molecule generated by</span>
|
|
|
844 831 <span class="c"># [Na+].[O-]c1ccccc1</span>
|
|
|
845 832 <span class="c">#</span>
|
|
|
846 <a name="GetMolecularFormula-"></a> 833 <span class="k">sub </span><span class="m">GetMolecularFormula</span> <span class="s">{</span>
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|
|
847 834 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$IncludeMissingHydrogens</span><span class="cm">,</span> <span class="i">$IncludeNonElements</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
848 835 <span class="k">my</span><span class="s">(</span><span class="i">$MolecularFormula</span><span class="cm">,</span> <span class="i">$AtomSymbol</span><span class="cm">,</span> <span class="i">$ElementsCountRef</span><span class="cm">,</span> <span class="i">$NonElementsCountRef</span><span class="s">)</span><span class="sc">;</span>
|
|
|
849 836
|
|
|
850 837 <span class="i">$IncludeMissingHydrogens</span> = <span class="k">defined</span><span class="s">(</span><span class="i">$IncludeMissingHydrogens</span><span class="s">)</span> ? <span class="i">$IncludeMissingHydrogens</span> <span class="co">:</span> <span class="n">1</span><span class="sc">;</span>
|
|
|
851 838 <span class="i">$IncludeNonElements</span> = <span class="k">defined</span><span class="s">(</span><span class="i">$IncludeNonElements</span><span class="s">)</span> ? <span class="i">$IncludeNonElements</span> <span class="co">:</span> <span class="n">1</span><span class="sc">;</span>
|
|
|
852 839
|
|
|
853 840 <span class="c"># Get elements count and setup molecular formula...</span>
|
|
|
854 841 <span class="s">(</span><span class="i">$ElementsCountRef</span><span class="cm">,</span> <span class="i">$NonElementsCountRef</span><span class="s">)</span> = <span class="i">$This</span><span class="i">->GetElementsAndNonElements</span><span class="s">(</span><span class="i">$IncludeMissingHydrogens</span><span class="s">)</span><span class="sc">;</span>
|
|
|
855 842 <span class="i">$MolecularFormula</span> = <span class="q">''</span><span class="sc">;</span>
|
|
|
856 843
|
|
|
857 844 <span class="c"># Count C and H first...</span>
|
|
|
858 845 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$ElementsCountRef</span>->{<span class="w">C</span>} <span class="s">)</span> <span class="s">{</span>
|
|
|
859 846 <span class="i">$MolecularFormula</span> .= <span class="q">'C'</span> . <span class="s">(</span><span class="i">$ElementsCountRef</span>->{<span class="w">C</span>} > <span class="n">1</span> ? <span class="i">$ElementsCountRef</span>->{<span class="w">C</span>} <span class="co">:</span> <span class="q">''</span><span class="s">)</span><span class="sc">;</span>
|
|
|
860 847 <span class="k">delete</span> <span class="i">$ElementsCountRef</span>->{<span class="w">C</span>}<span class="sc">;</span>
|
|
|
861 848
|
|
|
862 849 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$ElementsCountRef</span>->{<span class="w">H</span>} <span class="s">)</span> <span class="s">{</span>
|
|
|
863 850 <span class="i">$MolecularFormula</span> .= <span class="q">'H'</span> . <span class="s">(</span><span class="i">$ElementsCountRef</span>->{<span class="w">H</span>} > <span class="n">1</span> ? <span class="i">$ElementsCountRef</span>->{<span class="w">H</span>} <span class="co">:</span> <span class="q">''</span><span class="s">)</span><span class="sc">;</span>
|
|
|
864 851 <span class="k">delete</span> <span class="i">$ElementsCountRef</span>->{<span class="w">H</span>}<span class="sc">;</span>
|
|
|
865 852 <span class="s">}</span>
|
|
|
866 853 <span class="s">}</span>
|
|
|
867 854
|
|
|
868 855 <span class="c"># Sort elements...</span>
|
|
|
869 856 <span class="k">for</span> <span class="i">$AtomSymbol</span> <span class="s">(</span><span class="k">sort</span> <span class="s">{</span><span class="i">$a</span> <span class="k">cmp</span> <span class="i">$b</span><span class="s">}</span> <span class="k">keys</span> <span class="i">%</span>{<span class="i">$ElementsCountRef</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
870 857 <span class="i">$MolecularFormula</span> .= <span class="i">$AtomSymbol</span> . <span class="s">(</span><span class="i">$ElementsCountRef</span>->{<span class="i">$AtomSymbol</span>} > <span class="n">1</span> ? <span class="i">$ElementsCountRef</span>->{<span class="i">$AtomSymbol</span>} <span class="co">:</span> <span class="q">''</span><span class="s">)</span><span class="sc">;</span>
|
|
|
871 858 <span class="s">}</span>
|
|
|
872 859
|
|
|
873 860 <span class="c"># Sort non-elements...</span>
|
|
|
874 861 <span class="k">if</span> <span class="s">(</span><span class="i">$IncludeNonElements</span><span class="s">)</span> <span class="s">{</span>
|
|
|
875 862 <span class="k">for</span> <span class="i">$AtomSymbol</span> <span class="s">(</span><span class="k">sort</span> <span class="s">{</span><span class="i">$a</span> <span class="k">cmp</span> <span class="i">$b</span><span class="s">}</span> <span class="k">keys</span> <span class="i">%</span>{<span class="i">$NonElementsCountRef</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
876 863 <span class="i">$MolecularFormula</span> .= <span class="i">$AtomSymbol</span> . <span class="s">(</span><span class="i">$NonElementsCountRef</span>->{<span class="i">$AtomSymbol</span>} > <span class="n">1</span> ? <span class="i">$NonElementsCountRef</span>->{<span class="i">$AtomSymbol</span>} <span class="co">:</span> <span class="q">''</span><span class="s">)</span><span class="sc">;</span>
|
|
|
877 864 <span class="s">}</span>
|
|
|
878 865 <span class="s">}</span>
|
|
|
879 866
|
|
|
880 867 <span class="c"># Check formal charge...</span>
|
|
|
881 868 <span class="k">my</span><span class="s">(</span><span class="i">$FormalCharge</span><span class="s">)</span><span class="sc">;</span>
|
|
|
882 869 <span class="i">$FormalCharge</span> = <span class="i">$This</span><span class="i">->GetFormalCharge</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
883 870 <span class="k">if</span> <span class="s">(</span><span class="i">$FormalCharge</span><span class="s">)</span> <span class="s">{</span>
|
|
|
884 871 <span class="c"># Setup formal charge string...</span>
|
|
|
885 872 <span class="k">my</span><span class="s">(</span><span class="i">$FormalChargeString</span><span class="s">)</span><span class="sc">;</span>
|
|
|
886 873 <span class="k">if</span> <span class="s">(</span><span class="i">$FormalCharge</span> == <span class="n">1</span> <span class="s">)</span> <span class="s">{</span>
|
|
|
887 874 <span class="i">$FormalChargeString</span> = <span class="q">"+"</span><span class="sc">;</span>
|
|
|
888 875 <span class="s">}</span>
|
|
|
889 876 <span class="k">elsif</span> <span class="s">(</span><span class="i">$FormalCharge</span> == <span class="n">-1</span> <span class="s">)</span> <span class="s">{</span>
|
|
|
890 877 <span class="i">$FormalChargeString</span> = <span class="q">"-"</span><span class="sc">;</span>
|
|
|
891 878 <span class="s">}</span>
|
|
|
892 879 <span class="k">else</span> <span class="s">{</span>
|
|
|
893 880 <span class="i">$FormalChargeString</span> = <span class="s">(</span><span class="i">$FormalCharge</span> > <span class="n">0</span><span class="s">)</span> ? <span class="s">(</span><span class="q">"+"</span> . <span class="k">abs</span><span class="s">(</span><span class="i">$FormalCharge</span><span class="s">)</span><span class="s">)</span> <span class="co">:</span> <span class="s">(</span><span class="q">"-"</span> . <span class="k">abs</span><span class="s">(</span><span class="i">$FormalCharge</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span>
|
|
|
894 881 <span class="s">}</span>
|
|
|
895 882 <span class="i">$MolecularFormula</span> = <span class="q">"${MolecularFormula}${FormalChargeString}"</span><span class="sc">;</span>
|
|
|
896 883 <span class="s">}</span>
|
|
|
897 884
|
|
|
898 885 <span class="k">return</span> <span class="i">$MolecularFormula</span><span class="sc">;</span>
|
|
|
899 886 <span class="s">}</span>
|
|
|
900 887
|
|
|
901 888 <span class="c"># Count elements and non-elements in molecule and return references to hashes</span>
|
|
|
902 889 <span class="c"># containing count of elements and non-elements respectively. By default, missing</span>
|
|
|
903 890 <span class="c"># hydrogens are not added to the element hash.</span>
|
|
|
904 891 <span class="c">#</span>
|
|
|
905 892 <span class="c">#</span>
|
|
|
906 <a name="GetElementsAndNonElements-"></a> 893 <span class="k">sub </span><span class="m">GetElementsAndNonElements</span> <span class="s">{</span>
|
|
|
907 894 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$IncludeMissingHydrogens</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
908 895 <span class="k">my</span><span class="s">(</span><span class="i">$Atom</span><span class="cm">,</span> <span class="i">$AtomicNumber</span><span class="cm">,</span> <span class="i">$AtomSymbol</span><span class="cm">,</span> <span class="i">$NumOfMissingHydrogens</span><span class="cm">,</span> <span class="i">@Atoms</span><span class="cm">,</span> <span class="i">%ElementsCount</span><span class="cm">,</span> <span class="i">%NonElementsCount</span><span class="s">)</span><span class="sc">;</span>
|
|
|
909 896
|
|
|
910 897 <span class="i">$IncludeMissingHydrogens</span> = <span class="k">defined</span><span class="s">(</span><span class="i">$IncludeMissingHydrogens</span><span class="s">)</span> ? <span class="i">$IncludeMissingHydrogens</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
911 898
|
|
|
912 899 <span class="i">%ElementsCount</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> <span class="i">%NonElementsCount</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
913 900 <span class="i">$NumOfMissingHydrogens</span> = <span class="n">0</span><span class="sc">;</span>
|
|
|
914 901
|
|
|
915 902 <span class="c"># Count elements and non elements...</span>
|
|
|
916 903 <span class="i">@Atoms</span> = <span class="i">$This</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
917 904 <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="i">@Atoms</span><span class="s">)</span> <span class="s">{</span>
|
|
|
918 905 <span class="i">$AtomicNumber</span> = <span class="i">$Atom</span><span class="i">->GetAtomicNumber</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
919 906 <span class="i">$AtomSymbol</span> = <span class="i">$Atom</span><span class="i">->GetAtomSymbol</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
920 907 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomicNumber</span><span class="s">)</span> <span class="s">{</span>
|
|
|
921 908 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$ElementsCount</span>{<span class="i">$AtomSymbol</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
922 909 <span class="i">$ElementsCount</span>{<span class="i">$AtomSymbol</span>} += <span class="n">1</span><span class="sc">;</span>
|
|
|
923 910 <span class="s">}</span>
|
|
|
924 911 <span class="k">else</span> <span class="s">{</span>
|
|
|
925 912 <span class="i">$ElementsCount</span>{<span class="i">$AtomSymbol</span>} = <span class="n">1</span><span class="sc">;</span>
|
|
|
926 913 <span class="s">}</span>
|
|
|
927 914 <span class="k">if</span> <span class="s">(</span><span class="i">$IncludeMissingHydrogens</span><span class="s">)</span> <span class="s">{</span>
|
|
|
928 915 <span class="i">$NumOfMissingHydrogens</span> += <span class="i">$Atom</span><span class="i">->GetNumOfMissingHydrogens</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
929 916 <span class="s">}</span>
|
|
|
930 917 <span class="s">}</span>
|
|
|
931 918 <span class="k">else</span> <span class="s">{</span>
|
|
|
932 919 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$NonElementsCount</span>{<span class="i">$AtomSymbol</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
933 920 <span class="i">$NonElementsCount</span>{<span class="i">$AtomSymbol</span>} += <span class="n">1</span><span class="sc">;</span>
|
|
|
934 921 <span class="s">}</span>
|
|
|
935 922 <span class="k">else</span> <span class="s">{</span>
|
|
|
936 923 <span class="i">$NonElementsCount</span>{<span class="i">$AtomSymbol</span>} = <span class="n">1</span><span class="sc">;</span>
|
|
|
937 924 <span class="s">}</span>
|
|
|
938 925 <span class="s">}</span>
|
|
|
939 926 <span class="s">}</span>
|
|
|
940 927 <span class="k">if</span> <span class="s">(</span><span class="i">$IncludeMissingHydrogens</span> && <span class="i">$NumOfMissingHydrogens</span><span class="s">)</span> <span class="s">{</span>
|
|
|
941 928 <span class="i">$AtomSymbol</span> = <span class="q">'H'</span><span class="sc">;</span>
|
|
|
942 929 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$ElementsCount</span>{<span class="i">$AtomSymbol</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
943 930 <span class="i">$ElementsCount</span>{<span class="i">$AtomSymbol</span>} += <span class="i">$NumOfMissingHydrogens</span><span class="sc">;</span>
|
|
|
944 931 <span class="s">}</span>
|
|
|
945 932 <span class="k">else</span> <span class="s">{</span>
|
|
|
946 933 <span class="i">$ElementsCount</span>{<span class="i">$AtomSymbol</span>} = <span class="i">$NumOfMissingHydrogens</span><span class="sc">;</span>
|
|
|
947 934 <span class="s">}</span>
|
|
|
948 935 <span class="s">}</span>
|
|
|
949 936
|
|
|
950 937 <span class="k">return</span> <span class="s">(</span>\<span class="i">%ElementsCount</span><span class="cm">,</span> \<span class="i">%NonElementsCount</span><span class="s">)</span><span class="sc">;</span>
|
|
|
951 938 <span class="s">}</span>
|
|
|
952 939
|
|
|
953 940 <span class="c"># Get number of element and non-elements in molecule. By default, missing</span>
|
|
|
954 941 <span class="c"># hydrogens are not added to element count.</span>
|
|
|
955 942 <span class="c">#</span>
|
|
|
956 <a name="GetNumOfElementsAndNonElements-"></a> 943 <span class="k">sub </span><span class="m">GetNumOfElementsAndNonElements</span> <span class="s">{</span>
|
|
|
957 944 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$IncludeMissingHydrogens</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
958 945 <span class="k">my</span><span class="s">(</span><span class="i">$ElementCount</span><span class="cm">,</span> <span class="i">$NonElementCount</span><span class="cm">,</span> <span class="i">$Atom</span><span class="s">)</span><span class="sc">;</span>
|
|
|
959 946
|
|
|
960 947 <span class="i">$IncludeMissingHydrogens</span> = <span class="k">defined</span><span class="s">(</span><span class="i">$IncludeMissingHydrogens</span><span class="s">)</span> ? <span class="i">$IncludeMissingHydrogens</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
961 948
|
|
|
962 949 <span class="s">(</span><span class="i">$ElementCount</span><span class="cm">,</span> <span class="i">$NonElementCount</span><span class="s">)</span> = <span class="s">(</span><span class="n">0</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span><span class="sc">;</span>
|
|
|
963 950
|
|
|
964 951 <span class="j">ATOM:</span> <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="i">$This</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
965 952 <span class="k">if</span> <span class="s">(</span>!<span class="i">$Atom</span><span class="i">->GetAtomicNumber</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
966 953 <span class="i">$NonElementCount</span>++<span class="sc">;</span>
|
|
|
967 954 <span class="k">next</span> <span class="j">ATOM</span><span class="sc">;</span>
|
|
|
968 955 <span class="s">}</span>
|
|
|
969 956 <span class="c"># Process element...</span>
|
|
|
970 957 <span class="i">$ElementCount</span>++<span class="sc">;</span>
|
|
|
971 958 <span class="k">if</span> <span class="s">(</span><span class="i">$IncludeMissingHydrogens</span><span class="s">)</span> <span class="s">{</span>
|
|
|
972 959 <span class="k">if</span> <span class="s">(</span>!<span class="i">$Atom</span><span class="i">->IsHydrogen</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
973 960 <span class="i">$ElementCount</span> += <span class="i">$Atom</span><span class="i">->GetNumOfMissingHydrogens</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
974 961 <span class="s">}</span>
|
|
|
975 962 <span class="s">}</span>
|
|
|
976 963 <span class="s">}</span>
|
|
|
977 964
|
|
|
978 965 <span class="k">return</span> <span class="s">(</span><span class="i">$ElementCount</span><span class="cm">,</span> <span class="i">$NonElementCount</span><span class="s">)</span><span class="sc">;</span>
|
|
|
979 966 <span class="s">}</span>
|
|
|
980 967
|
|
|
981 968 <span class="c"># Calculate elemental composition and return reference to arrays</span>
|
|
|
982 969 <span class="c"># containing elements and their percent composition.</span>
|
|
|
983 970 <span class="c">#</span>
|
|
|
984 971 <span class="c"># Caveats:</span>
|
|
|
985 972 <span class="c"># . By default, missing hydrogens are included</span>
|
|
|
986 973 <span class="c"># . Non elemnents are ignored</span>
|
|
|
987 974 <span class="c"># . Mass number are ignored</span>
|
|
|
988 975 <span class="c">#</span>
|
|
|
989 <a name="GetElementalComposition-"></a> 976 <span class="k">sub </span><span class="m">GetElementalComposition</span> <span class="s">{</span>
|
|
|
990 977 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$IncludeMissingHydrogens</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
991 978 <span class="k">my</span><span class="s">(</span><span class="i">$MolecularFormula</span><span class="cm">,</span> <span class="i">$IncludeNonElements</span><span class="cm">,</span> <span class="i">$ElementsCountRef</span><span class="cm">,</span> <span class="i">$NonElementsCountRef</span><span class="cm">,</span> <span class="i">$ElementsRef</span><span class="cm">,</span> <span class="i">$ElementsCompositionRef</span><span class="s">)</span><span class="sc">;</span>
|
|
|
992 979
|
|
|
993 980 <span class="i">$IncludeMissingHydrogens</span> = <span class="k">defined</span><span class="s">(</span><span class="i">$IncludeMissingHydrogens</span><span class="s">)</span> ? <span class="i">$IncludeMissingHydrogens</span> <span class="co">:</span> <span class="n">1</span><span class="sc">;</span>
|
|
|
994 981
|
|
|
995 982 <span class="i">$IncludeNonElements</span> = <span class="n">0</span><span class="sc">;</span>
|
|
|
996 983 <span class="s">(</span><span class="i">$ElementsCountRef</span><span class="cm">,</span> <span class="i">$NonElementsCountRef</span><span class="s">)</span> = <span class="i">$This</span><span class="i">->GetElementsAndNonElements</span><span class="s">(</span><span class="i">$IncludeMissingHydrogens</span><span class="s">)</span><span class="sc">;</span>
|
|
|
997 984
|
|
|
998 985 <span class="i">$MolecularFormula</span> = <span class="i">$This</span><span class="i">->GetMolecularFormula</span><span class="s">(</span><span class="i">$IncludeMissingHydrogens</span><span class="cm">,</span> <span class="i">$IncludeNonElements</span><span class="s">)</span><span class="sc">;</span>
|
|
|
999 986
|
|
|
1000 987 <span class="s">(</span><span class="i">$ElementsRef</span><span class="cm">,</span> <span class="i">$ElementsCompositionRef</span><span class="s">)</span> = <span class="i">MolecularFormula::CalculateElementalComposition</span><span class="s">(</span><span class="i">$MolecularFormula</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1001 988
|
|
|
1002 989 <span class="k">return</span> <span class="s">(</span><span class="i">$ElementsRef</span><span class="cm">,</span> <span class="i">$ElementsCompositionRef</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1003 990 <span class="s">}</span>
|
|
|
1004 991
|
|
|
1005 992 <span class="c"># Using refernece to element and its composition arrays, format composition information</span>
|
|
|
1006 993 <span class="c"># as: Element: Composition;...</span>
|
|
|
1007 994 <span class="c">#</span>
|
|
|
1008 <a name="FormatElementalCompositionInformation-"></a> 995 <span class="k">sub </span><span class="m">FormatElementalCompositionInformation</span> <span class="s">{</span>
|
|
|
1009 996 <span class="k">my</span><span class="s">(</span><span class="i">$FirstParameter</span><span class="cm">,</span> <span class="i">$SecondParameter</span><span class="cm">,</span> <span class="i">$ThirdParameter</span><span class="cm">,</span> <span class="i">$FourthParameter</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
1010 997 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$ElementsRef</span><span class="cm">,</span> <span class="i">$ElementCompositionRef</span><span class="cm">,</span> <span class="i">$Precision</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1011 998
|
|
|
1012 999 <span class="k">if</span> <span class="s">(</span><span class="i">_IsMolecule</span><span class="s">(</span><span class="i">$FirstParameter</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1013 1000 <span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$ElementsRef</span><span class="cm">,</span> <span class="i">$ElementCompositionRef</span><span class="cm">,</span> <span class="i">$Precision</span><span class="s">)</span> = <span class="s">(</span><span class="i">$FirstParameter</span><span class="cm">,</span> <span class="i">$SecondParameter</span><span class="cm">,</span> <span class="i">$ThirdParameter</span><span class="cm">,</span> <span class="i">$FourthParameter</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1014 1001 <span class="s">}</span>
|
|
|
1015 1002 <span class="k">else</span> <span class="s">{</span>
|
|
|
1016 1003 <span class="s">(</span><span class="i">$ElementsRef</span><span class="cm">,</span> <span class="i">$ElementCompositionRef</span><span class="cm">,</span> <span class="i">$Precision</span><span class="s">)</span> = <span class="s">(</span><span class="i">$FirstParameter</span><span class="cm">,</span> <span class="i">$SecondParameter</span><span class="cm">,</span> <span class="i">$ThirdParameter</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1017 1004 <span class="s">}</span>
|
|
|
1018 1005 <span class="k">my</span><span class="s">(</span><span class="i">$FormattedInfo</span><span class="s">)</span> = <span class="q">''</span><span class="sc">;</span>
|
|
|
1019 1006
|
|
|
1020 1007 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$ElementsRef</span><span class="s">)</span> && <span class="i">@</span>{<span class="i">$ElementsRef</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1021 1008 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->FormatElementalCompositionInformation: Elements list is not defined or empty..."</span><span class="sc">;</span>
|
|
|
1022 1009 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
|
|
|
1023 1010 <span class="s">}</span>
|
|
|
1024 1011 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$ElementCompositionRef</span><span class="s">)</span> && <span class="i">@</span>{<span class="i">$ElementCompositionRef</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1025 1012 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->FormatElementalCompositionInformation: Elements composition list is not defined or empty..."</span><span class="sc">;</span>
|
|
|
1026 1013 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
|
|
|
1027 1014 <span class="s">}</span>
|
|
|
1028 1015
|
|
|
1029 1016 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$Precision</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1030 1017 <span class="i">$Precision</span> = <span class="n">2</span><span class="sc">;</span>
|
|
|
1031 1018 <span class="s">}</span>
|
|
|
1032 1019
|
|
|
1033 1020 <span class="i">$FormattedInfo</span> = <span class="i">MolecularFormula::FormatCompositionInfomation</span><span class="s">(</span><span class="i">$ElementsRef</span><span class="cm">,</span> <span class="i">$ElementCompositionRef</span><span class="cm">,</span> <span class="i">$Precision</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1034 1021
|
|
|
1035 1022 <span class="k">return</span> <span class="i">$FormattedInfo</span><span class="sc">;</span>
|
|
|
1036 1023 <span class="s">}</span>
|
|
|
1037 1024
|
|
|
1038 1025 <span class="c"># Copy molecule and its associated data using Storable::dclone and update:</span>
|
|
|
1039 1026 <span class="c">#</span>
|
|
|
1040 1027 <span class="c"># o Atom references corresponding atoms and bonds objects</span>
|
|
|
1041 1028 <span class="c"># o Bond object references</span>
|
|
|
1042 1029 <span class="c">#</span>
|
|
|
1043 1030 <span class="c"># Object IDs for Atoms and Bonds don't get changed. So there is no need to clear</span>
|
|
|
1044 1031 <span class="c"># up any exisiting ring data attached to molecule via graph as vertex IDs.</span>
|
|
|
1045 1032 <span class="c">#</span>
|
|
|
1046 <a name="Copy-"></a>1033 <span class="k">sub </span><span class="m">Copy</span> <span class="s">{</span>
|
|
|
1047 1034 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
1048 1035 <span class="k">my</span><span class="s">(</span><span class="i">$NewMolecule</span><span class="cm">,</span> <span class="i">$Atom</span><span class="cm">,</span> <span class="i">$NewAtom</span><span class="cm">,</span> <span class="i">$AtomID</span><span class="cm">,</span> <span class="i">@Atoms</span><span class="cm">,</span> <span class="i">@AtomIDs</span><span class="cm">,</span> <span class="i">%AtomsIDsToNewAtoms</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1049 1036
|
|
|
1050 1037 <span class="i">$NewMolecule</span> = <span class="i">Storable::dclone</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1051 1038
|
|
|
1052 1039 <span class="c"># Update atom references stored as vertex property...</span>
|
|
|
1053 1040
|
|
|
1054 1041 <span class="i">@Atoms</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> <span class="i">@AtomIDs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1055 1042 <span class="i">%AtomsIDsToNewAtoms</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1056 1043
|
|
|
1057 1044 <span class="i">@AtomIDs</span> = <span class="i">$This</span><span class="i">->GetVertices</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1058 1045 <span class="k">if</span> <span class="s">(</span><span class="i">@AtomIDs</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1059 1046 <span class="i">@Atoms</span> = <span class="i">$This</span><span class="i">->GetVerticesProperty</span><span class="s">(</span><span class="q">'Atom'</span><span class="cm">,</span> <span class="i">@AtomIDs</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1060 1047 <span class="s">}</span>
|
|
|
1061 1048
|
|
|
1062 1049 <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="i">@Atoms</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1063 1050 <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>
|
|
|
1064 1051
|
|
|
1065 1052 <span class="c"># Setup a reference to copied atom object...</span>
|
|
|
1066 1053 <span class="i">$NewAtom</span> = <span class="i">$Atom</span><span class="i">->Copy</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1067 1054 <span class="i">$AtomsIDsToNewAtoms</span>{<span class="i">$AtomID</span>} = <span class="i">$NewAtom</span><span class="sc">;</span>
|
|
|
1068 1055
|
|
|
1069 1056 <span class="c"># Update atom reference to new atom object...</span>
|
|
|
1070 1057 <span class="i">$NewMolecule</span><span class="i">->UpdateVertexProperty</span><span class="s">(</span><span class="q">'Atom'</span><span class="cm">,</span> <span class="i">$NewAtom</span><span class="cm">,</span> <span class="i">$AtomID</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1071 1058 <span class="s">}</span>
|
|
|
1072 1059
|
|
|
1073 1060 <span class="c"># Update bond object and bond atom references stored as edge property...</span>
|
|
|
1074 1061 <span class="k">my</span><span class="s">(</span><span class="i">$Index</span><span class="cm">,</span> <span class="i">$AtomID1</span><span class="cm">,</span> <span class="i">$AtomID2</span><span class="cm">,</span> <span class="i">$Bond</span><span class="cm">,</span> <span class="i">$NewBond</span><span class="cm">,</span> <span class="i">$NewAtom1</span><span class="cm">,</span> <span class="i">$NewAtom2</span><span class="cm">,</span> <span class="i">@EdgesAtomsIDs</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1075 1062 <span class="i">@EdgesAtomsIDs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1076 1063 <span class="i">@EdgesAtomsIDs</span> = <span class="i">$This</span><span class="i">->GetEdges</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1077 1064 <span class="k">for</span> <span class="s">(</span><span class="i">$Index</span> = <span class="n">0</span><span class="sc">;</span> <span class="i">$Index</span> < <span class="i">$#EdgesAtomsIDs</span><span class="sc">;</span> <span class="i">$Index</span> += <span class="n">2</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1078 1065 <span class="i">$AtomID1</span> = <span class="i">$EdgesAtomsIDs</span>[<span class="i">$Index</span>]<span class="sc">;</span> <span class="i">$AtomID2</span> = <span class="i">$EdgesAtomsIDs</span>[<span class="i">$Index</span> + <span class="n">1</span>]<span class="sc">;</span>
|
|
|
1079 1066
|
|
|
1080 1067 <span class="c"># Get reference to bond object...</span>
|
|
|
1081 1068 <span class="i">$Bond</span> = <span class="i">$This</span><span class="i">->GetEdgeProperty</span><span class="s">(</span><span class="q">'Bond'</span><span class="cm">,</span> <span class="i">$AtomID1</span><span class="cm">,</span> <span class="i">$AtomID2</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1082 1069
|
|
|
1083 1070 <span class="c"># Make a new bond object and update its atom references...</span>
|
|
|
1084 1071 <span class="i">$NewBond</span> = <span class="i">$Bond</span><span class="i">->Copy</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1085 1072 <span class="i">$NewAtom1</span> = <span class="i">$AtomsIDsToNewAtoms</span>{<span class="i">$AtomID1</span>}<span class="sc">;</span>
|
|
|
1086 1073 <span class="i">$NewAtom2</span> = <span class="i">$AtomsIDsToNewAtoms</span>{<span class="i">$AtomID2</span>}<span class="sc">;</span>
|
|
|
1087 1074 <span class="i">$NewBond</span><span class="i">->SetAtoms</span><span class="s">(</span><span class="i">$NewAtom1</span><span class="cm">,</span> <span class="i">$NewAtom2</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1088 1075
|
|
|
1089 1076 <span class="c"># Update bond object reference in the new molecule...</span>
|
|
|
1090 1077 <span class="i">$NewMolecule</span><span class="i">->UpdateEdgeProperty</span><span class="s">(</span><span class="q">'Bond'</span><span class="cm">,</span> <span class="i">$NewBond</span><span class="cm">,</span> <span class="i">$AtomID1</span><span class="cm">,</span> <span class="i">$AtomID2</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1091 1078 <span class="s">}</span>
|
|
|
1092 1079
|
|
|
1093 1080 <span class="k">return</span> <span class="i">$NewMolecule</span><span class="sc">;</span>
|
|
|
1094 1081 <span class="s">}</span>
|
|
|
1095 1082
|
|
|
1096 1083 <span class="c"># Get number of connected components...</span>
|
|
|
1097 1084 <span class="c">#</span>
|
|
|
1098 <a name="GetNumOfConnectedComponents-"></a>1085 <span class="k">sub </span><span class="m">GetNumOfConnectedComponents</span> <span class="s">{</span>
|
|
|
1099 1086 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
1100 1087 <span class="k">my</span><span class="s">(</span><span class="i">$NumOfComponents</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1101 1088
|
|
|
1102 1089 <span class="i">$NumOfComponents</span> = <span class="i">$This</span><span class="i">->GetConnectedComponentsVertices</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1103 1090
|
|
|
1104 1091 <span class="k">return</span> <span class="i">$NumOfComponents</span><span class="sc">;</span>
|
|
|
1105 1092 <span class="s">}</span>
|
|
|
1106 1093
|
|
|
1107 1094 <span class="c"># Return a reference to an array containing molecules corresponding</span>
|
|
|
1108 1095 <span class="c"># to connected components sorted in decreasing order of component size...</span>
|
|
|
1109 1096 <span class="c">#</span>
|
|
|
1110 <a name="GetConnectedComponents-"></a>1097 <span class="k">sub </span><span class="m">GetConnectedComponents</span> <span class="s">{</span>
|
|
|
1111 1098 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
1112 1099 <span class="k">my</span><span class="s">(</span><span class="i">$Index</span><span class="cm">,</span> <span class="i">@ComponentMolecules</span><span class="cm">,</span> <span class="i">@ConnectedComponents</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1113 1100
|
|
|
1114 1101 <span class="i">@ConnectedComponents</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1115 1102 <span class="i">@ConnectedComponents</span> = <span class="i">$This</span><span class="i">->GetConnectedComponentsVertices</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1116 1103 <span class="i">@ComponentMolecules</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1117 1104
|
|
|
1118 1105 <span class="k">for</span> <span class="i">$Index</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#ConnectedComponents</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1119 1106 <span class="k">push</span> <span class="i">@ComponentMolecules</span><span class="cm">,</span> <span class="i">$This</span><span class="i">->_GetConnectedComponent</span><span class="s">(</span>\<span class="i">@ConnectedComponents</span><span class="cm">,</span> <span class="i">$Index</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1120 1107 <span class="s">}</span>
|
|
|
1121 1108 <span class="k">return</span> <span class="i">@ComponentMolecules</span><span class="sc">;</span>
|
|
|
1122 1109 <span class="s">}</span>
|
|
|
1123 1110
|
|
|
1124 1111 <span class="c"># Return a reference to largest connected component as a molecule object...</span>
|
|
|
1125 1112 <span class="c">#</span>
|
|
|
1126 <a name="GetLargestConnectedComponent-"></a>1113 <span class="k">sub </span><span class="m">GetLargestConnectedComponent</span> <span class="s">{</span>
|
|
|
1127 1114 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
1128 1115 <span class="k">my</span><span class="s">(</span><span class="i">$LargestComponentIndex</span><span class="cm">,</span> <span class="i">@ConnectedComponents</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1129 1116
|
|
|
1130 1117 <span class="i">$LargestComponentIndex</span> = <span class="n">0</span><span class="sc">;</span>
|
|
|
1131 1118 <span class="i">@ConnectedComponents</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1132 1119 <span class="i">@ConnectedComponents</span> = <span class="i">$This</span><span class="i">->GetConnectedComponentsVertices</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1133 1120
|
|
|
1134 1121 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetConnectedComponent</span><span class="s">(</span>\<span class="i">@ConnectedComponents</span><span class="cm">,</span> <span class="i">$LargestComponentIndex</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1135 1122 <span class="s">}</span>
|
|
|
1136 1123
|
|
|
1137 1124 <span class="c"># Return connected component as a molecule...</span>
|
|
|
1138 1125 <span class="c">#</span>
|
|
|
1139 <a name="_GetConnectedComponent-"></a>1126 <span class="k">sub </span><span class="m">_GetConnectedComponent</span> <span class="s">{</span>
|
|
|
1140 1127 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$ConnectedComponentsRef</span><span class="cm">,</span> <span class="i">$ComponentIndex</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
1141 1128 <span class="k">my</span><span class="s">(</span><span class="i">$ComponentMolecule</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1142 1129
|
|
|
1143 1130 <span class="c"># Copy existing molecule...</span>
|
|
|
1144 1131 <span class="i">$ComponentMolecule</span> = <span class="i">$This</span><span class="i">->Copy</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1145 1132
|
|
|
1146 1133 <span class="c"># Delete all atoms besides the ones in specified component...</span>
|
|
|
1147 1134 <span class="i">$ComponentMolecule</span><span class="i">->_DeleteConnectedComponents</span><span class="s">(</span><span class="i">$ConnectedComponentsRef</span><span class="cm">,</span> <span class="i">$ComponentIndex</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1148 1135
|
|
|
1149 1136 <span class="c"># Clear any deteced rings...</span>
|
|
|
1150 1137 <span class="k">if</span> <span class="s">(</span><span class="i">$ComponentMolecule</span><span class="i">->HasRings</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1151 1138 <span class="i">$ComponentMolecule</span><span class="i">->ClearRings</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1152 1139 <span class="s">}</span>
|
|
|
1153 1140 <span class="k">return</span> <span class="i">$ComponentMolecule</span><span class="sc">;</span>
|
|
|
1154 1141 <span class="s">}</span>
|
|
|
1155 1142
|
|
|
1156 1143 <span class="c"># Delete atoms corresponding to all connected components except the one specified...</span>
|
|
|
1157 1144 <span class="c">#</span>
|
|
|
1158 <a name="_DeleteConnectedComponents-"></a>1145 <span class="k">sub </span><span class="m">_DeleteConnectedComponents</span> <span class="s">{</span>
|
|
|
1159 1146 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$ConnectedComponentsRef</span><span class="cm">,</span> <span class="i">$KeepComponentIndex</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
1160 1147 <span class="k">my</span><span class="s">(</span><span class="i">$Index</span><span class="cm">,</span> <span class="i">$AtomID</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1161 1148
|
|
|
1162 1149 <span class="j">INDEX:</span> <span class="k">for</span> <span class="i">$Index</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#</span>{<span class="i">$ConnectedComponentsRef</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
1163 1150 <span class="k">if</span> <span class="s">(</span><span class="i">$Index</span> == <span class="i">$KeepComponentIndex</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1164 1151 <span class="k">next</span> <span class="j">INDEX</span><span class="sc">;</span>
|
|
|
1165 1152 <span class="s">}</span>
|
|
|
1166 1153 <span class="k">for</span> <span class="i">$AtomID</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$ConnectedComponentsRef</span>->[<span class="i">$Index</span>]}<span class="s">)</span> <span class="s">{</span>
|
|
|
1167 1154 <span class="i">$This</span><span class="i">->DeleteVertex</span><span class="s">(</span><span class="i">$AtomID</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1168 1155 <span class="s">}</span>
|
|
|
1169 1156 <span class="s">}</span>
|
|
|
1170 1157 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
1171 1158 <span class="s">}</span>
|
|
|
1172 1159
|
|
|
1173 1160 <span class="c"># Return an array containing references to atom arrays corresponding to atoms of</span>
|
|
|
1174 1161 <span class="c"># connected components sorted in order of their decreasing size...</span>
|
|
|
1175 1162 <span class="c">#</span>
|
|
|
1176 <a name="GetConnectedComponentsAtoms-"></a>1163 <span class="k">sub </span><span class="m">GetConnectedComponentsAtoms</span> <span class="s">{</span>
|
|
|
1177 1164 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
1178 1165 <span class="k">my</span><span class="s">(</span><span class="i">$Index</span><span class="cm">,</span> <span class="i">@ComponentsAtoms</span><span class="cm">,</span> <span class="i">@ConnectedComponents</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1179 1166
|
|
|
1180 1167 <span class="i">@ConnectedComponents</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1181 1168 <span class="i">@ConnectedComponents</span> = <span class="i">$This</span><span class="i">->GetConnectedComponentsVertices</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1182 1169
|
|
|
1183 1170 <span class="i">@ComponentsAtoms</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1184 1171 <span class="k">for</span> <span class="i">$Index</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#ConnectedComponents</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1185 1172 <span class="k">my</span><span class="s">(</span><span class="i">@ComponentAtoms</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1186 1173
|
|
|
1187 1174 <span class="i">@ComponentAtoms</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1188 1175 <span class="i">@ComponentAtoms</span> = <span class="i">$This</span><span class="i">->_GetConnectedComponentAtoms</span><span class="s">(</span>\<span class="i">@ConnectedComponents</span><span class="cm">,</span> <span class="i">$Index</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1189 1176 <span class="k">push</span> <span class="i">@ComponentsAtoms</span><span class="cm">,</span> \<span class="i">@ComponentAtoms</span><span class="sc">;</span>
|
|
|
1190 1177 <span class="s">}</span>
|
|
|
1191 1178 <span class="k">return</span> <span class="i">@ComponentsAtoms</span><span class="sc">;</span>
|
|
|
1192 1179 <span class="s">}</span>
|
|
|
1193 1180
|
|
|
1194 1181 <span class="c"># Return an array containing atoms correspondig to largest connected component...</span>
|
|
|
1195 1182 <span class="c">#</span>
|
|
|
1196 <a name="GetLargestConnectedComponentAtoms-"></a>1183 <span class="k">sub </span><span class="m">GetLargestConnectedComponentAtoms</span> <span class="s">{</span>
|
|
|
1197 1184 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
1198 1185 <span class="k">my</span><span class="s">(</span><span class="i">$LargestComponentIndex</span><span class="cm">,</span> <span class="i">@ConnectedComponents</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1199 1186
|
|
|
1200 1187 <span class="i">$LargestComponentIndex</span> = <span class="n">0</span><span class="sc">;</span>
|
|
|
1201 1188 <span class="i">@ConnectedComponents</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1202 1189 <span class="i">@ConnectedComponents</span> = <span class="i">$This</span><span class="i">->GetConnectedComponentsVertices</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1203 1190
|
|
|
1204 1191 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetConnectedComponentAtoms</span><span class="s">(</span>\<span class="i">@ConnectedComponents</span><span class="cm">,</span> <span class="i">$LargestComponentIndex</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1205 1192 <span class="s">}</span>
|
|
|
1206 1193
|
|
|
1207 1194 <span class="c"># Return an array containing atoms corresponding to specified connected component...</span>
|
|
|
1208 1195 <span class="c">#</span>
|
|
|
1209 <a name="_GetConnectedComponentAtoms-"></a>1196 <span class="k">sub </span><span class="m">_GetConnectedComponentAtoms</span> <span class="s">{</span>
|
|
|
1210 1197 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$ConnectedComponentsRef</span><span class="cm">,</span> <span class="i">$ComponentIndex</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
1211 1198 <span class="k">my</span><span class="s">(</span><span class="i">$AtomID</span><span class="cm">,</span> <span class="i">@AtomIDs</span><span class="cm">,</span> <span class="i">@ComponentAtoms</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1212 1199
|
|
|
1213 1200 <span class="i">@ComponentAtoms</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1214 1201 <span class="i">@AtomIDs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1215 1202
|
|
|
1216 1203 <span class="k">for</span> <span class="i">$AtomID</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$ConnectedComponentsRef</span>->[<span class="i">$ComponentIndex</span>]}<span class="s">)</span> <span class="s">{</span>
|
|
|
1217 1204 <span class="k">push</span> <span class="i">@AtomIDs</span><span class="cm">,</span> <span class="i">$AtomID</span><span class="sc">;</span>
|
|
|
1218 1205 <span class="s">}</span>
|
|
|
1219 1206 <span class="i">@ComponentAtoms</span> = <span class="i">$This</span><span class="i">->_GetAtomsFromAtomIDs</span><span class="s">(</span><span class="i">@AtomIDs</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1220 1207
|
|
|
1221 1208 <span class="k">return</span> <span class="i">@ComponentAtoms</span><span class="sc">;</span>
|
|
|
1222 1209 <span class="s">}</span>
|
|
|
1223 1210
|
|
|
1224 1211 <span class="c"># Except for the largest connected component, delete atoms corresponding to all other</span>
|
|
|
1225 1212 <span class="c"># connected components...</span>
|
|
|
1226 1213 <span class="c">#</span>
|
|
|
1227 <a name="KeepLargestComponent-"></a>1214 <span class="k">sub </span><span class="m">KeepLargestComponent</span> <span class="s">{</span>
|
|
|
1228 1215 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
1229 1216 <span class="k">my</span><span class="s">(</span><span class="i">$LargestComponentIndex</span><span class="cm">,</span> <span class="i">@ConnectedComponents</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1230 1217
|
|
|
1231 1218 <span class="i">@ConnectedComponents</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1232 1219 <span class="i">@ConnectedComponents</span> = <span class="i">$This</span><span class="i">->GetConnectedComponentsVertices</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1233 1220 <span class="k">if</span> <span class="s">(</span><span class="i">@ConnectedComponents</span> == <span class="n">1</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1234 1221 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
1235 1222 <span class="s">}</span>
|
|
|
1236 1223 <span class="i">$LargestComponentIndex</span> = <span class="n">0</span><span class="sc">;</span>
|
|
|
1237 1224 <span class="i">$This</span><span class="i">->_DeleteConnectedComponents</span><span class="s">(</span>\<span class="i">@ConnectedComponents</span><span class="cm">,</span> <span class="i">$LargestComponentIndex</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1238 1225
|
|
|
1239 1226 <span class="c"># Clear any deteced rings...</span>
|
|
|
1240 1227 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span><span class="i">->HasRings</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1241 1228 <span class="i">$This</span><span class="i">->ClearRings</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1242 1229 <span class="s">}</span>
|
|
|
1243 1230
|
|
|
1244 1231 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
1245 1232 <span class="s">}</span>
|
|
|
1246 1233
|
|
|
1247 1234 <span class="c"># Get an array of topologically sorted atoms starting from a specified atom or</span>
|
|
|
1248 1235 <span class="c"># an arbitrary atom in the molecule...</span>
|
|
|
1249 1236 <span class="c">#</span>
|
|
|
1250 <a name="GetTopologicallySortedAtoms-"></a>1237 <span class="k">sub </span><span class="m">GetTopologicallySortedAtoms</span> <span class="s">{</span>
|
|
|
1251 1238 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$StartAtom</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
1252 1239 <span class="k">my</span><span class="s">(</span><span class="i">@SortedAtoms</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1253 1240
|
|
|
1254 1241 <span class="i">@SortedAtoms</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1255 1242 <span class="k">if</span> <span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$StartAtom</span><span class="s">)</span> && !<span class="i">$This</span><span class="i">->HasAtom</span><span class="s">(</span><span class="i">$StartAtom</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1256 1243 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->_GetTopologicallySortedAtoms: No atoms retrieved: Start atom doesn't exist..."</span><span class="sc">;</span>
|
|
|
1257 1244 <span class="k">return</span> <span class="i">@SortedAtoms</span><span class="sc">;</span>
|
|
|
1258 1245 <span class="s">}</span>
|
|
|
1259 1246 <span class="k">my</span><span class="s">(</span><span class="i">$StartAtomID</span><span class="cm">,</span> <span class="i">@AtomIDs</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1260 1247
|
|
|
1261 1248 <span class="i">@AtomIDs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1262 1249 <span class="i">$StartAtomID</span> = <span class="k">defined</span><span class="s">(</span><span class="i">$StartAtom</span><span class="s">)</span> ? <span class="i">$StartAtom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span> <span class="co">:</span> <span class="k">undef</span><span class="sc">;</span>
|
|
|
1263 1250
|
|
|
1264 1251 <span class="i">@AtomIDs</span> = <span class="i">$This</span><span class="i">->GetTopologicallySortedVertices</span><span class="s">(</span><span class="i">$StartAtomID</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1265 1252 <span class="i">@SortedAtoms</span> = <span class="i">$This</span><span class="i">->_GetAtomsFromAtomIDs</span><span class="s">(</span><span class="i">@AtomIDs</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1266 1253
|
|
|
1267 1254 <span class="k">return</span> <span class="i">@SortedAtoms</span><span class="sc">;</span>
|
|
|
1268 1255 <span class="s">}</span>
|
|
|
1269 1256
|
|
|
1270 1257 <span class="c"># Detect rings in molecule...</span>
|
|
|
1271 1258 <span class="c">#</span>
|
|
|
1272 <a name="DetectRings-"></a>1259 <span class="k">sub </span><span class="m">DetectRings</span> <span class="s">{</span>
|
|
|
1273 1260 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
1274 1261
|
|
|
1275 1262 <span class="c"># Use graph method to detect all cycles and associate 'em to graph as graph</span>
|
|
|
1276 1263 <span class="c"># and vertex properties...</span>
|
|
|
1277 1264 <span class="k">return</span> <span class="i">$This</span><span class="i">->DetectCycles</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1278 1265 <span class="s">}</span>
|
|
|
1279 1266
|
|
|
1280 1267 <span class="c"># Clear rings in molecule...</span>
|
|
|
1281 1268 <span class="c">#</span>
|
|
|
1282 <a name="ClearRings-"></a>1269 <span class="k">sub </span><span class="m">ClearRings</span> <span class="s">{</span>
|
|
|
1283 1270 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
1284 1271
|
|
|
1285 1272 <span class="c"># Use graph method to clear all cycles...</span>
|
|
|
1286 1273 <span class="i">$This</span><span class="i">->ClearCycles</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1287 1274
|
|
|
1288 1275 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
1289 1276 <span class="s">}</span>
|
|
|
1290 1277
|
|
|
1291 1278 <span class="c"># Setup rings type paths to use during all ring related methods. Possible values:</span>
|
|
|
1292 1279 <span class="c"># Independent or All. Default is to use Independent rings.</span>
|
|
|
1293 1280 <span class="c">#</span>
|
|
|
1294 <a name="SetActiveRings-"></a>1281 <span class="k">sub </span><span class="m">SetActiveRings</span> <span class="s">{</span>
|
|
|
1295 1282 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$RingsType</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
1296 1283
|
|
|
1297 1284 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$This</span><span class="i">->SetActiveCyclicPaths</span><span class="s">(</span><span class="i">$RingsType</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1298 1285 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
|
|
|
1299 1286 <span class="s">}</span>
|
|
|
1300 1287 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
1301 1288 <span class="s">}</span>
|
|
|
1302 1289
|
|
|
1303 1290 <span class="c"># Is it a supported aromaticity model?</span>
|
|
|
1304 1291 <span class="c">#</span>
|
|
|
1305 <a name="IsSupportedAromaticityModel-"></a>1292 <span class="k">sub </span><span class="m">IsSupportedAromaticityModel</span> <span class="s">{</span>
|
|
|
1306 1293 <span class="k">my</span><span class="s">(</span><span class="i">$FirstParameter</span><span class="cm">,</span> <span class="i">$SecondParameter</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
1307 1294 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$AromaticityModel</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1308 1295
|
|
|
1309 1296 <span class="k">if</span> <span class="s">(</span><span class="i">_IsMolecule</span><span class="s">(</span><span class="i">$FirstParameter</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1310 1297 <span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$AromaticityModel</span><span class="s">)</span> = <span class="s">(</span><span class="i">$FirstParameter</span><span class="cm">,</span> <span class="i">$SecondParameter</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1311 1298 <span class="s">}</span>
|
|
|
1312 1299 <span class="k">else</span> <span class="s">{</span>
|
|
|
1313 1300 <span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$AromaticityModel</span><span class="s">)</span> = <span class="s">(</span><span class="k">undef</span><span class="cm">,</span> <span class="i">$FirstParameter</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1314 1301 <span class="s">}</span>
|
|
|
1315 1302
|
|
|
1316 1303 <span class="k">return</span> <span class="k">exists</span> <span class="i">$CanonicalAromaticityModelNamesMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$AromaticityModel</span><span class="s">)</span>} ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
1317 1304 <span class="s">}</span>
|
|
|
1318 1305
|
|
|
1319 1306 <span class="c"># Get a list of supported aromaticity model names...</span>
|
|
|
1320 1307 <span class="c">#</span>
|
|
|
1321 <a name="GetSupportedAromaticityModels-"></a>1308 <span class="k">sub </span><span class="m">GetSupportedAromaticityModels</span> <span class="s">{</span>
|
|
|
1322 1309 <span class="k">return</span> <span class="s">(</span><span class="k">sort</span> <span class="k">values</span> <span class="i">%CanonicalAromaticityModelNamesMap</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1323 1310 <span class="s">}</span>
|
|
|
1324 1311
|
|
|
1325 1312 <span class="c"># Set aromaticity model...</span>
|
|
|
1326 1313 <span class="c">#</span>
|
|
|
1327 <a name="SetAromaticityModel-"></a>1314 <span class="k">sub </span><span class="m">SetAromaticityModel</span> <span class="s">{</span>
|
|
|
1328 1315 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$AromaticityModel</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
1329 1316
|
|
|
1330 1317 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->IsSupportedAromaticityModel</span><span class="s">(</span><span class="i">$AromaticityModel</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1331 1318 <span class="k">my</span><span class="s">(</span><span class="i">@SupportedModels</span><span class="s">)</span> = <span class="i">$This</span><span class="i">->GetSupportedAromaticityModels</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1332 1319
|
|
|
1333 1320 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->SetAromaticityModel: The current release of MayaChemTools doesn't support the specified aromaticity model $AromaticityModel. Supported aromaticity models defined in AromaticityModelsData.csv file are: @SupportedModels . Using MayaChemToolsAromaticityModel..."</span><span class="sc">;</span>
|
|
|
1334 1321 <span class="i">$AromaticityModel</span> = <span class="q">'MayaChemToolsAromaticityModel'</span><span class="sc">;</span>
|
|
|
1335 1322 <span class="s">}</span>
|
|
|
1336 1323
|
|
|
1337 1324 <span class="i">$This</span><span class="i">->SetProperty</span><span class="s">(</span><span class="q">'AromaticityModel'</span><span class="cm">,</span> <span class="i">$AromaticityModel</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1338 1325
|
|
|
1339 1326 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
1340 1327 <span class="s">}</span>
|
|
|
1341 1328
|
|
|
1342 1329 <span class="c"># Get aromaticity model...</span>
|
|
|
1343 1330 <span class="c">#</span>
|
|
|
1344 <a name="GetAromaticityModel-"></a>1331 <span class="k">sub </span><span class="m">GetAromaticityModel</span> <span class="s">{</span>
|
|
|
1345 1332 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
1346 1333
|
|
|
1347 1334 <span class="c"># Is ValenceModel property explicitly set?</span>
|
|
|
1348 1335 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'AromaticityModel'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1349 1336 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'AromaticityModel'</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1350 1337 <span class="s">}</span>
|
|
|
1351 1338
|
|
|
1352 1339 <span class="c"># Used internal aromaticity model as default model...</span>
|
|
|
1353 1340 <span class="k">return</span> <span class="q">'MayaChemToolsAromaticityModel'</span><span class="sc">;</span>
|
|
|
1354 1341 <span class="s">}</span>
|
|
|
1355 1342
|
|
|
1356 1343 <span class="c"># Identify aromatic rings and ring systems in a molecule and set aromaticity for</span>
|
|
|
1357 1344 <span class="c"># corresponding atoms and bonds.</span>
|
|
|
1358 1345 <span class="c">#</span>
|
|
|
1359 1346 <span class="c"># What is aromaticity? [ Ref 124 ] It's in the code of the implementer, did you</span>
|
|
|
1360 1347 <span class="c"># say? Agree. The implementation of aromaticity varies widely across different</span>
|
|
|
1361 1348 <span class="c"># packages [ Ref 125 ]; additionally, the implementation details are not always</span>
|
|
|
1362 1349 <span class="c"># completely available, and it's not possible to figure out the exact implementation</span>
|
|
|
1363 1350 <span class="c"># of aromaticity across various packages. Using the publicly available information,</span>
|
|
|
1364 1351 <span class="c"># however, one can try to reproduce the available results to the extent possible,</span>
|
|
|
1365 1352 <span class="c"># along with parameterizing all the control parameters used to implement different</span>
|
|
|
1366 1353 <span class="c"># aromaticity models, and that's exactly what the current release of MayaChemTools</span>
|
|
|
1367 1354 <span class="c"># does.</span>
|
|
|
1368 1355 <span class="c">#</span>
|
|
|
1369 1356 <span class="c"># The implementation of aromaticity corresponding to various aromaticity models in</span>
|
|
|
1370 1357 <span class="c"># MayaChemTools package is driven by an external CSV file AromaticityModelsData.csv,</span>
|
|
|
1371 1358 <span class="c"># which is distributed with the package and is available in lib/data directory. The CSV</span>
|
|
|
1372 1359 <span class="c"># files contains names of supported aromaticity models, along with various control</span>
|
|
|
1373 1360 <span class="c"># parameters and their values. This file is loaded and processed during instantiation</span>
|
|
|
1374 1361 <span class="c"># of Molecule class and data corresponding to specific aromaticity model are used</span>
|
|
|
1375 1362 <span class="c"># to detect aromaticity for that model. Any new aromaticity model added to the</span>
|
|
|
1376 1363 <span class="c"># aromaticity data file, using different combinations of values for existing control</span>
|
|
|
1377 1364 <span class="c"># parameters would work without any changes to the code; the addition of any new</span>
|
|
|
1378 1365 <span class="c"># control parameters, however, requires its implementation in the code used to</span>
|
|
|
1379 1366 <span class="c"># calculate number of pi electrons available towards delocalization in a ring or ring</span>
|
|
|
1380 1367 <span class="c"># systems.</span>
|
|
|
1381 1368 <span class="c">#</span>
|
|
|
1382 1369 <span class="c"># The current release of MayaChemTools package supports these aromaticity</span>
|
|
|
1383 1370 <span class="c"># models: MDLAromaticityModel, TriposAromaticityModel, MMFFAromaticityModel,</span>
|
|
|
1384 1371 <span class="c"># ChemAxonBasicAromaticityModel, ChemAxonGeneralAromaticityModel,</span>
|
|
|
1385 1372 <span class="c"># DaylightAromaticityModel, MayaChemToolsAromaticityModel.</span>
|
|
|
1386 1373 <span class="c">#</span>
|
|
|
1387 1374 <span class="c"># The current list of control parameters available to detect aromaticity corresponding</span>
|
|
|
1388 1375 <span class="c"># to different aromaticity models are: AllowHeteroRingAtoms, HeteroRingAtomsList,</span>
|
|
|
1389 1376 <span class="c"># AllowExocyclicDoubleBonds, AllowHomoNuclearExocyclicDoubleBonds,</span>
|
|
|
1390 1377 <span class="c"># AllowElectronegativeRingAtomExocyclicDoubleBonds, AllowRingAtomFormalCharge,</span>
|
|
|
1391 1378 <span class="c"># AllowHeteroRingAtomFormalCharge, MinimumRingSize. The values for these control</span>
|
|
|
1392 1379 <span class="c"># parameters are specified in AromaticityModelsData.csv file.</span>
|
|
|
1393 1380 <span class="c">#</span>
|
|
|
1394 1381 <span class="c"># Although definition of aromaticity differs across various aromaticity models, a ring</span>
|
|
|
1395 1382 <span class="c"># or a ring system containing 4n + 2 pi electrons (Huckel's rule) corresponding to</span>
|
|
|
1396 1383 <span class="c"># alternate single and double bonds, in general, is considered aromatic.</span>
|
|
|
1397 1384 <span class="c">#</span>
|
|
|
1398 1385 <span class="c"># The available valence free electrons on heterocyclic ring atoms, involved in two single</span>
|
|
|
1399 1386 <span class="c"># ring bonds, are also allowed to participate in pi electron delocalizaiton for most of</span>
|
|
|
1400 1387 <span class="c"># the supported aromaticity models.</span>
|
|
|
1401 1388 <span class="c">#</span>
|
|
|
1402 1389 <span class="c"># The presence of exocyclic terminal double bond on ring atoms involved in pi electron</span>
|
|
|
1403 1390 <span class="c"># delocalization is only allowed for some of the aromaticity models. Additionally, the type</span>
|
|
|
1404 1391 <span class="c"># atoms involved in exocyclic terminal double bonds may result in making a ring or ring</span>
|
|
|
1405 1392 <span class="c"># system non-aromatic.</span>
|
|
|
1406 1393 <span class="c">#</span>
|
|
|
1407 <a name="DetectAromaticity-"></a>1394 <span class="k">sub </span><span class="m">DetectAromaticity</span> <span class="s">{</span>
|
|
|
1408 1395 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
1409 1396
|
|
|
1410 1397 <span class="c"># Delete aromaticity property for atoms and bonds...</span>
|
|
|
1411 1398 <span class="i">$This</span><span class="i">->DeleteAromaticity</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1412 1399
|
|
|
1413 1400 <span class="c"># Any ring out there...</span>
|
|
|
1414 1401 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasRings</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1415 1402 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
1416 1403 <span class="s">}</span>
|
|
|
1417 1404
|
|
|
1418 1405 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span><span class="i">->HasFusedRings</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1419 1406 <span class="i">$This</span><span class="i">->_DetectAromaticityUsingFusedRingSets</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1420 1407 <span class="s">}</span>
|
|
|
1421 1408 <span class="k">else</span> <span class="s">{</span>
|
|
|
1422 1409 <span class="i">$This</span><span class="i">->_DetectAromaticityUsingIndividualRings</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1423 1410 <span class="s">}</span>
|
|
|
1424 1411 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
1425 1412 <span class="s">}</span>
|
|
|
1426 1413
|
|
|
1427 1414 <span class="c"># Go over all rings and set aromaticity property for corresponding ring atoms</span>
|
|
|
1428 1415 <span class="c"># and bonds involved in aromatic rings...</span>
|
|
|
1429 1416 <span class="c">#</span>
|
|
|
1430 <a name="_DetectAromaticityUsingIndividualRings-"></a>1417 <span class="k">sub </span><span class="m">_DetectAromaticityUsingIndividualRings</span> <span class="s">{</span>
|
|
|
1431 1418 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
1432 1419
|
|
|
1433 1420 <span class="k">return</span> <span class="i">$This</span><span class="i">->_DetectRingsAromaticity</span><span class="s">(</span><span class="i">$This</span><span class="i">->GetRings</span><span class="s">(</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1434 1421 <span class="s">}</span>
|
|
|
1435 1422
|
|
|
1436 1423 <span class="c"># For each fused ring set, detect aromaticity by treating all of its ring as one aromatic</span>
|
|
|
1437 1424 <span class="c"># system for counting pi electrons to satisfy Huckel's rule; In case of a failure, rings in</span>
|
|
|
1438 1425 <span class="c"># fused set are treated individually for aromaticity detection. Additionally, non-fused</span>
|
|
|
1439 1426 <span class="c"># rings are handled on their own during aromaticity detection.</span>
|
|
|
1440 1427 <span class="c">#</span>
|
|
|
1441 1428 <span class="c"># Note:</span>
|
|
|
1442 1429 <span class="c"># . pi electrons in common bonds involved in fused ring sets are only counted once.</span>
|
|
|
1443 1430 <span class="c">#</span>
|
|
|
1444 1431 <span class="c">#</span>
|
|
|
1445 <a name="_DetectAromaticityUsingFusedRingSets-"></a>1432 <span class="k">sub </span><span class="m">_DetectAromaticityUsingFusedRingSets</span> <span class="s">{</span>
|
|
|
1446 1433 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
1447 1434 <span class="k">my</span><span class="s">(</span><span class="i">$Index</span><span class="cm">,</span> <span class="i">$RingAtomsRef</span><span class="cm">,</span> <span class="i">$FusedRingSetRef</span><span class="cm">,</span> <span class="i">$FusedRingSetsRef</span><span class="cm">,</span> <span class="i">$NonFusedRingsRef</span><span class="cm">,</span> <span class="i">@FusedRingSetIsAromatic</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1448 1435
|
|
|
1449 1436 <span class="s">(</span><span class="i">$FusedRingSetsRef</span><span class="cm">,</span> <span class="i">$NonFusedRingsRef</span><span class="s">)</span> = <span class="i">$This</span><span class="i">->GetFusedAndNonFusedRings</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1450 1437
|
|
|
1451 1438 <span class="i">@FusedRingSetIsAromatic</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1452 1439 <span class="j">RINGSET:</span> <span class="k">for</span> <span class="i">$Index</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#</span>{<span class="i">$FusedRingSetsRef</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
1453 1440 <span class="i">$FusedRingSetRef</span> = <span class="i">$FusedRingSetsRef</span>->[<span class="i">$Index</span>]<span class="sc">;</span>
|
|
|
1454 1441 <span class="i">$FusedRingSetIsAromatic</span>[<span class="i">$Index</span>] = <span class="n">0</span><span class="sc">;</span>
|
|
|
1455 1442
|
|
|
1456 1443 <span class="k">my</span><span class="s">(</span><span class="i">$NumOfPiElectronsInRingSet</span><span class="cm">,</span> <span class="i">$NumOfPiElectronsInRing</span><span class="cm">,</span> <span class="i">$Bond</span><span class="cm">,</span> <span class="i">$BondID</span><span class="cm">,</span> <span class="i">%FusedRingSetsBondsMap</span><span class="cm">,</span> <span class="i">%FusedRingSetsBondsVisitedMap</span><span class="cm">,</span> <span class="i">%FusedRingBondsMap</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1457 1444
|
|
|
1458 1445 <span class="i">$NumOfPiElectronsInRingSet</span> = <span class="n">0</span><span class="sc">;</span>
|
|
|
1459 1446
|
|
|
1460 1447 <span class="i">%FusedRingSetsBondsMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1461 1448 <span class="i">%FusedRingSetsBondsVisitedMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1462 1449 <span class="i">%FusedRingBondsMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1463 1450
|
|
|
1464 1451 <span class="c"># Setup a bond ID map for all bonds in fused ring set and another one</span>
|
|
|
1465 1452 <span class="c"># for bonds involved in more than one ring...</span>
|
|
|
1466 1453 <span class="c">#</span>
|
|
|
1467 1454 <span class="k">for</span> <span class="i">$RingAtomsRef</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$FusedRingSetRef</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
1468 1455 <span class="k">for</span> <span class="i">$Bond</span> <span class="s">(</span><span class="i">$This</span><span class="i">->GetRingBonds</span><span class="s">(</span><span class="i">@</span>{<span class="i">$RingAtomsRef</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1469 1456 <span class="i">$BondID</span> = <span class="i">$Bond</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1470 1457 <span class="i">$FusedRingSetsBondsMap</span>{<span class="i">$BondID</span>} = <span class="i">$BondID</span><span class="sc">;</span>
|
|
|
1471 1458
|
|
|
1472 1459 <span class="k">if</span> <span class="s">(</span><span class="i">$Bond</span><span class="i">->GetNumOfRings</span><span class="s">(</span><span class="s">)</span> == <span class="n">2</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1473 1460 <span class="i">$FusedRingBondsMap</span>{<span class="i">$BondID</span>} = <span class="i">$BondID</span><span class="sc">;</span>
|
|
|
1474 1461 <span class="s">}</span>
|
|
|
1475 1462 <span class="s">}</span>
|
|
|
1476 1463 <span class="s">}</span>
|
|
|
1477 1464
|
|
|
1478 1465 <span class="k">for</span> <span class="i">$RingAtomsRef</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$FusedRingSetRef</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
1479 1466 <span class="k">my</span><span class="s">(</span><span class="i">@RingBonds</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1480 1467
|
|
|
1481 1468 <span class="i">@RingBonds</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1482 1469 <span class="i">@RingBonds</span> = <span class="i">$This</span><span class="i">->GetRingBonds</span><span class="s">(</span><span class="i">@</span>{<span class="i">$RingAtomsRef</span>}<span class="s">)</span><span class="sc">;</span>
|
|
|
1483 1470 <span class="i">$NumOfPiElectronsInRing</span> = <span class="i">$This</span><span class="i">->_GetNumOfPiElectronsAvailableForDelocalization</span><span class="s">(</span><span class="i">$RingAtomsRef</span><span class="cm">,</span> \<span class="i">@RingBonds</span><span class="cm">,</span> \<span class="i">%FusedRingSetsBondsMap</span><span class="cm">,</span> \<span class="i">%FusedRingSetsBondsVisitedMap</span><span class="cm">,</span> \<span class="i">%FusedRingBondsMap</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1484 1471
|
|
|
1485 1472 <span class="k">if</span> <span class="s">(</span>!<span class="i">$NumOfPiElectronsInRing</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1486 1473 <span class="k">next</span> <span class="j">RINGSET</span><span class="sc">;</span>
|
|
|
1487 1474 <span class="s">}</span>
|
|
|
1488 1475 <span class="i">$NumOfPiElectronsInRingSet</span> += <span class="i">$NumOfPiElectronsInRing</span><span class="sc">;</span>
|
|
|
1489 1476 <span class="s">}</span>
|
|
|
1490 1477 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span><span class="i">->_DoPiElectronSatifyHuckelsRule</span><span class="s">(</span><span class="i">$NumOfPiElectronsInRingSet</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1491 1478 <span class="i">$FusedRingSetIsAromatic</span>[<span class="i">$Index</span>] = <span class="n">1</span><span class="sc">;</span>
|
|
|
1492 1479 <span class="s">}</span>
|
|
|
1493 1480 <span class="s">}</span>
|
|
|
1494 1481
|
|
|
1495 1482 <span class="c"># Set atom and bond aromatic flags for ring sets whose pi electrons satisfy Huckel's rule; otherwise,</span>
|
|
|
1496 1483 <span class="c"># treat rings in a ring set as individual rings for detecting aromaticity...</span>
|
|
|
1497 1484 <span class="k">for</span> <span class="i">$Index</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#</span>{<span class="i">$FusedRingSetsRef</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
1498 1485 <span class="i">$FusedRingSetRef</span> = <span class="i">$FusedRingSetsRef</span>->[<span class="i">$Index</span>]<span class="sc">;</span>
|
|
|
1499 1486 <span class="k">if</span> <span class="s">(</span><span class="i">$FusedRingSetIsAromatic</span>[<span class="i">$Index</span>]<span class="s">)</span> <span class="s">{</span>
|
|
|
1500 1487 <span class="i">$This</span><span class="i">->_SetRingsAromaticity</span><span class="s">(</span><span class="i">@</span>{<span class="i">$FusedRingSetRef</span>}<span class="s">)</span><span class="sc">;</span>
|
|
|
1501 1488 <span class="s">}</span>
|
|
|
1502 1489 <span class="k">else</span> <span class="s">{</span>
|
|
|
1503 1490 <span class="i">$This</span><span class="i">->_DetectRingsAromaticity</span><span class="s">(</span><span class="i">@</span>{<span class="i">$FusedRingSetRef</span>}<span class="s">)</span><span class="sc">;</span>
|
|
|
1504 1491 <span class="s">}</span>
|
|
|
1505 1492 <span class="s">}</span>
|
|
|
1506 1493
|
|
|
1507 1494 <span class="i">$This</span><span class="i">->_DetectRingsAromaticity</span><span class="s">(</span><span class="i">@</span>{<span class="i">$NonFusedRingsRef</span>}<span class="s">)</span><span class="sc">;</span>
|
|
|
1508 1495
|
|
|
1509 1496 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
1510 1497 <span class="s">}</span>
|
|
|
1511 1498
|
|
|
1512 1499 <span class="c"># Detect and set aromaticity for rings...</span>
|
|
|
1513 1500 <span class="c">#</span>
|
|
|
1514 <a name="_DetectRingsAromaticity-"></a>1501 <span class="k">sub </span><span class="m">_DetectRingsAromaticity</span> <span class="s">{</span>
|
|
|
1515 1502 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">@Rings</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
1516 1503 <span class="k">my</span><span class="s">(</span><span class="i">$RingAtom</span><span class="cm">,</span> <span class="i">$RingBond</span><span class="cm">,</span> <span class="i">$RingAtomsRef</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1517 1504
|
|
|
1518 1505 <span class="j">RING:</span> <span class="k">for</span> <span class="i">$RingAtomsRef</span> <span class="s">(</span><span class="i">@Rings</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1519 1506 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->_CheckRingAromaticity</span><span class="s">(</span><span class="i">@</span>{<span class="i">$RingAtomsRef</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1520 1507 <span class="k">next</span> <span class="j">RING</span><span class="sc">;</span>
|
|
|
1521 1508 <span class="s">}</span>
|
|
|
1522 1509 <span class="i">$This</span><span class="i">->_SetRingAromaticity</span><span class="s">(</span><span class="i">@</span>{<span class="i">$RingAtomsRef</span>}<span class="s">)</span><span class="sc">;</span>
|
|
|
1523 1510 <span class="s">}</span>
|
|
|
1524 1511 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
1525 1512 <span class="s">}</span>
|
|
|
1526 1513
|
|
|
1527 1514 <span class="c"># Set aromatic property for all all atoms and bonds involved in all specified rings..</span>
|
|
|
1528 1515 <span class="c">#</span>
|
|
|
1529 <a name="_SetRingsAromaticity-"></a>1516 <span class="k">sub </span><span class="m">_SetRingsAromaticity</span> <span class="s">{</span>
|
|
|
1530 1517 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">@Rings</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
1531 1518 <span class="k">my</span><span class="s">(</span><span class="i">$RingAtomsRef</span> <span class="s">)</span><span class="sc">;</span>
|
|
|
1532 1519
|
|
|
1533 1520 <span class="k">for</span> <span class="i">$RingAtomsRef</span> <span class="s">(</span><span class="i">@Rings</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1534 1521 <span class="i">$This</span><span class="i">->_SetRingAromaticity</span><span class="s">(</span><span class="i">@</span>{<span class="i">$RingAtomsRef</span>}<span class="s">)</span><span class="sc">;</span>
|
|
|
1535 1522 <span class="s">}</span>
|
|
|
1536 1523 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
1537 1524 <span class="s">}</span>
|
|
|
1538 1525
|
|
|
1539 1526 <span class="c"># Set aromatic property for all all atoms and bonds involved in ring..</span>
|
|
|
1540 1527 <span class="c">#</span>
|
|
|
1541 <a name="_SetRingAromaticity-"></a>1528 <span class="k">sub </span><span class="m">_SetRingAromaticity</span> <span class="s">{</span>
|
|
|
1542 1529 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">@RingAtoms</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
1543 1530 <span class="k">my</span><span class="s">(</span><span class="i">$RingAtom</span><span class="cm">,</span> <span class="i">$RingBond</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1544 1531
|
|
|
1545 1532 <span class="k">for</span> <span class="i">$RingAtom</span> <span class="s">(</span><span class="i">@RingAtoms</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1546 1533 <span class="i">$RingAtom</span><span class="i">->SetAromatic</span><span class="s">(</span><span class="n">1</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1547 1534 <span class="s">}</span>
|
|
|
1548 1535 <span class="k">for</span> <span class="i">$RingBond</span> <span class="s">(</span><span class="i">$This</span><span class="i">->GetRingBonds</span><span class="s">(</span><span class="i">@RingAtoms</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1549 1536 <span class="i">$RingBond</span><span class="i">->SetAromatic</span><span class="s">(</span><span class="n">1</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1550 1537 <span class="s">}</span>
|
|
|
1551 1538 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
1552 1539 <span class="s">}</span>
|
|
|
1553 1540
|
|
|
1554 1541
|
|
|
1555 1542 <span class="c"># For a ring to be an aromatic ring, all of its atoms must have aromatic property</span>
|
|
|
1556 1543 <span class="c"># set.</span>
|
|
|
1557 1544 <span class="c">#</span>
|
|
|
1558 <a name="IsRingAromatic-"></a>1545 <span class="k">sub </span><span class="m">IsRingAromatic</span> <span class="s">{</span>
|
|
|
1559 1546 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">@RingAtoms</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
1560 1547 <span class="k">my</span><span class="s">(</span><span class="i">$RingAtom</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1561 1548
|
|
|
1562 1549 <span class="k">for</span> <span class="i">$RingAtom</span> <span class="s">(</span><span class="i">@RingAtoms</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1563 1550 <span class="k">if</span> <span class="s">(</span>!<span class="i">$RingAtom</span><span class="i">->IsAromatic</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1564 1551 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
1565 1552 <span class="s">}</span>
|
|
|
1566 1553 <span class="s">}</span>
|
|
|
1567 1554 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span>
|
|
|
1568 1555 <span class="s">}</span>
|
|
|
1569 1556
|
|
|
1570 1557 <span class="c"># Delete aromatic property for all atoms and bonds...</span>
|
|
|
1571 1558 <span class="c">#</span>
|
|
|
1572 <a name="DeleteAromaticity-"></a>1559 <span class="k">sub </span><span class="m">DeleteAromaticity</span> <span class="s">{</span>
|
|
|
1573 1560 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
1574 1561
|
|
|
1575 1562 <span class="k">return</span> <span class="i">$This</span><span class="i">->_DeleteAtomsAndBondsAromaticity</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1576 1563 <span class="s">}</span>
|
|
|
1577 1564
|
|
|
1578 1565 <span class="c"># Check ring aromaticity...</span>
|
|
|
1579 1566 <span class="c">#</span>
|
|
|
1580 <a name="_CheckRingAromaticity-"></a>1567 <span class="k">sub </span><span class="m">_CheckRingAromaticity</span> <span class="s">{</span>
|
|
|
1581 1568 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">@RingAtoms</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
1582 1569 <span class="k">my</span><span class="s">(</span><span class="i">$NumOfPiElectrons</span><span class="cm">,</span> <span class="i">$BondID</span><span class="cm">,</span> <span class="i">@RingBonds</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1583 1570
|
|
|
1584 1571 <span class="i">@RingBonds</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1585 1572 <span class="i">@RingBonds</span> = <span class="i">$This</span><span class="i">->GetRingBonds</span><span class="s">(</span><span class="i">@RingAtoms</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1586 1573
|
|
|
1587 1574 <span class="i">$NumOfPiElectrons</span> = <span class="i">$This</span><span class="i">->_GetNumOfPiElectronsAvailableForDelocalization</span><span class="s">(</span>\<span class="i">@RingAtoms</span><span class="cm">,</span> \<span class="i">@RingBonds</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1588 1575
|
|
|
1589 1576 <span class="k">return</span> <span class="i">$This</span><span class="i">->_DoPiElectronSatifyHuckelsRule</span><span class="s">(</span><span class="i">$NumOfPiElectrons</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1590 1577 <span class="s">}</span>
|
|
|
1591 1578
|
|
|
1592 1579 <span class="c"># Get number of pi electrons available for delocalizaiton in a ring or ring system...</span>
|
|
|
1593 1580 <span class="c">#</span>
|
|
|
1594 <a name="_GetNumOfPiElectronsAvailableForDelocalization-"></a>1581 <span class="k">sub </span><span class="m">_GetNumOfPiElectronsAvailableForDelocalization</span> <span class="s">{</span>
|
|
|
1595 1582 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$RingAtomsRef</span><span class="cm">,</span> <span class="i">$RingBondsRef</span><span class="cm">,</span> <span class="i">$FusedRingSetsBondsMapRef</span><span class="cm">,</span> <span class="i">$FusedRingSetsBondsVisitedMapRef</span><span class="cm">,</span> <span class="i">$FusedRingBondsMapRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
1596 1583 <span class="k">my</span><span class="s">(</span><span class="i">$AromaticityModelName</span><span class="cm">,</span> <span class="i">$AromaticityModelDataRef</span><span class="cm">,</span> <span class="i">$ExocyclicDoubleBondsDataMapRef</span><span class="cm">,</span> <span class="i">$NumOfConjugatedDoubleBonds</span><span class="cm">,</span> <span class="i">$NumOfExplicitAromaticBonds</span><span class="cm">,</span> <span class="i">$NumOfRingAtomElectronPairs</span><span class="cm">,</span> <span class="i">$NumOfRingBondsProcessed</span><span class="cm">,</span> <span class="i">$NumOfPiElectrons</span><span class="cm">,</span> <span class="i">$Index</span><span class="cm">,</span> <span class="i">$RingBond</span><span class="cm">,</span> <span class="i">$RingAtom</span><span class="cm">,</span> <span class="i">$RingAtomSymbol</span><span class="cm">,</span> <span class="i">$BondOrder</span><span class="cm">,</span> <span class="i">$RingAtomID</span><span class="cm">,</span> <span class="i">$RingBondID</span><span class="cm">,</span> <span class="i">$PreviousIndex</span><span class="cm">,</span> <span class="i">$PreviousRingBond</span><span class="cm">,</span> <span class="i">$ExcludeFreeRadicalElectrons</span><span class="cm">,</span> <span class="i">%ElectronPairContributionProcessedMap</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1597 1584
|
|
|
1598 1585 <span class="i">$AromaticityModelName</span> = <span class="i">$CanonicalAromaticityModelNamesMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$This</span><span class="i">->GetAromaticityModel</span><span class="s">(</span><span class="s">)</span><span class="s">)</span>}<span class="sc">;</span>
|
|
|
1599 1586 <span class="i">$AromaticityModelDataRef</span> = \<span class="i">%</span>{<span class="i">$AromaticityModelsDataMap</span>{<span class="i">$AromaticityModelName</span>}}<span class="sc">;</span>
|
|
|
1600 1587
|
|
|
1601 1588 <span class="c"># Perform an intial check for potential atomatic ring atoms..</span>
|
|
|
1602 1589 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->_CheckRingAtomsForPotentialAromaticity</span><span class="s">(</span><span class="i">$RingAtomsRef</span><span class="cm">,</span> <span class="i">$RingBondsRef</span><span class="cm">,</span> <span class="i">$AromaticityModelDataRef</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1603 1590 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
1604 1591 <span class="s">}</span>
|
|
|
1605 1592
|
|
|
1606 1593 <span class="i">$ExocyclicDoubleBondsDataMapRef</span> = <span class="k">undef</span><span class="sc">;</span>
|
|
|
1607 1594 <span class="i">$ExcludeFreeRadicalElectrons</span> = <span class="n">1</span><span class="sc">;</span>
|
|
|
1608 1595
|
|
|
1609 1596 <span class="i">%ElectronPairContributionProcessedMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1610 1597
|
|
|
1611 1598 <span class="s">(</span><span class="i">$NumOfPiElectrons</span><span class="cm">,</span> <span class="i">$NumOfRingBondsProcessed</span><span class="cm">,</span> <span class="i">$NumOfConjugatedDoubleBonds</span><span class="cm">,</span> <span class="i">$NumOfExplicitAromaticBonds</span><span class="cm">,</span> <span class="i">$NumOfRingAtomElectronPairs</span><span class="s">)</span> = <span class="s">(</span><span class="q">'0'</span><span class="s">)</span> x <span class="n">5</span><span class="sc">;</span>
|
|
|
1612 1599
|
|
|
1613 1600 <span class="c"># Go over ring atoms and bonds to check their participation in aromaticity and count</span>
|
|
|
1614 1601 <span class="c"># pi electrons available for delocalization corresponding to various aromaticity models...</span>
|
|
|
1615 1602 <span class="c">#</span>
|
|
|
1616 1603 <span class="j">RINGBOND:</span> <span class="k">for</span> <span class="i">$Index</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#</span>{<span class="i">$RingBondsRef</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
1617 1604 <span class="i">$RingBond</span> = <span class="i">$RingBondsRef</span>->[<span class="i">$Index</span>]<span class="sc">;</span>
|
|
|
1618 1605 <span class="i">$RingAtom</span> = <span class="i">$RingAtomsRef</span>->[<span class="i">$Index</span>]<span class="sc">;</span>
|
|
|
1619 1606 <span class="i">$BondOrder</span> = <span class="i">$RingBond</span><span class="i">->GetBondOrder</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1620 1607
|
|
|
1621 1608 <span class="c"># Is this ring bond part of a fused ring system which has been already processed?</span>
|
|
|
1622 1609 <span class="k">if</span> <span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$FusedRingSetsBondsVisitedMapRef</span><span class="s">)</span> && <span class="i">$RingBond</span><span class="i">->GetNumOfRings</span><span class="s">(</span><span class="s">)</span> == <span class="n">2</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1623 1610 <span class="i">$RingBondID</span> = <span class="i">$RingBond</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1624 1611 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$FusedRingSetsBondsVisitedMapRef</span>->{<span class="i">$RingBondID</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
1625 1612 <span class="k">next</span> <span class="j">RINGBOND</span><span class="sc">;</span>
|
|
|
1626 1613 <span class="s">}</span>
|
|
|
1627 1614 <span class="i">$FusedRingSetsBondsVisitedMapRef</span>->{<span class="i">$RingBondID</span>} = <span class="i">$RingBondID</span><span class="sc">;</span>
|
|
|
1628 1615 <span class="s">}</span>
|
|
|
1629 1616 <span class="i">$NumOfRingBondsProcessed</span>++<span class="sc">;</span>
|
|
|
1630 1617
|
|
|
1631 1618 <span class="c"># For first ring, previous ring bond corrresponds to last ring bond...</span>
|
|
|
1632 1619 <span class="i">$PreviousIndex</span> = <span class="i">$Index</span> ? <span class="s">(</span><span class="i">$Index</span> -<span class="n">1</span><span class="s">)</span> <span class="co">:</span> <span class="i">$#</span>{<span class="i">$RingBondsRef</span>}<span class="sc">;</span>
|
|
|
1633 1620 <span class="i">$PreviousRingBond</span> = <span class="i">$RingBondsRef</span>->[<span class="i">$PreviousIndex</span>]<span class="sc">;</span>
|
|
|
1634 1621
|
|
|
1635 1622 <span class="c"># Check for presence of alternate single/double bond configuration, and pesence of</span>
|
|
|
1636 1623 <span class="c"># hetero atoms with two single ring bonds along with any exocyclic double bonds...</span>
|
|
|
1637 1624 <span class="c">#</span>
|
|
|
1638 1625 <span class="j">BONDORDER:</span> <span class="s">{</span>
|
|
|
1639 1626 <span class="c"># Is current ring double bond in an alternate single/double bond configuration?</span>
|
|
|
1640 1627 <span class="k">if</span> <span class="s">(</span><span class="i">$BondOrder</span> == <span class="n">2</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1641 1628 <span class="k">if</span> <span class="s">(</span><span class="i">$PreviousRingBond</span><span class="i">->GetBondOrder</span><span class="s">(</span><span class="s">)</span> != <span class="n">1</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1642 1629 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
1643 1630 <span class="s">}</span>
|
|
|
1644 1631 <span class="i">$NumOfConjugatedDoubleBonds</span> += <span class="n">1</span><span class="sc">;</span>
|
|
|
1645 1632 <span class="k">last</span> <span class="j">BONDORDER</span><span class="sc">;</span>
|
|
|
1646 1633 <span class="s">}</span>
|
|
|
1647 1634
|
|
|
1648 1635 <span class="c"># Is current ring bond order correspond to an explicit aromatic bond?</span>
|
|
|
1649 1636 <span class="k">if</span> <span class="s">(</span><span class="i">$BondOrder</span> == <span class="n">1.5</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1650 1637 <span class="k">if</span> <span class="s">(</span><span class="i">$PreviousRingBond</span><span class="i">->GetBondOrder</span><span class="s">(</span><span class="s">)</span> != <span class="n">1.5</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1651 1638 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
1652 1639 <span class="s">}</span>
|
|
|
1653 1640 <span class="i">$NumOfExplicitAromaticBonds</span> += <span class="n">1</span><span class="sc">;</span>
|
|
|
1654 1641 <span class="k">last</span> <span class="j">BONDORDER</span><span class="sc">;</span>
|
|
|
1655 1642 <span class="s">}</span>
|
|
|
1656 1643
|
|
|
1657 1644 <span class="c"># Check for potential hetero atoms involved in two single ring bonds along</span>
|
|
|
1658 1645 <span class="c"># with any terminal exocyclic bonds...</span>
|
|
|
1659 1646 <span class="k">if</span> <span class="s">(</span><span class="i">$BondOrder</span> == <span class="n">1</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1660 1647 <span class="k">if</span> <span class="s">(</span><span class="i">$PreviousRingBond</span><span class="i">->GetBondOrder</span><span class="s">(</span><span class="s">)</span> != <span class="n">1</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1661 1648 <span class="c"># Part of a conjugated system...</span>
|
|
|
1662 1649 <span class="k">last</span> <span class="j">BONDORDER</span><span class="sc">;</span>
|
|
|
1663 1650 <span class="s">}</span>
|
|
|
1664 1651
|
|
|
1665 1652 <span class="c"># Identify any exocylic bonds on rings atoms...</span>
|
|
|
1666 1653 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$ExocyclicDoubleBondsDataMapRef</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1667 1654 <span class="i">$ExocyclicDoubleBondsDataMapRef</span> = <span class="i">$This</span><span class="i">->_IdentifyRingAtomsInvolvedInExocyclicDoubleBonds</span><span class="s">(</span><span class="i">$RingAtomsRef</span><span class="cm">,</span> <span class="i">$RingBondsRef</span><span class="cm">,</span> <span class="i">$FusedRingSetsBondsMapRef</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1668 1655 <span class="s">}</span>
|
|
|
1669 1656
|
|
|
1670 1657 <span class="c"># Is current ring atom part of an allowed exocyclic terminal bond?</span>
|
|
|
1671 1658 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->_CheckPotentialAromaticRingAtomForExocylicDoubleBonds</span><span class="s">(</span><span class="i">$RingAtom</span><span class="cm">,</span> <span class="i">$AromaticityModelDataRef</span><span class="cm">,</span> <span class="i">$ExocyclicDoubleBondsDataMapRef</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1672 1659 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
1673 1660 <span class="s">}</span>
|
|
|
1674 1661
|
|
|
1675 1662 <span class="c"># Is it allowed to have any formal charge?</span>
|
|
|
1676 1663 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->_CheckPotentialAromaticRingAtomForFormalCharge</span><span class="s">(</span><span class="i">$RingAtom</span><span class="cm">,</span> <span class="i">$AromaticityModelDataRef</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1677 1664 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
1678 1665 <span class="s">}</span>
|
|
|
1679 1666
|
|
|
1680 1667 <span class="c"># It it an allowed hetero ring atom or a carbon atom?</span>
|
|
|
1681 1668 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->_CheckPotentialAromaticRingAtomForAllowedHeteroAtoms</span><span class="s">(</span><span class="i">$RingAtom</span><span class="cm">,</span> <span class="i">$AromaticityModelDataRef</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1682 1669 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
1683 1670 <span class="s">}</span>
|
|
|
1684 1671
|
|
|
1685 1672 <span class="i">$RingAtomID</span> = <span class="i">$RingAtom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1686 1673 <span class="i">$ElectronPairContributionProcessedMap</span>{<span class="i">$RingAtomID</span>} = <span class="i">$RingAtomID</span><span class="sc">;</span>
|
|
|
1687 1674
|
|
|
1688 1675 <span class="c"># Is it able to donate a pair for electrons towards pi electron delocalization?</span>
|
|
|
1689 1676 <span class="k">if</span> <span class="s">(</span><span class="i">$RingAtom</span><span class="i">->GetValenceFreeElectrons</span><span class="s">(</span><span class="i">$ExcludeFreeRadicalElectrons</span><span class="s">)</span> >= <span class="n">2</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1690 1677 <span class="c"># Possibilites:</span>
|
|
|
1691 1678 <span class="c"># . Hetero atom with or without formal charge and an available electron pair</span>
|
|
|
1692 1679 <span class="c"># . Carbon atom with -ve formal charge and with an available electron pair</span>
|
|
|
1693 1680 <span class="c">#</span>
|
|
|
1694 1681 <span class="i">$NumOfRingAtomElectronPairs</span> += <span class="n">1</span><span class="sc">;</span>
|
|
|
1695 1682 <span class="s">}</span>
|
|
|
1696 1683 <span class="k">else</span> <span class="s">{</span>
|
|
|
1697 1684 <span class="c"># Is ring atom involved in two single bonds without any electron pair allowed?</span>
|
|
|
1698 1685 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->_AllowRingAtomInTwoSingleBondsWithoutElectronPair</span><span class="s">(</span><span class="i">$RingAtom</span><span class="cm">,</span> <span class="i">$RingBond</span><span class="cm">,</span> <span class="i">$PreviousRingBond</span><span class="cm">,</span> <span class="i">$ExocyclicDoubleBondsDataMapRef</span><span class="cm">,</span> <span class="i">$FusedRingBondsMapRef</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1699 1686 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
1700 1687 <span class="s">}</span>
|
|
|
1701 1688 <span class="s">}</span>
|
|
|
1702 1689 <span class="k">last</span> <span class="j">BONDORDER</span><span class="sc">;</span>
|
|
|
1703 1690 <span class="s">}</span>
|
|
|
1704 1691
|
|
|
1705 1692 <span class="c"># Any other type of ring atom/bond is not allowed to contribute towards pi electron count</span>
|
|
|
1706 1693 <span class="c"># and caused loss of aromaticity...</span>
|
|
|
1707 1694 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
1708 1695 <span class="s">}</span>
|
|
|
1709 1696 <span class="s">}</span>
|
|
|
1710 1697
|
|
|
1711 1698 <span class="c"># Check for any electron pair contributions towards pi electron delocalization due to</span>
|
|
|
1712 1699 <span class="c"># -ve formal charge on ring atoms which haven't been already processed and part of</span>
|
|
|
1713 1700 <span class="c"># conjugated single/double bond system...</span>
|
|
|
1714 1701 <span class="c">#</span>
|
|
|
1715 1702 <span class="i">$NumOfRingAtomElectronPairs</span> += <span class="i">$This</span><span class="i">->_GetElectronPairsContributionFromConjugatedRingAtoms</span><span class="s">(</span><span class="i">$RingAtomsRef</span><span class="cm">,</span> <span class="i">$RingBondsRef</span><span class="cm">,</span> <span class="i">$ExcludeFreeRadicalElectrons</span><span class="cm">,</span> <span class="i">$AromaticityModelDataRef</span><span class="cm">,</span> \<span class="i">%ElectronPairContributionProcessedMap</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1716 1703
|
|
|
1717 1704 <span class="c"># Setup pi electron count available for delocalization...</span>
|
|
|
1718 1705 <span class="j">COUNT:</span> <span class="s">{</span>
|
|
|
1719 1706 <span class="k">if</span> <span class="s">(</span><span class="i">$NumOfExplicitAromaticBonds</span> == <span class="i">$NumOfRingBondsProcessed</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1720 1707 <span class="c"># Each aromatic bond contribute one electron towards pi electron delocalization...</span>
|
|
|
1721 1708 <span class="i">$NumOfPiElectrons</span> = <span class="i">$NumOfExplicitAromaticBonds</span><span class="sc">;</span>
|
|
|
1722 1709 <span class="k">last</span> <span class="j">COUNT</span><span class="sc">;</span>
|
|
|
1723 1710 <span class="s">}</span>
|
|
|
1724 1711
|
|
|
1725 1712 <span class="c"># Each conjugated double bond contribute two electrons towards pi electron delocalization...</span>
|
|
|
1726 1713 <span class="i">$NumOfPiElectrons</span> = <span class="n">2</span>*<span class="i">$NumOfConjugatedDoubleBonds</span> + <span class="n">2</span>*<span class="i">$NumOfRingAtomElectronPairs</span><span class="sc">;</span>
|
|
|
1727 1714 <span class="s">}</span>
|
|
|
1728 1715
|
|
|
1729 1716 <span class="k">return</span> <span class="i">$NumOfPiElectrons</span><span class="sc">;</span>
|
|
|
1730 1717 <span class="s">}</span>
|
|
|
1731 1718
|
|
|
1732 1719 <span class="c"># Check ring atoms for their potential participation in aromatic systems..</span>
|
|
|
1733 1720 <span class="c">#</span>
|
|
|
1734 <a name="_CheckRingAtomsForPotentialAromaticity-"></a>1721 <span class="k">sub </span><span class="m">_CheckRingAtomsForPotentialAromaticity</span> <span class="s">{</span>
|
|
|
1735 1722 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$RingAtomsRef</span><span class="cm">,</span> <span class="i">$RingBondsRef</span><span class="cm">,</span> <span class="i">$AromaticityModelDataRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
1736 1723 <span class="k">my</span><span class="s">(</span><span class="i">$Index</span><span class="cm">,</span> <span class="i">$RingBond</span><span class="cm">,</span> <span class="i">$RingAtom</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1737 1724
|
|
|
1738 1725 <span class="c"># Check availability of ring atoms and bonds...</span>
|
|
|
1739 1726 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$RingAtomsRef</span><span class="s">)</span> && <span class="i">@</span>{<span class="i">$RingBondsRef</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1740 1727 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
1741 1728 <span class="s">}</span>
|
|
|
1742 1729
|
|
|
1743 1730 <span class="c"># Is there any minimum ring size limit?</span>
|
|
|
1744 1731 <span class="k">if</span> <span class="s">(</span><span class="i">$AromaticityModelDataRef</span>->{<span class="w">MinimumRingSize</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
1745 1732 <span class="k">if</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$RingAtomsRef</span>} < <span class="i">$AromaticityModelDataRef</span>->{<span class="w">MinimumRingSize</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
1746 1733 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
1747 1734 <span class="s">}</span>
|
|
|
1748 1735 <span class="s">}</span>
|
|
|
1749 1736
|
|
|
1750 1737 <span class="c"># Make sure ring bond order is not greater than 2 and ring atom is not connected to more</span>
|
|
|
1751 1738 <span class="c"># than 3 other atoms to eliminate any non sp2 carbon atoms and still allow for hetero atoms</span>
|
|
|
1752 1739 <span class="c"># to contrbute towards electron delocalization...</span>
|
|
|
1753 1740 <span class="c">#</span>
|
|
|
1754 1741 <span class="k">for</span> <span class="i">$Index</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#</span>{<span class="i">$RingBondsRef</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
1755 1742 <span class="i">$RingBond</span> = <span class="i">$RingBondsRef</span>->[<span class="i">$Index</span>]<span class="sc">;</span>
|
|
|
1756 1743 <span class="i">$RingAtom</span> = <span class="i">$RingAtomsRef</span>->[<span class="i">$Index</span>]<span class="sc">;</span>
|
|
|
1757 1744
|
|
|
1758 1745 <span class="k">if</span> <span class="s">(</span><span class="s">(</span><span class="i">$RingBond</span><span class="i">->GetBondOrder</span><span class="s">(</span><span class="s">)</span> > <span class="n">2</span><span class="s">)</span> || <span class="s">(</span><span class="i">$RingAtom</span><span class="i">->GetNumOfBonds</span><span class="s">(</span><span class="s">)</span> + <span class="i">$RingAtom</span><span class="i">->GetNumOfMissingHydrogens</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> > <span class="n">3</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1759 1746 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
1760 1747 <span class="s">}</span>
|
|
|
1761 1748 <span class="s">}</span>
|
|
|
1762 1749
|
|
|
1763 1750 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span>
|
|
|
1764 1751 <span class="s">}</span>
|
|
|
1765 1752
|
|
|
1766 1753 <span class="c"># Identify any exocylic double bonds on ring atoms...</span>
|
|
|
1767 1754 <span class="c">#</span>
|
|
|
1768 <a name="_IdentifyRingAtomsInvolvedInExocyclicDoubleBonds-"></a>1755 <span class="k">sub </span><span class="m">_IdentifyRingAtomsInvolvedInExocyclicDoubleBonds</span> <span class="s">{</span>
|
|
|
1769 1756 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$RingAtomsRef</span><span class="cm">,</span> <span class="i">$RingBondsRef</span><span class="cm">,</span> <span class="i">$FusedRingSetsBondsMapRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
1770 1757 <span class="k">my</span><span class="s">(</span><span class="i">$Index</span><span class="cm">,</span> <span class="i">$RingAtom</span><span class="cm">,</span> <span class="i">$RingBond</span><span class="cm">,</span> <span class="i">$RingAtomID</span><span class="cm">,</span> <span class="i">$Bond</span><span class="cm">,</span> <span class="i">$BondID</span><span class="cm">,</span> <span class="i">$BondedAtom</span><span class="cm">,</span> <span class="i">$RingBondsMapRef</span><span class="cm">,</span> <span class="i">%RingBondsMap</span><span class="cm">,</span> <span class="i">%ExocyclicDoubleBondsDataMap</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1771 1758
|
|
|
1772 1759 <span class="c"># Setup a ring bond map to process exocyclic bonds...</span>
|
|
|
1773 1760 <span class="i">$RingBondsMapRef</span> = <span class="k">undef</span><span class="sc">;</span>
|
|
|
1774 1761 <span class="i">%RingBondsMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1775 1762
|
|
|
1776 1763 <span class="k">if</span> <span class="s">(</span><span class="k">defined</span> <span class="i">$FusedRingSetsBondsMapRef</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1777 1764 <span class="i">$RingBondsMapRef</span> = <span class="i">$FusedRingSetsBondsMapRef</span><span class="sc">;</span>
|
|
|
1778 1765 <span class="s">}</span>
|
|
|
1779 1766 <span class="k">else</span> <span class="s">{</span>
|
|
|
1780 1767 <span class="k">for</span> <span class="i">$BondID</span> <span class="s">(</span><span class="k">map</span> <span class="s">{</span> <span class="i">$_</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span> <span class="s">}</span> <span class="i">@</span>{<span class="i">$RingBondsRef</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
1781 1768 <span class="i">$RingBondsMap</span>{<span class="i">$BondID</span>} = <span class="i">$BondID</span><span class="sc">;</span>
|
|
|
1782 1769 <span class="s">}</span>
|
|
|
1783 1770 <span class="i">$RingBondsMapRef</span> = \<span class="i">%RingBondsMap</span><span class="sc">;</span>
|
|
|
1784 1771 <span class="s">}</span>
|
|
|
1785 1772
|
|
|
1786 1773 <span class="c"># Intialize exocyclic terminal double bond data...</span>
|
|
|
1787 1774 <span class="i">%ExocyclicDoubleBondsDataMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1788 1775 <span class="i">%</span>{<span class="i">$ExocyclicDoubleBondsDataMap</span>{<span class="w">RingAtomID</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1789 1776
|
|
|
1790 1777 <span class="k">for</span> <span class="i">$Index</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#</span>{<span class="i">$RingBondsRef</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
1791 1778 <span class="i">$RingBond</span> = <span class="i">$RingBondsRef</span>->[<span class="i">$Index</span>]<span class="sc">;</span>
|
|
|
1792 1779 <span class="i">$RingAtom</span> = <span class="i">$RingAtomsRef</span>->[<span class="i">$Index</span>]<span class="sc">;</span>
|
|
|
1793 1780
|
|
|
1794 1781 <span class="i">$RingAtomID</span> = <span class="i">$RingAtom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1795 1782
|
|
|
1796 1783 <span class="j">BOND:</span> <span class="k">for</span> <span class="i">$Bond</span> <span class="s">(</span><span class="i">$RingAtom</span><span class="i">->GetBonds</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1797 1784 <span class="k">if</span> <span class="s">(</span><span class="i">$Bond</span><span class="i">->GetBondOrder</span> != <span class="n">2</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1798 1785 <span class="k">next</span> <span class="j">BOND</span><span class="sc">;</span>
|
|
|
1799 1786 <span class="s">}</span>
|
|
|
1800 1787
|
|
|
1801 1788 <span class="c"># Is it part of ring or ring system under consideration?</span>
|
|
|
1802 1789 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$RingBondsMapRef</span>->{<span class="i">$Bond</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
1803 1790 <span class="k">next</span> <span class="j">BOND</span><span class="sc">;</span>
|
|
|
1804 1791 <span class="s">}</span>
|
|
|
1805 1792
|
|
|
1806 1793 <span class="c"># Is bonded atom in a ring or a non-terminal atom?</span>
|
|
|
1807 1794 <span class="i">$BondedAtom</span> = <span class="i">$Bond</span><span class="i">->GetBondedAtom</span><span class="s">(</span><span class="i">$RingAtom</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1808 1795 <span class="k">if</span> <span class="s">(</span><span class="i">$BondedAtom</span><span class="i">->IsInRing</span><span class="s">(</span><span class="s">)</span> || !<span class="i">$BondedAtom</span><span class="i">->IsTerminal</span><span class="s">(</span><span class="s">)</span> <span class="s">)</span> <span class="s">{</span>
|
|
|
1809 1796 <span class="k">next</span> <span class="j">BOND</span><span class="sc">;</span>
|
|
|
1810 1797 <span class="s">}</span>
|
|
|
1811 1798
|
|
|
1812 1799 <span class="c"># Track exocyclic terminal double bond information...</span>
|
|
|
1813 1800 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$ExocyclicDoubleBondsDataMap</span>{<span class="w">RingAtomID</span>}{<span class="i">$RingAtomID</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
1814 1801 <span class="i">@</span>{<span class="i">$ExocyclicDoubleBondsDataMap</span>{<span class="w">RingAtomID</span>}{<span class="i">$RingAtomID</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1815 1802 <span class="s">}</span>
|
|
|
1816 1803 <span class="k">push</span> <span class="i">@</span>{<span class="i">$ExocyclicDoubleBondsDataMap</span>{<span class="w">RingAtomID</span>}{<span class="i">$RingAtomID</span>}}<span class="cm">,</span> <span class="i">$BondedAtom</span><span class="sc">;</span>
|
|
|
1817 1804 <span class="s">}</span>
|
|
|
1818 1805 <span class="s">}</span>
|
|
|
1819 1806
|
|
|
1820 1807 <span class="k">return</span> \<span class="i">%ExocyclicDoubleBondsDataMap</span><span class="sc">;</span>
|
|
|
1821 1808 <span class="s">}</span>
|
|
|
1822 1809
|
|
|
1823 1810 <span class="c"># Check to see whether ring atoms are allowed to participate in exocyclic terminal double</span>
|
|
|
1824 1811 <span class="c"># bonds...</span>
|
|
|
1825 1812 <span class="c">#</span>
|
|
|
1826 <a name="_CheckPotentialAromaticRingAtomForExocylicDoubleBonds-"></a>1813 <span class="k">sub </span><span class="m">_CheckPotentialAromaticRingAtomForExocylicDoubleBonds</span> <span class="s">{</span>
|
|
|
1827 1814 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$RingAtom</span><span class="cm">,</span> <span class="i">$AromaticityModelDataRef</span><span class="cm">,</span> <span class="i">$ExocyclicDoubleBondsDataMapRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
1828 1815 <span class="k">my</span><span class="s">(</span><span class="i">$RingAtomID</span><span class="cm">,</span> <span class="i">$ExocyclicTerminalAtom</span><span class="cm">,</span> <span class="i">$RingAtomElectronegativity</span><span class="cm">,</span> <span class="i">$TerminalAtomElectronagativity</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1829 1816
|
|
|
1830 1817 <span class="i">$RingAtomID</span> = <span class="i">$RingAtom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1831 1818
|
|
|
1832 1819 <span class="c"># Is it part of an exocyclic terminal double bond?</span>
|
|
|
1833 1820 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$ExocyclicDoubleBondsDataMapRef</span>->{<span class="w">RingAtomID</span>}{<span class="i">$RingAtomID</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
1834 1821 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span>
|
|
|
1835 1822 <span class="s">}</span>
|
|
|
1836 1823
|
|
|
1837 1824 <span class="c"># Are exocyclic terminal double bonds allowed?</span>
|
|
|
1838 1825 <span class="k">if</span> <span class="s">(</span>!<span class="i">$AromaticityModelDataRef</span>->{<span class="w">AllowExocyclicDoubleBonds</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
1839 1826 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
1840 1827 <span class="s">}</span>
|
|
|
1841 1828
|
|
|
1842 1829 <span class="c"># Are there multiple exocyclic double bonds?</span>
|
|
|
1843 1830 <span class="k">if</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$ExocyclicDoubleBondsDataMapRef</span>->{<span class="w">RingAtomID</span>}{<span class="i">$RingAtomID</span>}} > <span class="n">1</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1844 1831 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
1845 1832 <span class="s">}</span>
|
|
|
1846 1833 <span class="s">(</span><span class="i">$ExocyclicTerminalAtom</span><span class="s">)</span> = <span class="i">@</span>{<span class="i">$ExocyclicDoubleBondsDataMapRef</span>->{<span class="w">RingAtomID</span>}{<span class="i">$RingAtomID</span>}}<span class="sc">;</span>
|
|
|
1847 1834
|
|
|
1848 1835 <span class="c"># Are homo nuclear exocyclic terminal double bonds allowed?</span>
|
|
|
1849 1836 <span class="k">if</span> <span class="s">(</span>!<span class="i">$AromaticityModelDataRef</span>->{<span class="w">AllowHomoNuclearExocyclicDoubleBonds</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
1850 1837 <span class="k">if</span> <span class="s">(</span><span class="i">$RingAtom</span><span class="i">->GetAtomicNumber</span><span class="s">(</span><span class="s">)</span> == <span class="i">$ExocyclicTerminalAtom</span><span class="i">->GetAtomicNumber</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1851 1838 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
1852 1839 <span class="s">}</span>
|
|
|
1853 1840 <span class="s">}</span>
|
|
|
1854 1841
|
|
|
1855 1842 <span class="c"># Are ring atoms with higher electronegativity allowed in exocyclic double bonds?</span>
|
|
|
1856 1843 <span class="k">if</span> <span class="s">(</span>!<span class="i">$AromaticityModelDataRef</span>->{<span class="w">AllowElectronegativeRingAtomExocyclicDoubleBonds</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
1857 1844 <span class="i">$RingAtomElectronegativity</span> = <span class="i">PeriodicTable::GetElementPaulingElectronegativity</span><span class="s">(</span><span class="i">$RingAtom</span><span class="i">->GetAtomicNumber</span><span class="s">(</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1858 1845 <span class="i">$TerminalAtomElectronagativity</span> = <span class="i">PeriodicTable::GetElementPaulingElectronegativity</span><span class="s">(</span><span class="i">$ExocyclicTerminalAtom</span><span class="i">->GetAtomicNumber</span><span class="s">(</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1859 1846
|
|
|
1860 1847 <span class="k">if</span> <span class="s">(</span><span class="i">$RingAtomElectronegativity</span> && <span class="i">$TerminalAtomElectronagativity</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1861 1848 <span class="k">if</span> <span class="s">(</span><span class="i">$RingAtomElectronegativity</span> > <span class="i">$TerminalAtomElectronagativity</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1862 1849 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
1863 1850 <span class="s">}</span>
|
|
|
1864 1851 <span class="s">}</span>
|
|
|
1865 1852 <span class="s">}</span>
|
|
|
1866 1853
|
|
|
1867 1854 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span>
|
|
|
1868 1855 <span class="s">}</span>
|
|
|
1869 1856
|
|
|
1870 1857 <span class="c">#</span>
|
|
|
1871 1858 <span class="c"># Check for any formal charge participation into electron delocalization...</span>
|
|
|
1872 1859 <span class="c">#</span>
|
|
|
1873 <a name="_CheckPotentialAromaticRingAtomForFormalCharge-"></a>1860 <span class="k">sub </span><span class="m">_CheckPotentialAromaticRingAtomForFormalCharge</span> <span class="s">{</span>
|
|
|
1874 1861 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$RingAtom</span><span class="cm">,</span> <span class="i">$AromaticityModelDataRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
1875 1862 <span class="k">my</span><span class="s">(</span><span class="i">$FormalCharge</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1876 1863
|
|
|
1877 1864 <span class="c"># Does atom has any formal charge?</span>
|
|
|
1878 1865 <span class="i">$FormalCharge</span> = <span class="i">$RingAtom</span><span class="i">->GetFormalCharge</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1879 1866 <span class="k">if</span> <span class="s">(</span>!<span class="i">$FormalCharge</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1880 1867 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span>
|
|
|
1881 1868 <span class="s">}</span>
|
|
|
1882 1869
|
|
|
1883 1870 <span class="c"># Are ring atoms with formal charge allowed to participate in electron delocalization?</span>
|
|
|
1884 1871 <span class="k">if</span> <span class="s">(</span>!<span class="i">$AromaticityModelDataRef</span>->{<span class="w">AllowRingAtomFormalCharge</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
1885 1872 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
1886 1873 <span class="s">}</span>
|
|
|
1887 1874
|
|
|
1888 1875 <span class="c"># Are hetero ring atoms with formal charge allowed to participate in electron delocalization?</span>
|
|
|
1889 1876 <span class="k">if</span> <span class="s">(</span>!<span class="i">$RingAtom</span><span class="i">->IsCarbon</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1890 1877 <span class="k">if</span> <span class="s">(</span>!<span class="i">$AromaticityModelDataRef</span>->{<span class="w">AllowHeteroRingAtomFormalCharge</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
1891 1878 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
1892 1879 <span class="s">}</span>
|
|
|
1893 1880 <span class="s">}</span>
|
|
|
1894 1881
|
|
|
1895 1882 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span>
|
|
|
1896 1883 <span class="s">}</span>
|
|
|
1897 1884
|
|
|
1898 1885 <span class="c">#</span>
|
|
|
1899 1886 <span class="c"># Check ring atoms for allowed hetero atoms...</span>
|
|
|
1900 1887 <span class="c">#</span>
|
|
|
1901 <a name="_CheckPotentialAromaticRingAtomForAllowedHeteroAtoms-"></a>1888 <span class="k">sub </span><span class="m">_CheckPotentialAromaticRingAtomForAllowedHeteroAtoms</span> <span class="s">{</span>
|
|
|
1902 1889 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$RingAtom</span><span class="cm">,</span> <span class="i">$AromaticityModelDataRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
1903 1890 <span class="k">my</span><span class="s">(</span><span class="i">$RingAtomSymbol</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1904 1891
|
|
|
1905 1892 <span class="c"># Is it a Carbon atom?</span>
|
|
|
1906 1893 <span class="k">if</span> <span class="s">(</span><span class="i">$RingAtom</span><span class="i">->IsCarbon</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1907 1894 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span>
|
|
|
1908 1895 <span class="s">}</span>
|
|
|
1909 1896
|
|
|
1910 1897 <span class="c"># Are heteroatoms allowed?</span>
|
|
|
1911 1898 <span class="k">if</span> <span class="s">(</span>!<span class="i">$AromaticityModelDataRef</span>->{<span class="w">AllowHeteroRingAtoms</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
1912 1899 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
1913 1900 <span class="s">}</span>
|
|
|
1914 1901
|
|
|
1915 1902 <span class="c"># Is it an allowed hetero atom?</span>
|
|
|
1916 1903 <span class="i">$RingAtomSymbol</span> = <span class="i">$RingAtom</span><span class="i">->GetAtomSymbol</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1917 1904 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$AromaticityModelDataRef</span>->{<span class="w">HeteroRingAtomsListMapRef</span>}->{<span class="i">$RingAtomSymbol</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
1918 1905 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
1919 1906 <span class="s">}</span>
|
|
|
1920 1907
|
|
|
1921 1908 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span>
|
|
|
1922 1909 <span class="s">}</span>
|
|
|
1923 1910
|
|
|
1924 1911 <span class="c"># Check for any electron pair contributions toward pi electron delocalization due to</span>
|
|
|
1925 1912 <span class="c"># -ve formal charge on ring atoms which haven't been already processed and part of</span>
|
|
|
1926 1913 <span class="c"># conjugated single/double bond system...</span>
|
|
|
1927 1914 <span class="c">#</span>
|
|
|
1928 <a name="_GetElectronPairsContributionFromConjugatedRingAtoms-"></a>1915 <span class="k">sub </span><span class="m">_GetElectronPairsContributionFromConjugatedRingAtoms</span> <span class="s">{</span>
|
|
|
1929 1916 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$RingAtomsRef</span><span class="cm">,</span> <span class="i">$RingBondsRef</span><span class="cm">,</span> <span class="i">$ExcludeFreeRadicalElectrons</span><span class="cm">,</span> <span class="i">$AromaticityModelDataRef</span><span class="cm">,</span> <span class="i">$ElectronPairContributionProcessedMapRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
1930 1917 <span class="k">my</span><span class="s">(</span><span class="i">$Index</span><span class="cm">,</span> <span class="i">$RingBond</span><span class="cm">,</span> <span class="i">$RingAtom</span><span class="cm">,</span> <span class="i">$NumOfRingAtomElectronPairs</span><span class="cm">,</span> <span class="i">$RingAtomID</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1931 1918
|
|
|
1932 1919 <span class="c"># Is formal charge allowed on ring atoms?</span>
|
|
|
1933 1920 <span class="k">if</span> <span class="s">(</span>!<span class="i">$AromaticityModelDataRef</span>->{<span class="w">AllowRingAtomFormalCharge</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
1934 1921 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
1935 1922 <span class="s">}</span>
|
|
|
1936 1923
|
|
|
1937 1924 <span class="i">$NumOfRingAtomElectronPairs</span> = <span class="n">0</span><span class="sc">;</span>
|
|
|
1938 1925
|
|
|
1939 1926 <span class="c"># Process ring atoms...</span>
|
|
|
1940 1927 <span class="j">RINGBOND:</span> <span class="k">for</span> <span class="i">$Index</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#</span>{<span class="i">$RingBondsRef</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
1941 1928 <span class="i">$RingBond</span> = <span class="i">$RingBondsRef</span>->[<span class="i">$Index</span>]<span class="sc">;</span>
|
|
|
1942 1929 <span class="i">$RingAtom</span> = <span class="i">$RingAtomsRef</span>->[<span class="i">$Index</span>]<span class="sc">;</span>
|
|
|
1943 1930 <span class="i">$RingAtomID</span> = <span class="i">$RingAtom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
1944 1931
|
|
|
1945 1932 <span class="c"># Is is already processed?</span>
|
|
|
1946 1933 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$ElectronPairContributionProcessedMapRef</span>->{<span class="i">$RingAtomID</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
1947 1934 <span class="k">next</span> <span class="j">RINGBOND</span><span class="sc">;</span>
|
|
|
1948 1935 <span class="s">}</span>
|
|
|
1949 1936 <span class="i">$ElectronPairContributionProcessedMapRef</span>->{<span class="i">$RingAtomID</span>} = <span class="i">$RingAtomID</span><span class="sc">;</span>
|
|
|
1950 1937
|
|
|
1951 1938 <span class="c"># Is it allowed to have any formal charge?</span>
|
|
|
1952 1939 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->_CheckPotentialAromaticRingAtomForFormalCharge</span><span class="s">(</span><span class="i">$RingAtom</span><span class="cm">,</span> <span class="i">$AromaticityModelDataRef</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1953 1940 <span class="k">next</span> <span class="j">RINGBOND</span><span class="sc">;</span>
|
|
|
1954 1941 <span class="s">}</span>
|
|
|
1955 1942
|
|
|
1956 1943 <span class="c"># It it an allowed hetero ring atom or a carbon atom?</span>
|
|
|
1957 1944 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->_CheckPotentialAromaticRingAtomForAllowedHeteroAtoms</span><span class="s">(</span><span class="i">$RingAtom</span><span class="cm">,</span> <span class="i">$AromaticityModelDataRef</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1958 1945 <span class="k">next</span> <span class="j">RINGBOND</span><span class="sc">;</span>
|
|
|
1959 1946 <span class="s">}</span>
|
|
|
1960 1947
|
|
|
1961 1948 <span class="c"># It is an atom with -ve formal charge?</span>
|
|
|
1962 1949 <span class="k">if</span> <span class="s">(</span><span class="i">$RingAtom</span><span class="i">->GetFormalCharge</span><span class="s">(</span><span class="s">)</span> >= <span class="n">0</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1963 1950 <span class="k">next</span> <span class="j">RINGBOND</span><span class="sc">;</span>
|
|
|
1964 1951 <span class="s">}</span>
|
|
|
1965 1952
|
|
|
1966 1953 <span class="c"># Is it able to donate a pair for electrons towards pi electron delocalization?</span>
|
|
|
1967 1954 <span class="k">if</span> <span class="s">(</span><span class="i">$RingAtom</span><span class="i">->GetValenceFreeElectrons</span><span class="s">(</span><span class="i">$ExcludeFreeRadicalElectrons</span><span class="s">)</span> < <span class="n">2</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1968 1955 <span class="k">next</span> <span class="j">RINGBOND</span><span class="sc">;</span>
|
|
|
1969 1956 <span class="s">}</span>
|
|
|
1970 1957 <span class="i">$NumOfRingAtomElectronPairs</span> += <span class="n">1</span><span class="sc">;</span>
|
|
|
1971 1958 <span class="s">}</span>
|
|
|
1972 1959
|
|
|
1973 1960 <span class="k">return</span> <span class="i">$NumOfRingAtomElectronPairs</span><span class="sc">;</span>
|
|
|
1974 1961 <span class="s">}</span>
|
|
|
1975 1962
|
|
|
1976 1963 <span class="c"># Check for ring atoms involved in two single ring bonds without any available electron</span>
|
|
|
1977 1964 <span class="c"># pair which are allowed to participate in aromatic system, after all other checks</span>
|
|
|
1978 1965 <span class="c"># corresponding to specified aromaticity models have already been performed...</span>
|
|
|
1979 1966 <span class="c">#</span>
|
|
|
1980 <a name="_AllowRingAtomInTwoSingleBondsWithoutElectronPair-"></a>1967 <span class="k">sub </span><span class="m">_AllowRingAtomInTwoSingleBondsWithoutElectronPair</span> <span class="s">{</span>
|
|
|
1981 1968 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$RingAtom</span><span class="cm">,</span> <span class="i">$RingBond</span><span class="cm">,</span> <span class="i">$PreviousRingBond</span><span class="cm">,</span> <span class="i">$ExocyclicDoubleBondsDataMapRef</span><span class="cm">,</span> <span class="i">$FusedRingBondsMapRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
1982 1969
|
|
|
1983 1970 <span class="j">ALLOWRINGATOM:</span> <span class="s">{</span>
|
|
|
1984 1971 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$ExocyclicDoubleBondsDataMapRef</span>->{<span class="w">RingAtomID</span>}{<span class="i">$RingAtom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
1985 1972 <span class="c"># Ring atom in an exocylic terminal double bond without any available electron pair...</span>
|
|
|
1986 1973 <span class="k">last</span> <span class="j">ALLOWRINGATOM</span><span class="sc">;</span>
|
|
|
1987 1974 <span class="s">}</span>
|
|
|
1988 1975
|
|
|
1989 1976 <span class="k">if</span> <span class="s">(</span><span class="i">$RingAtom</span><span class="i">->GetFormalCharge</span><span class="s">(</span><span class="s">)</span> > <span class="n">0</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1990 1977 <span class="c"># Ring atom with positive formal charge without any available electron pair...</span>
|
|
|
1991 1978 <span class="k">last</span> <span class="j">ALLOWRINGATOM</span><span class="sc">;</span>
|
|
|
1992 1979 <span class="s">}</span>
|
|
|
1993 1980
|
|
|
1994 1981 <span class="k">if</span> <span class="s">(</span><span class="k">defined</span> <span class="i">$FusedRingBondsMapRef</span> && <span class="s">(</span><span class="k">exists</span> <span class="i">$FusedRingBondsMapRef</span>->{<span class="i">$RingBond</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span>} || <span class="k">exists</span> <span class="i">$FusedRingBondsMapRef</span>->{<span class="i">$PreviousRingBond</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
1995 1982 <span class="c"># Ring atom involved in fused ring bond, which might end up being part of a conjugated</span>
|
|
|
1996 1983 <span class="c"># system in another fused ring...</span>
|
|
|
1997 1984 <span class="k">last</span> <span class="j">ALLOWRINGATOM</span><span class="sc">;</span>
|
|
|
1998 1985 <span class="s">}</span>
|
|
|
1999 1986
|
|
|
2000 1987 <span class="c"># Ring atom in any other environment is not allowed...</span>
|
|
|
2001 1988 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
2002 1989 <span class="s">}</span>
|
|
|
2003 1990
|
|
|
2004 1991 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span>
|
|
|
2005 1992 <span class="s">}</span>
|
|
|
2006 1993
|
|
|
2007 1994 <span class="c"># Do pi electrons satify huckel's rule: Number of pi electrons correspond to 4n + 2 where</span>
|
|
|
2008 1995 <span class="c"># n is a positive integer...</span>
|
|
|
2009 1996 <span class="c">#</span>
|
|
|
2010 <a name="_DoPiElectronSatifyHuckelsRule-"></a>1997 <span class="k">sub </span><span class="m">_DoPiElectronSatifyHuckelsRule</span> <span class="s">{</span>
|
|
|
2011 1998 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$NumOfPiElectrons</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
2012 1999
|
|
|
2013 2000 <span class="i">$NumOfPiElectrons</span> = <span class="i">$NumOfPiElectrons</span> - <span class="n">2</span><span class="sc">;</span>
|
|
|
2014 2001
|
|
|
2015 2002 <span class="k">return</span> <span class="s">(</span><span class="i">$NumOfPiElectrons</span> > <span class="n">0</span><span class="s">)</span> ? <span class="s">(</span><span class="s">(</span><span class="i">$NumOfPiElectrons</span> % <span class="n">4</span><span class="s">)</span> ? <span class="n">0</span> <span class="co">:</span> <span class="n">1</span><span class="s">)</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
2016 2003 <span class="s">}</span>
|
|
|
2017 2004
|
|
|
2018 2005 <span class="c"># Delete aromatic property for all atoms and bonds...</span>
|
|
|
2019 2006 <span class="c">#</span>
|
|
|
2020 <a name="_DeleteAtomsAndBondsAromaticity-"></a>2007 <span class="k">sub </span><span class="m">_DeleteAtomsAndBondsAromaticity</span> <span class="s">{</span>
|
|
|
2021 2008 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
2022 2009 <span class="k">my</span><span class="s">(</span><span class="i">$Atom</span><span class="cm">,</span> <span class="i">$Bond</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2023 2010
|
|
|
2024 2011 <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="i">$This</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
2025 2012 <span class="i">$Atom</span><span class="i">->DeleteAromatic</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2026 2013 <span class="s">}</span>
|
|
|
2027 2014 <span class="k">for</span> <span class="i">$Bond</span> <span class="s">(</span><span class="i">$This</span><span class="i">->GetBonds</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
2028 2015 <span class="i">$Bond</span><span class="i">->DeleteAromatic</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2029 2016 <span class="s">}</span>
|
|
|
2030 2017 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
2031 2018 <span class="s">}</span>
|
|
|
2032 2019
|
|
|
2033 2020 <span class="c"># Kekulize marked ring and non-ring aromatic atoms in a molecule...</span>
|
|
|
2034 2021 <span class="c">#</span>
|
|
|
2035 <a name="KekulizeAromaticAtoms-"></a>2022 <span class="k">sub </span><span class="m">KekulizeAromaticAtoms</span> <span class="s">{</span>
|
|
|
2036 2023 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
2037 2024
|
|
|
2038 2025 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->_KekulizeAromaticAtomsInRings</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
2039 2026 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
2040 2027 <span class="s">}</span>
|
|
|
2041 2028
|
|
|
2042 2029 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->_KekulizeAromaticAtomsNotInRings</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
2043 2030 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
2044 2031 <span class="s">}</span>
|
|
|
2045 2032
|
|
|
2046 2033 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span>
|
|
|
2047 2034 <span class="s">}</span>
|
|
|
2048 2035
|
|
|
2049 2036 <span class="c"># Kekulize marked aromatic atoms in rings and fused ring sets...</span>
|
|
|
2050 2037 <span class="c">#</span>
|
|
|
2051 <a name="_KekulizeAromaticAtomsInRings-"></a>2038 <span class="k">sub </span><span class="m">_KekulizeAromaticAtomsInRings</span> <span class="s">{</span>
|
|
|
2052 2039 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
2053 2040
|
|
|
2054 2041 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasRings</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
2055 2042 <span class="c"># Nothing to do...</span>
|
|
|
2056 2043 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span>
|
|
|
2057 2044 <span class="s">}</span>
|
|
|
2058 2045
|
|
|
2059 2046 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasAromaticAtomsInRings</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
2060 2047 <span class="c"># Nothing to do...</span>
|
|
|
2061 2048 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span>
|
|
|
2062 2049 <span class="s">}</span>
|
|
|
2063 2050
|
|
|
2064 2051 <span class="c"># Identify fully aromatic fused and individual rings along with any partially aromatic ring components</span>
|
|
|
2065 2052 <span class="c"># using marked aromatic atoms in a molecule and kekulize them as individual stes...</span>
|
|
|
2066 2053 <span class="c">#</span>
|
|
|
2067 2054 <span class="k">my</span><span class="s">(</span><span class="i">$AromaticFusedRingSetsRef</span><span class="cm">,</span> <span class="i">$AromaticRingsRef</span><span class="cm">,</span> <span class="i">$PartiallyAromaticRingComponentsRef</span><span class="s">)</span> = <span class="s">(</span><span class="k">undef</span><span class="s">)</span> x <span class="n">3</span><span class="sc">;</span>
|
|
|
2068 2055 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span><span class="i">->HasFusedRings</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
2069 2056 <span class="s">(</span><span class="i">$AromaticFusedRingSetsRef</span><span class="cm">,</span> <span class="i">$AromaticRingsRef</span><span class="cm">,</span> <span class="i">$PartiallyAromaticRingComponentsRef</span><span class="s">)</span> = <span class="i">$This</span><span class="i">->_GetFusedAndNonFusedRingsContainingAromaticAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2070 2057 <span class="s">}</span>
|
|
|
2071 2058 <span class="k">else</span> <span class="s">{</span>
|
|
|
2072 2059 <span class="s">(</span><span class="i">$AromaticRingsRef</span><span class="cm">,</span> <span class="i">$PartiallyAromaticRingComponentsRef</span><span class="s">)</span> = <span class="i">$This</span><span class="i">->_GetIndividualRingsContainingAromaticAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2073 2060 <span class="s">}</span>
|
|
|
2074 2061
|
|
|
2075 2062 <span class="k">return</span> <span class="i">$This</span><span class="i">->_KekulizeCompleteAndPartialAromaticRings</span><span class="s">(</span><span class="i">$AromaticFusedRingSetsRef</span><span class="cm">,</span> <span class="i">$AromaticRingsRef</span><span class="cm">,</span> <span class="i">$PartiallyAromaticRingComponentsRef</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2076 2063 <span class="s">}</span>
|
|
|
2077 2064
|
|
|
2078 2065 <span class="c"># Identify fully aromatic fused and individual rings along with any partially aromatic ring components</span>
|
|
|
2079 2066 <span class="c"># using marked aromatic atoms in a molecule...</span>
|
|
|
2080 2067 <span class="c">#</span>
|
|
|
2081 <a name="_GetFusedAndNonFusedRingsContainingAromaticAtoms-"></a>2068 <span class="k">sub </span><span class="m">_GetFusedAndNonFusedRingsContainingAromaticAtoms</span> <span class="s">{</span>
|
|
|
2082 2069 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
2083 2070 <span class="k">my</span><span class="s">(</span><span class="i">$Index</span><span class="cm">,</span> <span class="i">$SetAtomsCount</span><span class="cm">,</span> <span class="i">$SetAromaticAtomsCount</span><span class="cm">,</span> <span class="i">$FusedRingSetRef</span><span class="cm">,</span> <span class="i">$FusedRingSetsRef</span><span class="cm">,</span> <span class="i">$NonFusedRingsRef</span><span class="cm">,</span> <span class="i">$IndividualRingsRef</span><span class="cm">,</span> <span class="i">$RingAtomsRef</span><span class="cm">,</span> <span class="i">$RingAtomsCount</span><span class="cm">,</span> <span class="i">$AromaticAtomsCount</span><span class="cm">,</span> <span class="i">$RingAtom</span><span class="cm">,</span> <span class="i">$NonFusedFullyAromaticRingsRef</span><span class="cm">,</span> <span class="i">$NonFusedPartiallyAromaticRingComponentsRef</span><span class="cm">,</span> <span class="i">$PartiallyAromaticRingComponentsRef</span><span class="cm">,</span> <span class="i">@FullyAromaticFusedRingSets</span><span class="cm">,</span> <span class="i">@PotentialFullyAromaticRings</span><span class="cm">,</span> <span class="i">@FullyAromaticRings</span><span class="cm">,</span> <span class="i">@PotentialPartiallyAromaticRings</span><span class="cm">,</span> <span class="i">@PartiallyAromaticRingComponents</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2084 2071
|
|
|
2085 2072 <span class="i">@FullyAromaticFusedRingSets</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2086 2073
|
|
|
2087 2074 <span class="i">@PotentialFullyAromaticRings</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2088 2075 <span class="i">@FullyAromaticRings</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2089 2076
|
|
|
2090 2077 <span class="i">@PotentialPartiallyAromaticRings</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2091 2078 <span class="i">@PartiallyAromaticRingComponents</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2092 2079
|
|
|
2093 2080 <span class="s">(</span><span class="i">$FusedRingSetsRef</span><span class="cm">,</span> <span class="i">$NonFusedRingsRef</span><span class="s">)</span> = <span class="i">$This</span><span class="i">->GetFusedAndNonFusedRings</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2094 2081
|
|
|
2095 2082 <span class="c"># Go over fused ring sets...</span>
|
|
|
2096 2083 <span class="j">RINGSET:</span> <span class="k">for</span> <span class="i">$Index</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#</span>{<span class="i">$FusedRingSetsRef</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
2097 2084 <span class="i">$FusedRingSetRef</span> = <span class="i">$FusedRingSetsRef</span>->[<span class="i">$Index</span>]<span class="sc">;</span>
|
|
|
2098 2085
|
|
|
2099 2086 <span class="i">$SetAtomsCount</span> = <span class="n">0</span><span class="sc">;</span>
|
|
|
2100 2087 <span class="i">$SetAromaticAtomsCount</span> = <span class="n">0</span><span class="sc">;</span>
|
|
|
2101 2088
|
|
|
2102 2089 <span class="k">for</span> <span class="i">$RingAtomsRef</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$FusedRingSetRef</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
2103 2090 <span class="i">$SetAtomsCount</span> += <span class="k">scalar</span> <span class="i">@</span>{<span class="i">$RingAtomsRef</span>}<span class="sc">;</span>
|
|
|
2104 2091
|
|
|
2105 2092 <span class="k">for</span> <span class="i">$RingAtom</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$RingAtomsRef</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
2106 2093 <span class="k">if</span> <span class="s">(</span><span class="i">$RingAtom</span><span class="i">->IsAromatic</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
2107 2094 <span class="i">$SetAromaticAtomsCount</span> += <span class="n">1</span><span class="sc">;</span>
|
|
|
2108 2095 <span class="s">}</span>
|
|
|
2109 2096 <span class="s">}</span>
|
|
|
2110 2097 <span class="s">}</span>
|
|
|
2111 2098
|
|
|
2112 2099 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="i">$SetAtomsCount</span> && <span class="i">$SetAromaticAtomsCount</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
2113 2100 <span class="k">next</span> <span class="j">RINGSET</span><span class="sc">;</span>
|
|
|
2114 2101 <span class="s">}</span>
|
|
|
2115 2102
|
|
|
2116 2103 <span class="k">if</span> <span class="s">(</span><span class="i">$SetAromaticAtomsCount</span> == <span class="i">$SetAtomsCount</span><span class="s">)</span> <span class="s">{</span>
|
|
|
2117 2104 <span class="k">push</span> <span class="i">@FullyAromaticFusedRingSets</span><span class="cm">,</span> <span class="i">$FusedRingSetRef</span><span class="sc">;</span>
|
|
|
2118 2105 <span class="s">}</span>
|
|
|
2119 2106 <span class="k">else</span> <span class="s">{</span>
|
|
|
2120 2107 <span class="c"># Identify any individual rings in partial aromatic fused ring sets which might be</span>
|
|
|
2121 2108 <span class="c"># fully or partially aromatic...</span>
|
|
|
2122 2109 <span class="c">#</span>
|
|
|
2123 2110 <span class="j">RING:</span> <span class="k">for</span> <span class="i">$RingAtomsRef</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$FusedRingSetRef</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
2124 2111 <span class="i">$RingAtomsCount</span> = <span class="k">scalar</span> <span class="i">@</span>{<span class="i">$RingAtomsRef</span>}<span class="sc">;</span>
|
|
|
2125 2112 <span class="i">$AromaticAtomsCount</span> = <span class="n">0</span><span class="sc">;</span>
|
|
|
2126 2113
|
|
|
2127 2114 <span class="j">RINGATOM:</span> <span class="k">for</span> <span class="i">$RingAtom</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$RingAtomsRef</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
2128 2115 <span class="k">if</span> <span class="s">(</span>!<span class="i">$RingAtom</span><span class="i">->IsAromatic</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
2129 2116 <span class="k">next</span> <span class="j">RINGATOM</span><span class="sc">;</span>
|
|
|
2130 2117 <span class="s">}</span>
|
|
|
2131 2118 <span class="i">$AromaticAtomsCount</span> += <span class="n">1</span><span class="sc">;</span>
|
|
|
2132 2119 <span class="s">}</span>
|
|
|
2133 2120
|
|
|
2134 2121 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="i">$RingAtomsCount</span> && <span class="i">$AromaticAtomsCount</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
2135 2122 <span class="k">next</span> <span class="j">RING</span><span class="sc">;</span>
|
|
|
2136 2123 <span class="s">}</span>
|
|
|
2137 2124
|
|
|
2138 2125 <span class="k">if</span> <span class="s">(</span><span class="i">$RingAtomsCount</span> == <span class="i">$AromaticAtomsCount</span><span class="s">)</span> <span class="s">{</span>
|
|
|
2139 2126 <span class="k">push</span> <span class="i">@PotentialFullyAromaticRings</span><span class="cm">,</span> <span class="i">$RingAtomsRef</span><span class="sc">;</span>
|
|
|
2140 2127 <span class="s">}</span>
|
|
|
2141 2128 <span class="k">else</span> <span class="s">{</span>
|
|
|
2142 2129 <span class="c"># Track partially aromatic rings in an different list before removing them for</span>
|
|
|
2143 2130 <span class="c"># any overlap with other rings and then add to fully aromatic rings...</span>
|
|
|
2144 2131 <span class="k">push</span> <span class="i">@PotentialPartiallyAromaticRings</span><span class="cm">,</span> <span class="i">$RingAtomsRef</span><span class="sc">;</span>
|
|
|
2145 2132 <span class="s">}</span>
|
|
|
2146 2133 <span class="s">}</span>
|
|
|
2147 2134 <span class="s">}</span>
|
|
|
2148 2135 <span class="s">}</span>
|
|
|
2149 2136
|
|
|
2150 2137 <span class="k">if</span> <span class="s">(</span><span class="i">@PotentialFullyAromaticRings</span> > <span class="n">1</span><span class="s">)</span> <span class="s">{</span>
|
|
|
2151 2138 <span class="c"># Get any fully aromatic fused ring subsets from potentially fully aromatic rings...</span>
|
|
|
2152 2139 <span class="k">my</span><span class="s">(</span><span class="i">$FullyAromaticFusedRingSetsRefs</span><span class="cm">,</span> <span class="i">$FullyAromaticNonFusedRingsRef</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2153 2140 <span class="s">(</span><span class="i">$FullyAromaticFusedRingSetsRefs</span><span class="cm">,</span> <span class="i">$FullyAromaticNonFusedRingsRef</span><span class="s">)</span> = <span class="i">$This</span><span class="i">->_GetFullyAromaticFusedAndNonFusedRingsInFusedSubset</span><span class="s">(</span>\<span class="i">@PotentialFullyAromaticRings</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2154 2141
|
|
|
2155 2142 <span class="k">if</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$FullyAromaticFusedRingSetsRefs</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
2156 2143 <span class="k">push</span> <span class="i">@FullyAromaticFusedRingSets</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$FullyAromaticFusedRingSetsRefs</span>}<span class="sc">;</span>
|
|
|
2157 2144 <span class="s">}</span>
|
|
|
2158 2145 <span class="k">if</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$FullyAromaticNonFusedRingsRef</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
2159 2146 <span class="k">push</span> <span class="i">@FullyAromaticRings</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$FullyAromaticNonFusedRingsRef</span>}<span class="sc">;</span>
|
|
|
2160 2147 <span class="s">}</span>
|
|
|
2161 2148 <span class="s">}</span>
|
|
|
2162 2149 <span class="k">else</span> <span class="s">{</span>
|
|
|
2163 2150 <span class="k">push</span> <span class="i">@FullyAromaticRings</span><span class="cm">,</span> <span class="i">@PotentialFullyAromaticRings</span><span class="sc">;</span>
|
|
|
2164 2151 <span class="s">}</span>
|
|
|
2165 2152
|
|
|
2166 2153 <span class="c"># Go over partial aromatic ring components...</span>
|
|
|
2167 2154 <span class="k">if</span> <span class="s">(</span><span class="i">@PotentialPartiallyAromaticRings</span><span class="s">)</span> <span class="s">{</span>
|
|
|
2168 2155 <span class="i">$PartiallyAromaticRingComponentsRef</span> = <span class="i">$This</span><span class="i">->_GetPartiallyAromaticRingComponents</span><span class="s">(</span>\<span class="i">@PotentialPartiallyAromaticRings</span><span class="cm">,</span> \<span class="i">@PotentialFullyAromaticRings</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2169 2156 <span class="k">if</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$PartiallyAromaticRingComponentsRef</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
2170 2157 <span class="k">push</span> <span class="i">@PartiallyAromaticRingComponents</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$PartiallyAromaticRingComponentsRef</span>}<span class="sc">;</span>
|
|
|
2171 2158 <span class="s">}</span>
|
|
|
2172 2159 <span class="s">}</span>
|
|
|
2173 2160
|
|
|
2174 2161 <span class="c"># Go over non-fused rings...</span>
|
|
|
2175 2162 <span class="k">if</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$NonFusedRingsRef</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
2176 2163 <span class="s">(</span><span class="i">$NonFusedFullyAromaticRingsRef</span><span class="cm">,</span> <span class="i">$NonFusedPartiallyAromaticRingComponentsRef</span><span class="s">)</span> = <span class="i">$This</span><span class="i">->_GetRingsContainingAromaticAtoms</span><span class="s">(</span><span class="i">@</span>{<span class="i">$NonFusedRingsRef</span>}<span class="s">)</span><span class="sc">;</span>
|
|
|
2177 2164
|
|
|
2178 2165 <span class="k">if</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$NonFusedFullyAromaticRingsRef</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
2179 2166 <span class="k">push</span> <span class="i">@FullyAromaticRings</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$NonFusedFullyAromaticRingsRef</span>}<span class="sc">;</span>
|
|
|
2180 2167 <span class="s">}</span>
|
|
|
2181 2168 <span class="k">if</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$NonFusedPartiallyAromaticRingComponentsRef</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
2182 2169 <span class="k">push</span> <span class="i">@PartiallyAromaticRingComponents</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$NonFusedPartiallyAromaticRingComponentsRef</span>}<span class="sc">;</span>
|
|
|
2183 2170 <span class="s">}</span>
|
|
|
2184 2171 <span class="s">}</span>
|
|
|
2185 2172
|
|
|
2186 2173 <span class="k">return</span> <span class="s">(</span>\<span class="i">@FullyAromaticFusedRingSets</span><span class="cm">,</span> \<span class="i">@FullyAromaticRings</span><span class="cm">,</span> \<span class="i">@PartiallyAromaticRingComponents</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2187 2174 <span class="s">}</span>
|
|
|
2188 2175
|
|
|
2189 2176 <span class="c"># Identify fully aromatic fused sets and non-fused rings in potentially fully aromatic</span>
|
|
|
2190 2177 <span class="c"># rings in fused ring sets...</span>
|
|
|
2191 2178 <span class="c">#</span>
|
|
|
2192 2179 <span class="c"># Fully aromatic rings in fused ring sets might contain fully aromatic fused subsets. These</span>
|
|
|
2193 2180 <span class="c"># fused subets need to be tracked and treated as fused sets.</span>
|
|
|
2194 2181 <span class="c">#</span>
|
|
|
2195 2182 <span class="c"># Note:</span>
|
|
|
2196 2183 <span class="c"># . Fused ring sets share at least one common bond, which could be used to identify</span>
|
|
|
2197 2184 <span class="c"># any multiple fully aromatic fused rings sets; absence of a shared ring bond implies</span>
|
|
|
2198 2185 <span class="c"># there are no fused ring sets.</span>
|
|
|
2199 2186 <span class="c">#</span>
|
|
|
2200 2187 <span class="c">#</span>
|
|
|
2201 <a name="_GetFullyAromaticFusedAndNonFusedRingsInFusedSubset-"></a>2188 <span class="k">sub </span><span class="m">_GetFullyAromaticFusedAndNonFusedRingsInFusedSubset</span> <span class="s">{</span>
|
|
|
2202 2189 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$PotentialFullyAromaticFusedRingsRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
2203 2190 <span class="k">my</span><span class="s">(</span><span class="i">$RingIndex</span><span class="cm">,</span> <span class="i">$RingIndex1</span><span class="cm">,</span> <span class="i">$RingIndex2</span><span class="cm">,</span> <span class="i">$RingAtom</span><span class="cm">,</span> <span class="i">$RingAtomID</span><span class="cm">,</span> <span class="i">$RingIsFuesd</span><span class="cm">,</span> <span class="i">$RingIndicesGraph</span><span class="cm">,</span> <span class="i">$FusedRingSetIndicesRef</span><span class="cm">,</span> <span class="i">@RingIndices</span><span class="cm">,</span> <span class="i">@FusedRingPairIndices</span><span class="cm">,</span> <span class="i">@FusedRingSetIndicesRefs</span><span class="cm">,</span> <span class="i">@FullyAromaticFusedRingSets</span><span class="cm">,</span> <span class="i">@FullyAromaticRings</span><span class="cm">,</span> <span class="i">%RingIndexToAtomIDMap</span><span class="cm">,</span> <span class="i">%FullyAromaticFusedRingIndexMap</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2204 2191
|
|
|
2205 2192 <span class="i">@FullyAromaticFusedRingSets</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2206 2193 <span class="i">@FullyAromaticRings</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2207 2194
|
|
|
2208 2195 <span class="c"># Setup a ring index map for ring atoms...</span>
|
|
|
2209 2196 <span class="c">#</span>
|
|
|
2210 2197 <span class="i">%RingIndexToAtomIDMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2211 2198 <span class="k">for</span> <span class="i">$RingIndex</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#</span>{<span class="i">$PotentialFullyAromaticFusedRingsRef</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
2212 2199 <span class="i">%</span>{<span class="i">$RingIndexToAtomIDMap</span>{<span class="i">$RingIndex</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2213 2200 <span class="k">for</span> <span class="i">$RingAtom</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$PotentialFullyAromaticFusedRingsRef</span>->[<span class="i">$RingIndex</span>]}<span class="s">)</span> <span class="s">{</span>
|
|
|
2214 2201 <span class="i">$RingAtomID</span> = <span class="i">$RingAtom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2215 2202 <span class="i">$RingIndexToAtomIDMap</span>{<span class="i">$RingIndex</span>}{<span class="i">$RingAtomID</span>} = <span class="i">$RingAtomID</span><span class="sc">;</span>
|
|
|
2216 2203 <span class="s">}</span>
|
|
|
2217 2204 <span class="s">}</span>
|
|
|
2218 2205
|
|
|
2219 2206 <span class="c"># Identify fused ring pairs...</span>
|
|
|
2220 2207 <span class="c">#</span>
|
|
|
2221 2208 <span class="i">@RingIndices</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2222 2209 <span class="i">@FusedRingPairIndices</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2223 2210
|
|
|
2224 2211 <span class="k">for</span> <span class="i">$RingIndex1</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#</span>{<span class="i">$PotentialFullyAromaticFusedRingsRef</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
2225 2212 <span class="k">push</span> <span class="i">@RingIndices</span><span class="cm">,</span> <span class="i">$RingIndex1</span><span class="sc">;</span>
|
|
|
2226 2213 <span class="k">for</span> <span class="i">$RingIndex2</span> <span class="s">(</span><span class="s">(</span><span class="i">$RingIndex1</span> + <span class="n">1</span><span class="s">)</span> .. <span class="i">$#</span>{<span class="i">$PotentialFullyAromaticFusedRingsRef</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
2227 2214 <span class="i">$RingIsFuesd</span> = <span class="n">0</span><span class="sc">;</span>
|
|
|
2228 2215 <span class="j">RINGATOM:</span> <span class="k">for</span> <span class="i">$RingAtom</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$PotentialFullyAromaticFusedRingsRef</span>->[<span class="i">$RingIndex2</span>]}<span class="s">)</span> <span class="s">{</span>
|
|
|
2229 2216 <span class="i">$RingAtomID</span> = <span class="i">$RingAtom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2230 2217 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$RingIndexToAtomIDMap</span>{<span class="i">$RingIndex1</span>}{<span class="i">$RingAtomID</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
2231 2218 <span class="i">$RingIsFuesd</span> = <span class="n">1</span><span class="sc">;</span>
|
|
|
2232 2219 <span class="k">last</span> <span class="j">RINGATOM</span><span class="sc">;</span>
|
|
|
2233 2220 <span class="s">}</span>
|
|
|
2234 2221 <span class="s">}</span>
|
|
|
2235 2222 <span class="k">if</span> <span class="s">(</span><span class="i">$RingIsFuesd</span><span class="s">)</span> <span class="s">{</span>
|
|
|
2236 2223 <span class="k">push</span> <span class="i">@FusedRingPairIndices</span><span class="cm">,</span> <span class="s">(</span><span class="i">$RingIndex1</span><span class="cm">,</span> <span class="i">$RingIndex2</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2237 2224 <span class="s">}</span>
|
|
|
2238 2225 <span class="s">}</span>
|
|
|
2239 2226 <span class="s">}</span>
|
|
|
2240 2227
|
|
|
2241 2228 <span class="k">if</span> <span class="s">(</span>!<span class="i">@FusedRingPairIndices</span><span class="s">)</span> <span class="s">{</span>
|
|
|
2242 2229 <span class="c"># No fused ring subset out there...</span>
|
|
|
2243 2230 <span class="k">push</span> <span class="i">@FullyAromaticRings</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$PotentialFullyAromaticFusedRingsRef</span>}<span class="sc">;</span>
|
|
|
2244 2231
|
|
|
2245 2232 <span class="k">return</span> <span class="s">(</span>\<span class="i">@FullyAromaticFusedRingSets</span><span class="cm">,</span> \<span class="i">@FullyAromaticRings</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2246 2233 <span class="s">}</span>
|
|
|
2247 2234
|
|
|
2248 2235 <span class="c"># Identify fused ring sets...</span>
|
|
|
2249 2236 <span class="c">#</span>
|
|
|
2250 2237 <span class="i">$RingIndicesGraph</span> = <span class="i">new</span> <span class="i">Graph</span><span class="s">(</span><span class="i">@RingIndices</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2251 2238 <span class="i">$RingIndicesGraph</span><span class="i">->AddEdges</span><span class="s">(</span><span class="i">@FusedRingPairIndices</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2252 2239 <span class="i">@FusedRingSetIndicesRefs</span> = <span class="i">$RingIndicesGraph</span><span class="i">->GetConnectedComponentsVertices</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2253 2240
|
|
|
2254 2241 <span class="c"># Collect fully aromatic fused ring sets...</span>
|
|
|
2255 2242 <span class="c">#</span>
|
|
|
2256 2243 <span class="i">%FullyAromaticFusedRingIndexMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2257 2244 <span class="k">for</span> <span class="i">$FusedRingSetIndicesRef</span> <span class="s">(</span><span class="i">@FusedRingSetIndicesRefs</span><span class="s">)</span> <span class="s">{</span>
|
|
|
2258 2245 <span class="k">my</span><span class="s">(</span><span class="i">@FullyAromaticFusedRingSet</span><span class="s">)</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2259 2246 <span class="k">for</span> <span class="i">$RingIndex</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$FusedRingSetIndicesRef</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
2260 2247 <span class="i">$FullyAromaticFusedRingIndexMap</span>{<span class="i">$RingIndex</span>} = <span class="i">$RingIndex</span><span class="sc">;</span>
|
|
|
2261 2248 <span class="k">push</span> <span class="i">@FullyAromaticFusedRingSet</span><span class="cm">,</span> <span class="i">$PotentialFullyAromaticFusedRingsRef</span>->[<span class="i">$RingIndex</span>]<span class="sc">;</span>
|
|
|
2262 2249 <span class="s">}</span>
|
|
|
2263 2250 <span class="k">if</span> <span class="s">(</span><span class="i">@FullyAromaticFusedRingSet</span><span class="s">)</span> <span class="s">{</span>
|
|
|
2264 2251 <span class="c"># Sort rings by size with in the fused ring set...</span>
|
|
|
2265 2252 <span class="i">@FullyAromaticFusedRingSet</span> = <span class="k">sort</span> <span class="s">{</span> <span class="k">scalar</span> <span class="i">@$a</span> <=> <span class="k">scalar</span> <span class="i">@$b</span> <span class="s">}</span> <span class="i">@FullyAromaticFusedRingSet</span><span class="sc">;</span>
|
|
|
2266 2253 <span class="k">push</span> <span class="i">@FullyAromaticFusedRingSets</span><span class="cm">,</span> \<span class="i">@FullyAromaticFusedRingSet</span><span class="sc">;</span>
|
|
|
2267 2254 <span class="s">}</span>
|
|
|
2268 2255 <span class="s">}</span>
|
|
|
2269 2256
|
|
|
2270 2257 <span class="c"># Collect fully aromatic non-fused rings...</span>
|
|
|
2271 2258 <span class="c">#</span>
|
|
|
2272 2259 <span class="j">RINGINDEX:</span> <span class="k">for</span> <span class="i">$RingIndex</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#</span>{<span class="i">$PotentialFullyAromaticFusedRingsRef</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
2273 2260 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$FullyAromaticFusedRingIndexMap</span>{<span class="i">$RingIndex</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
2274 2261 <span class="k">next</span> <span class="j">RINGINDEX</span><span class="sc">;</span>
|
|
|
2275 2262 <span class="s">}</span>
|
|
|
2276 2263 <span class="k">push</span> <span class="i">@FullyAromaticRings</span><span class="cm">,</span> <span class="i">$PotentialFullyAromaticFusedRingsRef</span>->[<span class="i">$RingIndex</span>]<span class="sc">;</span>
|
|
|
2277 2264 <span class="s">}</span>
|
|
|
2278 2265
|
|
|
2279 2266 <span class="k">return</span> <span class="s">(</span>\<span class="i">@FullyAromaticFusedRingSets</span><span class="cm">,</span> \<span class="i">@FullyAromaticRings</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2280 2267 <span class="s">}</span>
|
|
|
2281 2268
|
|
|
2282 2269 <span class="c"># Identify individual non-fused rings containing aromatic atoms...</span>
|
|
|
2283 2270 <span class="c">#</span>
|
|
|
2284 <a name="_GetIndividualRingsContainingAromaticAtoms-"></a>2271 <span class="k">sub </span><span class="m">_GetIndividualRingsContainingAromaticAtoms</span> <span class="s">{</span>
|
|
|
2285 2272 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
2286 2273
|
|
|
2287 2274 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetRingsContainingAromaticAtoms</span><span class="s">(</span><span class="i">$This</span><span class="i">->GetRings</span><span class="s">(</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2288 2275 <span class="s">}</span>
|
|
|
2289 2276
|
|
|
2290 2277 <span class="c"># Identify individual non-fused rings containing aromatic atoms...</span>
|
|
|
2291 2278 <span class="c">#</span>
|
|
|
2292 <a name="_GetRingsContainingAromaticAtoms-"></a>2279 <span class="k">sub </span><span class="m">_GetRingsContainingAromaticAtoms</span> <span class="s">{</span>
|
|
|
2293 2280 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">@Rings</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
2294 2281 <span class="k">my</span><span class="s">(</span><span class="i">$RingAtom</span><span class="cm">,</span> <span class="i">$RingAtomsRef</span><span class="cm">,</span> <span class="i">$RingAtomsCount</span><span class="cm">,</span> <span class="i">$AromaticAtomsCount</span><span class="cm">,</span> <span class="i">$PartiallyAromaticRingComponentsRef</span><span class="cm">,</span> <span class="i">@FullyAromaticRings</span><span class="cm">,</span> <span class="i">@PartiallyAromaticRings</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2295 2282
|
|
|
2296 2283 <span class="i">@FullyAromaticRings</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2297 2284 <span class="i">@PartiallyAromaticRings</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2298 2285
|
|
|
2299 2286 <span class="j">RING:</span> <span class="k">for</span> <span class="i">$RingAtomsRef</span> <span class="s">(</span><span class="i">@Rings</span><span class="s">)</span> <span class="s">{</span>
|
|
|
2300 2287 <span class="i">$RingAtomsCount</span> = <span class="k">scalar</span> <span class="i">@</span>{<span class="i">$RingAtomsRef</span>}<span class="sc">;</span>
|
|
|
2301 2288 <span class="i">$AromaticAtomsCount</span> = <span class="n">0</span><span class="sc">;</span>
|
|
|
2302 2289
|
|
|
2303 2290 <span class="k">for</span> <span class="i">$RingAtom</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$RingAtomsRef</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
2304 2291 <span class="k">if</span> <span class="s">(</span><span class="i">$RingAtom</span><span class="i">->IsAromatic</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
2305 2292 <span class="i">$AromaticAtomsCount</span> += <span class="n">1</span><span class="sc">;</span>
|
|
|
2306 2293 <span class="s">}</span>
|
|
|
2307 2294 <span class="s">}</span>
|
|
|
2308 2295
|
|
|
2309 2296 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="i">$AromaticAtomsCount</span> && <span class="i">$RingAtomsCount</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
2310 2297 <span class="k">next</span> <span class="j">RING</span><span class="sc">;</span>
|
|
|
2311 2298 <span class="s">}</span>
|
|
|
2312 2299
|
|
|
2313 2300 <span class="k">if</span> <span class="s">(</span><span class="i">$AromaticAtomsCount</span> == <span class="i">$RingAtomsCount</span><span class="s">)</span> <span class="s">{</span>
|
|
|
2314 2301 <span class="k">push</span> <span class="i">@FullyAromaticRings</span><span class="cm">,</span> <span class="i">$RingAtomsRef</span><span class="sc">;</span>
|
|
|
2315 2302 <span class="s">}</span>
|
|
|
2316 2303 <span class="k">else</span> <span class="s">{</span>
|
|
|
2317 2304 <span class="k">push</span> <span class="i">@PartiallyAromaticRings</span><span class="cm">,</span> <span class="i">$RingAtomsRef</span><span class="sc">;</span>
|
|
|
2318 2305 <span class="s">}</span>
|
|
|
2319 2306 <span class="s">}</span>
|
|
|
2320 2307
|
|
|
2321 2308 <span class="i">$PartiallyAromaticRingComponentsRef</span> = <span class="i">$This</span><span class="i">->_GetPartiallyAromaticRingComponents</span><span class="s">(</span>\<span class="i">@PartiallyAromaticRings</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2322 2309
|
|
|
2323 2310 <span class="k">return</span> <span class="s">(</span>\<span class="i">@FullyAromaticRings</span><span class="cm">,</span> <span class="i">$PartiallyAromaticRingComponentsRef</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2324 2311 <span class="s">}</span>
|
|
|
2325 2312
|
|
|
2326 2313 <span class="c"># Get connected aromatic components with in partially aromatic rings...</span>
|
|
|
2327 2314 <span class="c">#</span>
|
|
|
2328 <a name="_GetPartiallyAromaticRingComponents-"></a>2315 <span class="k">sub </span><span class="m">_GetPartiallyAromaticRingComponents</span> <span class="s">{</span>
|
|
|
2329 2316 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$PotentialPartiallyAromaticRingsRef</span><span class="cm">,</span> <span class="i">$FullyAromaticRingsRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
2330 2317 <span class="k">my</span><span class="s">(</span><span class="i">$RingAtomsRef</span><span class="cm">,</span> <span class="i">$RingAtom</span><span class="cm">,</span> <span class="i">$RingAtomID</span><span class="cm">,</span> <span class="i">$Index</span><span class="cm">,</span> <span class="i">@PartiallyAromaticRingComponents</span><span class="cm">,</span> <span class="i">%FullyAromaticRingAtomsMap</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2331 2318
|
|
|
2332 2319 <span class="i">@PartiallyAromaticRingComponents</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2333 2320
|
|
|
2334 2321 <span class="c"># Setup a map for atoms involve in fully aromatic rings to remove remove partial rings</span>
|
|
|
2335 2322 <span class="c"># containing only those atoms which are already part of some other fully aromatic ring</span>
|
|
|
2336 2323 <span class="c"># in fused ring scenarios or some other partially aromatic ring...</span>
|
|
|
2337 2324 <span class="c">#</span>
|
|
|
2338 2325 <span class="i">%FullyAromaticRingAtomsMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2339 2326 <span class="k">if</span> <span class="s">(</span><span class="k">defined</span> <span class="i">$FullyAromaticRingsRef</span><span class="s">)</span> <span class="s">{</span>
|
|
|
2340 2327 <span class="k">for</span> <span class="i">$RingAtomsRef</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$FullyAromaticRingsRef</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
2341 2328 <span class="k">for</span> <span class="i">$RingAtom</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$RingAtomsRef</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
2342 2329 <span class="i">$RingAtomID</span> = <span class="i">$RingAtom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2343 2330 <span class="i">$FullyAromaticRingAtomsMap</span>{<span class="i">$RingAtomID</span>} = <span class="i">$RingAtomID</span><span class="sc">;</span>
|
|
|
2344 2331 <span class="s">}</span>
|
|
|
2345 2332 <span class="s">}</span>
|
|
|
2346 2333 <span class="s">}</span>
|
|
|
2347 2334
|
|
|
2348 2335 <span class="c"># . Identify any connected components with in each partially aromatic ring.</span>
|
|
|
2349 2336 <span class="c"># . Use ring atom indices to figure out connnected components in rings: All ring atoms</span>
|
|
|
2350 2337 <span class="c"># in a connected component have sequential indices and a difference by more than</span>
|
|
|
2351 2338 <span class="c"># 1 indicates a new component in the list.</span>
|
|
|
2352 2339 <span class="c">#</span>
|
|
|
2353 2340 <span class="j">RING:</span> <span class="k">for</span> <span class="i">$RingAtomsRef</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$PotentialPartiallyAromaticRingsRef</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
2354 2341 <span class="k">my</span><span class="s">(</span><span class="i">@AromaticRingAtoms</span><span class="cm">,</span> <span class="i">@AromaticRingAtomsIndices</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2355 2342
|
|
|
2356 2343 <span class="i">@AromaticRingAtoms</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2357 2344 <span class="i">@AromaticRingAtomsIndices</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2358 2345
|
|
|
2359 2346 <span class="j">RINGATOM:</span> <span class="k">for</span> <span class="i">$Index</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#</span>{<span class="i">$RingAtomsRef</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
2360 2347 <span class="i">$RingAtom</span> = <span class="i">$RingAtomsRef</span>->[<span class="i">$Index</span>]<span class="sc">;</span>
|
|
|
2361 2348 <span class="i">$RingAtomID</span> = <span class="i">$RingAtom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2362 2349
|
|
|
2363 2350 <span class="k">if</span> <span class="s">(</span><span class="k">defined</span> <span class="i">$FullyAromaticRingsRef</span> && <span class="k">exists</span> <span class="i">$FullyAromaticRingAtomsMap</span>{<span class="i">$RingAtomID</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
2364 2351 <span class="k">next</span> <span class="j">RINGATOM</span><span class="sc">;</span>
|
|
|
2365 2352 <span class="s">}</span>
|
|
|
2366 2353 <span class="k">if</span> <span class="s">(</span>!<span class="i">$RingAtom</span><span class="i">->IsAromatic</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
2367 2354 <span class="k">next</span> <span class="j">RINGATOM</span><span class="sc">;</span>
|
|
|
2368 2355 <span class="s">}</span>
|
|
|
2369 2356 <span class="k">push</span> <span class="i">@AromaticRingAtoms</span><span class="cm">,</span> <span class="i">$RingAtom</span><span class="sc">;</span>
|
|
|
2370 2357 <span class="k">push</span> <span class="i">@AromaticRingAtomsIndices</span><span class="cm">,</span> <span class="i">$Index</span><span class="sc">;</span>
|
|
|
2371 2358
|
|
|
2372 2359 <span class="s">}</span>
|
|
|
2373 2360 <span class="k">if</span> <span class="s">(</span>!<span class="i">@AromaticRingAtoms</span><span class="s">)</span> <span class="s">{</span>
|
|
|
2374 2361 <span class="k">next</span> <span class="j">RING</span><span class="sc">;</span>
|
|
|
2375 2362 <span class="s">}</span>
|
|
|
2376 2363
|
|
|
2377 2364 <span class="c"># Start off with a new connected component...</span>
|
|
|
2378 2365 <span class="c">#</span>
|
|
|
2379 2366 <span class="k">my</span><span class="s">(</span><span class="i">$ComponentNum</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2380 2367 <span class="i">$ComponentNum</span> = <span class="k">scalar</span> <span class="i">@PartiallyAromaticRingComponents</span><span class="sc">;</span>
|
|
|
2381 2368 <span class="i">@</span>{<span class="i">$PartiallyAromaticRingComponents</span>[<span class="i">$ComponentNum</span>]} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2382 2369
|
|
|
2383 2370 <span class="i">$Index</span> = <span class="n">0</span><span class="sc">;</span>
|
|
|
2384 2371 <span class="k">push</span> <span class="i">@</span>{<span class="i">$PartiallyAromaticRingComponents</span>[<span class="i">$ComponentNum</span>]}<span class="cm">,</span> <span class="i">$AromaticRingAtoms</span>[<span class="i">$Index</span>]<span class="sc">;</span>
|
|
|
2385 2372
|
|
|
2386 2373 <span class="k">for</span> <span class="i">$Index</span> <span class="s">(</span><span class="n">1</span> .. <span class="i">$#AromaticRingAtoms</span><span class="s">)</span> <span class="s">{</span>
|
|
|
2387 2374 <span class="k">if</span> <span class="s">(</span><span class="s">(</span><span class="i">$AromaticRingAtomsIndices</span>[<span class="i">$Index</span>] - <span class="i">$AromaticRingAtomsIndices</span>[<span class="i">$Index</span> -<span class="n">1</span>]<span class="s">)</span> > <span class="n">1</span><span class="s">)</span> <span class="s">{</span>
|
|
|
2388 2375 <span class="c"># New connected component...</span>
|
|
|
2389 2376 <span class="i">$ComponentNum</span> += <span class="n">1</span><span class="sc">;</span>
|
|
|
2390 2377 <span class="i">@</span>{<span class="i">$PartiallyAromaticRingComponents</span>[<span class="i">$ComponentNum</span>]} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2391 2378 <span class="s">}</span>
|
|
|
2392 2379 <span class="k">push</span> <span class="i">@</span>{<span class="i">$PartiallyAromaticRingComponents</span>[<span class="i">$ComponentNum</span>]}<span class="cm">,</span> <span class="i">$AromaticRingAtoms</span>[<span class="i">$Index</span>]<span class="sc">;</span>
|
|
|
2393 2380 <span class="s">}</span>
|
|
|
2394 2381 <span class="s">}</span>
|
|
|
2395 2382
|
|
|
2396 2383 <span class="k">return</span> <span class="s">(</span>\<span class="i">@PartiallyAromaticRingComponents</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2397 2384 <span class="s">}</span>
|
|
|
2398 2385
|
|
|
2399 2386 <span class="c"># Kekulize fully aromatic fused and individual rings along with any partially aromatic ring</span>
|
|
|
2400 2387 <span class="c"># components...</span>
|
|
|
2401 2388 <span class="c">#</span>
|
|
|
2402 <a name="_KekulizeCompleteAndPartialAromaticRings-"></a>2389 <span class="k">sub </span><span class="m">_KekulizeCompleteAndPartialAromaticRings</span> <span class="s">{</span>
|
|
|
2403 2390 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$AromaticFusedRingSetsRef</span><span class="cm">,</span> <span class="i">$AromaticRingsRef</span><span class="cm">,</span> <span class="i">$PartiallyAromaticRingComponentsRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
2404 2391 <span class="k">my</span><span class="s">(</span><span class="i">$Status</span><span class="cm">,</span> <span class="i">$ConnectedPathsAtomsSetsRef</span><span class="cm">,</span> <span class="i">$ConnectedPathsBondsSetsRef</span><span class="cm">,</span> <span class="i">$ConnectdPathsSetsTypesRef</span><span class="cm">,</span> <span class="i">$PathSetIndex</span><span class="cm">,</span> <span class="i">$PathAtom</span><span class="cm">,</span> <span class="i">$AtomID</span><span class="cm">,</span> <span class="i">$BondID</span><span class="cm">,</span> <span class="i">$PathBondsRef</span><span class="cm">,</span> <span class="i">$DeleteAtomsAromaticity</span><span class="cm">,</span> <span class="i">$DeleteBondsAromaticity</span><span class="cm">,</span> <span class="i">%PathAtomsProcessingStatusMap</span><span class="cm">,</span> <span class="i">%PathBondsProcessingStatusMap</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2405 2392
|
|
|
2406 2393 <span class="s">(</span><span class="i">$ConnectedPathsAtomsSetsRef</span><span class="cm">,</span> <span class="i">$ConnectedPathsBondsSetsRef</span><span class="cm">,</span> <span class="i">$ConnectdPathsSetsTypesRef</span><span class="s">)</span> = <span class="i">$This</span><span class="i">->_SetupCompleteAndPartialAromaticRingsForKekulizaiton</span><span class="s">(</span><span class="i">$AromaticFusedRingSetsRef</span><span class="cm">,</span> <span class="i">$AromaticRingsRef</span><span class="cm">,</span> <span class="i">$PartiallyAromaticRingComponentsRef</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2407 2394
|
|
|
2408 2395 <span class="k">if</span> <span class="s">(</span>!<span class="i">@</span>{<span class="i">$ConnectedPathsAtomsSetsRef</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
2409 2396 <span class="c"># Nothing to do...</span>
|
|
|
2410 2397 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span>
|
|
|
2411 2398 <span class="s">}</span>
|
|
|
2412 2399
|
|
|
2413 2400 <span class="c"># Delete any aromaticity property set for non-ring bonds connected any two ring</span>
|
|
|
2414 2401 <span class="c"># aromatic atoms...</span>
|
|
|
2415 2402 <span class="c">#</span>
|
|
|
2416 2403 <span class="i">$This</span><span class="i">->_ProcessNonRingAromaticBondsBetweenAromaticRingAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2417 2404
|
|
|
2418 2405 <span class="i">%PathAtomsProcessingStatusMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2419 2406 <span class="i">%PathBondsProcessingStatusMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2420 2407
|
|
|
2421 2408 <span class="i">$Status</span> = <span class="n">1</span><span class="sc">;</span>
|
|
|
2422 2409
|
|
|
2423 2410 <span class="j">PATHSET:</span> <span class="k">for</span> <span class="i">$PathSetIndex</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#</span>{<span class="i">$ConnectedPathsAtomsSetsRef</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
2424 2411 <span class="k">my</span><span class="s">(</span><span class="i">$AtomProcessingStatusMapRef</span><span class="cm">,</span> <span class="i">$BondProcessingStatusMapRef</span><span class="cm">,</span> <span class="i">$PathSetProcessingStatusRef</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2425 2412
|
|
|
2426 2413 <span class="s">(</span><span class="i">$AtomProcessingStatusMapRef</span><span class="cm">,</span> <span class="i">$BondProcessingStatusMapRef</span><span class="cm">,</span> <span class="i">$PathSetProcessingStatusRef</span><span class="s">)</span> = <span class="s">(</span><span class="k">undef</span><span class="s">)</span> x <span class="n">3</span><span class="sc">;</span>
|
|
|
2427 2414
|
|
|
2428 2415 <span class="k">if</span> <span class="s">(</span><span class="i">$ConnectdPathsSetsTypesRef</span>->[<span class="i">$PathSetIndex</span>] =~ <span class="q">/^FusedAromatic$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
2429 2416 <span class="c"># Fused set of connected paths...</span>
|
|
|
2430 2417 <span class="c">#</span>
|
|
|
2431 2418 <span class="k">my</span><span class="s">(</span><span class="i">$FusedConnectedPathAtomsSetRef</span><span class="cm">,</span> <span class="i">$FusedConnectedPathBondsSetRef</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2432 2419
|
|
|
2433 2420 <span class="i">$FusedConnectedPathAtomsSetRef</span> = <span class="i">$ConnectedPathsAtomsSetsRef</span>->[<span class="i">$PathSetIndex</span>]<span class="sc">;</span>
|
|
|
2434 2421 <span class="i">$FusedConnectedPathBondsSetRef</span> = <span class="i">$ConnectedPathsBondsSetsRef</span>->[<span class="i">$PathSetIndex</span>]<span class="sc">;</span>
|
|
|
2435 2422
|
|
|
2436 2423 <span class="c"># Prepare for kekulization...</span>
|
|
|
2437 2424 <span class="s">(</span><span class="i">$AtomProcessingStatusMapRef</span><span class="cm">,</span> <span class="i">$BondProcessingStatusMapRef</span><span class="cm">,</span> <span class="i">$PathSetProcessingStatusRef</span><span class="s">)</span> = <span class="i">$This</span><span class="i">->_SetupConnectedPathSetsForKekulization</span><span class="s">(</span><span class="i">$FusedConnectedPathAtomsSetRef</span><span class="cm">,</span> <span class="i">$FusedConnectedPathBondsSetRef</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2438 2425
|
|
|
2439 2426 <span class="c"># Perform kekulization starting with the first path set...</span>
|
|
|
2440 2427 <span class="i">$PathSetProcessingStatusRef</span>->[<span class="n">0</span>] = <span class="q">'Processed'</span><span class="sc">;</span>
|
|
|
2441 2428 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->_KekulizeConnectedPathSets</span><span class="s">(</span><span class="i">$FusedConnectedPathAtomsSetRef</span>->[<span class="n">0</span>]<span class="cm">,</span> <span class="i">$FusedConnectedPathBondsSetRef</span>->[<span class="n">0</span>]<span class="cm">,</span> <span class="i">$AtomProcessingStatusMapRef</span><span class="cm">,</span> <span class="i">$BondProcessingStatusMapRef</span><span class="cm">,</span> <span class="i">$FusedConnectedPathAtomsSetRef</span><span class="cm">,</span> <span class="i">$FusedConnectedPathBondsSetRef</span><span class="cm">,</span> <span class="i">$PathSetProcessingStatusRef</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
2442 2429 <span class="c"># Kekulization failed for the current fused paths set...</span>
|
|
|
2443 2430 <span class="i">$Status</span> = <span class="n">0</span><span class="sc">;</span>
|
|
|
2444 2431 <span class="s">}</span>
|
|
|
2445 2432 <span class="s">}</span>
|
|
|
2446 2433 <span class="k">else</span> <span class="s">{</span>
|
|
|
2447 2434 <span class="c"># An individual connected path...</span>
|
|
|
2448 2435 <span class="c">#</span>
|
|
|
2449 2436 <span class="k">my</span><span class="s">(</span><span class="i">@ConnectedPathAtomsSet</span><span class="cm">,</span> <span class="i">@ConnectedPathBondsSet</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2450 2437
|
|
|
2451 2438 <span class="i">@ConnectedPathAtomsSet</span> = <span class="s">(</span><span class="i">$ConnectedPathsAtomsSetsRef</span>->[<span class="i">$PathSetIndex</span>]<span class="s">)</span><span class="sc">;</span>
|
|
|
2452 2439 <span class="i">@ConnectedPathBondsSet</span> = <span class="s">(</span><span class="i">$ConnectedPathsBondsSetsRef</span>->[<span class="i">$PathSetIndex</span>]<span class="s">)</span><span class="sc">;</span>
|
|
|
2453 2440
|
|
|
2454 2441 <span class="c"># Prepare for kekulization...</span>
|
|
|
2455 2442 <span class="s">(</span><span class="i">$AtomProcessingStatusMapRef</span><span class="cm">,</span> <span class="i">$BondProcessingStatusMapRef</span><span class="s">)</span> = <span class="i">$This</span><span class="i">->_SetupConnectedPathSetsForKekulization</span><span class="s">(</span>\<span class="i">@ConnectedPathAtomsSet</span><span class="cm">,</span> \<span class="i">@ConnectedPathBondsSet</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2456 2443
|
|
|
2457 2444 <span class="c"># Perform kekulization...</span>
|
|
|
2458 2445 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->_KekulizeConnectedPathSets</span><span class="s">(</span><span class="i">$ConnectedPathsAtomsSetsRef</span>->[<span class="i">$PathSetIndex</span>]<span class="cm">,</span> <span class="i">$ConnectedPathsBondsSetsRef</span>->[<span class="i">$PathSetIndex</span>]<span class="cm">,</span> <span class="i">$AtomProcessingStatusMapRef</span><span class="cm">,</span> <span class="i">$BondProcessingStatusMapRef</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
2459 2446 <span class="c"># Kekulization failed for the current path...</span>
|
|
|
2460 2447 <span class="i">$Status</span> = <span class="n">0</span><span class="sc">;</span>
|
|
|
2461 2448 <span class="s">}</span>
|
|
|
2462 2449 <span class="s">}</span>
|
|
|
2463 2450
|
|
|
2464 2451 <span class="c"># Did kekulization succeed for the current path or path set?</span>
|
|
|
2465 2452 <span class="k">if</span> <span class="s">(</span>!<span class="i">$Status</span><span class="s">)</span> <span class="s">{</span>
|
|
|
2466 2453 <span class="k">last</span> <span class="j">PATHSET</span><span class="sc">;</span>
|
|
|
2467 2454 <span class="s">}</span>
|
|
|
2468 2455
|
|
|
2469 2456 <span class="c"># Track atom and bond processing state for final assignment after kekulization</span>
|
|
|
2470 2457 <span class="c"># is successfully completed for all the paths and fused path sets...</span>
|
|
|
2471 2458 <span class="c">#</span>
|
|
|
2472 2459 <span class="k">for</span> <span class="i">$AtomID</span> <span class="s">(</span><span class="k">keys</span> <span class="i">%</span>{<span class="i">$AtomProcessingStatusMapRef</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
2473 2460 <span class="i">$PathAtomsProcessingStatusMap</span>{<span class="i">$AtomID</span>} = <span class="i">$AtomProcessingStatusMapRef</span>->{<span class="i">$AtomID</span>}<span class="sc">;</span>
|
|
|
2474 2461 <span class="s">}</span>
|
|
|
2475 2462
|
|
|
2476 2463 <span class="k">for</span> <span class="i">$BondID</span> <span class="s">(</span><span class="k">keys</span> <span class="i">%</span>{<span class="i">$BondProcessingStatusMapRef</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
2477 2464 <span class="i">$PathBondsProcessingStatusMap</span>{<span class="i">$BondID</span>} = <span class="i">$BondProcessingStatusMapRef</span>->{<span class="i">$BondID</span>}<span class="sc">;</span>
|
|
|
2478 2465 <span class="s">}</span>
|
|
|
2479 2466 <span class="s">}</span>
|
|
|
2480 2467
|
|
|
2481 2468 <span class="k">if</span> <span class="s">(</span>!<span class="i">$Status</span><span class="s">)</span> <span class="s">{</span>
|
|
|
2482 2469 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->_KekulizeCompleteAndPartialAromaticRings: Couldn't perform kekulization for marked ring aromatic atoms..."</span><span class="sc">;</span>
|
|
|
2483 2470 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
2484 2471 <span class="s">}</span>
|
|
|
2485 2472
|
|
|
2486 2473 <span class="c"># Use PathAtomsProcessingStatusMap and PathBondsProcessingStatusMap to set</span>
|
|
|
2487 2474 <span class="c"># single/double bonds in the molecule after successful kekulization along with modification of</span>
|
|
|
2488 2475 <span class="c"># any aromatic flags...</span>
|
|
|
2489 2476
|
|
|
2490 2477 <span class="k">for</span> <span class="i">$PathSetIndex</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#</span>{<span class="i">$ConnectedPathsAtomsSetsRef</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
2491 2478 <span class="i">$DeleteAtomsAromaticity</span> = <span class="n">0</span><span class="sc">;</span> <span class="i">$DeleteBondsAromaticity</span> = <span class="n">0</span><span class="sc">;</span>
|
|
|
2492 2479
|
|
|
2493 2480 <span class="k">if</span> <span class="s">(</span><span class="i">$ConnectdPathsSetsTypesRef</span>->[<span class="i">$PathSetIndex</span>] =~ <span class="q">/^FusedAromatic$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
2494 2481 <span class="k">for</span> <span class="i">$PathBondsRef</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$ConnectedPathsBondsSetsRef</span>->[<span class="i">$PathSetIndex</span>]}<span class="s">)</span> <span class="s">{</span>
|
|
|
2495 2482 <span class="i">$This</span><span class="i">->_ProcessBondOrdersAssignedDuringSuccessfulKekulization</span><span class="s">(</span><span class="i">$PathBondsRef</span><span class="cm">,</span> \<span class="i">%PathBondsProcessingStatusMap</span><span class="cm">,</span> <span class="i">$DeleteBondsAromaticity</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2496 2483 <span class="s">}</span>
|
|
|
2497 2484 <span class="s">}</span>
|
|
|
2498 2485 <span class="k">else</span> <span class="s">{</span>
|
|
|
2499 2486 <span class="k">if</span> <span class="s">(</span><span class="i">$ConnectdPathsSetsTypesRef</span>->[<span class="i">$PathSetIndex</span>] =~ <span class="q">/^PartiallyAromatic$/i</span> <span class="s">)</span> <span class="s">{</span>
|
|
|
2500 2487 <span class="i">$DeleteBondsAromaticity</span> = <span class="n">1</span><span class="sc">;</span> <span class="i">$DeleteAtomsAromaticity</span> = <span class="n">1</span><span class="sc">;</span>
|
|
|
2501 2488 <span class="s">}</span>
|
|
|
2502 2489
|
|
|
2503 2490 <span class="k">if</span> <span class="s">(</span><span class="i">$DeleteAtomsAromaticity</span><span class="s">)</span> <span class="s">{</span>
|
|
|
2504 2491 <span class="k">for</span> <span class="i">$PathAtom</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$ConnectedPathsAtomsSetsRef</span>->[<span class="i">$PathSetIndex</span>]}<span class="s">)</span> <span class="s">{</span>
|
|
|
2505 2492 <span class="i">$PathAtom</span><span class="i">->DeleteAromatic</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2506 2493 <span class="s">}</span>
|
|
|
2507 2494 <span class="s">}</span>
|
|
|
2508 2495
|
|
|
2509 2496 <span class="i">$This</span><span class="i">->_ProcessBondOrdersAssignedDuringSuccessfulKekulization</span><span class="s">(</span><span class="i">$ConnectedPathsBondsSetsRef</span>->[<span class="i">$PathSetIndex</span>]<span class="cm">,</span> \<span class="i">%PathBondsProcessingStatusMap</span><span class="cm">,</span> <span class="i">$DeleteBondsAromaticity</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2510 2497 <span class="s">}</span>
|
|
|
2511 2498 <span class="s">}</span>
|
|
|
2512 2499
|
|
|
2513 2500 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span>
|
|
|
2514 2501 <span class="s">}</span>
|
|
|
2515 2502
|
|
|
2516 2503 <span class="c"># Look for any aromatic bonds outside the rings between two ring aromatic atoms</span>
|
|
|
2517 2504 <span class="c"># and turn them into single non-aromatic bonds before kekulization; otherwise, kekulization</span>
|
|
|
2518 2505 <span class="c"># fails.</span>
|
|
|
2519 2506 <span class="c">#</span>
|
|
|
2520 2507 <span class="c"># Note:</span>
|
|
|
2521 2508 <span class="c"># . Two atoms marked as aromatic atoms in two different rings, such as two rings</span>
|
|
|
2522 2509 <span class="c"># connected through a single bond, are still aromatic, but the bond is outside</span>
|
|
|
2523 2510 <span class="c"># the ring and shouldn't be marked as aromatic. It should be set to single bond without</span>
|
|
|
2524 2511 <span class="c"># any aromatic property for kekulization to succeed.</span>
|
|
|
2525 2512 <span class="c">#</span>
|
|
|
2526 2513 <span class="c"># For example, the molecule generated by SMILES parser for biphenyl SMILES string</span>
|
|
|
2527 2514 <span class="c"># "c1ccccc1c2ccccc2" sets up an aromatic bond between the two phenyl rings, as</span>
|
|
|
2528 2515 <span class="c"># it's connected to two aromatic atoms.</span>
|
|
|
2529 2516 <span class="c">#</span>
|
|
|
2530 <a name="_ProcessNonRingAromaticBondsBetweenAromaticRingAtoms-"></a>2517 <span class="k">sub </span><span class="m">_ProcessNonRingAromaticBondsBetweenAromaticRingAtoms</span> <span class="s">{</span>
|
|
|
2531 2518 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
2532 2519 <span class="k">my</span><span class="s">(</span><span class="i">$Bond</span><span class="cm">,</span> <span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2533 2520
|
|
|
2534 2521 <span class="j">BOND:</span> <span class="k">for</span> <span class="i">$Bond</span> <span class="s">(</span><span class="i">$This</span><span class="i">->GetBonds</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
2535 2522 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="i">$Bond</span><span class="i">->IsAromatic</span><span class="s">(</span><span class="s">)</span> && <span class="i">$Bond</span><span class="i">->IsNotInRing</span><span class="s">(</span><span class="s">)</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
2536 2523 <span class="k">next</span> <span class="j">BOND</span><span class="sc">;</span>
|
|
|
2537 2524 <span class="s">}</span>
|
|
|
2538 2525
|
|
|
2539 2526 <span class="s">(</span><span class="i">$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>
|
|
|
2540 2527 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="i">$Atom1</span><span class="i">->IsAromatic</span><span class="s">(</span><span class="s">)</span> && <span class="i">$Atom2</span><span class="i">->IsAromatic</span><span class="s">(</span><span class="s">)</span> && <span class="i">$Atom1</span><span class="i">->IsInRing</span><span class="s">(</span><span class="s">)</span> && <span class="i">$Atom2</span><span class="i">->IsInRing</span><span class="s">(</span><span class="s">)</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
2541 2528 <span class="k">next</span> <span class="j">BOND</span><span class="sc">;</span>
|
|
|
2542 2529 <span class="s">}</span>
|
|
|
2543 2530
|
|
|
2544 2531 <span class="i">$Bond</span><span class="i">->SetBondOrder</span><span class="s">(</span><span class="n">1</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2545 2532 <span class="i">$Bond</span><span class="i">->DeleteAromatic</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2546 2533 <span class="s">}</span>
|
|
|
2547 2534
|
|
|
2548 2535 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
2549 2536 <span class="s">}</span>
|
|
|
2550 2537
|
|
|
2551 2538 <span class="c"># Setup completelty aromatic fused and individual rings along with partially aromatic ring</span>
|
|
|
2552 2539 <span class="c"># components as sets of connected paths...</span>
|
|
|
2553 2540 <span class="c">#</span>
|
|
|
2554 <a name="_SetupCompleteAndPartialAromaticRingsForKekulizaiton-"></a>2541 <span class="k">sub </span><span class="m">_SetupCompleteAndPartialAromaticRingsForKekulizaiton</span> <span class="s">{</span>
|
|
|
2555 2542 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$AromaticFusedRingSetsRef</span><span class="cm">,</span> <span class="i">$AromaticRingsRef</span><span class="cm">,</span> <span class="i">$PartiallyAromaticRingComponentsRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
2556 2543 <span class="k">my</span><span class="s">(</span><span class="i">@ConnectedPathsSets</span><span class="cm">,</span> <span class="i">@ConnectedPathsBondsSets</span><span class="cm">,</span> <span class="i">@ConnectdPathsSetsTypes</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2557 2544
|
|
|
2558 2545 <span class="i">@ConnectedPathsSets</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2559 2546 <span class="i">@ConnectedPathsBondsSets</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2560 2547 <span class="i">@ConnectdPathsSetsTypes</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2561 2548
|
|
|
2562 2549 <span class="c"># Setup atoms and bonds for connected paths in fused aromatic ring sets...</span>
|
|
|
2563 2550 <span class="c">#</span>
|
|
|
2564 2551 <span class="k">if</span> <span class="s">(</span><span class="k">defined</span> <span class="i">$AromaticFusedRingSetsRef</span> && <span class="i">@</span>{<span class="i">$AromaticFusedRingSetsRef</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
2565 2552 <span class="k">my</span><span class="s">(</span><span class="i">$RingSetIndex</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2566 2553
|
|
|
2567 2554 <span class="k">push</span> <span class="i">@ConnectdPathsSetsTypes</span><span class="cm">,</span> <span class="s">(</span><span class="q">'FusedAromatic'</span><span class="s">)</span> x <span class="k">scalar</span> <span class="i">@</span>{<span class="i">$AromaticFusedRingSetsRef</span>}<span class="sc">;</span>
|
|
|
2568 2555 <span class="k">push</span> <span class="i">@ConnectedPathsSets</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$AromaticFusedRingSetsRef</span>}<span class="sc">;</span>
|
|
|
2569 2556
|
|
|
2570 2557 <span class="k">for</span> <span class="i">$RingSetIndex</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#</span>{<span class="i">$AromaticFusedRingSetsRef</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
2571 2558 <span class="k">my</span><span class="s">(</span><span class="i">@AromaticFusedRingBondsSet</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2572 2559
|
|
|
2573 2560 <span class="c"># Get ring bonds for each ring set...</span>
|
|
|
2574 2561 <span class="c">#</span>
|
|
|
2575 2562 <span class="i">@AromaticFusedRingBondsSet</span> = <span class="i">$This</span><span class="i">->GetRingBondsFromRings</span><span class="s">(</span><span class="i">@</span>{<span class="i">$AromaticFusedRingSetsRef</span>->[<span class="i">$RingSetIndex</span>]}<span class="s">)</span><span class="sc">;</span>
|
|
|
2576 2563 <span class="k">push</span> <span class="i">@ConnectedPathsBondsSets</span><span class="cm">,</span> \<span class="i">@AromaticFusedRingBondsSet</span><span class="sc">;</span>
|
|
|
2577 2564 <span class="s">}</span>
|
|
|
2578 2565 <span class="s">}</span>
|
|
|
2579 2566
|
|
|
2580 2567 <span class="c"># Set up atoms and bonds for connected paths in aromatic rings...</span>
|
|
|
2581 2568 <span class="c">#</span>
|
|
|
2582 2569 <span class="k">if</span> <span class="s">(</span><span class="k">defined</span> <span class="i">$AromaticRingsRef</span> && <span class="i">@</span>{<span class="i">$AromaticRingsRef</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
2583 2570 <span class="k">my</span><span class="s">(</span><span class="i">@AromaticRingBondsSets</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2584 2571
|
|
|
2585 2572 <span class="k">push</span> <span class="i">@ConnectdPathsSetsTypes</span><span class="cm">,</span> <span class="s">(</span><span class="q">'Aromatic'</span><span class="s">)</span> x <span class="k">scalar</span> <span class="i">@</span>{<span class="i">$AromaticRingsRef</span>}<span class="sc">;</span>
|
|
|
2586 2573 <span class="k">push</span> <span class="i">@ConnectedPathsSets</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$AromaticRingsRef</span>}<span class="sc">;</span>
|
|
|
2587 2574
|
|
|
2588 2575 <span class="c"># Get ring bonds for each ring...</span>
|
|
|
2589 2576 <span class="i">@AromaticRingBondsSets</span> = <span class="i">$This</span><span class="i">->GetRingBondsFromRings</span><span class="s">(</span><span class="i">@</span>{<span class="i">$AromaticRingsRef</span>}<span class="s">)</span><span class="sc">;</span>
|
|
|
2590 2577 <span class="k">push</span> <span class="i">@ConnectedPathsBondsSets</span><span class="cm">,</span> <span class="i">@AromaticRingBondsSets</span><span class="sc">;</span>
|
|
|
2591 2578 <span class="s">}</span>
|
|
|
2592 2579
|
|
|
2593 2580 <span class="c"># Set up atoms and bonds for connected paths in partially aromatic rings...</span>
|
|
|
2594 2581 <span class="c">#</span>
|
|
|
2595 2582 <span class="k">if</span> <span class="s">(</span><span class="k">defined</span> <span class="i">$PartiallyAromaticRingComponentsRef</span> && <span class="i">@</span>{<span class="i">$PartiallyAromaticRingComponentsRef</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
2596 2583 <span class="k">my</span><span class="s">(</span><span class="i">$ComponentIndex</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2597 2584
|
|
|
2598 2585 <span class="k">push</span> <span class="i">@ConnectedPathsSets</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$PartiallyAromaticRingComponentsRef</span>}<span class="sc">;</span>
|
|
|
2599 2586 <span class="k">push</span> <span class="i">@ConnectdPathsSetsTypes</span><span class="cm">,</span> <span class="s">(</span><span class="q">'PartiallyAromatic'</span><span class="s">)</span> x <span class="k">scalar</span> <span class="i">@</span>{<span class="i">$PartiallyAromaticRingComponentsRef</span>}<span class="sc">;</span>
|
|
|
2600 2587
|
|
|
2601 2588 <span class="k">for</span> <span class="i">$ComponentIndex</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#</span>{<span class="i">$PartiallyAromaticRingComponentsRef</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
2602 2589 <span class="k">my</span><span class="s">(</span><span class="i">@ComponentBonds</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2603 2590 <span class="i">@ComponentBonds</span> = <span class="i">$This</span><span class="i">->_GetPathBonds</span><span class="s">(</span><span class="i">$This</span><span class="i">->_GetAtomsIDsFromAtoms</span><span class="s">(</span><span class="i">@</span>{<span class="i">$PartiallyAromaticRingComponentsRef</span>->[<span class="i">$ComponentIndex</span>]}<span class="s">)</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2604 2591 <span class="k">push</span> <span class="i">@ConnectedPathsBondsSets</span><span class="cm">,</span> \<span class="i">@ComponentBonds</span><span class="sc">;</span>
|
|
|
2605 2592 <span class="s">}</span>
|
|
|
2606 2593 <span class="s">}</span>
|
|
|
2607 2594
|
|
|
2608 2595 <span class="k">return</span> <span class="s">(</span>\<span class="i">@ConnectedPathsSets</span><span class="cm">,</span> \<span class="i">@ConnectedPathsBondsSets</span><span class="cm">,</span> \<span class="i">@ConnectdPathsSetsTypes</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2609 2596 <span class="s">}</span>
|
|
|
2610 2597
|
|
|
2611 2598 <span class="c"># Process non-ring connected atoms which are marked aromatic and set connected</span>
|
|
|
2612 2599 <span class="c"># bonds as alternate single/double bonds...</span>
|
|
|
2613 2600 <span class="c">#</span>
|
|
|
2614 2601 <span class="c"># Notes:</span>
|
|
|
2615 2602 <span class="c"># . Atom and bond aromaticity is deleted during kekulization of non-ring atoms.</span>
|
|
|
2616 2603 <span class="c">#</span>
|
|
|
2617 <a name="_KekulizeAromaticAtomsNotInRings-"></a>2604 <span class="k">sub </span><span class="m">_KekulizeAromaticAtomsNotInRings</span> <span class="s">{</span>
|
|
|
2618 2605 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
2619 2606 <span class="k">my</span><span class="s">(</span><span class="i">$Status</span><span class="cm">,</span> <span class="i">$PathIndex</span><span class="cm">,</span> <span class="i">$PathAtom</span><span class="cm">,</span> <span class="i">$PathAtomID</span><span class="cm">,</span> <span class="i">$PathBondID</span><span class="cm">,</span> <span class="i">$ConnectedPathsAtomsRef</span><span class="cm">,</span> <span class="i">$ConnectedPathsBondsRef</span><span class="cm">,</span> <span class="i">$DeleteAtomsAromaticity</span><span class="cm">,</span> <span class="i">$DeleteBondsAromaticity</span><span class="cm">,</span> <span class="i">%PathAtomsProcessingStatusMap</span><span class="cm">,</span> <span class="i">%PathBondsProcessingStatusMap</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2620 2607
|
|
|
2621 2608 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasAromaticAtomsNotInRings</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
2622 2609 <span class="c"># Nothing to do...</span>
|
|
|
2623 2610 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span>
|
|
|
2624 2611 <span class="s">}</span>
|
|
|
2625 2612
|
|
|
2626 2613 <span class="c"># Identify paths for connected components containing non-ring aromatic atoms...</span>
|
|
|
2627 2614 <span class="s">(</span><span class="i">$ConnectedPathsAtomsRef</span><span class="cm">,</span> <span class="i">$ConnectedPathsBondsRef</span><span class="s">)</span> = <span class="i">$This</span><span class="i">->_GetConnectedComponentsPathsForNonRingAromaticAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2628 2615
|
|
|
2629 2616 <span class="k">if</span> <span class="s">(</span>!<span class="i">@</span>{<span class="i">$ConnectedPathsAtomsRef</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
2630 2617 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->_KekulizeAromaticAtomsNotInRings: Couldn't perform kekulization for marked non-ring aromatic atoms..."</span><span class="sc">;</span>
|
|
|
2631 2618 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
2632 2619 <span class="s">}</span>
|
|
|
2633 2620
|
|
|
2634 2621 <span class="i">%PathAtomsProcessingStatusMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2635 2622 <span class="i">%PathBondsProcessingStatusMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2636 2623
|
|
|
2637 2624 <span class="i">$Status</span> = <span class="n">1</span><span class="sc">;</span>
|
|
|
2638 2625
|
|
|
2639 2626 <span class="j">PATH:</span> <span class="k">for</span> <span class="i">$PathIndex</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#</span>{<span class="i">$ConnectedPathsAtomsRef</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
2640 2627 <span class="k">my</span><span class="s">(</span><span class="i">$AtomProcessingStatusMapRef</span><span class="cm">,</span> <span class="i">$BondProcessingStatusMapRef</span><span class="cm">,</span> <span class="i">@ConnectedPathAtomsSet</span><span class="cm">,</span> <span class="i">@ConnectedPathBondsSet</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2641 2628
|
|
|
2642 2629 <span class="s">(</span><span class="i">$AtomProcessingStatusMapRef</span><span class="cm">,</span> <span class="i">$BondProcessingStatusMapRef</span><span class="s">)</span> = <span class="s">(</span><span class="k">undef</span><span class="s">)</span> x <span class="n">2</span><span class="sc">;</span>
|
|
|
2643 2630
|
|
|
2644 2631 <span class="i">@ConnectedPathAtomsSet</span> = <span class="s">(</span><span class="i">$ConnectedPathsAtomsRef</span>->[<span class="i">$PathIndex</span>]<span class="s">)</span><span class="sc">;</span>
|
|
|
2645 2632 <span class="i">@ConnectedPathBondsSet</span> = <span class="s">(</span><span class="i">$ConnectedPathsBondsRef</span>->[<span class="i">$PathIndex</span>]<span class="s">)</span><span class="sc">;</span>
|
|
|
2646 2633
|
|
|
2647 2634 <span class="c"># Prepare for kekulization...</span>
|
|
|
2648 2635 <span class="s">(</span><span class="i">$AtomProcessingStatusMapRef</span><span class="cm">,</span> <span class="i">$BondProcessingStatusMapRef</span><span class="s">)</span> = <span class="i">$This</span><span class="i">->_SetupConnectedPathSetsForKekulization</span><span class="s">(</span>\<span class="i">@ConnectedPathAtomsSet</span><span class="cm">,</span> \<span class="i">@ConnectedPathBondsSet</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2649 2636
|
|
|
2650 2637 <span class="c"># Perform kekulization...</span>
|
|
|
2651 2638 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->_KekulizeConnectedPathSets</span><span class="s">(</span><span class="i">$ConnectedPathsAtomsRef</span>->[<span class="i">$PathIndex</span>]<span class="cm">,</span> <span class="i">$ConnectedPathsBondsRef</span>->[<span class="i">$PathIndex</span>]<span class="cm">,</span> <span class="i">$AtomProcessingStatusMapRef</span><span class="cm">,</span> <span class="i">$BondProcessingStatusMapRef</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
2652 2639 <span class="c"># Kekulization failed for the current path...</span>
|
|
|
2653 2640 <span class="i">$Status</span> = <span class="n">0</span><span class="sc">;</span>
|
|
|
2654 2641 <span class="k">last</span> <span class="j">PATH</span><span class="sc">;</span>
|
|
|
2655 2642 <span class="s">}</span>
|
|
|
2656 2643
|
|
|
2657 2644 <span class="c"># Track atom and bond processing state for final assignment after kekulization</span>
|
|
|
2658 2645 <span class="c"># is successfully completed for all the paths and fused path sets...</span>
|
|
|
2659 2646 <span class="c">#</span>
|
|
|
2660 2647 <span class="k">for</span> <span class="i">$PathAtomID</span> <span class="s">(</span><span class="k">keys</span> <span class="i">%</span>{<span class="i">$AtomProcessingStatusMapRef</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
2661 2648 <span class="i">$PathAtomsProcessingStatusMap</span>{<span class="i">$PathAtomID</span>} = <span class="i">$AtomProcessingStatusMapRef</span>->{<span class="i">$PathAtomID</span>}<span class="sc">;</span>
|
|
|
2662 2649 <span class="s">}</span>
|
|
|
2663 2650
|
|
|
2664 2651 <span class="k">for</span> <span class="i">$PathBondID</span> <span class="s">(</span><span class="k">keys</span> <span class="i">%</span>{<span class="i">$BondProcessingStatusMapRef</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
2665 2652 <span class="i">$PathBondsProcessingStatusMap</span>{<span class="i">$PathBondID</span>} = <span class="i">$BondProcessingStatusMapRef</span>->{<span class="i">$PathBondID</span>}<span class="sc">;</span>
|
|
|
2666 2653 <span class="s">}</span>
|
|
|
2667 2654 <span class="s">}</span>
|
|
|
2668 2655
|
|
|
2669 2656 <span class="k">if</span> <span class="s">(</span>!<span class="i">$Status</span><span class="s">)</span> <span class="s">{</span>
|
|
|
2670 2657 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->_KekulizeAromaticAtomsNotInRings: Couldn't perform kekulization for marked non-ring aromatic atoms..."</span><span class="sc">;</span>
|
|
|
2671 2658 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
2672 2659 <span class="s">}</span>
|
|
|
2673 2660
|
|
|
2674 2661 <span class="i">$DeleteAtomsAromaticity</span> = <span class="n">1</span><span class="sc">;</span> <span class="i">$DeleteBondsAromaticity</span> = <span class="n">1</span><span class="sc">;</span>
|
|
|
2675 2662 <span class="k">for</span> <span class="i">$PathIndex</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#</span>{<span class="i">$ConnectedPathsAtomsRef</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
2676 2663 <span class="k">if</span> <span class="s">(</span><span class="i">$DeleteAtomsAromaticity</span><span class="s">)</span> <span class="s">{</span>
|
|
|
2677 2664 <span class="k">for</span> <span class="i">$PathAtom</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$ConnectedPathsAtomsRef</span>->[<span class="i">$PathIndex</span>]}<span class="s">)</span> <span class="s">{</span>
|
|
|
2678 2665 <span class="i">$PathAtom</span><span class="i">->DeleteAromatic</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2679 2666 <span class="s">}</span>
|
|
|
2680 2667 <span class="s">}</span>
|
|
|
2681 2668 <span class="i">$This</span><span class="i">->_ProcessBondOrdersAssignedDuringSuccessfulKekulization</span><span class="s">(</span><span class="i">$ConnectedPathsBondsRef</span>->[<span class="i">$PathIndex</span>]<span class="cm">,</span> \<span class="i">%PathBondsProcessingStatusMap</span><span class="cm">,</span> <span class="i">$DeleteBondsAromaticity</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2682 2669 <span class="s">}</span>
|
|
|
2683 2670
|
|
|
2684 2671 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span>
|
|
|
2685 2672 <span class="s">}</span>
|
|
|
2686 2673
|
|
|
2687 2674 <span class="c"># Collect path atoms for connected components paths containing non-ring aromatic atoms...</span>
|
|
|
2688 2675 <span class="c">#</span>
|
|
|
2689 <a name="_GetConnectedComponentsPathsForNonRingAromaticAtoms-"></a>2676 <span class="k">sub </span><span class="m">_GetConnectedComponentsPathsForNonRingAromaticAtoms</span> <span class="s">{</span>
|
|
|
2690 2677 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
2691 2678 <span class="k">my</span><span class="s">(</span><span class="i">$ComponentRef</span><span class="cm">,</span> <span class="i">$AtomIDsRef</span><span class="cm">,</span> <span class="i">$AtomIDsMapRef</span><span class="cm">,</span> <span class="i">$ConnectedComponentsAtomIDsRef</span><span class="cm">,</span> <span class="i">$ConnectedComponentsAtomIDsMapRef</span><span class="cm">,</span> <span class="i">$ConnectedComponentsPathsAtomIDsRef</span><span class="cm">,</span> <span class="i">$ConnectedComponentsPathsAtomsRef</span><span class="cm">,</span> <span class="i">$ConnectedComponentsPathsBondsRef</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2692 2679
|
|
|
2693 2680 <span class="c"># Retrieve information for marked aromatic atoms not in the rings...</span>
|
|
|
2694 2681 <span class="s">(</span><span class="i">$AtomIDsRef</span><span class="cm">,</span> <span class="i">$AtomIDsMapRef</span><span class="s">)</span> = <span class="i">$This</span><span class="i">->_GetNonRingAromaticAtomIDs</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2695 2682
|
|
|
2696 2683 <span class="c"># Identify connected components containing marked aromatic atoms not in the rings...</span>
|
|
|
2697 2684 <span class="s">(</span><span class="i">$ConnectedComponentsAtomIDsRef</span><span class="cm">,</span> <span class="i">$ConnectedComponentsAtomIDsMapRef</span><span class="s">)</span> = <span class="i">$This</span><span class="i">->_GetConnectedComponentsForNonRingAromaticAtoms</span><span class="s">(</span><span class="i">$AtomIDsRef</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2698 2685
|
|
|
2699 2686 <span class="c"># Identify paths for connected components containing non-ring aromatic atoms...</span>
|
|
|
2700 2687 <span class="s">(</span><span class="i">$ConnectedComponentsPathsAtomsRef</span><span class="cm">,</span> <span class="i">$ConnectedComponentsPathsBondsRef</span><span class="s">)</span> = <span class="i">$This</span><span class="i">->_GetConnectedComponentsPathsAtomsAndBondsForNonRingAromaticAtoms</span><span class="s">(</span><span class="i">$AtomIDsMapRef</span><span class="cm">,</span> <span class="i">$ConnectedComponentsAtomIDsRef</span><span class="cm">,</span> <span class="i">$ConnectedComponentsAtomIDsMapRef</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2701 2688
|
|
|
2702 2689 <span class="k">return</span> <span class="s">(</span><span class="i">$ConnectedComponentsPathsAtomsRef</span><span class="cm">,</span> <span class="i">$ConnectedComponentsPathsBondsRef</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2703 2690 <span class="s">}</span>
|
|
|
2704 2691
|
|
|
2705 2692 <span class="c"># Collect information for marked aromatic atoms not in the rings...</span>
|
|
|
2706 2693 <span class="c">#</span>
|
|
|
2707 <a name="_GetNonRingAromaticAtomIDs-"></a>2694 <span class="k">sub </span><span class="m">_GetNonRingAromaticAtomIDs</span> <span class="s">{</span>
|
|
|
2708 2695 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
2709 2696 <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">@AtomIDs</span><span class="cm">,</span> <span class="i">%AtomIDsMap</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2710 2697
|
|
|
2711 2698 <span class="i">@AtomIDs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2712 2699 <span class="i">%AtomIDsMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2713 2700
|
|
|
2714 2701 <span class="j">ATOM:</span> <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="i">$This</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
2715 2702 <span class="k">if</span> <span class="s">(</span>!<span class="i">$Atom</span><span class="i">->IsAromatic</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
2716 2703 <span class="k">next</span> <span class="j">ATOM</span><span class="sc">;</span>
|
|
|
2717 2704 <span class="s">}</span>
|
|
|
2718 2705 <span class="k">if</span> <span class="s">(</span><span class="i">$Atom</span><span class="i">->IsInRing</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
2719 2706 <span class="k">next</span> <span class="j">ATOM</span><span class="sc">;</span>
|
|
|
2720 2707 <span class="s">}</span>
|
|
|
2721 2708 <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>
|
|
|
2722 2709
|
|
|
2723 2710 <span class="k">push</span> <span class="i">@AtomIDs</span><span class="cm">,</span> <span class="i">$AtomID</span><span class="sc">;</span>
|
|
|
2724 2711 <span class="i">$AtomIDsMap</span>{<span class="i">$AtomID</span>} = <span class="i">$Atom</span><span class="sc">;</span>
|
|
|
2725 2712 <span class="s">}</span>
|
|
|
2726 2713
|
|
|
2727 2714 <span class="k">return</span> <span class="s">(</span>\<span class="i">@AtomIDs</span><span class="cm">,</span> \<span class="i">%AtomIDsMap</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2728 2715 <span class="s">}</span>
|
|
|
2729 2716
|
|
|
2730 2717 <span class="c"># Retrieve connected non-ring atom components as a reference to an array of references</span>
|
|
|
2731 2718 <span class="c"># containing atom IDs of connecnted components...</span>
|
|
|
2732 2719 <span class="c">#</span>
|
|
|
2733 <a name="_GetConnectedComponentsForNonRingAromaticAtoms-"></a>2720 <span class="k">sub </span><span class="m">_GetConnectedComponentsForNonRingAromaticAtoms</span> <span class="s">{</span>
|
|
|
2734 2721 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$AtomIDsRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
2735 2722 <span class="k">my</span><span class="s">(</span><span class="i">$Index</span><span class="cm">,</span> <span class="i">$AtomID</span><span class="cm">,</span> <span class="i">$AtomIDsGraph</span><span class="cm">,</span> <span class="i">@BondedAtomPairIDs</span><span class="cm">,</span> <span class="i">@ComponentsAtomIDsRefs</span><span class="cm">,</span> <span class="i">@ComponentsAtomIDsMapRefs</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2736 2723
|
|
|
2737 2724 <span class="i">@ComponentsAtomIDsRefs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2738 2725 <span class="i">@ComponentsAtomIDsMapRefs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2739 2726
|
|
|
2740 2727 <span class="c"># Get bonded atom pair IDs...</span>
|
|
|
2741 2728 <span class="i">@BondedAtomPairIDs</span> = <span class="i">$This</span><span class="i">->_GetBondedAtomPairAtomIDsFromAtomIDs</span><span class="s">(</span><span class="i">@</span>{<span class="i">$AtomIDsRef</span>}<span class="s">)</span><span class="sc">;</span>
|
|
|
2742 2729
|
|
|
2743 2730 <span class="k">if</span> <span class="s">(</span>!<span class="i">@BondedAtomPairIDs</span><span class="s">)</span> <span class="s">{</span>
|
|
|
2744 2731 <span class="k">return</span> <span class="s">(</span>\<span class="i">@ComponentsAtomIDsRefs</span><span class="cm">,</span> \<span class="i">@ComponentsAtomIDsMapRefs</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2745 2732 <span class="s">}</span>
|
|
|
2746 2733
|
|
|
2747 2734 <span class="i">$AtomIDsGraph</span> = <span class="i">new</span> <span class="i">Graph</span><span class="s">(</span><span class="i">@</span>{<span class="i">$AtomIDsRef</span>}<span class="s">)</span><span class="sc">;</span>
|
|
|
2748 2735 <span class="i">$AtomIDsGraph</span><span class="i">->AddEdges</span><span class="s">(</span><span class="i">@BondedAtomPairIDs</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2749 2736
|
|
|
2750 2737 <span class="i">@ComponentsAtomIDsRefs</span> = <span class="i">$AtomIDsGraph</span><span class="i">->GetConnectedComponentsVertices</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2751 2738
|
|
|
2752 2739 <span class="c"># Setup atom IDs map for each component...</span>
|
|
|
2753 2740 <span class="k">for</span> <span class="i">$Index</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#ComponentsAtomIDsRefs</span><span class="s">)</span> <span class="s">{</span>
|
|
|
2754 2741 <span class="i">%</span>{<span class="i">$ComponentsAtomIDsMapRefs</span>[<span class="i">$Index</span>]} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2755 2742
|
|
|
2756 2743 <span class="k">for</span> <span class="i">$AtomID</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$ComponentsAtomIDsRefs</span>[<span class="i">$Index</span>]}<span class="s">)</span> <span class="s">{</span>
|
|
|
2757 2744 <span class="i">$ComponentsAtomIDsMapRefs</span>[<span class="i">$Index</span>]{<span class="i">$AtomID</span>} = <span class="i">$AtomID</span><span class="sc">;</span>
|
|
|
2758 2745 <span class="s">}</span>
|
|
|
2759 2746 <span class="s">}</span>
|
|
|
2760 2747
|
|
|
2761 2748 <span class="k">return</span> <span class="s">(</span>\<span class="i">@ComponentsAtomIDsRefs</span><span class="cm">,</span> \<span class="i">@ComponentsAtomIDsMapRefs</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2762 2749 <span class="s">}</span>
|
|
|
2763 2750
|
|
|
2764 2751 <span class="c"># Get linear paths for connected components starting and ending at terminal aromatic atoms,</span>
|
|
|
2765 2752 <span class="c"># which are connected to only one other aromatic atom in the connected component..</span>
|
|
|
2766 2753 <span class="c">#</span>
|
|
|
2767 <a name="_GetConnectedComponentsPathsAtomsAndBondsForNonRingAromaticAtoms-"></a>2754 <span class="k">sub </span><span class="m">_GetConnectedComponentsPathsAtomsAndBondsForNonRingAromaticAtoms</span> <span class="s">{</span>
|
|
|
2768 2755 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$AtomIDsMapRef</span><span class="cm">,</span> <span class="i">$ComponentsAtomIDsRef</span><span class="cm">,</span> <span class="i">$ComponentsAtomIDsMapRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
2769 2756 <span class="k">my</span><span class="s">(</span><span class="i">$Index</span><span class="cm">,</span> <span class="i">$AtomID</span><span class="cm">,</span> <span class="i">$Atom</span><span class="cm">,</span> <span class="i">$AtomNbr</span><span class="cm">,</span> <span class="i">$AtomNbrID</span><span class="cm">,</span> <span class="i">$NumOfNonRingAromaticNbrs</span><span class="cm">,</span> <span class="i">$AtomIndex1</span><span class="cm">,</span> <span class="i">$AtomIndex2</span><span class="cm">,</span> <span class="i">$AtomID1</span><span class="cm">,</span> <span class="i">$AtomID2</span><span class="cm">,</span> <span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="cm">,</span> <span class="i">$AtomIDsGraph</span><span class="cm">,</span> <span class="i">$StartTerminalAtomID</span><span class="cm">,</span> <span class="i">$EndTerminalAtomID</span><span class="cm">,</span> <span class="i">@Paths</span><span class="cm">,</span> <span class="i">@PathAtomIDs</span><span class="cm">,</span> <span class="i">@PathsAtoms</span><span class="cm">,</span> <span class="i">@PathsBonds</span><span class="cm">,</span> <span class="i">@TerminalAtomIDs</span><span class="cm">,</span> <span class="i">@AtomIDs</span><span class="cm">,</span> <span class="i">@BondedAtomPairIDs</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2770 2757
|
|
|
2771 2758 <span class="i">@PathsAtoms</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2772 2759 <span class="i">@PathsBonds</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2773 2760
|
|
|
2774 2761 <span class="i">@TerminalAtomIDs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2775 2762
|
|
|
2776 2763 <span class="i">$Index</span> = <span class="n">0</span><span class="sc">;</span>
|
|
|
2777 2764 <span class="j">COMPONENT:</span> <span class="k">for</span> <span class="i">$Index</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#</span>{<span class="i">$ComponentsAtomIDsRef</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
2778 2765 <span class="i">@</span>{<span class="i">$TerminalAtomIDs</span>[<span class="i">$Index</span>]} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2779 2766
|
|
|
2780 2767 <span class="c"># Identify terminal atoms for connected components...</span>
|
|
|
2781 2768 <span class="c">#</span>
|
|
|
2782 2769 <span class="c"># Notes:</span>
|
|
|
2783 2770 <span class="c"># . Terminal atoms are defined as atoms connected to only one marked</span>
|
|
|
2784 2771 <span class="c"># aromatic atom.</span>
|
|
|
2785 2772 <span class="c"># . Linear connected compoents contain only two terminal atoms.</span>
|
|
|
2786 2773 <span class="c">#</span>
|
|
|
2787 2774 <span class="j">ATOM:</span> <span class="k">for</span> <span class="i">$AtomID</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$ComponentsAtomIDsRef</span>->[<span class="i">$Index</span>]}<span class="s">)</span> <span class="s">{</span>
|
|
|
2788 2775 <span class="i">$Atom</span> = <span class="i">$AtomIDsMapRef</span>->{<span class="i">$AtomID</span>}<span class="sc">;</span>
|
|
|
2789 2776 <span class="i">$NumOfNonRingAromaticNbrs</span> = <span class="n">0</span><span class="sc">;</span>
|
|
|
2790 2777
|
|
|
2791 2778 <span class="j">ATOMNBRID:</span> <span class="k">for</span> <span class="i">$AtomNbr</span> <span class="s">(</span><span class="i">$Atom</span><span class="i">->GetNeighbors</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
2792 2779 <span class="i">$AtomNbrID</span> = <span class="i">$AtomNbr</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2793 2780
|
|
|
2794 2781 <span class="c"># Is neighbor in the same connected components containing aromatic atoms?</span>
|
|
|
2795 2782 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$ComponentsAtomIDsMapRef</span>->[<span class="i">$Index</span>]{<span class="i">$AtomNbrID</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
2796 2783 <span class="k">next</span> <span class="j">ATOMNBRID</span><span class="sc">;</span>
|
|
|
2797 2784 <span class="s">}</span>
|
|
|
2798 2785 <span class="i">$NumOfNonRingAromaticNbrs</span>++<span class="sc">;</span>
|
|
|
2799 2786 <span class="s">}</span>
|
|
|
2800 2787
|
|
|
2801 2788 <span class="c"># Is it a terminal atom?</span>
|
|
|
2802 2789 <span class="k">if</span> <span class="s">(</span><span class="i">$NumOfNonRingAromaticNbrs</span> != <span class="n">1</span><span class="s">)</span> <span class="s">{</span>
|
|
|
2803 2790 <span class="k">next</span> <span class="j">ATOM</span><span class="sc">;</span>
|
|
|
2804 2791 <span class="s">}</span>
|
|
|
2805 2792 <span class="k">push</span> <span class="i">@</span>{<span class="i">$TerminalAtomIDs</span>[<span class="i">$Index</span>]}<span class="cm">,</span> <span class="i">$AtomID</span><span class="sc">;</span>
|
|
|
2806 2793 <span class="s">}</span>
|
|
|
2807 2794
|
|
|
2808 2795 <span class="k">if</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$TerminalAtomIDs</span>[<span class="i">$Index</span>]} != <span class="n">2</span><span class="s">)</span> <span class="s">{</span>
|
|
|
2809 2796 <span class="k">next</span> <span class="j">COMPONENT</span><span class="sc">;</span>
|
|
|
2810 2797 <span class="s">}</span>
|
|
|
2811 2798
|
|
|
2812 2799 <span class="c"># Setup bonded atom pair IDs for connected component...</span>
|
|
|
2813 2800 <span class="c">#</span>
|
|
|
2814 2801 <span class="i">@AtomIDs</span> = <span class="i">@</span>{<span class="i">$ComponentsAtomIDsRef</span>->[<span class="i">$Index</span>]}<span class="sc">;</span>
|
|
|
2815 2802 <span class="i">@BondedAtomPairIDs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2816 2803
|
|
|
2817 2804 <span class="k">for</span> <span class="i">$AtomIndex1</span> <span class="s">(</span> <span class="n">0</span> .. <span class="i">$#AtomIDs</span><span class="s">)</span> <span class="s">{</span>
|
|
|
2818 2805 <span class="i">$AtomID1</span> = <span class="i">$AtomIDs</span>[<span class="i">$AtomIndex1</span>]<span class="sc">;</span>
|
|
|
2819 2806 <span class="i">$Atom1</span> = <span class="i">$AtomIDsMapRef</span>->{<span class="i">$AtomID1</span>}<span class="sc">;</span>
|
|
|
2820 2807
|
|
|
2821 2808 <span class="k">for</span> <span class="i">$AtomIndex2</span> <span class="s">(</span> <span class="s">(</span><span class="i">$AtomIndex1</span> + <span class="n">1</span><span class="s">)</span> .. <span class="i">$#AtomIDs</span><span class="s">)</span> <span class="s">{</span>
|
|
|
2822 2809 <span class="i">$AtomID2</span> = <span class="i">$AtomIDs</span>[<span class="i">$AtomIndex2</span>]<span class="sc">;</span>
|
|
|
2823 2810 <span class="i">$Atom2</span> = <span class="i">$AtomIDsMapRef</span>->{<span class="i">$AtomID2</span>}<span class="sc">;</span>
|
|
|
2824 2811
|
|
|
2825 2812 <span class="k">if</span> <span class="s">(</span><span class="i">$Atom1</span><span class="i">->IsBondedToAtom</span><span class="s">(</span><span class="i">$Atom2</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
2826 2813 <span class="k">push</span> <span class="i">@BondedAtomPairIDs</span><span class="cm">,</span> <span class="s">(</span><span class="i">$AtomID1</span><span class="cm">,</span> <span class="i">$AtomID2</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2827 2814 <span class="s">}</span>
|
|
|
2828 2815 <span class="s">}</span>
|
|
|
2829 2816 <span class="s">}</span>
|
|
|
2830 2817
|
|
|
2831 2818 <span class="k">if</span> <span class="s">(</span>!<span class="i">@BondedAtomPairIDs</span><span class="s">)</span> <span class="s">{</span>
|
|
|
2832 2819 <span class="k">next</span> <span class="j">COMPONENT</span><span class="sc">;</span>
|
|
|
2833 2820 <span class="s">}</span>
|
|
|
2834 2821
|
|
|
2835 2822 <span class="c"># Get path for connected component...</span>
|
|
|
2836 2823 <span class="i">$AtomIDsGraph</span> = <span class="i">new</span> <span class="i">Graph</span><span class="s">(</span><span class="i">@AtomIDs</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2837 2824 <span class="i">$AtomIDsGraph</span><span class="i">->AddEdges</span><span class="s">(</span><span class="i">@BondedAtomPairIDs</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2838 2825
|
|
|
2839 2826 <span class="s">(</span><span class="i">$StartTerminalAtomID</span><span class="cm">,</span> <span class="i">$EndTerminalAtomID</span><span class="s">)</span> = <span class="k">sort</span> <span class="s">{</span> <span class="i">$a</span> <=> <span class="i">$b</span> <span class="s">}</span> <span class="i">@</span>{<span class="i">$TerminalAtomIDs</span>[<span class="i">$Index</span>]}<span class="sc">;</span>
|
|
|
2840 2827 <span class="i">@Paths</span> = <span class="i">$AtomIDsGraph</span><span class="i">->GetPathsBetween</span><span class="s">(</span><span class="i">$StartTerminalAtomID</span><span class="cm">,</span> <span class="i">$EndTerminalAtomID</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2841 2828
|
|
|
2842 2829 <span class="k">if</span> <span class="s">(</span><span class="i">@Paths</span> != <span class="n">1</span><span class="s">)</span> <span class="s">{</span>
|
|
|
2843 2830 <span class="k">next</span> <span class="j">COMPONENT</span><span class="sc">;</span>
|
|
|
2844 2831 <span class="s">}</span>
|
|
|
2845 2832
|
|
|
2846 2833 <span class="i">@PathAtomIDs</span> = <span class="i">$Paths</span>[<span class="n">0</span>]<span class="i">->GetVertices</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2847 2834
|
|
|
2848 2835 <span class="k">my</span><span class="s">(</span><span class="i">@PathAtoms</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2849 2836 <span class="i">@PathAtoms</span> = <span class="i">$This</span><span class="i">->_GetAtomsFromAtomIDs</span><span class="s">(</span><span class="i">@PathAtomIDs</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2850 2837 <span class="k">push</span> <span class="i">@PathsAtoms</span><span class="cm">,</span> \<span class="i">@PathAtoms</span><span class="sc">;</span>
|
|
|
2851 2838
|
|
|
2852 2839 <span class="k">my</span><span class="s">(</span><span class="i">@PathBonds</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2853 2840 <span class="i">@PathBonds</span> = <span class="i">$This</span><span class="i">->_GetPathBonds</span><span class="s">(</span><span class="i">@PathAtomIDs</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2854 2841 <span class="k">push</span> <span class="i">@PathsBonds</span><span class="cm">,</span> \<span class="i">@PathBonds</span><span class="sc">;</span>
|
|
|
2855 2842
|
|
|
2856 2843 <span class="s">}</span>
|
|
|
2857 2844
|
|
|
2858 2845 <span class="k">return</span> <span class="s">(</span>\<span class="i">@PathsAtoms</span><span class="cm">,</span> \<span class="i">@PathsBonds</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2859 2846 <span class="s">}</span>
|
|
|
2860 2847
|
|
|
2861 2848 <span class="c"># Setup initial processing status of atoms and bonds involved in connected paths</span>
|
|
|
2862 2849 <span class="c"># before starting kekulization...</span>
|
|
|
2863 2850 <span class="c">#</span>
|
|
|
2864 2851 <span class="c"># Possible atom processing status: DoubleBondPossible, DoubleBondAssigned, DoubleBondNotPossible</span>
|
|
|
2865 2852 <span class="c"># Initial status: DoubleBondPossible or DoubleBondNotPossible</span>
|
|
|
2866 2853 <span class="c">#</span>
|
|
|
2867 2854 <span class="c"># Possible bond processing status: DoubleBondAssigned, SingleBondAssigned, NotProcessed</span>
|
|
|
2868 2855 <span class="c">#</span>
|
|
|
2869 2856 <span class="c"># Possible paths processing status: Processed, NotProcessed</span>
|
|
|
2870 2857 <span class="c"># Initial status: NotProcessed</span>
|
|
|
2871 2858 <span class="c">#</span>
|
|
|
2872 <a name="_SetupConnectedPathSetsForKekulization-"></a>2859 <span class="k">sub </span><span class="m">_SetupConnectedPathSetsForKekulization</span> <span class="s">{</span>
|
|
|
2873 2860 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$PathAtomsSetsRef</span><span class="cm">,</span> <span class="i">$PathBondsSetsRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
2874 2861 <span class="k">my</span><span class="s">(</span><span class="i">$PathIndex</span><span class="cm">,</span> <span class="i">$PathAtomsRef</span><span class="cm">,</span> <span class="i">$PathBondsRef</span><span class="cm">,</span> <span class="i">$Atom</span><span class="cm">,</span> <span class="i">$AtomID</span><span class="cm">,</span> <span class="i">$Bond</span><span class="cm">,</span> <span class="i">$BondID</span><span class="cm">,</span> <span class="i">%AtomProcessingStatusMap</span><span class="cm">,</span> <span class="i">%BondProcessingStatusMap</span><span class="cm">,</span> <span class="i">@PathsProcessingStatus</span><span class="cm">,</span> <span class="i">%InitialPathBondOrderMap</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2875 2862
|
|
|
2876 2863 <span class="c"># Possible path set status values: Processed, NotProcessed</span>
|
|
|
2877 2864 <span class="c"># Initial value: NotProcessed</span>
|
|
|
2878 2865 <span class="c">#</span>
|
|
|
2879 2866 <span class="i">@PathsProcessingStatus</span> = <span class="s">(</span><span class="q">'NotProcessed'</span><span class="s">)</span> x <span class="k">scalar</span> <span class="i">@</span>{<span class="i">$PathAtomsSetsRef</span>}<span class="sc">;</span>
|
|
|
2880 2867
|
|
|
2881 2868 <span class="c"># Collect initial bond order of path bonds before setting bond orders to 1</span>
|
|
|
2882 2869 <span class="c"># and use it to set the bond order back to intial value after it has been processed for</span>
|
|
|
2883 2870 <span class="c"># availability of double bonds...</span>
|
|
|
2884 2871 <span class="c">#</span>
|
|
|
2885 2872 <span class="i">%InitialPathBondOrderMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2886 2873 <span class="k">for</span> <span class="i">$PathBondsRef</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$PathBondsSetsRef</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
2887 2874 <span class="j">BOND:</span> <span class="k">for</span> <span class="i">$Bond</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$PathBondsRef</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
2888 2875 <span class="i">$BondID</span> = <span class="i">$Bond</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2889 2876 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$InitialPathBondOrderMap</span>{<span class="i">$BondID</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
2890 2877 <span class="k">next</span> <span class="j">BOND</span><span class="sc">;</span>
|
|
|
2891 2878 <span class="s">}</span>
|
|
|
2892 2879 <span class="i">$InitialPathBondOrderMap</span>{<span class="i">$BondID</span>} = <span class="i">$Bond</span><span class="i">->GetBondOrder</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2893 2880 <span class="i">$Bond</span><span class="i">->SetBondOrder</span><span class="s">(</span><span class="n">1</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2894 2881 <span class="s">}</span>
|
|
|
2895 2882 <span class="s">}</span>
|
|
|
2896 2883
|
|
|
2897 2884 <span class="i">%AtomProcessingStatusMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2898 2885 <span class="i">%BondProcessingStatusMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2899 2886
|
|
|
2900 2887 <span class="k">for</span> <span class="i">$PathIndex</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#</span>{<span class="i">$PathAtomsSetsRef</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
2901 2888
|
|
|
2902 2889 <span class="i">$PathAtomsRef</span> = <span class="i">$PathAtomsSetsRef</span>->[<span class="i">$PathIndex</span>]<span class="sc">;</span>
|
|
|
2903 2890 <span class="j">ATOM:</span> <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$PathAtomsRef</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
2904 2891 <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>
|
|
|
2905 2892 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$AtomProcessingStatusMap</span>{<span class="i">$AtomID</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
2906 2893 <span class="k">next</span> <span class="j">ATOM</span><span class="sc">;</span>
|
|
|
2907 2894 <span class="s">}</span>
|
|
|
2908 2895 <span class="i">$AtomProcessingStatusMap</span>{<span class="i">$AtomID</span>} = <span class="s">(</span><span class="i">$Atom</span><span class="i">->GetNumOfBondsAvailableForNonHydrogenAtoms</span><span class="s">(</span><span class="s">)</span> >= <span class="n">1</span><span class="s">)</span> ? <span class="q">'DoubleBondPossible'</span> <span class="co">:</span> <span class="q">'DoubleBondNotPossible'</span><span class="sc">;</span>
|
|
|
2909 2896 <span class="s">}</span>
|
|
|
2910 2897
|
|
|
2911 2898 <span class="i">$PathBondsRef</span> = <span class="i">$PathBondsSetsRef</span>->[<span class="i">$PathIndex</span>]<span class="sc">;</span>
|
|
|
2912 2899 <span class="j">BOND:</span> <span class="k">for</span> <span class="i">$Bond</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$PathBondsRef</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
2913 2900 <span class="i">$BondID</span> = <span class="i">$Bond</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2914 2901 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$BondProcessingStatusMap</span>{<span class="i">$BondID</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
2915 2902 <span class="k">next</span> <span class="j">BOND</span><span class="sc">;</span>
|
|
|
2916 2903 <span class="s">}</span>
|
|
|
2917 2904 <span class="i">$BondProcessingStatusMap</span>{<span class="i">$BondID</span>} = <span class="q">'NotProcessed'</span><span class="sc">;</span>
|
|
|
2918 2905 <span class="s">}</span>
|
|
|
2919 2906 <span class="s">}</span>
|
|
|
2920 2907
|
|
|
2921 2908 <span class="c"># Set bond orders back to initial bond orders...</span>
|
|
|
2922 2909 <span class="k">for</span> <span class="i">$PathIndex</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#</span>{<span class="i">$PathAtomsSetsRef</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
2923 2910 <span class="i">$PathBondsRef</span> = <span class="i">$PathBondsSetsRef</span>->[<span class="i">$PathIndex</span>]<span class="sc">;</span>
|
|
|
2924 2911
|
|
|
2925 2912 <span class="k">for</span> <span class="i">$Bond</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$PathBondsRef</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
2926 2913 <span class="i">$BondID</span> = <span class="i">$Bond</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2927 2914 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$InitialPathBondOrderMap</span>{<span class="i">$BondID</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
2928 2915 <span class="i">$Bond</span><span class="i">->SetBondOrder</span><span class="s">(</span><span class="i">$InitialPathBondOrderMap</span>{<span class="i">$BondID</span>}<span class="s">)</span><span class="sc">;</span>
|
|
|
2929 2916 <span class="s">}</span>
|
|
|
2930 2917 <span class="s">}</span>
|
|
|
2931 2918 <span class="s">}</span>
|
|
|
2932 2919
|
|
|
2933 2920 <span class="k">return</span> <span class="s">(</span>\<span class="i">%AtomProcessingStatusMap</span><span class="cm">,</span> \<span class="i">%BondProcessingStatusMap</span><span class="cm">,</span> \<span class="i">@PathsProcessingStatus</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2934 2921 <span class="s">}</span>
|
|
|
2935 2922
|
|
|
2936 2923 <span class="c"># Kekulize connected path sets corresponding to fused rings, individual rings, or any other</span>
|
|
|
2937 2924 <span class="c"># connected path...</span>
|
|
|
2938 2925 <span class="c">#</span>
|
|
|
2939 2926 <span class="c"># Note:</span>
|
|
|
2940 2927 <span class="c"># . PathAtomsRef and PathBondsRef contain paths and bonds corresponding to path</span>
|
|
|
2941 2928 <span class="c"># under consideration for kekulization</span>
|
|
|
2942 2929 <span class="c"># . PathAtomsSetsRef and PathBondsSetsRef contain any other available paths fused</span>
|
|
|
2943 2930 <span class="c"># to the path being kekulized</span>
|
|
|
2944 2931 <span class="c"># . _KekulizeConnectedPathSets is invoked recursively to kekulize all available paths</span>
|
|
|
2945 2932 <span class="c">#</span>
|
|
|
2946 <a name="_KekulizeConnectedPathSets-"></a>2933 <span class="k">sub </span><span class="m">_KekulizeConnectedPathSets</span> <span class="s">{</span>
|
|
|
2947 2934 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$PathAtomsRef</span><span class="cm">,</span> <span class="i">$PathBondsRef</span><span class="cm">,</span> <span class="i">$AtomProcessingStatusMapRef</span><span class="cm">,</span> <span class="i">$BondProcessingStatusMapRef</span><span class="cm">,</span> <span class="i">$PathAtomsSetsRef</span><span class="cm">,</span> <span class="i">$PathBondsSetsRef</span><span class="cm">,</span> <span class="i">$PathsProcessingStatusRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
2948 2935 <span class="k">my</span><span class="s">(</span><span class="i">$PathBond</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2949 2936
|
|
|
2950 2937 <span class="c"># Get next available path bond...</span>
|
|
|
2951 2938 <span class="i">$PathBond</span> = <span class="i">$This</span><span class="i">->_GetNextAvailablePathBondForKekulization</span><span class="s">(</span><span class="i">$PathBondsRef</span><span class="cm">,</span> <span class="i">$BondProcessingStatusMapRef</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2952 2939
|
|
|
2953 2940 <span class="k">if</span> <span class="s">(</span><span class="i">$PathBond</span><span class="s">)</span> <span class="s">{</span>
|
|
|
2954 2941 <span class="k">return</span> <span class="i">$This</span><span class="i">->_ProcessNextAvailablePathBondForKekulization</span><span class="s">(</span><span class="i">$PathBond</span><span class="cm">,</span> <span class="i">$PathAtomsRef</span><span class="cm">,</span> <span class="i">$PathBondsRef</span><span class="cm">,</span> <span class="i">$AtomProcessingStatusMapRef</span><span class="cm">,</span> <span class="i">$BondProcessingStatusMapRef</span><span class="cm">,</span> <span class="i">$PathAtomsSetsRef</span><span class="cm">,</span> <span class="i">$PathBondsSetsRef</span><span class="cm">,</span> <span class="i">$PathsProcessingStatusRef</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2955 2942 <span class="s">}</span>
|
|
|
2956 2943
|
|
|
2957 2944 <span class="c"># Did kekulization succeed for the current path bonds?</span>
|
|
|
2958 2945 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->_DidKekulizationSucceedForPathBonds</span><span class="s">(</span><span class="i">$PathAtomsRef</span><span class="cm">,</span> <span class="i">$PathBondsRef</span><span class="cm">,</span> <span class="i">$AtomProcessingStatusMapRef</span><span class="cm">,</span> <span class="i">$BondProcessingStatusMapRef</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
2959 2946 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
2960 2947 <span class="s">}</span>
|
|
|
2961 2948
|
|
|
2962 2949 <span class="c"># Is there any other path available for kekulization?</span>
|
|
|
2963 2950 <span class="s">(</span><span class="i">$PathAtomsRef</span><span class="cm">,</span> <span class="i">$PathBondsRef</span><span class="s">)</span> = <span class="i">$This</span><span class="i">->_GetNextAvailablePathForKekulization</span><span class="s">(</span><span class="i">$PathAtomsSetsRef</span><span class="cm">,</span> <span class="i">$PathBondsSetsRef</span><span class="cm">,</span> <span class="i">$PathsProcessingStatusRef</span><span class="cm">,</span> <span class="i">$AtomProcessingStatusMapRef</span><span class="cm">,</span> <span class="i">$BondProcessingStatusMapRef</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2964 2951
|
|
|
2965 2952 <span class="k">if</span> <span class="s">(</span><span class="i">$PathAtomsRef</span> && <span class="i">$PathBondsRef</span><span class="s">)</span> <span class="s">{</span>
|
|
|
2966 2953 <span class="c"># Recursively call itself to kekulize next path, which could either be a new path or part</span>
|
|
|
2967 2954 <span class="c"># of a fused paths corresponding to fused ring sets...</span>
|
|
|
2968 2955 <span class="c">#</span>
|
|
|
2969 2956 <span class="k">return</span> <span class="i">$This</span><span class="i">->_KekulizeConnectedPathSets</span><span class="s">(</span><span class="i">$PathAtomsRef</span><span class="cm">,</span> <span class="i">$PathBondsRef</span><span class="cm">,</span> <span class="i">$AtomProcessingStatusMapRef</span><span class="cm">,</span> <span class="i">$BondProcessingStatusMapRef</span><span class="cm">,</span> <span class="i">$PathAtomsSetsRef</span><span class="cm">,</span> <span class="i">$PathBondsSetsRef</span><span class="cm">,</span> <span class="i">$PathsProcessingStatusRef</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2970 2957 <span class="s">}</span>
|
|
|
2971 2958
|
|
|
2972 2959 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span>
|
|
|
2973 2960 <span class="s">}</span>
|
|
|
2974 2961
|
|
|
2975 2962 <span class="c"># Get next available path bond in a list of path bonds...</span>
|
|
|
2976 2963 <span class="c">#</span>
|
|
|
2977 <a name="_GetNextAvailablePathBondForKekulization-"></a>2964 <span class="k">sub </span><span class="m">_GetNextAvailablePathBondForKekulization</span> <span class="s">{</span>
|
|
|
2978 2965 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$PathBondsRef</span><span class="cm">,</span> <span class="i">$BondProcessingStatusMapRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
2979 2966 <span class="k">my</span><span class="s">(</span><span class="i">$AvailablePathBond</span><span class="cm">,</span> <span class="i">$PathBond</span><span class="cm">,</span> <span class="i">$PathBondID</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2980 2967
|
|
|
2981 2968 <span class="i">$AvailablePathBond</span> = <span class="k">undef</span><span class="sc">;</span>
|
|
|
2982 2969
|
|
|
2983 2970 <span class="j">BOND:</span> <span class="k">for</span> <span class="i">$PathBond</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$PathBondsRef</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
2984 2971 <span class="i">$PathBondID</span> = <span class="i">$PathBond</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2985 2972 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$BondProcessingStatusMapRef</span>->{<span class="i">$PathBondID</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
2986 2973 <span class="k">next</span> <span class="j">BOND</span><span class="sc">;</span>
|
|
|
2987 2974 <span class="s">}</span>
|
|
|
2988 2975 <span class="k">if</span> <span class="s">(</span><span class="i">$BondProcessingStatusMapRef</span>->{<span class="i">$PathBondID</span>} =~ <span class="q">/^NotProcessed$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
2989 2976 <span class="i">$AvailablePathBond</span> = <span class="i">$PathBond</span><span class="sc">;</span>
|
|
|
2990 2977 <span class="k">last</span> <span class="j">BOND</span><span class="sc">;</span>
|
|
|
2991 2978 <span class="s">}</span>
|
|
|
2992 2979 <span class="s">}</span>
|
|
|
2993 2980
|
|
|
2994 2981 <span class="k">return</span> <span class="s">(</span><span class="i">$AvailablePathBond</span><span class="s">)</span><span class="sc">;</span>
|
|
|
2995 2982 <span class="s">}</span>
|
|
|
2996 2983
|
|
|
2997 2984 <span class="c"># Process next available path bond for kekulizaiton...</span>
|
|
|
2998 2985 <span class="c">#</span>
|
|
|
2999 <a name="_ProcessNextAvailablePathBondForKekulization-"></a>2986 <span class="k">sub </span><span class="m">_ProcessNextAvailablePathBondForKekulization</span> <span class="s">{</span>
|
|
|
3000 2987 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$PathBond</span><span class="cm">,</span> <span class="i">$PathAtomsRef</span><span class="cm">,</span> <span class="i">$PathBondsRef</span><span class="cm">,</span> <span class="i">$AtomProcessingStatusMapRef</span><span class="cm">,</span> <span class="i">$BondProcessingStatusMapRef</span><span class="cm">,</span> <span class="i">$PathAtomsSetsRef</span><span class="cm">,</span> <span class="i">$PathBondsSetsRef</span><span class="cm">,</span> <span class="i">$PathsProcessingStatusRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
3001 2988 <span class="k">my</span><span class="s">(</span><span class="i">$PathBondID</span><span class="cm">,</span> <span class="i">$PathAtom1</span><span class="cm">,</span> <span class="i">$PathAtom2</span><span class="cm">,</span> <span class="i">$PathAtomID1</span><span class="cm">,</span> <span class="i">$PathAtomID2</span><span class="cm">,</span> <span class="i">%CurrentAtomProcessingStatusMap</span><span class="cm">,</span> <span class="i">%CurrentBondProcessingStatusMap</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3002 2989
|
|
|
3003 2990 <span class="i">$PathBondID</span> = <span class="i">$PathBond</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3004 2991
|
|
|
3005 2992 <span class="s">(</span><span class="i">$PathAtom1</span><span class="cm">,</span> <span class="i">$PathAtom2</span><span class="s">)</span> = <span class="i">$PathBond</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3006 2993 <span class="s">(</span><span class="i">$PathAtomID1</span><span class="cm">,</span> <span class="i">$PathAtomID2</span><span class="s">)</span> = <span class="s">(</span><span class="i">$PathAtom1</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="cm">,</span> <span class="i">$PathAtom2</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3007 2994
|
|
|
3008 2995 <span class="i">%CurrentAtomProcessingStatusMap</span> = <span class="i">%</span>{<span class="i">$AtomProcessingStatusMapRef</span>}<span class="sc">;</span>
|
|
|
3009 2996 <span class="i">%CurrentBondProcessingStatusMap</span> = <span class="i">%</span>{<span class="i">$BondProcessingStatusMapRef</span>}<span class="sc">;</span>
|
|
|
3010 2997
|
|
|
3011 2998 <span class="c"># Is it possible to assign a double bond to the current path bond?</span>
|
|
|
3012 2999 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomProcessingStatusMapRef</span>->{<span class="i">$PathAtomID1</span>} =~ <span class="q">/^DoubleBondPossible$/i</span> && <span class="i">$AtomProcessingStatusMapRef</span>->{<span class="i">$PathAtomID2</span>} =~ <span class="q">/^DoubleBondPossible$/i</span> <span class="s">)</span> <span class="s">{</span>
|
|
|
3013 3000 <span class="c"># Set current bond to double bond by appropriately marking atom and bond process status...</span>
|
|
|
3014 3001 <span class="i">$AtomProcessingStatusMapRef</span>->{<span class="i">$PathAtomID1</span>} = <span class="q">'DoubleBondAssigned'</span><span class="sc">;</span>
|
|
|
3015 3002 <span class="i">$AtomProcessingStatusMapRef</span>->{<span class="i">$PathAtomID2</span>} = <span class="q">'DoubleBondAssigned'</span><span class="sc">;</span>
|
|
|
3016 3003
|
|
|
3017 3004 <span class="i">$BondProcessingStatusMapRef</span>->{<span class="i">$PathBondID</span>} = <span class="q">'DoubleBondAssigned'</span><span class="sc">;</span>
|
|
|
3018 3005
|
|
|
3019 3006 <span class="c"># Recursively call _KekulizeConnectedPathSets to kekulize next available bond...</span>
|
|
|
3020 3007 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span><span class="i">->_KekulizeConnectedPathSets</span><span class="s">(</span><span class="i">$PathAtomsRef</span><span class="cm">,</span> <span class="i">$PathBondsRef</span><span class="cm">,</span> <span class="i">$AtomProcessingStatusMapRef</span><span class="cm">,</span> <span class="i">$BondProcessingStatusMapRef</span><span class="cm">,</span> <span class="i">$PathAtomsSetsRef</span><span class="cm">,</span> <span class="i">$PathBondsSetsRef</span><span class="cm">,</span> <span class="i">$PathsProcessingStatusRef</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
3021 3008 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span>
|
|
|
3022 3009 <span class="s">}</span>
|
|
|
3023 3010
|
|
|
3024 3011 <span class="c"># Double bond at the current ring bond position didn't lead to successful kekulization...</span>
|
|
|
3025 3012 <span class="i">%</span>{<span class="i">$AtomProcessingStatusMapRef</span>} = <span class="i">%CurrentAtomProcessingStatusMap</span><span class="sc">;</span>
|
|
|
3026 3013 <span class="i">%</span>{<span class="i">$BondProcessingStatusMapRef</span>} = <span class="i">%CurrentBondProcessingStatusMap</span><span class="sc">;</span>
|
|
|
3027 3014 <span class="s">}</span>
|
|
|
3028 3015
|
|
|
3029 3016 <span class="c"># Try single bond at the current ring bond position and recursively call _KekulizeConnectedPathSets to kekulize</span>
|
|
|
3030 3017 <span class="c"># rest of the ring bonds...</span>
|
|
|
3031 3018 <span class="c">#</span>
|
|
|
3032 3019 <span class="i">$BondProcessingStatusMapRef</span>->{<span class="i">$PathBondID</span>} = <span class="q">'SingleBondAssigned'</span><span class="sc">;</span>
|
|
|
3033 3020
|
|
|
3034 3021 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span><span class="i">->_KekulizeConnectedPathSets</span><span class="s">(</span><span class="i">$PathAtomsRef</span><span class="cm">,</span> <span class="i">$PathBondsRef</span><span class="cm">,</span> <span class="i">$AtomProcessingStatusMapRef</span><span class="cm">,</span> <span class="i">$BondProcessingStatusMapRef</span><span class="cm">,</span> <span class="i">$PathAtomsSetsRef</span><span class="cm">,</span> <span class="i">$PathBondsSetsRef</span><span class="cm">,</span> <span class="i">$PathsProcessingStatusRef</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
3035 3022 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span>
|
|
|
3036 3023 <span class="s">}</span>
|
|
|
3037 3024
|
|
|
3038 3025 <span class="i">%</span>{<span class="i">$AtomProcessingStatusMapRef</span>} = <span class="i">%CurrentAtomProcessingStatusMap</span><span class="sc">;</span>
|
|
|
3039 3026 <span class="i">%</span>{<span class="i">$BondProcessingStatusMapRef</span>} = <span class="i">%CurrentBondProcessingStatusMap</span><span class="sc">;</span>
|
|
|
3040 3027
|
|
|
3041 3028 <span class="c"># Kekulization didn't work out for path bonds...</span>
|
|
|
3042 3029
|
|
|
3043 3030 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
3044 3031
|
|
|
3045 3032 <span class="s">}</span>
|
|
|
3046 3033
|
|
|
3047 3034 <span class="c"># Get next available path for kekulization from a set of fused ring paths...</span>
|
|
|
3048 3035 <span class="c">#</span>
|
|
|
3049 <a name="_GetNextAvailablePathForKekulization-"></a>3036 <span class="k">sub </span><span class="m">_GetNextAvailablePathForKekulization</span> <span class="s">{</span>
|
|
|
3050 3037 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$PathAtomsSetsRef</span><span class="cm">,</span> <span class="i">$PathBondsSetsRef</span><span class="cm">,</span> <span class="i">$PathsProcessingStatusRef</span><span class="cm">,</span> <span class="i">$AtomProcessingStatusMapRef</span><span class="cm">,</span> <span class="i">$BondProcessingStatusMapRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
3051 3038 <span class="k">my</span><span class="s">(</span><span class="i">$PathIndex</span><span class="cm">,</span> <span class="i">$AvailablePathIndex</span><span class="cm">,</span> <span class="i">$PathAtomsRef</span><span class="cm">,</span> <span class="i">$PathBondsRef</span><span class="cm">,</span> <span class="i">$PathBond</span><span class="cm">,</span> <span class="i">$PathBondID</span><span class="cm">,</span> <span class="i">$MaxNumOfPathBondsProcessed</span><span class="cm">,</span> <span class="i">$NumOfPathBondsProcessed</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3052 3039
|
|
|
3053 3040 <span class="s">(</span><span class="i">$PathAtomsRef</span><span class="cm">,</span> <span class="i">$PathBondsRef</span><span class="cm">,</span> <span class="i">$AvailablePathIndex</span><span class="s">)</span> = <span class="s">(</span><span class="k">undef</span><span class="s">)</span> x <span class="n">3</span><span class="sc">;</span>
|
|
|
3054 3041
|
|
|
3055 3042 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$PathAtomsSetsRef</span><span class="s">)</span> && <span class="k">defined</span><span class="s">(</span><span class="i">$PathBondsSetsRef</span><span class="s">)</span> && <span class="k">defined</span><span class="s">(</span><span class="i">$PathsProcessingStatusRef</span><span class="s">)</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
3056 3043 <span class="k">return</span> <span class="s">(</span><span class="i">$PathAtomsRef</span><span class="cm">,</span> <span class="i">$PathBondsRef</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3057 3044 <span class="s">}</span>
|
|
|
3058 3045
|
|
|
3059 3046 <span class="i">$MaxNumOfPathBondsProcessed</span> = <span class="n">-999</span><span class="sc">;</span>
|
|
|
3060 3047 <span class="i">$AvailablePathIndex</span> = <span class="k">undef</span><span class="sc">;</span>
|
|
|
3061 3048
|
|
|
3062 3049 <span class="j">PATHINDEX:</span> <span class="k">for</span> <span class="i">$PathIndex</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#</span>{<span class="i">$PathsProcessingStatusRef</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
3063 3050 <span class="k">if</span> <span class="s">(</span><span class="i">$PathsProcessingStatusRef</span>->[<span class="i">$PathIndex</span>] =~ <span class="q">/^Processed$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
3064 3051 <span class="k">next</span> <span class="j">PATHINDEX</span><span class="sc">;</span>
|
|
|
3065 3052 <span class="s">}</span>
|
|
|
3066 3053
|
|
|
3067 3054 <span class="c"># Count of already processed bonds in an unprocessed path bonds through</span>
|
|
|
3068 3055 <span class="c"># their participation in any fused bonds sets...</span>
|
|
|
3069 3056 <span class="c">#</span>
|
|
|
3070 3057 <span class="i">$NumOfPathBondsProcessed</span> = <span class="n">0</span><span class="sc">;</span>
|
|
|
3071 3058 <span class="j">PATHBOND:</span> <span class="k">for</span> <span class="i">$PathBond</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$PathBondsSetsRef</span>->[<span class="i">$PathIndex</span>]}<span class="s">)</span> <span class="s">{</span>
|
|
|
3072 3059 <span class="i">$PathBondID</span> = <span class="i">$PathBond</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3073 3060 <span class="k">if</span> <span class="s">(</span><span class="i">$BondProcessingStatusMapRef</span>->{<span class="i">$PathBondID</span>} =~ <span class="q">/^NotProcessed$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
3074 3061 <span class="k">next</span> <span class="j">PATHBOND</span><span class="sc">;</span>
|
|
|
3075 3062 <span class="s">}</span>
|
|
|
3076 3063 <span class="i">$NumOfPathBondsProcessed</span>++<span class="sc">;</span>
|
|
|
3077 3064 <span class="s">}</span>
|
|
|
3078 3065
|
|
|
3079 3066 <span class="k">if</span> <span class="s">(</span><span class="i">$NumOfPathBondsProcessed</span> > <span class="i">$MaxNumOfPathBondsProcessed</span><span class="s">)</span> <span class="s">{</span>
|
|
|
3080 3067 <span class="i">$AvailablePathIndex</span> = <span class="i">$PathIndex</span><span class="sc">;</span>
|
|
|
3081 3068 <span class="i">$MaxNumOfPathBondsProcessed</span> = <span class="i">$NumOfPathBondsProcessed</span><span class="sc">;</span>
|
|
|
3082 3069 <span class="s">}</span>
|
|
|
3083 3070
|
|
|
3084 3071 <span class="s">}</span>
|
|
|
3085 3072
|
|
|
3086 3073 <span class="c"># Is any path available?</span>
|
|
|
3087 3074 <span class="k">if</span> <span class="s">(</span>!<span class="i">$AvailablePathIndex</span><span class="s">)</span> <span class="s">{</span>
|
|
|
3088 3075 <span class="k">return</span> <span class="s">(</span><span class="i">$PathAtomsRef</span><span class="cm">,</span> <span class="i">$PathBondsRef</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3089 3076 <span class="s">}</span>
|
|
|
3090 3077
|
|
|
3091 3078 <span class="i">$PathsProcessingStatusRef</span>->[<span class="i">$AvailablePathIndex</span>] = <span class="q">'Processed'</span><span class="sc">;</span>
|
|
|
3092 3079
|
|
|
3093 3080 <span class="i">$PathAtomsRef</span> = <span class="i">$PathAtomsSetsRef</span>->[<span class="i">$AvailablePathIndex</span>]<span class="sc">;</span>
|
|
|
3094 3081 <span class="i">$PathBondsRef</span> = <span class="i">$PathBondsSetsRef</span>->[<span class="i">$AvailablePathIndex</span>]<span class="sc">;</span>
|
|
|
3095 3082
|
|
|
3096 3083 <span class="k">return</span> <span class="s">(</span><span class="i">$PathAtomsRef</span><span class="cm">,</span> <span class="i">$PathBondsRef</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3097 3084 <span class="s">}</span>
|
|
|
3098 3085
|
|
|
3099 3086 <span class="c"># Check for kekulization in a specific set of path bonds. For successful kekulization, all</span>
|
|
|
3100 3087 <span class="c"># all path atoms marked with DoubleBondPossible must be involved in a path double bond...</span>
|
|
|
3101 3088 <span class="c">#</span>
|
|
|
3102 <a name="_DidKekulizationSucceedForPathBonds-"></a>3089 <span class="k">sub </span><span class="m">_DidKekulizationSucceedForPathBonds</span> <span class="s">{</span>
|
|
|
3103 3090 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$PathAtomsRef</span><span class="cm">,</span> <span class="i">$PathBondsRef</span><span class="cm">,</span> <span class="i">$AtomProcessingStatusMapRef</span><span class="cm">,</span> <span class="i">$BondProcessingStatusMapRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
3104 3091 <span class="k">my</span><span class="s">(</span><span class="i">$PathAtom</span><span class="cm">,</span> <span class="i">$PathAtomID</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3105 3092
|
|
|
3106 3093 <span class="k">for</span> <span class="i">$PathAtom</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$PathAtomsRef</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
3107 3094 <span class="i">$PathAtomID</span> = <span class="i">$PathAtom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3108 3095 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$AtomProcessingStatusMapRef</span>->{<span class="i">$PathAtomID</span>} && <span class="i">$AtomProcessingStatusMapRef</span>->{<span class="i">$PathAtomID</span>} =~ <span class="q">/^DoubleBondPossible$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
3109 3096 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
3110 3097 <span class="s">}</span>
|
|
|
3111 3098 <span class="s">}</span>
|
|
|
3112 3099 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span>
|
|
|
3113 3100 <span class="s">}</span>
|
|
|
3114 3101
|
|
|
3115 3102 <span class="c"># Assign bond orders to the bonds in a molecule which have been successfully</span>
|
|
|
3116 3103 <span class="c"># kekulized along with optional clearing of aromaticty property...</span>
|
|
|
3117 3104 <span class="c">#</span>
|
|
|
3118 <a name="_ProcessBondOrdersAssignedDuringSuccessfulKekulization-"></a>3105 <span class="k">sub </span><span class="m">_ProcessBondOrdersAssignedDuringSuccessfulKekulization</span> <span class="s">{</span>
|
|
|
3119 3106 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$BondsRef</span><span class="cm">,</span> <span class="i">$BondsProcessingStatusMapRef</span><span class="cm">,</span> <span class="i">$DeleteBondsAromaticity</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
3120 3107 <span class="k">my</span><span class="s">(</span><span class="i">$Bond</span><span class="cm">,</span> <span class="i">$BondID</span><span class="cm">,</span> <span class="i">$BondOrder</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3121 3108
|
|
|
3122 3109 <span class="i">$DeleteBondsAromaticity</span> = <span class="k">defined</span> <span class="i">$DeleteBondsAromaticity</span> ? <span class="i">$DeleteBondsAromaticity</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
3123 3110
|
|
|
3124 3111 <span class="j">BOND:</span> <span class="k">for</span> <span class="i">$Bond</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$BondsRef</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
3125 3112 <span class="i">$BondID</span> = <span class="i">$Bond</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3126 3113
|
|
|
3127 3114 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$BondsProcessingStatusMapRef</span>->{<span class="i">$BondID</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
3128 3115 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->_ProcessBondOrdersAssignedDuringSuccessfulKekulization: Couldn't process bond with bond ID, $BondID: It's not available in the list of bonds processed for kekulization..."</span><span class="sc">;</span>
|
|
|
3129 3116 <span class="k">next</span> <span class="j">BOND</span><span class="sc">;</span>
|
|
|
3130 3117 <span class="s">}</span>
|
|
|
3131 3118
|
|
|
3132 3119 <span class="i">$BondOrder</span> = <span class="s">(</span><span class="i">$BondsProcessingStatusMapRef</span>->{<span class="i">$BondID</span>} =~ <span class="q">/^DoubleBondAssigned$/i</span><span class="s">)</span> ? <span class="n">2</span> <span class="co">:</span> <span class="n">1</span><span class="sc">;</span>
|
|
|
3133 3120 <span class="i">$Bond</span><span class="i">->SetBondOrder</span><span class="s">(</span><span class="i">$BondOrder</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3134 3121
|
|
|
3135 3122 <span class="k">if</span> <span class="s">(</span><span class="i">$DeleteBondsAromaticity</span><span class="s">)</span> <span class="s">{</span>
|
|
|
3136 3123 <span class="i">$Bond</span><span class="i">->DeleteAromatic</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3137 3124 <span class="s">}</span>
|
|
|
3138 3125 <span class="s">}</span>
|
|
|
3139 3126 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
3140 3127 <span class="s">}</span>
|
|
|
3141 3128
|
|
|
3142 3129 <span class="c"># Does molecule contains aromatic rings?</span>
|
|
|
3143 3130 <span class="c">#</span>
|
|
|
3144 <a name="HasAromaticRings-"></a>3131 <span class="k">sub </span><span class="m">HasAromaticRings</span> <span class="s">{</span>
|
|
|
3145 3132 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
3146 3133
|
|
|
3147 3134 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetNumOfAromaticRings</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>
|
|
|
3148 3135 <span class="s">}</span>
|
|
|
3149 3136
|
|
|
3150 3137 <span class="c"># Does molecule contains any aromatic atom in a ring?</span>
|
|
|
3151 3138 <span class="c">#</span>
|
|
|
3152 <a name="HasAromaticAtomsInRings-"></a>3139 <span class="k">sub </span><span class="m">HasAromaticAtomsInRings</span> <span class="s">{</span>
|
|
|
3153 3140 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
3154 3141 <span class="k">my</span><span class="s">(</span><span class="i">$Atom</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3155 3142
|
|
|
3156 3143 <span class="j">ATOM:</span> <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="i">$This</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
3157 3144 <span class="k">if</span> <span class="s">(</span>!<span class="i">$Atom</span><span class="i">->IsAromatic</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
3158 3145 <span class="k">next</span> <span class="j">ATOM</span><span class="sc">;</span>
|
|
|
3159 3146 <span class="s">}</span>
|
|
|
3160 3147 <span class="k">if</span> <span class="s">(</span><span class="i">$Atom</span><span class="i">->IsInRing</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
3161 3148 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span>
|
|
|
3162 3149 <span class="s">}</span>
|
|
|
3163 3150 <span class="s">}</span>
|
|
|
3164 3151 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
3165 3152 <span class="s">}</span>
|
|
|
3166 3153
|
|
|
3167 3154 <span class="c"># Does molecule contains any aromatic atom not in a ring?</span>
|
|
|
3168 3155 <span class="c">#</span>
|
|
|
3169 <a name="HasAromaticAtomsNotInRings-"></a>3156 <span class="k">sub </span><span class="m">HasAromaticAtomsNotInRings</span> <span class="s">{</span>
|
|
|
3170 3157 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
3171 3158 <span class="k">my</span><span class="s">(</span><span class="i">$Atom</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3172 3159
|
|
|
3173 3160 <span class="j">ATOM:</span> <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="i">$This</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
3174 3161 <span class="k">if</span> <span class="s">(</span>!<span class="i">$Atom</span><span class="i">->IsAromatic</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
3175 3162 <span class="k">next</span> <span class="j">ATOM</span><span class="sc">;</span>
|
|
|
3176 3163 <span class="s">}</span>
|
|
|
3177 3164 <span class="k">if</span> <span class="s">(</span><span class="i">$Atom</span><span class="i">->IsNotInRing</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
3178 3165 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span>
|
|
|
3179 3166 <span class="s">}</span>
|
|
|
3180 3167 <span class="s">}</span>
|
|
|
3181 3168 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
3182 3169 <span class="s">}</span>
|
|
|
3183 3170
|
|
|
3184 3171 <span class="c"># Does molecule contains rings?</span>
|
|
|
3185 3172 <span class="c">#</span>
|
|
|
3186 <a name="HasRings-"></a>3173 <span class="k">sub </span><span class="m">HasRings</span> <span class="s">{</span>
|
|
|
3187 3174 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
3188 3175
|
|
|
3189 3176 <span class="k">return</span> <span class="i">$This</span><span class="i">->IsCyclic</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3190 3177 <span class="s">}</span>
|
|
|
3191 3178
|
|
|
3192 3179 <span class="c"># Does molecule contains only one ring?</span>
|
|
|
3193 3180 <span class="c">#</span>
|
|
|
3194 <a name="HasOnlyOneRing-"></a>3181 <span class="k">sub </span><span class="m">HasOnlyOneRing</span> <span class="s">{</span>
|
|
|
3195 3182 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
3196 3183
|
|
|
3197 3184 <span class="k">return</span> <span class="i">$This</span><span class="i">->IsUnicyclic</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3198 3185 <span class="s">}</span>
|
|
|
3199 3186
|
|
|
3200 3187 <span class="c"># Does molecule contains any rings?</span>
|
|
|
3201 3188 <span class="c">#</span>
|
|
|
3202 <a name="HasNoRings-"></a>3189 <span class="k">sub </span><span class="m">HasNoRings</span> <span class="s">{</span>
|
|
|
3203 3190 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
3204 3191
|
|
|
3205 3192 <span class="k">return</span> <span class="i">$This</span><span class="i">->IsAcyclic</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3206 3193 <span class="s">}</span>
|
|
|
3207 3194
|
|
|
3208 3195 <span class="c"># Get size of smallest ring...</span>
|
|
|
3209 3196 <span class="c">#</span>
|
|
|
3210 <a name="GetSizeOfSmallestRing-"></a>3197 <span class="k">sub </span><span class="m">GetSizeOfSmallestRing</span> <span class="s">{</span>
|
|
|
3211 3198 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
3212 3199
|
|
|
3213 3200 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetSizeOfSmallestCycle</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3214 3201 <span class="s">}</span>
|
|
|
3215 3202
|
|
|
3216 3203 <span class="c"># Get size of largest ring...</span>
|
|
|
3217 3204 <span class="c">#</span>
|
|
|
3218 <a name="GetSizeOfLargestRing-"></a>3205 <span class="k">sub </span><span class="m">GetSizeOfLargestRing</span> <span class="s">{</span>
|
|
|
3219 3206 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
3220 3207
|
|
|
3221 3208 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetSizeOfLargestCycle</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3222 3209 <span class="s">}</span>
|
|
|
3223 3210
|
|
|
3224 3211 <span class="c"># Get number of rings...</span>
|
|
|
3225 3212 <span class="c">#</span>
|
|
|
3226 <a name="GetNumOfRings-"></a>3213 <span class="k">sub </span><span class="m">GetNumOfRings</span> <span class="s">{</span>
|
|
|
3227 3214 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
3228 3215
|
|
|
3229 3216 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetNumOfCycles</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3230 3217 <span class="s">}</span>
|
|
|
3231 3218
|
|
|
3232 3219 <span class="c"># Get number of aromatic rings...</span>
|
|
|
3233 3220 <span class="c">#</span>
|
|
|
3234 <a name="GetNumOfAromaticRings-"></a>3221 <span class="k">sub </span><span class="m">GetNumOfAromaticRings</span> <span class="s">{</span>
|
|
|
3235 3222 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
3236 3223 <span class="k">my</span><span class="s">(</span><span class="i">$NumOfRings</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3237 3224
|
|
|
3238 3225 <span class="i">$NumOfRings</span> = <span class="k">scalar</span> <span class="i">$This</span><span class="i">->GetAromaticRings</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3239 3226
|
|
|
3240 3227 <span class="k">return</span> <span class="i">$NumOfRings</span><span class="sc">;</span>
|
|
|
3241 3228 <span class="s">}</span>
|
|
|
3242 3229
|
|
|
3243 3230 <span class="c"># Get num of rings with odd size...</span>
|
|
|
3244 3231 <span class="c">#</span>
|
|
|
3245 <a name="GetNumOfRingsWithOddSize-"></a>3232 <span class="k">sub </span><span class="m">GetNumOfRingsWithOddSize</span> <span class="s">{</span>
|
|
|
3246 3233 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
3247 3234
|
|
|
3248 3235 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetNumOfCyclesWithOddSize</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3249 3236 <span class="s">}</span>
|
|
|
3250 3237
|
|
|
3251 3238 <span class="c"># Get num of rings with even size...</span>
|
|
|
3252 3239 <span class="c">#</span>
|
|
|
3253 <a name="GetNumOfRingsWithEvenSize-"></a>3240 <span class="k">sub </span><span class="m">GetNumOfRingsWithEvenSize</span> <span class="s">{</span>
|
|
|
3254 3241 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
3255 3242
|
|
|
3256 3243 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetNumOfCyclesWithEvenSize</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3257 3244 <span class="s">}</span>
|
|
|
3258 3245
|
|
|
3259 3246 <span class="c"># Get num of rings with specified size...</span>
|
|
|
3260 3247 <span class="c">#</span>
|
|
|
3261 <a name="GetNumOfRingsWithSize-"></a>3248 <span class="k">sub </span><span class="m">GetNumOfRingsWithSize</span> <span class="s">{</span>
|
|
|
3262 3249 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$RingSize</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
3263 3250
|
|
|
3264 3251 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetNumOfCyclesWithSize</span><span class="s">(</span><span class="i">$RingSize</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3265 3252 <span class="s">}</span>
|
|
|
3266 3253
|
|
|
3267 3254 <span class="c"># Get num of rings with size less than a specified size...</span>
|
|
|
3268 3255 <span class="c">#</span>
|
|
|
3269 <a name="GetNumOfRingsWithSizeLessThan-"></a>3256 <span class="k">sub </span><span class="m">GetNumOfRingsWithSizeLessThan</span> <span class="s">{</span>
|
|
|
3270 3257 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$RingSize</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
3271 3258
|
|
|
3272 3259 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetNumOfCyclesWithSizeLessThan</span><span class="s">(</span><span class="i">$RingSize</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3273 3260 <span class="s">}</span>
|
|
|
3274 3261
|
|
|
3275 3262 <span class="c"># Get num of rings with size greater than a specified size...</span>
|
|
|
3276 3263 <span class="c">#</span>
|
|
|
3277 <a name="GetNumOfRingsWithSizeGreaterThan-"></a>3264 <span class="k">sub </span><span class="m">GetNumOfRingsWithSizeGreaterThan</span> <span class="s">{</span>
|
|
|
3278 3265 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$RingSize</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
3279 3266
|
|
|
3280 3267 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetNumOfCyclesWithSizeGreaterThan</span><span class="s">(</span><span class="i">$RingSize</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3281 3268 <span class="s">}</span>
|
|
|
3282 3269
|
|
|
3283 3270 <span class="c"># Get largest ring as an array containing ring atoms...</span>
|
|
|
3284 3271 <span class="c">#</span>
|
|
|
3285 <a name="GetLargestRing-"></a>3272 <span class="k">sub </span><span class="m">GetLargestRing</span> <span class="s">{</span>
|
|
|
3286 3273 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
3287 3274
|
|
|
3288 3275 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetRing</span><span class="s">(</span><span class="i">$This</span><span class="i">->GetLargestCycle</span><span class="s">(</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3289 3276 <span class="s">}</span>
|
|
|
3290 3277
|
|
|
3291 3278 <span class="c"># Get smallest ring as an array containing ring atoms...</span>
|
|
|
3292 3279 <span class="c">#</span>
|
|
|
3293 <a name="GetSmallestRing-"></a>3280 <span class="k">sub </span><span class="m">GetSmallestRing</span> <span class="s">{</span>
|
|
|
3294 3281 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
3295 3282
|
|
|
3296 3283 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetRing</span><span class="s">(</span><span class="i">$This</span><span class="i">->GetSmallestCycle</span><span class="s">(</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3297 3284 <span class="s">}</span>
|
|
|
3298 3285
|
|
|
3299 3286 <span class="c"># Get rings as an array containing references to arrays with ring atoms...</span>
|
|
|
3300 3287 <span class="c">#</span>
|
|
|
3301 <a name="GetRings-"></a>3288 <span class="k">sub </span><span class="m">GetRings</span> <span class="s">{</span>
|
|
|
3302 3289 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
3303 3290
|
|
|
3304 3291 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetRings</span><span class="s">(</span><span class="i">$This</span><span class="i">->GetCycles</span><span class="s">(</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3305 3292 <span class="s">}</span>
|
|
|
3306 3293
|
|
|
3307 3294 <span class="c"># Get aromatic rings as an array containing references to arrays with ring atoms...</span>
|
|
|
3308 3295 <span class="c">#</span>
|
|
|
3309 <a name="GetAromaticRings-"></a>3296 <span class="k">sub </span><span class="m">GetAromaticRings</span> <span class="s">{</span>
|
|
|
3310 3297 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
3311 3298
|
|
|
3312 3299 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetAromaticRings</span><span class="s">(</span><span class="i">$This</span><span class="i">->GetCycles</span><span class="s">(</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3313 3300 <span class="s">}</span>
|
|
|
3314 3301
|
|
|
3315 3302 <span class="c"># Get odd size rings as an array containing references to arrays with ring atoms...</span>
|
|
|
3316 3303 <span class="c">#</span>
|
|
|
3317 <a name="GetRingsWithOddSize-"></a>3304 <span class="k">sub </span><span class="m">GetRingsWithOddSize</span> <span class="s">{</span>
|
|
|
3318 3305 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
3319 3306
|
|
|
3320 3307 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetRings</span><span class="s">(</span><span class="i">$This</span><span class="i">->GetCyclesWithOddSize</span><span class="s">(</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3321 3308 <span class="s">}</span>
|
|
|
3322 3309
|
|
|
3323 3310 <span class="c"># Get even size rings as an array containing references to arrays with ring atoms...</span>
|
|
|
3324 3311 <span class="c">#</span>
|
|
|
3325 <a name="GetRingsWithEvenSize-"></a>3312 <span class="k">sub </span><span class="m">GetRingsWithEvenSize</span> <span class="s">{</span>
|
|
|
3326 3313 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
3327 3314
|
|
|
3328 3315 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetRings</span><span class="s">(</span><span class="i">$This</span><span class="i">->GetCyclesWithEvenSize</span><span class="s">(</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3329 3316 <span class="s">}</span>
|
|
|
3330 3317
|
|
|
3331 3318 <span class="c"># Get rings with a specific size as an array containing references to arrays with ring atoms...</span>
|
|
|
3332 3319 <span class="c">#</span>
|
|
|
3333 <a name="GetRingsWithSize-"></a>3320 <span class="k">sub </span><span class="m">GetRingsWithSize</span> <span class="s">{</span>
|
|
|
3334 3321 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$RingSize</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
3335 3322
|
|
|
3336 3323 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetRings</span><span class="s">(</span><span class="i">$This</span><span class="i">->GetCyclesWithSize</span><span class="s">(</span><span class="i">$RingSize</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3337 3324 <span class="s">}</span>
|
|
|
3338 3325
|
|
|
3339 3326 <span class="c"># Get rings with size less than a specific size as an array containing references to arrays with ring atoms...</span>
|
|
|
3340 3327 <span class="c">#</span>
|
|
|
3341 <a name="GetRingsWithSizeLessThan-"></a>3328 <span class="k">sub </span><span class="m">GetRingsWithSizeLessThan</span> <span class="s">{</span>
|
|
|
3342 3329 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$RingSize</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
3343 3330
|
|
|
3344 3331 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetRings</span><span class="s">(</span><span class="i">$This</span><span class="i">->GetCyclesWithSizeLessThan</span><span class="s">(</span><span class="i">$RingSize</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3345 3332 <span class="s">}</span>
|
|
|
3346 3333
|
|
|
3347 3334 <span class="c"># Get rings with size greater than a specific size as an array containing references to arrays with ring atoms...</span>
|
|
|
3348 3335 <span class="c">#</span>
|
|
|
3349 <a name="GetRingsWithSizeGreaterThan-"></a>3336 <span class="k">sub </span><span class="m">GetRingsWithSizeGreaterThan</span> <span class="s">{</span>
|
|
|
3350 3337 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$RingSize</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
3351 3338
|
|
|
3352 3339 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetRings</span><span class="s">(</span><span class="i">$This</span><span class="i">->GetCyclesWithSizeGreaterThan</span><span class="s">(</span><span class="i">$RingSize</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3353 3340 <span class="s">}</span>
|
|
|
3354 3341
|
|
|
3355 3342 <span class="c"># Generate an array of bond objects for an array of ring atoms and return an array</span>
|
|
|
3356 3343 <span class="c"># of bond objects...</span>
|
|
|
3357 3344 <span class="c">#</span>
|
|
|
3358 <a name="GetRingBonds-"></a>3345 <span class="k">sub </span><span class="m">GetRingBonds</span> <span class="s">{</span>
|
|
|
3359 3346 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">@RingAtoms</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
3360 3347 <span class="k">my</span><span class="s">(</span><span class="i">@Bonds</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3361 3348
|
|
|
3362 3349 <span class="i">@Bonds</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3363 3350 <span class="k">if</span> <span class="s">(</span>!<span class="i">@RingAtoms</span><span class="s">)</span> <span class="s">{</span>
|
|
|
3364 3351 <span class="c"># Return an empty ring bonds list...</span>
|
|
|
3365 3352 <span class="k">return</span> <span class="i">@Bonds</span><span class="sc">;</span>
|
|
|
3366 3353 <span class="s">}</span>
|
|
|
3367 3354
|
|
|
3368 3355 <span class="k">my</span><span class="s">(</span><span class="i">@RingAtomIDs</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3369 3356
|
|
|
3370 3357 <span class="i">@RingAtomIDs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3371 3358 <span class="i">@RingAtomIDs</span> = <span class="i">$This</span><span class="i">->_GetAtomsIDsFromAtoms</span><span class="s">(</span><span class="i">@RingAtoms</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3372 3359 <span class="k">if</span> <span class="s">(</span>!<span class="i">@RingAtomIDs</span><span class="s">)</span> <span class="s">{</span>
|
|
|
3373 3360 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->GetRingBonds: No ring bonds retrieved: Atom IDs couldn't be retrieved for specified atoms..."</span><span class="sc">;</span>
|
|
|
3374 3361 <span class="k">return</span> <span class="i">@Bonds</span><span class="sc">;</span>
|
|
|
3375 3362 <span class="s">}</span>
|
|
|
3376 3363
|
|
|
3377 3364 <span class="c"># Add start atom to the end to make it a cyclic path for ring: It's taken out during conversion</span>
|
|
|
3378 3365 <span class="c"># of cyclic path to a ring...</span>
|
|
|
3379 3366 <span class="k">push</span> <span class="i">@RingAtomIDs</span><span class="cm">,</span> <span class="i">$RingAtomIDs</span>[<span class="n">0</span>]<span class="sc">;</span>
|
|
|
3380 3367
|
|
|
3381 3368 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetPathBonds</span><span class="s">(</span><span class="i">@RingAtomIDs</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3382 3369 <span class="s">}</span>
|
|
|
3383 3370
|
|
|
3384 3371 <span class="c"># Generate an array containing references to arrays of ring bond objects for rings specified</span>
|
|
|
3385 3372 <span class="c"># in an array of references to ring atoms...</span>
|
|
|
3386 3373 <span class="c">#</span>
|
|
|
3387 <a name="GetRingBondsFromRings-"></a>3374 <span class="k">sub </span><span class="m">GetRingBondsFromRings</span> <span class="s">{</span>
|
|
|
3388 3375 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">@RingAtomsSets</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
3389 3376 <span class="k">my</span><span class="s">(</span><span class="i">$RingAtomsRef</span><span class="cm">,</span> <span class="i">@RingBondsSets</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3390 3377
|
|
|
3391 3378 <span class="i">@RingBondsSets</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3392 3379 <span class="k">for</span> <span class="i">$RingAtomsRef</span> <span class="s">(</span><span class="i">@RingAtomsSets</span><span class="s">)</span> <span class="s">{</span>
|
|
|
3393 3380 <span class="k">my</span><span class="s">(</span><span class="i">@RingBonds</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3394 3381 <span class="i">@RingBonds</span> = <span class="i">$This</span><span class="i">->GetRingBonds</span><span class="s">(</span><span class="i">@</span>{<span class="i">$RingAtomsRef</span>}<span class="s">)</span><span class="sc">;</span>
|
|
|
3395 3382
|
|
|
3396 3383 <span class="k">push</span> <span class="i">@RingBondsSets</span><span class="cm">,</span> \<span class="i">@RingBonds</span><span class="sc">;</span>
|
|
|
3397 3384 <span class="s">}</span>
|
|
|
3398 3385
|
|
|
3399 3386 <span class="k">return</span> <span class="i">@RingBondsSets</span><span class="sc">;</span>
|
|
|
3400 3387 <span class="s">}</span>
|
|
|
3401 3388
|
|
|
3402 3389 <span class="c"># Does molecule has any fused rings?</span>
|
|
|
3403 3390 <span class="c">#</span>
|
|
|
3404 <a name="HasFusedRings-"></a>3391 <span class="k">sub </span><span class="m">HasFusedRings</span> <span class="s">{</span>
|
|
|
3405 3392 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
3406 3393
|
|
|
3407 3394 <span class="k">return</span> <span class="i">$This</span><span class="i">->HasFusedCycles</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3408 3395 <span class="s">}</span>
|
|
|
3409 3396
|
|
|
3410 3397 <span class="c"># Get references to array of fused ring sets and non-fused rings. Fused ring sets array reference</span>
|
|
|
3411 3398 <span class="c"># contains refernces to arrays of rings; Non-fused rings array reference contains references to</span>
|
|
|
3412 3399 <span class="c"># arrays of ring atoms...</span>
|
|
|
3413 3400 <span class="c"># rings.</span>
|
|
|
3414 3401 <span class="c">#</span>
|
|
|
3415 <a name="GetFusedAndNonFusedRings-"></a>3402 <span class="k">sub </span><span class="m">GetFusedAndNonFusedRings</span> <span class="s">{</span>
|
|
|
3416 3403 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
3417 3404 <span class="k">my</span><span class="s">(</span><span class="i">$FusedCyclesSetsRef</span><span class="cm">,</span> <span class="i">$NonFusedCyclesRef</span><span class="cm">,</span> <span class="i">@FusedRingSets</span><span class="cm">,</span> <span class="i">@NonFusedRings</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3418 3405
|
|
|
3419 3406 <span class="i">@FusedRingSets</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> <span class="i">@NonFusedRings</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3420 3407 <span class="s">(</span><span class="i">$FusedCyclesSetsRef</span><span class="cm">,</span> <span class="i">$NonFusedCyclesRef</span><span class="s">)</span> = <span class="i">$This</span><span class="i">->GetFusedAndNonFusedCycles</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3421 3408 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$FusedCyclesSetsRef</span><span class="s">)</span> && <span class="k">defined</span><span class="s">(</span><span class="i">$NonFusedCyclesRef</span><span class="s">)</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
3422 3409 <span class="k">return</span> <span class="s">(</span>\<span class="i">@FusedRingSets</span><span class="cm">,</span> \<span class="i">@NonFusedRings</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3423 3410 <span class="s">}</span>
|
|
|
3424 3411 <span class="k">my</span><span class="s">(</span><span class="i">$FusedCyclesSetRef</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3425 3412
|
|
|
3426 3413 <span class="k">for</span> <span class="i">$FusedCyclesSetRef</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$FusedCyclesSetsRef</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
3427 3414 <span class="k">my</span><span class="s">(</span><span class="i">@FusedRingSet</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3428 3415 <span class="i">@FusedRingSet</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3429 3416 <span class="i">@FusedRingSet</span> = <span class="i">$This</span><span class="i">->_GetRings</span><span class="s">(</span><span class="i">@</span>{<span class="i">$FusedCyclesSetRef</span>}<span class="s">)</span><span class="sc">;</span>
|
|
|
3430 3417 <span class="k">push</span> <span class="i">@FusedRingSets</span><span class="cm">,</span> \<span class="i">@FusedRingSet</span><span class="sc">;</span>
|
|
|
3431 3418 <span class="s">}</span>
|
|
|
3432 3419
|
|
|
3433 3420 <span class="i">@NonFusedRings</span> = <span class="i">$This</span><span class="i">->_GetRings</span><span class="s">(</span><span class="i">@</span>{<span class="i">$NonFusedCyclesRef</span>}<span class="s">)</span><span class="sc">;</span>
|
|
|
3434 3421
|
|
|
3435 3422 <span class="k">return</span> <span class="s">(</span>\<span class="i">@FusedRingSets</span><span class="cm">,</span> \<span class="i">@NonFusedRings</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3436 3423 <span class="s">}</span>
|
|
|
3437 3424
|
|
|
3438 3425 <span class="c"># Get rings as an array containing references to arrays with ring atoms...</span>
|
|
|
3439 3426 <span class="c">#</span>
|
|
|
3440 <a name="_GetRings-"></a>3427 <span class="k">sub </span><span class="m">_GetRings</span> <span class="s">{</span>
|
|
|
3441 3428 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">@CyclicPaths</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
3442 3429 <span class="k">my</span><span class="s">(</span><span class="i">$CyclicPath</span><span class="cm">,</span> <span class="i">@Rings</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3443 3430
|
|
|
3444 3431 <span class="i">@Rings</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3445 3432 <span class="k">if</span> <span class="s">(</span>!<span class="i">@CyclicPaths</span><span class="s">)</span> <span class="s">{</span>
|
|
|
3446 3433 <span class="k">return</span> <span class="i">@Rings</span><span class="sc">;</span>
|
|
|
3447 3434 <span class="s">}</span>
|
|
|
3448 3435 <span class="k">if</span> <span class="s">(</span>!<span class="i">@CyclicPaths</span><span class="s">)</span> <span class="s">{</span>
|
|
|
3449 3436 <span class="c"># Return an empty ring list...</span>
|
|
|
3450 3437 <span class="k">return</span> <span class="i">@Rings</span><span class="sc">;</span>
|
|
|
3451 3438 <span class="s">}</span>
|
|
|
3452 3439
|
|
|
3453 3440 <span class="k">for</span> <span class="i">$CyclicPath</span> <span class="s">(</span><span class="i">@CyclicPaths</span><span class="s">)</span> <span class="s">{</span>
|
|
|
3454 3441 <span class="k">my</span><span class="s">(</span><span class="i">@RingAtoms</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3455 3442 <span class="i">@RingAtoms</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3456 3443 <span class="k">push</span> <span class="i">@RingAtoms</span><span class="cm">,</span> <span class="i">$This</span><span class="i">->_GetRing</span><span class="s">(</span><span class="i">$CyclicPath</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3457 3444
|
|
|
3458 3445 <span class="k">push</span> <span class="i">@Rings</span><span class="cm">,</span> \<span class="i">@RingAtoms</span><span class="sc">;</span>
|
|
|
3459 3446 <span class="s">}</span>
|
|
|
3460 3447 <span class="k">return</span> <span class="i">@Rings</span><span class="sc">;</span>
|
|
|
3461 3448 <span class="s">}</span>
|
|
|
3462 3449
|
|
|
3463 3450 <span class="c"># Get aromatic rings as an array containing references to arrays with ring atoms...</span>
|
|
|
3464 3451 <span class="c">#</span>
|
|
|
3465 <a name="_GetAromaticRings-"></a>3452 <span class="k">sub </span><span class="m">_GetAromaticRings</span> <span class="s">{</span>
|
|
|
3466 3453 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">@CyclicPaths</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
3467 3454 <span class="k">my</span><span class="s">(</span><span class="i">$RingAtomsRef</span><span class="cm">,</span> <span class="i">@Rings</span><span class="cm">,</span> <span class="i">@AromaticRings</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3468 3455
|
|
|
3469 3456 <span class="i">@AromaticRings</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3470 3457 <span class="i">@Rings</span> = <span class="i">$This</span><span class="i">->_GetRings</span><span class="s">(</span><span class="i">@CyclicPaths</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3471 3458
|
|
|
3472 3459 <span class="k">if</span> <span class="s">(</span>!<span class="i">@Rings</span><span class="s">)</span> <span class="s">{</span>
|
|
|
3473 3460 <span class="k">return</span> <span class="i">@AromaticRings</span><span class="sc">;</span>
|
|
|
3474 3461 <span class="s">}</span>
|
|
|
3475 3462 <span class="j">RING:</span> <span class="k">for</span> <span class="i">$RingAtomsRef</span> <span class="s">(</span><span class="i">@Rings</span><span class="s">)</span> <span class="s">{</span>
|
|
|
3476 3463 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->IsRingAromatic</span><span class="s">(</span><span class="i">@</span>{<span class="i">$RingAtomsRef</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
3477 3464 <span class="k">next</span> <span class="j">RING</span><span class="sc">;</span>
|
|
|
3478 3465 <span class="s">}</span>
|
|
|
3479 3466 <span class="k">my</span><span class="s">(</span><span class="i">@RingAtoms</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3480 3467 <span class="i">@RingAtoms</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3481 3468 <span class="k">push</span> <span class="i">@RingAtoms</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$RingAtomsRef</span>}<span class="sc">;</span>
|
|
|
3482 3469
|
|
|
3483 3470 <span class="k">push</span> <span class="i">@AromaticRings</span><span class="cm">,</span> \<span class="i">@RingAtoms</span><span class="sc">;</span>
|
|
|
3484 3471 <span class="s">}</span>
|
|
|
3485 3472 <span class="k">return</span> <span class="i">@AromaticRings</span><span class="sc">;</span>
|
|
|
3486 3473 <span class="s">}</span>
|
|
|
3487 3474
|
|
|
3488 3475 <span class="c"># Map atom IDs in cyclic path to atoms and return a reference to an array containing ring atoms...</span>
|
|
|
3489 3476 <span class="c">#</span>
|
|
|
3490 3477 <span class="c"># Note:</span>
|
|
|
3491 3478 <span class="c"># . Start and end vertex is same for cyclic paths. So end atom is removed before</span>
|
|
|
3492 3479 <span class="c"># returning atoms array as ring atoms...</span>
|
|
|
3493 3480 <span class="c">#</span>
|
|
|
3494 <a name="_GetRing-"></a>3481 <span class="k">sub </span><span class="m">_GetRing</span> <span class="s">{</span>
|
|
|
3495 3482 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$CyclicPath</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
3496 3483 <span class="k">my</span><span class="s">(</span><span class="i">@RingAtoms</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3497 3484
|
|
|
3498 3485 <span class="i">@RingAtoms</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3499 3486 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$CyclicPath</span><span class="s">)</span> <span class="s">{</span>
|
|
|
3500 3487 <span class="c"># Return an empty atoms list...</span>
|
|
|
3501 3488 <span class="k">return</span> <span class="i">@RingAtoms</span><span class="sc">;</span>
|
|
|
3502 3489 <span class="s">}</span>
|
|
|
3503 3490
|
|
|
3504 3491 <span class="i">@RingAtoms</span> = <span class="i">$This</span><span class="i">->_GetPathAtoms</span><span class="s">(</span><span class="i">$CyclicPath</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3505 3492 <span class="k">if</span> <span class="s">(</span><span class="i">@RingAtoms</span><span class="s">)</span> <span class="s">{</span>
|
|
|
3506 3493 <span class="k">pop</span> <span class="i">@RingAtoms</span><span class="sc">;</span>
|
|
|
3507 3494 <span class="s">}</span>
|
|
|
3508 3495 <span class="k">return</span> <span class="i">@RingAtoms</span><span class="sc">;</span>
|
|
|
3509 3496 <span class="s">}</span>
|
|
|
3510 3497
|
|
|
3511 3498 <span class="c"># Map atom IDs to atoms and return a reference to an array containing these atoms...</span>
|
|
|
3512 3499 <span class="c">#</span>
|
|
|
3513 <a name="_GetPathAtoms-"></a>3500 <span class="k">sub </span><span class="m">_GetPathAtoms</span> <span class="s">{</span>
|
|
|
3514 3501 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Path</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
3515 3502 <span class="k">my</span><span class="s">(</span><span class="i">@PathAtoms</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3516 3503
|
|
|
3517 3504 <span class="i">@PathAtoms</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3518 3505 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$Path</span><span class="s">)</span> <span class="s">{</span>
|
|
|
3519 3506 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->_GetPathAtoms: No path atoms retrieved: Path must be defined..."</span><span class="sc">;</span>
|
|
|
3520 3507 <span class="k">return</span> <span class="i">@PathAtoms</span><span class="sc">;</span>
|
|
|
3521 3508 <span class="s">}</span>
|
|
|
3522 3509 <span class="k">my</span><span class="s">(</span><span class="i">@AtomIDs</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3523 3510
|
|
|
3524 3511 <span class="i">@AtomIDs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3525 3512 <span class="i">@AtomIDs</span> = <span class="i">$Path</span><span class="i">->GetVertices</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3526 3513
|
|
|
3527 3514 <span class="i">@PathAtoms</span> = <span class="i">$This</span><span class="i">->_GetAtomsFromAtomIDs</span><span class="s">(</span><span class="i">@AtomIDs</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3528 3515
|
|
|
3529 3516 <span class="k">return</span> <span class="i">@PathAtoms</span><span class="sc">;</span>
|
|
|
3530 3517 <span class="s">}</span>
|
|
|
3531 3518
|
|
|
3532 3519 <span class="c"># Get bonds for a path specified by atom IDs...</span>
|
|
|
3533 3520 <span class="c">#</span>
|
|
|
3534 <a name="_GetPathBonds-"></a>3521 <span class="k">sub </span><span class="m">_GetPathBonds</span> <span class="s">{</span>
|
|
|
3535 3522 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">@AtomIDs</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
3536 3523 <span class="k">my</span><span class="s">(</span><span class="i">$Index</span><span class="cm">,</span> <span class="i">$AtomID1</span><span class="cm">,</span> <span class="i">$AtomID2</span><span class="cm">,</span> <span class="i">@Bonds</span><span class="cm">,</span> <span class="i">@EdgesAtomIDs</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3537 3524
|
|
|
3538 3525 <span class="i">@Bonds</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> <span class="i">@EdgesAtomIDs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3539 3526
|
|
|
3540 3527 <span class="k">if</span> <span class="s">(</span>!<span class="i">@AtomIDs</span> || <span class="i">@AtomIDs</span> == <span class="n">1</span><span class="s">)</span> <span class="s">{</span>
|
|
|
3541 3528 <span class="k">return</span> <span class="i">@Bonds</span><span class="sc">;</span>
|
|
|
3542 3529 <span class="s">}</span>
|
|
|
3543 3530
|
|
|
3544 3531 <span class="c"># Setup edges...</span>
|
|
|
3545 3532 <span class="k">for</span> <span class="i">$Index</span> <span class="s">(</span><span class="n">0</span> .. <span class="s">(</span><span class="i">$#AtomIDs</span> - <span class="n">1</span><span class="s">)</span> <span class="s">)</span> <span class="s">{</span>
|
|
|
3546 3533 <span class="i">$AtomID1</span> = <span class="i">$AtomIDs</span>[<span class="i">$Index</span>]<span class="sc">;</span>
|
|
|
3547 3534 <span class="i">$AtomID2</span> = <span class="i">$AtomIDs</span>[<span class="i">$Index</span> + <span class="n">1</span>]<span class="sc">;</span>
|
|
|
3548 3535 <span class="k">push</span> <span class="i">@EdgesAtomIDs</span><span class="cm">,</span> <span class="s">(</span><span class="i">$AtomID1</span><span class="cm">,</span> <span class="i">$AtomID2</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3549 3536 <span class="s">}</span>
|
|
|
3550 3537 <span class="i">@Bonds</span> = <span class="i">$This</span><span class="i">->GetEdgesProperty</span><span class="s">(</span><span class="q">'Bond'</span><span class="cm">,</span> <span class="i">@EdgesAtomIDs</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3551 3538
|
|
|
3552 3539 <span class="k">return</span> <span class="i">@Bonds</span><span class="sc">;</span>
|
|
|
3553 3540 <span class="s">}</span>
|
|
|
3554 3541
|
|
|
3555 3542 <span class="c"># Map atom ID to an atom...</span>
|
|
|
3556 3543 <span class="c">#</span>
|
|
|
3557 <a name="_GetAtomFromAtomID-"></a>3544 <span class="k">sub </span><span class="m">_GetAtomFromAtomID</span> <span class="s">{</span>
|
|
|
3558 3545 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$AtomID</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
3559 3546
|
|
|
3560 3547 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetVertexProperty</span><span class="s">(</span><span class="q">'Atom'</span><span class="cm">,</span> <span class="i">$AtomID</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3561 3548 <span class="s">}</span>
|
|
|
3562 3549
|
|
|
3563 3550 <span class="c"># Map atom IDs to atoms and return an array containing these atoms...</span>
|
|
|
3564 3551 <span class="c">#</span>
|
|
|
3565 <a name="_GetAtomsFromAtomIDs-"></a>3552 <span class="k">sub </span><span class="m">_GetAtomsFromAtomIDs</span> <span class="s">{</span>
|
|
|
3566 3553 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">@AtomIDs</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
3567 3554
|
|
|
3568 3555 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetVerticesProperty</span><span class="s">(</span><span class="q">'Atom'</span><span class="cm">,</span> <span class="i">@AtomIDs</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3569 3556 <span class="s">}</span>
|
|
|
3570 3557
|
|
|
3571 3558 <span class="c"># Map atoms to atom IDs and return an array containing these atoms...</span>
|
|
|
3572 3559 <span class="c">#</span>
|
|
|
3573 <a name="_GetAtomsIDsFromAtoms-"></a>3560 <span class="k">sub </span><span class="m">_GetAtomsIDsFromAtoms</span> <span class="s">{</span>
|
|
|
3574 3561 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">@Atoms</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
3575 3562
|
|
|
3576 3563 <span class="k">return</span> <span class="k">map</span> <span class="s">{</span> <span class="i">$_</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span> <span class="s">}</span> <span class="i">@Atoms</span><span class="sc">;</span>
|
|
|
3577 3564 <span class="s">}</span>
|
|
|
3578 3565
|
|
|
3579 3566 <span class="c"># Get bonded atom pair atom IDs for specified list of atom IDs...</span>
|
|
|
3580 3567 <span class="c">#</span>
|
|
|
3581 <a name="_GetBondedAtomPairAtomIDsFromAtomIDs-"></a>3568 <span class="k">sub </span><span class="m">_GetBondedAtomPairAtomIDsFromAtomIDs</span> <span class="s">{</span>
|
|
|
3582 3569 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">@AtomIDs</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
3583 3570 <span class="k">my</span><span class="s">(</span><span class="i">$AtomIndex1</span><span class="cm">,</span> <span class="i">$AtomID1</span><span class="cm">,</span> <span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$AtomIndex2</span><span class="cm">,</span> <span class="i">$AtomID2</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="cm">,</span> <span class="i">@Atoms</span><span class="cm">,</span> <span class="i">@BondedAtomPairIDs</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3584 3571
|
|
|
3585 3572 <span class="i">@BondedAtomPairIDs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3586 3573 <span class="i">@Atoms</span> = <span class="i">$This</span><span class="i">->_GetAtomsFromAtomIDs</span><span class="s">(</span><span class="i">@AtomIDs</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3587 3574
|
|
|
3588 3575 <span class="k">for</span> <span class="i">$AtomIndex1</span> <span class="s">(</span> <span class="n">0</span> .. <span class="i">$#Atoms</span><span class="s">)</span> <span class="s">{</span>
|
|
|
3589 3576 <span class="i">$Atom1</span> = <span class="i">$Atoms</span>[<span class="i">$AtomIndex1</span>]<span class="sc">;</span>
|
|
|
3590 3577 <span class="i">$AtomID1</span> = <span class="i">$Atom1</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3591 3578
|
|
|
3592 3579 <span class="j">ATOMINDEX2:</span> <span class="k">for</span> <span class="i">$AtomIndex2</span> <span class="s">(</span> <span class="s">(</span><span class="i">$AtomIndex1</span> + <span class="n">1</span><span class="s">)</span> .. <span class="i">$#Atoms</span><span class="s">)</span> <span class="s">{</span>
|
|
|
3593 3580 <span class="i">$Atom2</span> = <span class="i">$Atoms</span>[<span class="i">$AtomIndex2</span>]<span class="sc">;</span>
|
|
|
3594 3581 <span class="k">if</span> <span class="s">(</span>!<span class="i">$Atom1</span><span class="i">->IsBondedToAtom</span><span class="s">(</span><span class="i">$Atom2</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
3595 3582 <span class="k">next</span> <span class="j">ATOMINDEX2</span><span class="sc">;</span>
|
|
|
3596 3583 <span class="s">}</span>
|
|
|
3597 3584 <span class="i">$AtomID2</span> = <span class="i">$Atom2</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3598 3585
|
|
|
3599 3586 <span class="k">push</span> <span class="i">@BondedAtomPairIDs</span><span class="cm">,</span> <span class="s">(</span><span class="i">$AtomID1</span><span class="cm">,</span> <span class="i">$AtomID2</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3600 3587 <span class="s">}</span>
|
|
|
3601 3588 <span class="s">}</span>
|
|
|
3602 3589
|
|
|
3603 3590 <span class="k">return</span> <span class="i">@BondedAtomPairIDs</span><span class="sc">;</span>
|
|
|
3604 3591 <span class="s">}</span>
|
|
|
3605 3592
|
|
|
3606 3593 <span class="c"># Get bonded atom pair atoms for specified list of atoms...</span>
|
|
|
3607 3594 <span class="c">#</span>
|
|
|
3608 <a name="_GetBondedAtomPairAtomsFromAtoms-"></a>3595 <span class="k">sub </span><span class="m">_GetBondedAtomPairAtomsFromAtoms</span> <span class="s">{</span>
|
|
|
3609 3596 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">@Atoms</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
3610 3597 <span class="k">my</span><span class="s">(</span><span class="i">$AtomIndex1</span><span class="cm">,</span> <span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$AtomIndex2</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="cm">,</span> <span class="i">@BondedAtomPairAtoms</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3611 3598
|
|
|
3612 3599 <span class="i">@BondedAtomPairAtoms</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3613 3600
|
|
|
3614 3601 <span class="k">for</span> <span class="i">$AtomIndex1</span> <span class="s">(</span> <span class="n">0</span> .. <span class="i">$#Atoms</span><span class="s">)</span> <span class="s">{</span>
|
|
|
3615 3602 <span class="i">$Atom1</span> = <span class="i">$Atoms</span>[<span class="i">$AtomIndex1</span>]<span class="sc">;</span>
|
|
|
3616 3603
|
|
|
3617 3604 <span class="j">ATOMINDEX2:</span> <span class="k">for</span> <span class="i">$AtomIndex2</span> <span class="s">(</span> <span class="s">(</span><span class="i">$AtomIndex1</span> + <span class="n">1</span><span class="s">)</span> .. <span class="i">$#Atoms</span><span class="s">)</span> <span class="s">{</span>
|
|
|
3618 3605 <span class="i">$Atom2</span> = <span class="i">$Atoms</span>[<span class="i">$AtomIndex2</span>]<span class="sc">;</span>
|
|
|
3619 3606 <span class="k">if</span> <span class="s">(</span><span class="i">$Atom1</span><span class="i">->IsBondedToAtom</span><span class="s">(</span><span class="i">$Atom2</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
3620 3607 <span class="k">next</span> <span class="j">ATOMINDEX2</span><span class="sc">;</span>
|
|
|
3621 3608 <span class="s">}</span>
|
|
|
3622 3609
|
|
|
3623 3610 <span class="k">push</span> <span class="i">@BondedAtomPairAtoms</span><span class="cm">,</span> <span class="s">(</span><span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3624 3611 <span class="s">}</span>
|
|
|
3625 3612 <span class="s">}</span>
|
|
|
3626 3613
|
|
|
3627 3614 <span class="k">return</span> <span class="i">@BondedAtomPairAtoms</span><span class="sc">;</span>
|
|
|
3628 3615 <span class="s">}</span>
|
|
|
3629 3616
|
|
|
3630 3617 <span class="c"># Is atom in a ring?</span>
|
|
|
3631 3618 <span class="c">#</span>
|
|
|
3632 <a name="_IsAtomInRing-"></a>3619 <span class="k">sub </span><span class="m">_IsAtomInRing</span> <span class="s">{</span>
|
|
|
3633 3620 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Atom</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
3634 3621
|
|
|
3635 3622 <span class="k">return</span> <span class="i">$This</span><span class="i">->IsCyclicVertex</span><span class="s">(</span><span class="i">$Atom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3636 3623 <span class="s">}</span>
|
|
|
3637 3624
|
|
|
3638 3625 <span class="c"># Is atom not in a ring?</span>
|
|
|
3639 3626 <span class="c">#</span>
|
|
|
3640 <a name="_IsAtomNotInRing-"></a>3627 <span class="k">sub </span><span class="m">_IsAtomNotInRing</span> <span class="s">{</span>
|
|
|
3641 3628 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Atom</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
3642 3629
|
|
|
3643 3630 <span class="k">return</span> <span class="i">$This</span><span class="i">->IsAcyclicVertex</span><span class="s">(</span><span class="i">$Atom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3644 3631 <span class="s">}</span>
|
|
|
3645 3632
|
|
|
3646 3633 <span class="c"># Is atom only in one ring?</span>
|
|
|
3647 3634 <span class="c">#</span>
|
|
|
3648 <a name="_IsAtomInOnlyOneRing-"></a>3635 <span class="k">sub </span><span class="m">_IsAtomInOnlyOneRing</span> <span class="s">{</span>
|
|
|
3649 3636 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Atom</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
3650 3637
|
|
|
3651 3638 <span class="k">return</span> <span class="i">$This</span><span class="i">->IsUnicyclicVertex</span><span class="s">(</span><span class="i">$Atom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3652 3639 <span class="s">}</span>
|
|
|
3653 3640
|
|
|
3654 3641 <span class="c"># Is atom in a ring of specified size?</span>
|
|
|
3655 3642 <span class="c">#</span>
|
|
|
3656 <a name="_IsAtomInRingOfSize-"></a>3643 <span class="k">sub </span><span class="m">_IsAtomInRingOfSize</span> <span class="s">{</span>
|
|
|
3657 3644 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Atom</span><span class="cm">,</span> <span class="i">$RingSize</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
3658 3645
|
|
|
3659 3646 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetNumOfVertexCyclesWithSize</span><span class="s">(</span><span class="i">$Atom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="cm">,</span> <span class="i">$RingSize</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
3660 3647 <span class="s">}</span>
|
|
|
3661 3648
|
|
|
3662 3649 <span class="c"># Get size of smallest ring containing specified atom...</span>
|
|
|
3663 3650 <span class="c">#</span>
|
|
|
3664 <a name="_GetSizeOfSmallestAtomRing-"></a>3651 <span class="k">sub </span><span class="m">_GetSizeOfSmallestAtomRing</span> <span class="s">{</span>
|
|
|
3665 3652 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Atom</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
3666 3653
|
|
|
3667 3654 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetSizeOfSmallestVertexCycle</span><span class="s">(</span><span class="i">$Atom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3668 3655 <span class="s">}</span>
|
|
|
3669 3656
|
|
|
3670 3657 <span class="c"># Get size of largest ring containing specified atom...</span>
|
|
|
3671 3658 <span class="c">#</span>
|
|
|
3672 <a name="_GetSizeOfLargestAtomRing-"></a>3659 <span class="k">sub </span><span class="m">_GetSizeOfLargestAtomRing</span> <span class="s">{</span>
|
|
|
3673 3660 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Atom</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
3674 3661
|
|
|
3675 3662 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetSizeOfLargestVertexCycle</span><span class="s">(</span><span class="i">$Atom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3676 3663 <span class="s">}</span>
|
|
|
3677 3664
|
|
|
3678 3665 <span class="c"># Get number of rings containing specified atom...</span>
|
|
|
3679 3666 <span class="c">#</span>
|
|
|
3680 <a name="_GetNumOfAtomRings-"></a>3667 <span class="k">sub </span><span class="m">_GetNumOfAtomRings</span> <span class="s">{</span>
|
|
|
3681 3668 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Atom</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
3682 3669
|
|
|
3683 3670 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetNumOfVertexCycles</span><span class="s">(</span><span class="i">$Atom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3684 3671 <span class="s">}</span>
|
|
|
3685 3672
|
|
|
3686 3673 <span class="c"># Get number of rings with odd size containing specified atom...</span>
|
|
|
3687 3674 <span class="c">#</span>
|
|
|
3688 <a name="_GetNumOfAtomRingsWithOddSize-"></a>3675 <span class="k">sub </span><span class="m">_GetNumOfAtomRingsWithOddSize</span> <span class="s">{</span>
|
|
|
3689 3676 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Atom</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
3690 3677
|
|
|
3691 3678 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetNumOfVertexCyclesWithOddSize</span><span class="s">(</span><span class="i">$Atom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3692 3679 <span class="s">}</span>
|
|
|
3693 3680
|
|
|
3694 3681 <span class="c"># Get number of rings with even size containing specified atom...</span>
|
|
|
3695 3682 <span class="c">#</span>
|
|
|
3696 <a name="_GetNumOfAtomRingsWithEvenSize-"></a>3683 <span class="k">sub </span><span class="m">_GetNumOfAtomRingsWithEvenSize</span> <span class="s">{</span>
|
|
|
3697 3684 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Atom</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
3698 3685
|
|
|
3699 3686 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetNumOfVertexCyclesWithEvenSize</span><span class="s">(</span><span class="i">$Atom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3700 3687 <span class="s">}</span>
|
|
|
3701 3688
|
|
|
3702 3689 <span class="c"># Get number of rings with specified size containing specified atom...</span>
|
|
|
3703 3690 <span class="c">#</span>
|
|
|
3704 <a name="_GetNumOfAtomRingsWithSize-"></a>3691 <span class="k">sub </span><span class="m">_GetNumOfAtomRingsWithSize</span> <span class="s">{</span>
|
|
|
3705 3692 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Atom</span><span class="cm">,</span> <span class="i">$RingSize</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
3706 3693
|
|
|
3707 3694 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetNumOfVertexCyclesWithSize</span><span class="s">(</span><span class="i">$Atom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="cm">,</span> <span class="i">$RingSize</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3708 3695 <span class="s">}</span>
|
|
|
3709 3696
|
|
|
3710 3697 <span class="c"># Get number of rings with size less than specified containing specified atom...</span>
|
|
|
3711 3698 <span class="c">#</span>
|
|
|
3712 <a name="_GetNumOfAtomRingsWithSizeLessThan-"></a>3699 <span class="k">sub </span><span class="m">_GetNumOfAtomRingsWithSizeLessThan</span> <span class="s">{</span>
|
|
|
3713 3700 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Atom</span><span class="cm">,</span> <span class="i">$RingSize</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
3714 3701
|
|
|
3715 3702 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetNumOfVertexCyclesWithSizeLessThan</span><span class="s">(</span><span class="i">$Atom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="cm">,</span> <span class="i">$RingSize</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3716 3703 <span class="s">}</span>
|
|
|
3717 3704
|
|
|
3718 3705 <span class="c"># Get number of rings with size greater than specified containing specified atom...</span>
|
|
|
3719 3706 <span class="c">#</span>
|
|
|
3720 <a name="_GetNumOfAtomRingsWithSizeGreaterThan-"></a>3707 <span class="k">sub </span><span class="m">_GetNumOfAtomRingsWithSizeGreaterThan</span> <span class="s">{</span>
|
|
|
3721 3708 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Atom</span><span class="cm">,</span> <span class="i">$RingSize</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
3722 3709
|
|
|
3723 3710 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetNumOfVertexCyclesWithSizeGreaterThan</span><span class="s">(</span><span class="i">$Atom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="cm">,</span> <span class="i">$RingSize</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3724 3711 <span class="s">}</span>
|
|
|
3725 3712
|
|
|
3726 3713 <span class="c"># Get smallest ring as an array containing ring atoms...</span>
|
|
|
3727 3714 <span class="c">#</span>
|
|
|
3728 <a name="_GetSmallestAtomRing-"></a>3715 <span class="k">sub </span><span class="m">_GetSmallestAtomRing</span> <span class="s">{</span>
|
|
|
3729 3716 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Atom</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
3730 3717
|
|
|
3731 3718 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetRing</span><span class="s">(</span><span class="i">$This</span><span class="i">->GetSmallestVertexCycle</span><span class="s">(</span><span class="i">$Atom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3732 3719 <span class="s">}</span>
|
|
|
3733 3720
|
|
|
3734 3721 <span class="c"># Get odd size rings an array of references to arrays containing ring atoms...</span>
|
|
|
3735 3722 <span class="c">#</span>
|
|
|
3736 <a name="_GetLargestAtomRing-"></a>3723 <span class="k">sub </span><span class="m">_GetLargestAtomRing</span> <span class="s">{</span>
|
|
|
3737 3724 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Atom</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
3738 3725
|
|
|
3739 3726 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetRing</span><span class="s">(</span><span class="i">$This</span><span class="i">->GetLargestVertexCycle</span><span class="s">(</span><span class="i">$Atom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3740 3727 <span class="s">}</span>
|
|
|
3741 3728
|
|
|
3742 3729 <span class="c"># Get all rings an array of references to arrays containing ring atoms...</span>
|
|
|
3743 3730 <span class="c">#</span>
|
|
|
3744 <a name="_GetAtomRings-"></a>3731 <span class="k">sub </span><span class="m">_GetAtomRings</span> <span class="s">{</span>
|
|
|
3745 3732 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Atom</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
3746 3733
|
|
|
3747 3734 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetRings</span><span class="s">(</span><span class="i">$This</span><span class="i">->GetVertexCycles</span><span class="s">(</span><span class="i">$Atom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3748 3735 <span class="s">}</span>
|
|
|
3749 3736
|
|
|
3750 3737 <span class="c"># Get odd size rings an array of references to arrays containing ring atoms...</span>
|
|
|
3751 3738 <span class="c">#</span>
|
|
|
3752 <a name="_GetAtomRingsWithOddSize-"></a>3739 <span class="k">sub </span><span class="m">_GetAtomRingsWithOddSize</span> <span class="s">{</span>
|
|
|
3753 3740 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Atom</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
3754 3741
|
|
|
3755 3742 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetRings</span><span class="s">(</span><span class="i">$This</span><span class="i">->GetVertexCyclesWithOddSize</span><span class="s">(</span><span class="i">$Atom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3756 3743 <span class="s">}</span>
|
|
|
3757 3744
|
|
|
3758 3745 <span class="c"># Get even size rings an array of references to arrays containing ring atoms...</span>
|
|
|
3759 3746 <span class="c">#</span>
|
|
|
3760 <a name="_GetAtomRingsWithEvenSize-"></a>3747 <span class="k">sub </span><span class="m">_GetAtomRingsWithEvenSize</span> <span class="s">{</span>
|
|
|
3761 3748 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Atom</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
3762 3749
|
|
|
3763 3750 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetRings</span><span class="s">(</span><span class="i">$This</span><span class="i">->GetVertexCyclesWithEvenSize</span><span class="s">(</span><span class="i">$Atom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3764 3751 <span class="s">}</span>
|
|
|
3765 3752
|
|
|
3766 3753 <span class="c"># Get rings with specified size an array of references to arrays containing ring atoms...</span>
|
|
|
3767 3754 <span class="c">#</span>
|
|
|
3768 <a name="_GetAtomRingsWithSize-"></a>3755 <span class="k">sub </span><span class="m">_GetAtomRingsWithSize</span> <span class="s">{</span>
|
|
|
3769 3756 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Atom</span><span class="cm">,</span> <span class="i">$RingSize</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
3770 3757
|
|
|
3771 3758 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetRings</span><span class="s">(</span><span class="i">$This</span><span class="i">->GetVertexCyclesWithSize</span><span class="s">(</span><span class="i">$Atom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="cm">,</span> <span class="i">$RingSize</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3772 3759 <span class="s">}</span>
|
|
|
3773 3760
|
|
|
3774 3761 <span class="c"># Get rings with size less than specfied size as an array of references to arrays containing ring atoms...</span>
|
|
|
3775 3762 <span class="c">#</span>
|
|
|
3776 <a name="_GetAtomRingsWithSizeLessThan-"></a>3763 <span class="k">sub </span><span class="m">_GetAtomRingsWithSizeLessThan</span> <span class="s">{</span>
|
|
|
3777 3764 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Atom</span><span class="cm">,</span> <span class="i">$RingSize</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
3778 3765
|
|
|
3779 3766 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetRings</span><span class="s">(</span><span class="i">$This</span><span class="i">->GetVertexCyclesWithSizeLessThan</span><span class="s">(</span><span class="i">$Atom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="cm">,</span> <span class="i">$RingSize</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3780 3767 <span class="s">}</span>
|
|
|
3781 3768
|
|
|
3782 3769 <span class="c"># Get rings with size less than specfied size as an array of references to arrays containing ring atoms...</span>
|
|
|
3783 3770 <span class="c">#</span>
|
|
|
3784 <a name="_GetAtomRingsWithSizeGreaterThan-"></a>3771 <span class="k">sub </span><span class="m">_GetAtomRingsWithSizeGreaterThan</span> <span class="s">{</span>
|
|
|
3785 3772 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Atom</span><span class="cm">,</span> <span class="i">$RingSize</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
3786 3773
|
|
|
3787 3774 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetRings</span><span class="s">(</span><span class="i">$This</span><span class="i">->GetVertexCyclesWithSizeGreaterThan</span><span class="s">(</span><span class="i">$Atom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="cm">,</span> <span class="i">$RingSize</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3788 3775 <span class="s">}</span>
|
|
|
3789 3776
|
|
|
3790 3777 <span class="c"># Is bond in a ring?</span>
|
|
|
3791 3778 <span class="c">#</span>
|
|
|
3792 <a name="_IsBondInRing-"></a>3779 <span class="k">sub </span><span class="m">_IsBondInRing</span> <span class="s">{</span>
|
|
|
3793 3780 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Bond</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
3794 3781 <span class="k">my</span><span class="s">(</span><span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3795 3782
|
|
|
3796 3783 <span class="s">(</span><span class="i">$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>
|
|
|
3797 3784
|
|
|
3798 3785 <span class="k">return</span> <span class="i">$This</span><span class="i">->IsCyclicEdge</span><span class="s">(</span><span class="i">$Atom1</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3799 3786 <span class="s">}</span>
|
|
|
3800 3787
|
|
|
3801 3788 <span class="c"># Is bond not in a ring?</span>
|
|
|
3802 3789 <span class="c">#</span>
|
|
|
3803 <a name="_IsBondNotInRing-"></a>3790 <span class="k">sub </span><span class="m">_IsBondNotInRing</span> <span class="s">{</span>
|
|
|
3804 3791 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Bond</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
3805 3792 <span class="k">my</span><span class="s">(</span><span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3806 3793
|
|
|
3807 3794 <span class="s">(</span><span class="i">$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>
|
|
|
3808 3795
|
|
|
3809 3796 <span class="k">return</span> <span class="i">$This</span><span class="i">->IsAcyclicEdge</span><span class="s">(</span><span class="i">$Atom1</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3810 3797 <span class="s">}</span>
|
|
|
3811 3798
|
|
|
3812 3799 <span class="c"># Is bond only in one ring?</span>
|
|
|
3813 3800 <span class="c">#</span>
|
|
|
3814 <a name="_IsBondInOnlyOneRing-"></a>3801 <span class="k">sub </span><span class="m">_IsBondInOnlyOneRing</span> <span class="s">{</span>
|
|
|
3815 3802 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Bond</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
3816 3803 <span class="k">my</span><span class="s">(</span><span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3817 3804
|
|
|
3818 3805 <span class="s">(</span><span class="i">$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>
|
|
|
3819 3806
|
|
|
3820 3807 <span class="k">return</span> <span class="i">$This</span><span class="i">->IsUnicyclicEdge</span><span class="s">(</span><span class="i">$Atom1</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3821 3808 <span class="s">}</span>
|
|
|
3822 3809
|
|
|
3823 3810 <span class="c"># Is bond in a ring of specified size?</span>
|
|
|
3824 3811 <span class="c">#</span>
|
|
|
3825 <a name="_IsBondInRingOfSize-"></a>3812 <span class="k">sub </span><span class="m">_IsBondInRingOfSize</span> <span class="s">{</span>
|
|
|
3826 3813 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Bond</span><span class="cm">,</span> <span class="i">$RingSize</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
3827 3814 <span class="k">my</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>
|
|
|
3828 3815
|
|
|
3829 3816 <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">$Bond</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3830 3817
|
|
|
3831 3818 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetNumOfEdgeCyclesWithSize</span><span class="s">(</span><span class="i">$Atom1</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="cm">,</span> <span class="i">$RingSize</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
3832 3819 <span class="s">}</span>
|
|
|
3833 3820
|
|
|
3834 3821 <span class="c"># Get size of smallest ring containing specified bond...</span>
|
|
|
3835 3822 <span class="c">#</span>
|
|
|
3836 <a name="_GetSizeOfSmallestBondRing-"></a>3823 <span class="k">sub </span><span class="m">_GetSizeOfSmallestBondRing</span> <span class="s">{</span>
|
|
|
3837 3824 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Bond</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
3838 3825 <span class="k">my</span><span class="s">(</span><span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3839 3826
|
|
|
3840 3827 <span class="s">(</span><span class="i">$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>
|
|
|
3841 3828
|
|
|
3842 3829 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetSizeOfSmallestEdgeCycle</span><span class="s">(</span><span class="i">$Atom1</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3843 3830 <span class="s">}</span>
|
|
|
3844 3831
|
|
|
3845 3832 <span class="c"># Get size of largest ring containing specified bond...</span>
|
|
|
3846 3833 <span class="c">#</span>
|
|
|
3847 <a name="_GetSizeOfLargestBondRing-"></a>3834 <span class="k">sub </span><span class="m">_GetSizeOfLargestBondRing</span> <span class="s">{</span>
|
|
|
3848 3835 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Bond</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
3849 3836 <span class="k">my</span><span class="s">(</span><span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3850 3837
|
|
|
3851 3838 <span class="s">(</span><span class="i">$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>
|
|
|
3852 3839
|
|
|
3853 3840 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetSizeOfLargestEdgeCycle</span><span class="s">(</span><span class="i">$Atom1</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3854 3841 <span class="s">}</span>
|
|
|
3855 3842
|
|
|
3856 3843 <span class="c"># Get number of rings containing specified bond...</span>
|
|
|
3857 3844 <span class="c">#</span>
|
|
|
3858 <a name="_GetNumOfBondRings-"></a>3845 <span class="k">sub </span><span class="m">_GetNumOfBondRings</span> <span class="s">{</span>
|
|
|
3859 3846 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Bond</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
3860 3847 <span class="k">my</span><span class="s">(</span><span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3861 3848
|
|
|
3862 3849 <span class="s">(</span><span class="i">$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>
|
|
|
3863 3850
|
|
|
3864 3851 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetNumOfEdgeCycles</span><span class="s">(</span><span class="i">$Atom1</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3865 3852 <span class="s">}</span>
|
|
|
3866 3853
|
|
|
3867 3854 <span class="c"># Get number of rings with odd size containing specified bond...</span>
|
|
|
3868 3855 <span class="c">#</span>
|
|
|
3869 <a name="_GetNumOfBondRingsWithOddSize-"></a>3856 <span class="k">sub </span><span class="m">_GetNumOfBondRingsWithOddSize</span> <span class="s">{</span>
|
|
|
3870 3857 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Bond</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
3871 3858 <span class="k">my</span><span class="s">(</span><span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3872 3859
|
|
|
3873 3860 <span class="s">(</span><span class="i">$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>
|
|
|
3874 3861
|
|
|
3875 3862 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetNumOfEdgeCyclesWithOddSize</span><span class="s">(</span><span class="i">$Atom1</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3876 3863 <span class="s">}</span>
|
|
|
3877 3864
|
|
|
3878 3865 <span class="c"># Get number of rings with even size containing specified bond...</span>
|
|
|
3879 3866 <span class="c">#</span>
|
|
|
3880 <a name="_GetNumOfBondRingsWithEvenSize-"></a>3867 <span class="k">sub </span><span class="m">_GetNumOfBondRingsWithEvenSize</span> <span class="s">{</span>
|
|
|
3881 3868 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Bond</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
3882 3869 <span class="k">my</span><span class="s">(</span><span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3883 3870
|
|
|
3884 3871 <span class="s">(</span><span class="i">$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>
|
|
|
3885 3872
|
|
|
3886 3873 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetNumOfEdgeCyclesWithEvenSize</span><span class="s">(</span><span class="i">$Atom1</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3887 3874 <span class="s">}</span>
|
|
|
3888 3875
|
|
|
3889 3876 <span class="c"># Get number of rings with specified size containing specified bond...</span>
|
|
|
3890 3877 <span class="c">#</span>
|
|
|
3891 <a name="_GetNumOfBondRingsWithSize-"></a>3878 <span class="k">sub </span><span class="m">_GetNumOfBondRingsWithSize</span> <span class="s">{</span>
|
|
|
3892 3879 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Bond</span><span class="cm">,</span> <span class="i">$RingSize</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
3893 3880 <span class="k">my</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>
|
|
|
3894 3881
|
|
|
3895 3882 <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">$Bond</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3896 3883
|
|
|
3897 3884 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetNumOfEdgeCyclesWithSize</span><span class="s">(</span><span class="i">$Atom1</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="cm">,</span> <span class="i">$RingSize</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3898 3885 <span class="s">}</span>
|
|
|
3899 3886
|
|
|
3900 3887 <span class="c"># Get number of rings with size less than specified containing specified bond...</span>
|
|
|
3901 3888 <span class="c">#</span>
|
|
|
3902 <a name="_GetNumOfBondRingsWithSizeLessThan-"></a>3889 <span class="k">sub </span><span class="m">_GetNumOfBondRingsWithSizeLessThan</span> <span class="s">{</span>
|
|
|
3903 3890 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Bond</span><span class="cm">,</span> <span class="i">$RingSize</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
3904 3891 <span class="k">my</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>
|
|
|
3905 3892
|
|
|
3906 3893 <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">$Bond</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3907 3894
|
|
|
3908 3895 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetNumOfEdgeCyclesWithSizeLessThan</span><span class="s">(</span><span class="i">$Atom1</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="cm">,</span> <span class="i">$RingSize</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3909 3896 <span class="s">}</span>
|
|
|
3910 3897
|
|
|
3911 3898 <span class="c"># Get number of rings with size greater than specified containing specified bond...</span>
|
|
|
3912 3899 <span class="c">#</span>
|
|
|
3913 <a name="_GetNumOfBondRingsWithSizeGreaterThan-"></a>3900 <span class="k">sub </span><span class="m">_GetNumOfBondRingsWithSizeGreaterThan</span> <span class="s">{</span>
|
|
|
3914 3901 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Bond</span><span class="cm">,</span> <span class="i">$RingSize</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
3915 3902 <span class="k">my</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>
|
|
|
3916 3903
|
|
|
3917 3904 <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">$Bond</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3918 3905
|
|
|
3919 3906 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetNumOfEdgeCyclesWithSizeGreaterThan</span><span class="s">(</span><span class="i">$Atom1</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="cm">,</span> <span class="i">$RingSize</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3920 3907 <span class="s">}</span>
|
|
|
3921 3908
|
|
|
3922 3909 <span class="c"># Get smallest ring as an array containing ring atoms...</span>
|
|
|
3923 3910 <span class="c">#</span>
|
|
|
3924 <a name="_GetSmallestBondRing-"></a>3911 <span class="k">sub </span><span class="m">_GetSmallestBondRing</span> <span class="s">{</span>
|
|
|
3925 3912 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Bond</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
3926 3913 <span class="k">my</span><span class="s">(</span><span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3927 3914
|
|
|
3928 3915 <span class="s">(</span><span class="i">$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>
|
|
|
3929 3916
|
|
|
3930 3917 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetRing</span><span class="s">(</span><span class="i">$This</span><span class="i">->GetSmallestEdgeCycle</span><span class="s">(</span><span class="i">$Atom1</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3931 3918 <span class="s">}</span>
|
|
|
3932 3919
|
|
|
3933 3920 <span class="c"># Get odd size rings an array of references to arrays containing ring atoms...</span>
|
|
|
3934 3921 <span class="c">#</span>
|
|
|
3935 <a name="_GetLargestBondRing-"></a>3922 <span class="k">sub </span><span class="m">_GetLargestBondRing</span> <span class="s">{</span>
|
|
|
3936 3923 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Bond</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
3937 3924 <span class="k">my</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>
|
|
|
3938 3925
|
|
|
3939 3926 <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">$Bond</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3940 3927
|
|
|
3941 3928 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetRing</span><span class="s">(</span><span class="i">$This</span><span class="i">->GetLargestEdgeCycle</span><span class="s">(</span><span class="i">$Atom1</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3942 3929 <span class="s">}</span>
|
|
|
3943 3930
|
|
|
3944 3931 <span class="c"># Get all rings an array of references to arrays containing ring atoms...</span>
|
|
|
3945 3932 <span class="c">#</span>
|
|
|
3946 <a name="_GetBondRings-"></a>3933 <span class="k">sub </span><span class="m">_GetBondRings</span> <span class="s">{</span>
|
|
|
3947 3934 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Bond</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
3948 3935 <span class="k">my</span><span class="s">(</span><span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3949 3936
|
|
|
3950 3937 <span class="s">(</span><span class="i">$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>
|
|
|
3951 3938
|
|
|
3952 3939 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetRings</span><span class="s">(</span><span class="i">$This</span><span class="i">->GetEdgeCycles</span><span class="s">(</span><span class="i">$Atom1</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3953 3940 <span class="s">}</span>
|
|
|
3954 3941
|
|
|
3955 3942 <span class="c"># Get odd size rings an array of references to arrays containing ring atoms...</span>
|
|
|
3956 3943 <span class="c">#</span>
|
|
|
3957 <a name="_GetBondRingsWithOddSize-"></a>3944 <span class="k">sub </span><span class="m">_GetBondRingsWithOddSize</span> <span class="s">{</span>
|
|
|
3958 3945 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Bond</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
3959 3946 <span class="k">my</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>
|
|
|
3960 3947
|
|
|
3961 3948 <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">$Bond</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3962 3949
|
|
|
3963 3950 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetRings</span><span class="s">(</span><span class="i">$This</span><span class="i">->GetEdgeCyclesWithOddSize</span><span class="s">(</span><span class="i">$Atom1</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3964 3951 <span class="s">}</span>
|
|
|
3965 3952
|
|
|
3966 3953 <span class="c"># Get even size rings an array of references to arrays containing ring atoms...</span>
|
|
|
3967 3954 <span class="c">#</span>
|
|
|
3968 <a name="_GetBondRingsWithEvenSize-"></a>3955 <span class="k">sub </span><span class="m">_GetBondRingsWithEvenSize</span> <span class="s">{</span>
|
|
|
3969 3956 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Bond</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
3970 3957 <span class="k">my</span><span class="s">(</span><span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3971 3958
|
|
|
3972 3959 <span class="s">(</span><span class="i">$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>
|
|
|
3973 3960
|
|
|
3974 3961 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetRings</span><span class="s">(</span><span class="i">$This</span><span class="i">->GetEdgeCyclesWithEvenSize</span><span class="s">(</span><span class="i">$Atom1</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3975 3962 <span class="s">}</span>
|
|
|
3976 3963
|
|
|
3977 3964 <span class="c"># Get rings with specified size an array of references to arrays containing ring atoms...</span>
|
|
|
3978 3965 <span class="c">#</span>
|
|
|
3979 <a name="_GetBondRingsWithSize-"></a>3966 <span class="k">sub </span><span class="m">_GetBondRingsWithSize</span> <span class="s">{</span>
|
|
|
3980 3967 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Bond</span><span class="cm">,</span> <span class="i">$RingSize</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
3981 3968 <span class="k">my</span><span class="s">(</span><span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3982 3969
|
|
|
3983 3970 <span class="s">(</span><span class="i">$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>
|
|
|
3984 3971
|
|
|
3985 3972 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetRings</span><span class="s">(</span><span class="i">$This</span><span class="i">->GetEdgeCyclesWithSize</span><span class="s">(</span><span class="i">$Atom1</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="cm">,</span> <span class="i">$RingSize</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3986 3973 <span class="s">}</span>
|
|
|
3987 3974
|
|
|
3988 3975 <span class="c"># Get rings with size less than specfied size as an array of references to arrays containing ring atoms...</span>
|
|
|
3989 3976 <span class="c">#</span>
|
|
|
3990 <a name="_GetBondRingsWithSizeLessThan-"></a>3977 <span class="k">sub </span><span class="m">_GetBondRingsWithSizeLessThan</span> <span class="s">{</span>
|
|
|
3991 3978 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Bond</span><span class="cm">,</span> <span class="i">$RingSize</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
3992 3979 <span class="k">my</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>
|
|
|
3993 3980
|
|
|
3994 3981 <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">$Bond</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3995 3982
|
|
|
3996 3983 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetRings</span><span class="s">(</span><span class="i">$This</span><span class="i">->GetEdgeCyclesWithSizeLessThan</span><span class="s">(</span><span class="i">$Atom1</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="cm">,</span> <span class="i">$RingSize</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span>
|
|
|
3997 3984 <span class="s">}</span>
|
|
|
3998 3985
|
|
|
3999 3986 <span class="c"># Get rings with size less than specfied size as an array of references to arrays containing ring atoms...</span>
|
|
|
4000 3987 <span class="c">#</span>
|
|
|
4001 <a name="_GetBondRingsWithSizeGreaterThan-"></a>3988 <span class="k">sub </span><span class="m">_GetBondRingsWithSizeGreaterThan</span> <span class="s">{</span>
|
|
|
4002 3989 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Bond</span><span class="cm">,</span> <span class="i">$RingSize</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
4003 3990 <span class="k">my</span><span class="s">(</span><span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4004 3991
|
|
|
4005 3992 <span class="s">(</span><span class="i">$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>
|
|
|
4006 3993
|
|
|
4007 3994 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetRings</span><span class="s">(</span><span class="i">$This</span><span class="i">->GetEdgeCyclesWithSizeGreaterThan</span><span class="s">(</span><span class="i">$Atom1</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="cm">,</span> <span class="i">$RingSize</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4008 3995 <span class="s">}</span>
|
|
|
4009 3996
|
|
|
4010 3997
|
|
|
4011 3998 <span class="c"># Get atom paths starting from a specified atom as a reference to an array containing references</span>
|
|
|
4012 3999 <span class="c"># to arrays with path atoms.</span>
|
|
|
4013 4000 <span class="c">#</span>
|
|
|
4014 4001 <span class="c"># Path atoms atoms correspond to to all possible paths for specified atom in molecule with length</span>
|
|
|
4015 4002 <span class="c"># upto a specified length and sharing of bonds in paths traversed. By default, rings are</span>
|
|
|
4016 4003 <span class="c"># included in paths. A path containing a ring is terminated at an atom completing the ring.</span>
|
|
|
4017 4004 <span class="c">#</span>
|
|
|
4018 4005 <span class="c"># Note:</span>
|
|
|
4019 4006 <span class="c"># . For molecule without any rings, this method returns the same set of atom paths</span>
|
|
|
4020 4007 <span class="c"># as GetAtomPathsStartingAtWithLengthUpto method.</span>
|
|
|
4021 4008 <span class="c">#</span>
|
|
|
4022 <a name="GetAllAtomPathsStartingAtWithLengthUpto-"></a>4009 <span class="k">sub </span><span class="m">GetAllAtomPathsStartingAtWithLengthUpto</span> <span class="s">{</span>
|
|
|
4023 4010 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$StartAtom</span><span class="cm">,</span> <span class="i">$Length</span><span class="cm">,</span> <span class="i">$AllowCycles</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
4024 4011
|
|
|
4025 4012 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetAtomPathsStartingAt</span><span class="s">(</span><span class="q">'AllAtomPathsWithLengthUpto'</span><span class="cm">,</span> <span class="i">$StartAtom</span><span class="cm">,</span> <span class="i">$Length</span><span class="cm">,</span> <span class="i">$AllowCycles</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4026 4013 <span class="s">}</span>
|
|
|
4027 4014
|
|
|
4028 4015 <span class="c"># Get atom paths starting from a specified atom as a reference to an array containing references</span>
|
|
|
4029 4016 <span class="c"># to arrays with path atoms.</span>
|
|
|
4030 4017 <span class="c">#</span>
|
|
|
4031 4018 <span class="c"># Path atoms atoms correspond to to all possible paths for specified atom in molecule with</span>
|
|
|
4032 4019 <span class="c"># specified length and sharing of bonds in paths traversed. By default, rings are</span>
|
|
|
4033 4020 <span class="c"># included in paths. A path containing a ring is terminated at an atom completing the ring.</span>
|
|
|
4034 4021 <span class="c">#</span>
|
|
|
4035 4022 <span class="c"># Note:</span>
|
|
|
4036 4023 <span class="c"># . For molecule without any rings, this method returns the same set of atom paths</span>
|
|
|
4037 4024 <span class="c"># as GetAtomPathsStartingAtWithLengthUpto method.</span>
|
|
|
4038 4025 <span class="c">#</span>
|
|
|
4039 <a name="GetAllAtomPathsStartingAtWithLength-"></a>4026 <span class="k">sub </span><span class="m">GetAllAtomPathsStartingAtWithLength</span> <span class="s">{</span>
|
|
|
4040 4027 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$StartAtom</span><span class="cm">,</span> <span class="i">$Length</span><span class="cm">,</span> <span class="i">$AllowCycles</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
4041 4028
|
|
|
4042 4029 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetAtomPathsStartingAt</span><span class="s">(</span><span class="q">'AllAtomPathsWithLength'</span><span class="cm">,</span> <span class="i">$StartAtom</span><span class="cm">,</span> <span class="i">$Length</span><span class="cm">,</span> <span class="i">$AllowCycles</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4043 4030 <span class="s">}</span>
|
|
|
4044 4031
|
|
|
4045 4032 <span class="c"># Get atom paths starting from a specified atom as a reference to an array containing references</span>
|
|
|
4046 4033 <span class="c"># to arrays with path atoms.</span>
|
|
|
4047 4034 <span class="c">#</span>
|
|
|
4048 4035 <span class="c"># Path atoms atoms correspond to to all possible paths for specified atom in molecule with all</span>
|
|
|
4049 4036 <span class="c"># possible lengths and sharing of bonds in paths traversed. By default, rings are</span>
|
|
|
4050 4037 <span class="c"># included in paths. A path containing a ring is terminated at an atom completing the ring.</span>
|
|
|
4051 4038 <span class="c">#</span>
|
|
|
4052 4039 <span class="c"># Note:</span>
|
|
|
4053 4040 <span class="c"># . For molecule without any rings, this method returns the same set of atom paths</span>
|
|
|
4054 4041 <span class="c"># as GetAtomPathsStartingAt method.</span>
|
|
|
4055 4042 <span class="c">#</span>
|
|
|
4056 <a name="GetAllAtomPathsStartingAt-"></a>4043 <span class="k">sub </span><span class="m">GetAllAtomPathsStartingAt</span> <span class="s">{</span>
|
|
|
4057 4044 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$StartAtom</span><span class="cm">,</span> <span class="i">$AllowCycles</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
4058 4045
|
|
|
4059 4046 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetAtomPathsStartingAt</span><span class="s">(</span><span class="q">'AllAtomPathsWithAllLengths'</span><span class="cm">,</span> <span class="i">$StartAtom</span><span class="cm">,</span> <span class="k">undef</span><span class="cm">,</span> <span class="i">$AllowCycles</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4060 4047 <span class="s">}</span>
|
|
|
4061 4048
|
|
|
4062 4049 <span class="c"># Get atom paths starting from a specified atom as a reference to an array containing references</span>
|
|
|
4063 4050 <span class="c"># to arrays with path atoms.</span>
|
|
|
4064 4051 <span class="c">#</span>
|
|
|
4065 4052 <span class="c"># Path atoms atoms correspond to to all possible paths for specified atom in molecule with length</span>
|
|
|
4066 4053 <span class="c"># upto a specified length and no sharing of bonds in paths traversed. By default, rings are</span>
|
|
|
4067 4054 <span class="c"># included in paths. A path containing a ring is terminated at an atom completing the ring.</span>
|
|
|
4068 4055 <span class="c">#</span>
|
|
|
4069 <a name="GetAtomPathsStartingAtWithLengthUpto-"></a>4056 <span class="k">sub </span><span class="m">GetAtomPathsStartingAtWithLengthUpto</span> <span class="s">{</span>
|
|
|
4070 4057 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$StartAtom</span><span class="cm">,</span> <span class="i">$Length</span><span class="cm">,</span> <span class="i">$AllowCycles</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
4071 4058
|
|
|
4072 4059 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetAtomPathsStartingAt</span><span class="s">(</span><span class="q">'AtomPathsWithLengthUpto'</span><span class="cm">,</span> <span class="i">$StartAtom</span><span class="cm">,</span> <span class="i">$Length</span><span class="cm">,</span> <span class="i">$AllowCycles</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4073 4060 <span class="s">}</span>
|
|
|
4074 4061
|
|
|
4075 4062 <span class="c"># Get atom paths starting from a specified atom as a reference to an array containing references</span>
|
|
|
4076 4063 <span class="c"># to arrays with path atoms.</span>
|
|
|
4077 4064 <span class="c">#</span>
|
|
|
4078 4065 <span class="c"># Path atoms atoms correspond to to all possible paths for specified atom in molecule with</span>
|
|
|
4079 4066 <span class="c"># specified length and no sharing of bonds in paths traversed. By default, rings are</span>
|
|
|
4080 4067 <span class="c"># included in paths. A path containing a ring is terminated at an atom completing the ring.</span>
|
|
|
4081 4068 <span class="c">#</span>
|
|
|
4082 <a name="GetAtomPathsStartingAtWithLength-"></a>4069 <span class="k">sub </span><span class="m">GetAtomPathsStartingAtWithLength</span> <span class="s">{</span>
|
|
|
4083 4070 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$StartAtom</span><span class="cm">,</span> <span class="i">$Length</span><span class="cm">,</span> <span class="i">$AllowCycles</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
4084 4071
|
|
|
4085 4072 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetAtomPathsStartingAt</span><span class="s">(</span><span class="q">'AtomPathsWithLength'</span><span class="cm">,</span> <span class="i">$StartAtom</span><span class="cm">,</span> <span class="i">$Length</span><span class="cm">,</span> <span class="i">$AllowCycles</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4086 4073 <span class="s">}</span>
|
|
|
4087 4074
|
|
|
4088 4075 <span class="c"># Get atom paths starting from a specified atom as a reference to an array containing references</span>
|
|
|
4089 4076 <span class="c"># to arrays with path atoms.</span>
|
|
|
4090 4077 <span class="c">#</span>
|
|
|
4091 4078 <span class="c"># Path atoms atoms correspond to to all possible paths for specified atom in molecule with all</span>
|
|
|
4092 4079 <span class="c"># possible lengths and no sharing of bonds in paths traversed. By default, rings are</span>
|
|
|
4093 4080 <span class="c"># included in paths. A path containing a ring is terminated at an atom completing the ring.</span>
|
|
|
4094 4081 <span class="c">#</span>
|
|
|
4095 4082 <span class="c">#</span>
|
|
|
4096 <a name="GetAtomPathsStartingAt-"></a>4083 <span class="k">sub </span><span class="m">GetAtomPathsStartingAt</span> <span class="s">{</span>
|
|
|
4097 4084 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$StartAtom</span><span class="cm">,</span> <span class="i">$AllowCycles</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
4098 4085
|
|
|
4099 4086 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetAtomPathsStartingAt</span><span class="s">(</span><span class="q">'AtomPathsWithAllLengths'</span><span class="cm">,</span> <span class="i">$StartAtom</span><span class="cm">,</span> <span class="k">undef</span><span class="cm">,</span> <span class="i">$AllowCycles</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4100 4087 <span class="s">}</span>
|
|
|
4101 4088
|
|
|
4102 4089 <span class="c"># Get atom paths as an array containing references to arrays with path atoms...</span>
|
|
|
4103 4090 <span class="c">#</span>
|
|
|
4104 <a name="_GetAtomPathsStartingAt-"></a>4091 <span class="k">sub </span><span class="m">_GetAtomPathsStartingAt</span> <span class="s">{</span>
|
|
|
4105 4092 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Mode</span><span class="cm">,</span> <span class="i">$StartAtom</span><span class="cm">,</span> <span class="i">$Length</span><span class="cm">,</span> <span class="i">$AllowCycles</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
4106 4093 <span class="k">my</span><span class="s">(</span><span class="i">@AtomPaths</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4107 4094
|
|
|
4108 4095 <span class="i">@AtomPaths</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4109 4096 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$StartAtom</span><span class="s">)</span> <span class="s">{</span>
|
|
|
4110 4097 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->_GetAtomPathsStartingAt: No atom paths retrieved: Start atom is not defined..."</span><span class="sc">;</span>
|
|
|
4111 4098 <span class="k">return</span> <span class="i">@AtomPaths</span><span class="sc">;</span>
|
|
|
4112 4099 <span class="s">}</span>
|
|
|
4113 4100 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasAtom</span><span class="s">(</span><span class="i">$StartAtom</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
4114 4101 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->_GetAtomPathsStartingAt: No atom paths retrieved: Start atom doesn't exist..."</span><span class="sc">;</span>
|
|
|
4115 4102 <span class="k">return</span> <span class="i">@AtomPaths</span><span class="sc">;</span>
|
|
|
4116 4103 <span class="s">}</span>
|
|
|
4117 4104 <span class="k">my</span><span class="s">(</span><span class="i">$StartAtomID</span><span class="cm">,</span> <span class="i">@Paths</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4118 4105
|
|
|
4119 4106 <span class="i">$StartAtomID</span> = <span class="i">$StartAtom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4120 4107 <span class="i">@Paths</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4121 4108
|
|
|
4122 4109 <span class="c"># Collect appropriate atom paths...</span>
|
|
|
4123 4110 <span class="j">MODE:</span> <span class="s">{</span>
|
|
|
4124 4111 <span class="k">if</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^AtomPathsWithLengthUpto$/i</span><span class="s">)</span> <span class="s">{</span> <span class="i">@Paths</span> = <span class="i">$This</span><span class="i">->GetPathsStartingAtWithLengthUpto</span><span class="s">(</span><span class="i">$StartAtomID</span><span class="cm">,</span> <span class="i">$Length</span><span class="cm">,</span> <span class="i">$AllowCycles</span><span class="s">)</span><span class="sc">;</span> <span class="k">last</span> <span class="j">MODE</span><span class="sc">;</span> <span class="s">}</span>
|
|
|
4125 4112 <span class="k">if</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^AtomPathsWithLength$/i</span><span class="s">)</span> <span class="s">{</span> <span class="i">@Paths</span> = <span class="i">$This</span><span class="i">->GetPathsStartingAtWithLength</span><span class="s">(</span><span class="i">$StartAtomID</span><span class="cm">,</span> <span class="i">$Length</span><span class="cm">,</span> <span class="i">$AllowCycles</span><span class="s">)</span><span class="sc">;</span> <span class="k">last</span> <span class="j">MODE</span><span class="sc">;</span> <span class="s">}</span>
|
|
|
4126 4113 <span class="k">if</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^AtomPathsWithAllLengths$/i</span><span class="s">)</span> <span class="s">{</span> <span class="i">@Paths</span> = <span class="i">$This</span><span class="i">->GetPathsStartingAt</span><span class="s">(</span><span class="i">$StartAtomID</span><span class="cm">,</span> <span class="i">$AllowCycles</span><span class="s">)</span><span class="sc">;</span> <span class="k">last</span> <span class="j">MODE</span><span class="sc">;</span> <span class="s">}</span>
|
|
|
4127 4114
|
|
|
4128 4115 <span class="k">if</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^AllAtomPathsWithLengthUpto$/i</span><span class="s">)</span> <span class="s">{</span> <span class="i">@Paths</span> = <span class="i">$This</span><span class="i">->GetAllPathsStartingAtWithLengthUpto</span><span class="s">(</span><span class="i">$StartAtomID</span><span class="cm">,</span> <span class="i">$Length</span><span class="cm">,</span> <span class="i">$AllowCycles</span><span class="s">)</span><span class="sc">;</span> <span class="k">last</span> <span class="j">MODE</span><span class="sc">;</span> <span class="s">}</span>
|
|
|
4129 4116 <span class="k">if</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^AllAtomPathsWithLength$/i</span><span class="s">)</span> <span class="s">{</span> <span class="i">@Paths</span> = <span class="i">$This</span><span class="i">->GetAllPathsStartingAtWithLength</span><span class="s">(</span><span class="i">$StartAtomID</span><span class="cm">,</span> <span class="i">$Length</span><span class="cm">,</span> <span class="i">$AllowCycles</span><span class="s">)</span><span class="sc">;</span> <span class="k">last</span> <span class="j">MODE</span><span class="sc">;</span> <span class="s">}</span>
|
|
|
4130 4117 <span class="k">if</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^AllAtomPathsWithAllLengths$/i</span><span class="s">)</span> <span class="s">{</span> <span class="i">@Paths</span> = <span class="i">$This</span><span class="i">->GetAllPathsStartingAt</span><span class="s">(</span><span class="i">$StartAtomID</span><span class="cm">,</span> <span class="i">$AllowCycles</span><span class="s">)</span><span class="sc">;</span> <span class="k">last</span> <span class="j">MODE</span><span class="sc">;</span> <span class="s">}</span>
|
|
|
4131 4118
|
|
|
4132 4119 <span class="k">print</span> <span class="q">"Warn: ${ClassName}->_GetAtomPathsStartingAt: No atom paths retrieved: Mode, $Mode, is not supported..."</span><span class="sc">;</span>
|
|
|
4133 4120 <span class="k">return</span> <span class="i">@AtomPaths</span><span class="sc">;</span>
|
|
|
4134 4121 <span class="s">}</span>
|
|
|
4135 4122 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetAtomPathsFromPaths</span><span class="s">(</span>\<span class="i">@Paths</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4136 4123 <span class="s">}</span>
|
|
|
4137 4124
|
|
|
4138 4125 <span class="c"># Get atom paths for all atoms as a reference to an array containing references to arrays with</span>
|
|
|
4139 4126 <span class="c"># path atoms.</span>
|
|
|
4140 4127 <span class="c">#</span>
|
|
|
4141 4128 <span class="c"># Path atoms correspond to to all possible paths for each atom in molecule with length</span>
|
|
|
4142 4129 <span class="c"># upto a specified length and sharing of bonds in paths traversed. By default, rings are</span>
|
|
|
4143 4130 <span class="c"># included in paths. A path containing a ring is terminated at an atom completing the ring.</span>
|
|
|
4144 4131 <span class="c">#</span>
|
|
|
4145 4132 <span class="c"># Notes:</span>
|
|
|
4146 4133 <span class="c"># . For molecule without any rings, this method returns the same set of atom paths</span>
|
|
|
4147 4134 <span class="c"># as GetAtomPathsWithLengthUpto method.</span>
|
|
|
4148 4135 <span class="c">#</span>
|
|
|
4149 <a name="GetAllAtomPathsWithLengthUpto-"></a>4136 <span class="k">sub </span><span class="m">GetAllAtomPathsWithLengthUpto</span> <span class="s">{</span>
|
|
|
4150 4137 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Length</span><span class="cm">,</span> <span class="i">$AllowCycles</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
4151 4138
|
|
|
4152 4139 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetAtomPaths</span><span class="s">(</span><span class="q">'AllAtomPathsWithLengthUpto'</span><span class="cm">,</span> <span class="i">$Length</span><span class="cm">,</span> <span class="i">$AllowCycles</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4153 4140 <span class="s">}</span>
|
|
|
4154 4141
|
|
|
4155 4142 <span class="c"># Get atom paths for all atoms as a reference to an array containing references to arrays with</span>
|
|
|
4156 4143 <span class="c"># path atoms.</span>
|
|
|
4157 4144 <span class="c">#</span>
|
|
|
4158 4145 <span class="c"># Path atoms correspond to to all possible paths for each atom in molecule with</span>
|
|
|
4159 4146 <span class="c"># a specified length and sharing of bonds in paths traversed. By default, rings are</span>
|
|
|
4160 4147 <span class="c"># included in paths. A path containing a ring is terminated at an atom completing the ring.</span>
|
|
|
4161 4148 <span class="c">#</span>
|
|
|
4162 4149 <span class="c"># Notes:</span>
|
|
|
4163 4150 <span class="c"># . For molecule without any rings, this method returns the same set of atom paths</span>
|
|
|
4164 4151 <span class="c"># as GetAtomPathsWithLengthUpto method.</span>
|
|
|
4165 4152 <span class="c">#</span>
|
|
|
4166 <a name="GetAllAtomPathsWithLength-"></a>4153 <span class="k">sub </span><span class="m">GetAllAtomPathsWithLength</span> <span class="s">{</span>
|
|
|
4167 4154 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Length</span><span class="cm">,</span> <span class="i">$AllowCycles</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
4168 4155
|
|
|
4169 4156 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetAtomPaths</span><span class="s">(</span><span class="q">'AllAtomPathsWithLength'</span><span class="cm">,</span> <span class="i">$Length</span><span class="cm">,</span> <span class="i">$AllowCycles</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4170 4157 <span class="s">}</span>
|
|
|
4171 4158
|
|
|
4172 4159 <span class="c"># Get atom paths for all atoms as a reference to an array containing references to arrays with</span>
|
|
|
4173 4160 <span class="c"># path atoms.</span>
|
|
|
4174 4161 <span class="c">#</span>
|
|
|
4175 4162 <span class="c"># Path atoms correspond to to all possible paths for each atom in molecule with all</span>
|
|
|
4176 4163 <span class="c"># possible lengths and sharing of bonds in paths traversed. By default, rings are</span>
|
|
|
4177 4164 <span class="c"># included in paths. A path containing a ring is terminated at an atom completing the ring.</span>
|
|
|
4178 4165 <span class="c">#</span>
|
|
|
4179 4166 <span class="c"># Notes:</span>
|
|
|
4180 4167 <span class="c"># . For molecule without any rings, this method returns the same set of atom paths</span>
|
|
|
4181 4168 <span class="c"># as GetAtomPaths method.</span>
|
|
|
4182 4169 <span class="c">#</span>
|
|
|
4183 <a name="GetAllAtomPaths-"></a>4170 <span class="k">sub </span><span class="m">GetAllAtomPaths</span> <span class="s">{</span>
|
|
|
4184 4171 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$AllowCycles</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
4185 4172
|
|
|
4186 4173 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetAtomPaths</span><span class="s">(</span><span class="q">'AllAtomPathsWithAllLengths'</span><span class="cm">,</span> <span class="k">undef</span><span class="cm">,</span> <span class="i">$AllowCycles</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4187 4174 <span class="s">}</span>
|
|
|
4188 4175
|
|
|
4189 4176 <span class="c"># Get atom paths for all atoms as a reference to an array containing references to arrays with</span>
|
|
|
4190 4177 <span class="c"># path atoms.</span>
|
|
|
4191 4178 <span class="c">#</span>
|
|
|
4192 4179 <span class="c"># Path atoms correspond to to all possible paths for each atom in molecule with length</span>
|
|
|
4193 4180 <span class="c"># upto a specified length and no sharing of bonds in paths traversed. By default, rings are</span>
|
|
|
4194 4181 <span class="c"># included in paths. A path containing a ring is terminated at an atom completing the ring.</span>
|
|
|
4195 4182 <span class="c">#</span>
|
|
|
4196 <a name="GetAtomPathsWithLengthUpto-"></a>4183 <span class="k">sub </span><span class="m">GetAtomPathsWithLengthUpto</span> <span class="s">{</span>
|
|
|
4197 4184 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Length</span><span class="cm">,</span> <span class="i">$AllowCycles</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
4198 4185
|
|
|
4199 4186 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetAtomPaths</span><span class="s">(</span><span class="q">'AtomPathsWithLengthUpto'</span><span class="cm">,</span> <span class="i">$Length</span><span class="cm">,</span> <span class="i">$AllowCycles</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4200 4187 <span class="s">}</span>
|
|
|
4201 4188
|
|
|
4202 4189 <span class="c"># Get atom paths for all atoms as a reference to an array containing references to arrays with</span>
|
|
|
4203 4190 <span class="c"># path atoms.</span>
|
|
|
4204 4191 <span class="c">#</span>
|
|
|
4205 4192 <span class="c"># Path atoms correspond to to all possible paths for each atom in molecule with</span>
|
|
|
4206 4193 <span class="c"># a specified length and no sharing of bonds in paths traversed. By default, rings are</span>
|
|
|
4207 4194 <span class="c"># included in paths. A path containing a ring is terminated at an atom completing the ring.</span>
|
|
|
4208 4195 <span class="c">#</span>
|
|
|
4209 <a name="GetAtomPathsWithLength-"></a>4196 <span class="k">sub </span><span class="m">GetAtomPathsWithLength</span> <span class="s">{</span>
|
|
|
4210 4197 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Length</span><span class="cm">,</span> <span class="i">$AllowCycles</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
4211 4198
|
|
|
4212 4199 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetAtomPaths</span><span class="s">(</span><span class="q">'AtomPathsWithLength'</span><span class="cm">,</span> <span class="i">$Length</span><span class="cm">,</span> <span class="i">$AllowCycles</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4213 4200 <span class="s">}</span>
|
|
|
4214 4201
|
|
|
4215 4202
|
|
|
4216 4203 <span class="c"># Get atom paths for all atoms as a reference to an array containing references to arrays with</span>
|
|
|
4217 4204 <span class="c"># path atoms.</span>
|
|
|
4218 4205 <span class="c">#</span>
|
|
|
4219 4206 <span class="c"># Path atoms correspond to to all possible paths for each atom in molecule with all</span>
|
|
|
4220 4207 <span class="c"># possible lengths and no sharing of bonds in paths traversed. By default, rings are</span>
|
|
|
4221 4208 <span class="c"># included in paths. A path containing a ring is terminated at an atom completing the ring.</span>
|
|
|
4222 4209 <span class="c">#</span>
|
|
|
4223 <a name="GetAtomPaths-"></a>4210 <span class="k">sub </span><span class="m">GetAtomPaths</span> <span class="s">{</span>
|
|
|
4224 4211 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$AllowCycles</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
4225 4212
|
|
|
4226 4213 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetAtomPaths</span><span class="s">(</span><span class="q">'AtomPathsWithAllLengths'</span><span class="cm">,</span> <span class="k">undef</span><span class="cm">,</span> <span class="i">$AllowCycles</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4227 4214 <span class="s">}</span>
|
|
|
4228 4215
|
|
|
4229 4216 <span class="c"># Get atom paths for all atoms as a reference to an array containing references to arrays with</span>
|
|
|
4230 4217 <span class="c"># path atoms.</span>
|
|
|
4231 4218 <span class="c">#</span>
|
|
|
4232 <a name="_GetAtomPaths-"></a>4219 <span class="k">sub </span><span class="m">_GetAtomPaths</span> <span class="s">{</span>
|
|
|
4233 4220 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Mode</span><span class="cm">,</span> <span class="i">$Length</span><span class="cm">,</span> <span class="i">$AllowCycles</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
4234 4221 <span class="k">my</span><span class="s">(</span><span class="i">$PathsRef</span><span class="cm">,</span> <span class="i">@AtomPaths</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4235 4222
|
|
|
4236 4223 <span class="i">@AtomPaths</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4237 4224 <span class="c"># Collect appropriate atom paths...</span>
|
|
|
4238 4225 <span class="j">MODE:</span> <span class="s">{</span>
|
|
|
4239 4226 <span class="k">if</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^AtomPathsWithLengthUpto$/i</span><span class="s">)</span> <span class="s">{</span> <span class="i">$PathsRef</span> = <span class="i">$This</span><span class="i">->GetPathsWithLengthUpto</span><span class="s">(</span><span class="i">$Length</span><span class="cm">,</span> <span class="i">$AllowCycles</span><span class="s">)</span><span class="sc">;</span> <span class="k">last</span> <span class="j">MODE</span><span class="sc">;</span> <span class="s">}</span>
|
|
|
4240 4227 <span class="k">if</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^AtomPathsWithLength$/i</span><span class="s">)</span> <span class="s">{</span> <span class="i">$PathsRef</span> = <span class="i">$This</span><span class="i">->GetPathsWithLength</span><span class="s">(</span><span class="i">$Length</span><span class="cm">,</span> <span class="i">$AllowCycles</span><span class="s">)</span><span class="sc">;</span> <span class="k">last</span> <span class="j">MODE</span><span class="sc">;</span> <span class="s">}</span>
|
|
|
4241 4228 <span class="k">if</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^AtomPathsWithAllLengths$/i</span><span class="s">)</span> <span class="s">{</span> <span class="i">$PathsRef</span> = <span class="i">$This</span><span class="i">->GetPaths</span><span class="s">(</span><span class="i">$AllowCycles</span><span class="s">)</span><span class="sc">;</span> <span class="k">last</span> <span class="j">MODE</span><span class="sc">;</span> <span class="s">}</span>
|
|
|
4242 4229
|
|
|
4243 4230 <span class="k">if</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^AllAtomPathsWithLengthUpto$/i</span><span class="s">)</span> <span class="s">{</span> <span class="i">$PathsRef</span> = <span class="i">$This</span><span class="i">->GetAllPathsWithLengthUpto</span><span class="s">(</span><span class="i">$Length</span><span class="cm">,</span> <span class="i">$AllowCycles</span><span class="s">)</span><span class="sc">;</span> <span class="k">last</span> <span class="j">MODE</span><span class="sc">;</span> <span class="s">}</span>
|
|
|
4244 4231 <span class="k">if</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^AllAtomPathsWithLength$/i</span><span class="s">)</span> <span class="s">{</span> <span class="i">$PathsRef</span> = <span class="i">$This</span><span class="i">->GetAllPathsWithLength</span><span class="s">(</span><span class="i">$Length</span><span class="cm">,</span> <span class="i">$AllowCycles</span><span class="s">)</span><span class="sc">;</span> <span class="k">last</span> <span class="j">MODE</span><span class="sc">;</span> <span class="s">}</span>
|
|
|
4245 4232 <span class="k">if</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^AllAtomPathsWithAllLengths$/i</span><span class="s">)</span> <span class="s">{</span> <span class="i">$PathsRef</span> = <span class="i">$This</span><span class="i">->GetAllPaths</span><span class="s">(</span><span class="i">$AllowCycles</span><span class="s">)</span><span class="sc">;</span> <span class="k">last</span> <span class="j">MODE</span><span class="sc">;</span> <span class="s">}</span>
|
|
|
4246 4233
|
|
|
4247 4234 <span class="k">print</span> <span class="q">"Warn: ${ClassName}->_GetAtomPaths: No atom paths retrieved: Mode, $Mode, is not supported..."</span><span class="sc">;</span>
|
|
|
4248 4235 <span class="k">return</span> \<span class="i">@AtomPaths</span><span class="sc">;</span>
|
|
|
4249 4236 <span class="s">}</span>
|
|
|
4250 4237 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetAtomPathsFromPaths</span><span class="s">(</span><span class="i">$PathsRef</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4251 4238 <span class="s">}</span>
|
|
|
4252 4239
|
|
|
4253 4240 <span class="c"># Get atom paths as an array reference containing references to arrays with path atoms...</span>
|
|
|
4254 4241 <span class="c">#</span>
|
|
|
4255 <a name="_GetAtomPathsFromPaths-"></a>4242 <span class="k">sub </span><span class="m">_GetAtomPathsFromPaths</span> <span class="s">{</span>
|
|
|
4256 4243 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$PathsRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
4257 4244 <span class="k">my</span><span class="s">(</span><span class="i">$Path</span><span class="cm">,</span> <span class="i">@AtomPaths</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4258 4245
|
|
|
4259 4246 <span class="i">@AtomPaths</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4260 4247 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$PathsRef</span><span class="s">)</span> <span class="s">{</span>
|
|
|
4261 4248 <span class="k">return</span> \<span class="i">@AtomPaths</span><span class="sc">;</span>
|
|
|
4262 4249 <span class="s">}</span>
|
|
|
4263 4250 <span class="k">if</span> <span class="s">(</span>!<span class="i">@</span>{<span class="i">$PathsRef</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
4264 4251 <span class="c"># Return an empty atom paths list...</span>
|
|
|
4265 4252 <span class="k">return</span> \<span class="i">@AtomPaths</span><span class="sc">;</span>
|
|
|
4266 4253 <span class="s">}</span>
|
|
|
4267 4254 <span class="k">for</span> <span class="i">$Path</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$PathsRef</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
4268 4255 <span class="k">my</span><span class="s">(</span><span class="i">@PathAtoms</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4269 4256 <span class="i">@PathAtoms</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4270 4257 <span class="i">@PathAtoms</span> = <span class="i">$This</span><span class="i">->_GetAtomPathFromPath</span><span class="s">(</span><span class="i">$Path</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4271 4258
|
|
|
4272 4259 <span class="k">push</span> <span class="i">@AtomPaths</span><span class="cm">,</span> \<span class="i">@PathAtoms</span><span class="sc">;</span>
|
|
|
4273 4260 <span class="s">}</span>
|
|
|
4274 4261 <span class="k">return</span> \<span class="i">@AtomPaths</span><span class="sc">;</span>
|
|
|
4275 4262 <span class="s">}</span>
|
|
|
4276 4263
|
|
|
4277 4264 <span class="c"># Generate an array of bond objects for an array of path atoms and return an array</span>
|
|
|
4278 4265 <span class="c"># of bond objects...</span>
|
|
|
4279 4266 <span class="c">#</span>
|
|
|
4280 <a name="GetAtomPathBonds-"></a>4267 <span class="k">sub </span><span class="m">GetAtomPathBonds</span> <span class="s">{</span>
|
|
|
4281 4268 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">@PathAtoms</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
4282 4269 <span class="k">my</span><span class="s">(</span><span class="i">@Bonds</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4283 4270
|
|
|
4284 4271 <span class="k">if</span> <span class="s">(</span>!<span class="i">@PathAtoms</span><span class="s">)</span> <span class="s">{</span>
|
|
|
4285 4272 <span class="c"># Return an empty ring bonds list...</span>
|
|
|
4286 4273 <span class="k">return</span> <span class="i">@Bonds</span><span class="sc">;</span>
|
|
|
4287 4274 <span class="s">}</span>
|
|
|
4288 4275 <span class="k">my</span><span class="s">(</span><span class="i">@PathAtomIDs</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4289 4276
|
|
|
4290 4277 <span class="i">@PathAtomIDs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4291 4278 <span class="i">@PathAtomIDs</span> = <span class="i">$This</span><span class="i">->_GetAtomsIDsFromAtoms</span><span class="s">(</span><span class="i">@PathAtoms</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4292 4279
|
|
|
4293 4280 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetPathBonds</span><span class="s">(</span><span class="i">@PathAtomIDs</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4294 4281 <span class="s">}</span>
|
|
|
4295 4282
|
|
|
4296 4283 <span class="c"># Map atom IDs in path to atoms and return a reference to an array containing ring atoms...</span>
|
|
|
4297 4284 <span class="c">#</span>
|
|
|
4298 <a name="_GetAtomPathFromPath-"></a>4285 <span class="k">sub </span><span class="m">_GetAtomPathFromPath</span> <span class="s">{</span>
|
|
|
4299 4286 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Path</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
4300 4287 <span class="k">my</span><span class="s">(</span><span class="i">@PathAtoms</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4301 4288
|
|
|
4302 4289 <span class="i">@PathAtoms</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4303 4290 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$Path</span><span class="s">)</span> <span class="s">{</span>
|
|
|
4304 4291 <span class="c"># Return an empty atoms list...</span>
|
|
|
4305 4292 <span class="k">return</span> <span class="i">@PathAtoms</span><span class="sc">;</span>
|
|
|
4306 4293 <span class="s">}</span>
|
|
|
4307 4294
|
|
|
4308 4295 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetPathAtoms</span><span class="s">(</span><span class="i">$Path</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4309 4296 <span class="s">}</span>
|
|
|
4310 4297
|
|
|
4311 4298 <span class="c"># Get atom paths between two specified atoms as a reference to an array containing references</span>
|
|
|
4312 4299 <span class="c"># to arrays with path atoms. For molecules with rings, atom paths array contains may contain</span>
|
|
|
4313 4300 <span class="c"># two paths.</span>
|
|
|
4314 4301 <span class="c">#</span>
|
|
|
4315 <a name="GetAtomPathsBetween-"></a>4302 <span class="k">sub </span><span class="m">GetAtomPathsBetween</span> <span class="s">{</span>
|
|
|
4316 4303 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$StartAtom</span><span class="cm">,</span> <span class="i">$EndAtom</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
4317 4304 <span class="k">my</span><span class="s">(</span><span class="i">@AtomPaths</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4318 4305
|
|
|
4319 4306 <span class="i">@AtomPaths</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4320 4307 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$StartAtom</span><span class="s">)</span> && <span class="i">$This</span><span class="i">->HasAtom</span><span class="s">(</span><span class="i">$StartAtom</span><span class="s">)</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
4321 4308 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->_GetAtomPathsBetween: No atom paths retrieved: Start atom is not defined or it doesn't exist..."</span><span class="sc">;</span>
|
|
|
4322 4309 <span class="k">return</span> <span class="i">@AtomPaths</span><span class="sc">;</span>
|
|
|
4323 4310 <span class="s">}</span>
|
|
|
4324 4311 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$EndAtom</span><span class="s">)</span> && <span class="i">$This</span><span class="i">->HasAtom</span><span class="s">(</span><span class="i">$EndAtom</span><span class="s">)</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
4325 4312 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->_GetAtomPathsBetween: No atom paths retrieved: End atom is not defined or it doesn't exist..."</span><span class="sc">;</span>
|
|
|
4326 4313 <span class="k">return</span> <span class="i">@AtomPaths</span><span class="sc">;</span>
|
|
|
4327 4314 <span class="s">}</span>
|
|
|
4328 4315 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetAtomPathsBetween</span><span class="s">(</span><span class="i">$StartAtom</span><span class="cm">,</span> <span class="i">$EndAtom</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4329 4316 <span class="s">}</span>
|
|
|
4330 4317
|
|
|
4331 4318 <span class="c"># Get atom paths between two specified atoms as a reference to an array containing references</span>
|
|
|
4332 4319 <span class="c"># to arrays with path atoms.</span>
|
|
|
4333 4320 <span class="c">#</span>
|
|
|
4334 <a name="_GetAtomPathsBetween-"></a>4321 <span class="k">sub </span><span class="m">_GetAtomPathsBetween</span> <span class="s">{</span>
|
|
|
4335 4322 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$StartAtom</span><span class="cm">,</span> <span class="i">$EndAtom</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
4336 4323 <span class="k">my</span><span class="s">(</span><span class="i">$StartAtomID</span><span class="cm">,</span> <span class="i">$EndAtomID</span><span class="cm">,</span> <span class="i">@Paths</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4337 4324
|
|
|
4338 4325 <span class="i">$StartAtomID</span> = <span class="i">$StartAtom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4339 4326 <span class="i">$EndAtomID</span> = <span class="i">$EndAtom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4340 4327
|
|
|
4341 4328 <span class="i">@Paths</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4342 4329 <span class="i">@Paths</span> = <span class="i">$This</span><span class="i">->GetPathsBetween</span><span class="s">(</span><span class="i">$StartAtomID</span><span class="cm">,</span> <span class="i">$EndAtomID</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4343 4330
|
|
|
4344 4331 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetAtomPathsFromPaths</span><span class="s">(</span>\<span class="i">@Paths</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4345 4332 <span class="s">}</span>
|
|
|
4346 4333
|
|
|
4347 4334 <span class="c"># Get atom neighborhoods around a specified atom as an array containing references</span>
|
|
|
4348 4335 <span class="c"># to arrays with neighborhood atoms at different radii upto specified radius...</span>
|
|
|
4349 4336 <span class="c">#</span>
|
|
|
4350 <a name="GetAtomNeighborhoodsWithRadiusUpto-"></a>4337 <span class="k">sub </span><span class="m">GetAtomNeighborhoodsWithRadiusUpto</span> <span class="s">{</span>
|
|
|
4351 4338 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$StartAtom</span><span class="cm">,</span> <span class="i">$Radius</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
4352 4339
|
|
|
4353 4340 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetAtomNeighborhoods</span><span class="s">(</span><span class="q">'RadiusUpto'</span><span class="cm">,</span> <span class="i">$StartAtom</span><span class="cm">,</span> <span class="i">$Radius</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4354 4341 <span class="s">}</span>
|
|
|
4355 4342
|
|
|
4356 4343 <span class="c"># Get atom neighborhoods around a specified atom as an array containing references</span>
|
|
|
4357 4344 <span class="c"># to arrays with neighborhood atoms at possible radii...</span>
|
|
|
4358 4345 <span class="c">#</span>
|
|
|
4359 <a name="GetAtomNeighborhoods-"></a>4346 <span class="k">sub </span><span class="m">GetAtomNeighborhoods</span> <span class="s">{</span>
|
|
|
4360 4347 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$StartAtom</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
4361 4348
|
|
|
4362 4349 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetAtomNeighborhoods</span><span class="s">(</span><span class="q">'AllRadii'</span><span class="cm">,</span> <span class="i">$StartAtom</span><span class="cm">,</span> <span class="k">undef</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4363 4350 <span class="s">}</span>
|
|
|
4364 4351
|
|
|
4365 4352 <span class="c"># Get atom neighborhood around a specified atom, along with their successor connected atoms, collected</span>
|
|
|
4366 4353 <span class="c"># with in a specified radius as a list containing references to lists with first value corresponding to neighborhood</span>
|
|
|
4367 4354 <span class="c"># atom at a specific radius and second value as reference to a list containing its successor connected atoms.</span>
|
|
|
4368 4355 <span class="c">#</span>
|
|
|
4369 4356 <span class="c"># For a neighborhood atom at each radius level, the successor connected atoms correspond to the</span>
|
|
|
4370 4357 <span class="c"># neighborhood atoms at the next radius level. Consequently, the neighborhood atoms at the last</span>
|
|
|
4371 4358 <span class="c"># radius level don't contain any successor atoms which fall outside the range of specified radius.</span>
|
|
|
4372 4359 <span class="c">#</span>
|
|
|
4373 <a name="GetAtomNeighborhoodsWithSuccessorAtomsAndRadiusUpto-"></a>4360 <span class="k">sub </span><span class="m">GetAtomNeighborhoodsWithSuccessorAtomsAndRadiusUpto</span> <span class="s">{</span>
|
|
|
4374 4361 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$StartAtom</span><span class="cm">,</span> <span class="i">$Radius</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
4375 4362
|
|
|
4376 4363 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetAtomNeighborhoods</span><span class="s">(</span><span class="q">'WithSuccessorsAndRadiusUpto'</span><span class="cm">,</span> <span class="i">$StartAtom</span><span class="cm">,</span> <span class="i">$Radius</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4377 4364 <span class="s">}</span>
|
|
|
4378 4365
|
|
|
4379 4366 <span class="c"># Get atom neighborhood around a specified atom, along with their successor connected atoms, collected</span>
|
|
|
4380 4367 <span class="c"># at all radii as a list containing references to lists with first value corresponding to neighborhood</span>
|
|
|
4381 4368 <span class="c"># atom at a specific radius and second value as reference to a list containing its successor connected atoms.</span>
|
|
|
4382 4369 <span class="c">#</span>
|
|
|
4383 4370 <span class="c"># For a neighborhood atom at each radius level, the successor connected atoms correspond to the</span>
|
|
|
4384 4371 <span class="c"># neighborhood atoms at the next radius level. Consequently, the neighborhood atoms at the last</span>
|
|
|
4385 4372 <span class="c"># radius level don't contain any successor atoms which fall outside the range of specified radius.</span>
|
|
|
4386 4373 <span class="c">#</span>
|
|
|
4387 4374 <span class="c">#</span>
|
|
|
4388 <a name="GetAtomNeighborhoodsWithSuccessorAtoms-"></a>4375 <span class="k">sub </span><span class="m">GetAtomNeighborhoodsWithSuccessorAtoms</span> <span class="s">{</span>
|
|
|
4389 4376 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$StartAtom</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
4390 4377
|
|
|
4391 4378 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetAtomNeighborhoods</span><span class="s">(</span><span class="q">'WithSuccessorsAndAllRadii'</span><span class="cm">,</span> <span class="i">$StartAtom</span><span class="cm">,</span> <span class="k">undef</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4392 4379 <span class="s">}</span>
|
|
|
4393 4380
|
|
|
4394 4381 <span class="c"># Get atom neighborhoods...</span>
|
|
|
4395 4382 <span class="c">#</span>
|
|
|
4396 <a name="_GetAtomNeighborhoods-"></a>4383 <span class="k">sub </span><span class="m">_GetAtomNeighborhoods</span> <span class="s">{</span>
|
|
|
4397 4384 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Mode</span><span class="cm">,</span> <span class="i">$StartAtom</span><span class="cm">,</span> <span class="i">$Radius</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
4398 4385 <span class="k">my</span><span class="s">(</span><span class="i">@AtomNeighborhoods</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4399 4386
|
|
|
4400 4387 <span class="i">@AtomNeighborhoods</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4401 4388
|
|
|
4402 4389 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$StartAtom</span><span class="s">)</span> && <span class="i">$This</span><span class="i">->HasAtom</span><span class="s">(</span><span class="i">$StartAtom</span><span class="s">)</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
4403 4390 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->_GetAtomNeighborhoods: No atom neighborhoods retrieved: Start atom is not defined or it doesn't exist..."</span><span class="sc">;</span>
|
|
|
4404 4391 <span class="k">return</span> <span class="i">@AtomNeighborhoods</span><span class="sc">;</span>
|
|
|
4405 4392 <span class="s">}</span>
|
|
|
4406 4393 <span class="k">if</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^(RadiusUpto|WithSuccessorsAndRadiusUpto)$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
4407 4394 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$Radius</span><span class="s">)</span> && <span class="i">$Radius</span> > <span class="n">0</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
4408 4395 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->_GetAtomNeighborhoods: No atom neighborhoods retrieved: Radius is not defined or it's <= 0 ..."</span><span class="sc">;</span>
|
|
|
4409 4396 <span class="k">return</span> <span class="i">@AtomNeighborhoods</span><span class="sc">;</span>
|
|
|
4410 4397 <span class="s">}</span>
|
|
|
4411 4398 <span class="s">}</span>
|
|
|
4412 4399
|
|
|
4413 4400 <span class="c"># Collect neighborhood atom IDs...</span>
|
|
|
4414 4401 <span class="k">my</span><span class="s">(</span><span class="i">$StartAtomID</span><span class="cm">,</span> <span class="i">@NeighborhoodAtomIDs</span><span class="cm">,</span> <span class="i">@NeighborhoodAtomIDsWithSuccessors</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4415 4402
|
|
|
4416 4403 <span class="i">@NeighborhoodAtomIDs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> <span class="i">@NeighborhoodAtomIDsWithSuccessors</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4417 4404 <span class="i">$StartAtomID</span> = <span class="i">$StartAtom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4418 4405
|
|
|
4419 4406 <span class="j">MODE:</span> <span class="s">{</span>
|
|
|
4420 4407 <span class="k">if</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^RadiusUpto$/i</span><span class="s">)</span> <span class="s">{</span> <span class="i">@NeighborhoodAtomIDs</span> = <span class="i">$This</span><span class="i">->GetNeighborhoodVerticesWithRadiusUpto</span><span class="s">(</span><span class="i">$StartAtomID</span><span class="cm">,</span> <span class="i">$Radius</span><span class="s">)</span><span class="sc">;</span> <span class="k">last</span> <span class="j">MODE</span><span class="sc">;</span> <span class="s">}</span>
|
|
|
4421 4408 <span class="k">if</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^AllRadii$/i</span><span class="s">)</span> <span class="s">{</span> <span class="i">@NeighborhoodAtomIDs</span> = <span class="i">$This</span><span class="i">->GetNeighborhoodVertices</span><span class="s">(</span><span class="i">$StartAtomID</span><span class="s">)</span><span class="sc">;</span> <span class="k">last</span> <span class="j">MODE</span><span class="sc">;</span> <span class="s">}</span>
|
|
|
4422 4409
|
|
|
4423 4410 <span class="k">if</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^WithSuccessorsAndRadiusUpto$/i</span><span class="s">)</span> <span class="s">{</span> <span class="i">@NeighborhoodAtomIDsWithSuccessors</span> = <span class="i">$This</span><span class="i">->GetNeighborhoodVerticesWithSuccessorsAndRadiusUpto</span><span class="s">(</span><span class="i">$StartAtomID</span><span class="cm">,</span> <span class="i">$Radius</span><span class="s">)</span><span class="sc">;</span> <span class="k">last</span> <span class="j">MODE</span><span class="sc">;</span> <span class="s">}</span>
|
|
|
4424 4411 <span class="k">if</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^WithSuccessorsAndAllRadii$/i</span><span class="s">)</span> <span class="s">{</span> <span class="i">@NeighborhoodAtomIDsWithSuccessors</span> = <span class="i">$This</span><span class="i">->GetNeighborhoodVerticesWithSuccessors</span><span class="s">(</span><span class="i">$StartAtomID</span><span class="s">)</span><span class="sc">;</span> <span class="k">last</span> <span class="j">MODE</span><span class="sc">;</span> <span class="s">}</span>
|
|
|
4425 4412
|
|
|
4426 4413 <span class="k">print</span> <span class="q">"Warn: ${ClassName}->_GetAtomNeighborhood: No atom neighborhoods retrieved: Mode, $Mode, is not supported..."</span><span class="sc">;</span>
|
|
|
4427 4414 <span class="k">return</span> <span class="i">@AtomNeighborhoods</span><span class="sc">;</span>
|
|
|
4428 4415 <span class="s">}</span>
|
|
|
4429 4416 <span class="k">if</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^(RadiusUpto|AllRadii)$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
4430 4417 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetNeighborhoodAtomsFromAtomIDs</span><span class="s">(</span>\<span class="i">@NeighborhoodAtomIDs</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4431 4418 <span class="s">}</span>
|
|
|
4432 4419 <span class="k">elsif</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^(WithSuccessorsAndRadiusUpto|WithSuccessorsAndAllRadii)$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
4433 4420 <span class="k">return</span> <span class="i">$This</span><span class="i">->_GetNeighborhoodAtomsWithSuccessorsFromAtomIDs</span><span class="s">(</span>\<span class="i">@NeighborhoodAtomIDsWithSuccessors</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4434 4421 <span class="s">}</span>
|
|
|
4435 4422
|
|
|
4436 4423 <span class="k">return</span> <span class="i">@AtomNeighborhoods</span><span class="sc">;</span>
|
|
|
4437 4424 <span class="s">}</span>
|
|
|
4438 4425
|
|
|
4439 4426 <span class="c"># Map neighborhood atom IDs to atoms...</span>
|
|
|
4440 4427 <span class="c">#</span>
|
|
|
4441 <a name="_GetNeighborhoodAtomsFromAtomIDs-"></a>4428 <span class="k">sub </span><span class="m">_GetNeighborhoodAtomsFromAtomIDs</span> <span class="s">{</span>
|
|
|
4442 4429 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$NeighborhoodsAtomIDsRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
4443 4430 <span class="k">my</span><span class="s">(</span><span class="i">$NeighborhoodAtomIDsRef</span><span class="cm">,</span> <span class="i">@AtomNeighborhoods</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4444 4431
|
|
|
4445 4432 <span class="i">@AtomNeighborhoods</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4446 4433 <span class="k">for</span> <span class="i">$NeighborhoodAtomIDsRef</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$NeighborhoodsAtomIDsRef</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
4447 4434 <span class="k">my</span><span class="s">(</span><span class="i">@AtomNeighborhood</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4448 4435
|
|
|
4449 4436 <span class="i">@AtomNeighborhood</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4450 4437 <span class="i">@AtomNeighborhood</span> = <span class="i">$This</span><span class="i">->_GetAtomsFromAtomIDs</span><span class="s">(</span><span class="i">@</span>{<span class="i">$NeighborhoodAtomIDsRef</span>}<span class="s">)</span><span class="sc">;</span>
|
|
|
4451 4438 <span class="k">push</span> <span class="i">@AtomNeighborhoods</span><span class="cm">,</span> \<span class="i">@AtomNeighborhood</span><span class="sc">;</span>
|
|
|
4452 4439 <span class="s">}</span>
|
|
|
4453 4440 <span class="k">return</span> <span class="i">@AtomNeighborhoods</span><span class="sc">;</span>
|
|
|
4454 4441 <span class="s">}</span>
|
|
|
4455 4442
|
|
|
4456 4443 <span class="c"># Map neighborhood atom IDs with successors to atoms...</span>
|
|
|
4457 4444 <span class="c">#</span>
|
|
|
4458 <a name="_GetNeighborhoodAtomsWithSuccessorsFromAtomIDs-"></a>4445 <span class="k">sub </span><span class="m">_GetNeighborhoodAtomsWithSuccessorsFromAtomIDs</span> <span class="s">{</span>
|
|
|
4459 4446 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$NeighborhoodsAtomIDsWithSuccessorsRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
4460 4447 <span class="k">my</span><span class="s">(</span><span class="i">$Depth</span><span class="cm">,</span> <span class="i">$NeighborhoodAtomIDsWithSuccessorsRef</span><span class="cm">,</span> <span class="i">$NeighborhoodAtomIDWithSuccessorsRef</span><span class="cm">,</span> <span class="i">$NeighborhoodAtomID</span><span class="cm">,</span> <span class="i">$NeighborhoodAtomSuccessorsIDsRef</span><span class="cm">,</span> <span class="i">@AtomNeighborhoods</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4461 4448
|
|
|
4462 4449 <span class="i">$Depth</span> = <span class="n">0</span><span class="sc">;</span>
|
|
|
4463 4450 <span class="i">@AtomNeighborhoods</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4464 4451
|
|
|
4465 4452 <span class="c"># Go over neighborhoods at each level...</span>
|
|
|
4466 4453 <span class="k">for</span> <span class="i">$NeighborhoodAtomIDsWithSuccessorsRef</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$NeighborhoodsAtomIDsWithSuccessorsRef</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
4467 4454 <span class="i">@</span>{<span class="i">$AtomNeighborhoods</span>[<span class="i">$Depth</span>]} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4468 4455
|
|
|
4469 4456 <span class="c"># Go over the neighborhood atoms and their successors at a specific level..</span>
|
|
|
4470 4457 <span class="k">for</span> <span class="i">$NeighborhoodAtomIDWithSuccessorsRef</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$NeighborhoodAtomIDsWithSuccessorsRef</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
4471 4458 <span class="k">my</span><span class="s">(</span><span class="i">$NeighborhoodAtom</span><span class="cm">,</span> <span class="i">@NeighborhoodAtomWithSuccessors</span><span class="cm">,</span> <span class="i">@NeighborhoodAtomSuccessorAtoms</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4472 4459
|
|
|
4473 4460 <span class="i">@NeighborhoodAtomWithSuccessors</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> <span class="i">@NeighborhoodAtomSuccessorAtoms</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4474 4461 <span class="s">(</span><span class="i">$NeighborhoodAtomID</span><span class="cm">,</span> <span class="i">$NeighborhoodAtomSuccessorsIDsRef</span><span class="s">)</span> = <span class="i">@</span>{<span class="i">$NeighborhoodAtomIDWithSuccessorsRef</span>}<span class="sc">;</span>
|
|
|
4475 4462
|
|
|
4476 4463 <span class="c"># Map atom IDs to atoms...</span>
|
|
|
4477 4464 <span class="i">$NeighborhoodAtom</span> = <span class="i">$This</span><span class="i">->_GetAtomFromAtomID</span><span class="s">(</span><span class="i">$NeighborhoodAtomID</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4478 4465 <span class="k">if</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$NeighborhoodAtomSuccessorsIDsRef</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
4479 4466 <span class="i">@NeighborhoodAtomSuccessorAtoms</span> = <span class="i">$This</span><span class="i">->_GetAtomsFromAtomIDs</span><span class="s">(</span><span class="i">@</span>{<span class="i">$NeighborhoodAtomSuccessorsIDsRef</span>}<span class="s">)</span><span class="sc">;</span>
|
|
|
4480 4467 <span class="s">}</span>
|
|
|
4481 4468
|
|
|
4482 4469 <span class="c"># Store an atom and its successors at each level in an array...</span>
|
|
|
4483 4470 <span class="k">push</span> <span class="i">@NeighborhoodAtomWithSuccessors</span><span class="cm">,</span> <span class="s">(</span><span class="i">$NeighborhoodAtom</span><span class="cm">,</span> \<span class="i">@NeighborhoodAtomSuccessorAtoms</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4484 4471
|
|
|
4485 4472 <span class="k">push</span> <span class="i">@</span>{<span class="i">$AtomNeighborhoods</span>[<span class="i">$Depth</span>]} <span class="cm">,</span> \<span class="i">@NeighborhoodAtomWithSuccessors</span><span class="sc">;</span>
|
|
|
4486 4473 <span class="s">}</span>
|
|
|
4487 4474 <span class="i">$Depth</span>++<span class="sc">;</span>
|
|
|
4488 4475 <span class="s">}</span>
|
|
|
4489 4476 <span class="k">return</span> <span class="i">@AtomNeighborhoods</span><span class="sc">;</span>
|
|
|
4490 4477 <span class="s">}</span>
|
|
|
4491 4478
|
|
|
4492 4479 <span class="c"># Get next object ID...</span>
|
|
|
4493 <a name="_GetNewObjectID-"></a>4480 <span class="k">sub </span><span class="m">_GetNewObjectID</span> <span class="s">{</span>
|
|
|
4494 4481 <span class="i">$ObjectID</span>++<span class="sc">;</span>
|
|
|
4495 4482 <span class="k">return</span> <span class="i">$ObjectID</span><span class="sc">;</span>
|
|
|
4496 4483 <span class="s">}</span>
|
|
|
4497 4484
|
|
|
4498 4485 <span class="c"># Is aromatic property set for the molecule?</span>
|
|
|
4499 <a name="IsAromatic-"></a>4486 <span class="k">sub </span><span class="m">IsAromatic</span> <span class="s">{</span>
|
|
|
4500 4487 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
4501 4488 <span class="k">my</span><span class="s">(</span><span class="i">$Aromatic</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4502 4489
|
|
|
4503 4490 <span class="i">$Aromatic</span> = <span class="i">$This</span><span class="i">->GetAromatic</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4504 4491
|
|
|
4505 4492 <span class="k">return</span> <span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$Aromatic</span><span class="s">)</span> && <span class="i">$Aromatic</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
4506 4493 <span class="s">}</span>
|
|
|
4507 4494
|
|
|
4508 4495 <span class="c"># Does molecule contains any atoms with non-zero Z coordiantes?</span>
|
|
|
4509 <a name="IsThreeDimensional-"></a>4496 <span class="k">sub </span><span class="m">IsThreeDimensional</span> <span class="s">{</span>
|
|
|
4510 4497 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
4511 4498 <span class="k">my</span><span class="s">(</span><span class="i">$Atom</span><span class="cm">,</span> <span class="i">@Atoms</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4512 4499
|
|
|
4513 4500 <span class="i">@Atoms</span> = <span class="i">$This</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4514 4501 <span class="j">ATOM:</span> <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="i">@Atoms</span><span class="s">)</span> <span class="s">{</span>
|
|
|
4515 4502 <span class="k">if</span> <span class="s">(</span><span class="i">$Atom</span><span class="i">->GetZ</span><span class="s">(</span><span class="s">)</span> != <span class="n">0</span><span class="s">)</span> <span class="s">{</span>
|
|
|
4516 4503 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span>
|
|
|
4517 4504 <span class="s">}</span>
|
|
|
4518 4505 <span class="s">}</span>
|
|
|
4519 4506 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
4520 4507 <span class="s">}</span>
|
|
|
4521 4508
|
|
|
4522 4509 <span class="c"># Does molecule contains any atoms with non-zero X or Y coordinates</span>
|
|
|
4523 4510 <span class="c"># and only zero Z-coordinates?</span>
|
|
|
4524 <a name="IsTwoDimensional-"></a>4511 <span class="k">sub </span><span class="m">IsTwoDimensional</span> <span class="s">{</span>
|
|
|
4525 4512 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
4526 4513 <span class="k">my</span><span class="s">(</span><span class="i">$Atom</span><span class="cm">,</span> <span class="i">@Atoms</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4527 4514
|
|
|
4528 4515 <span class="i">@Atoms</span> = <span class="i">$This</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4529 4516 <span class="j">ATOM:</span> <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="i">@Atoms</span><span class="s">)</span> <span class="s">{</span>
|
|
|
4530 4517 <span class="k">if</span> <span class="s">(</span><span class="i">$Atom</span><span class="i">->GetZ</span><span class="s">(</span><span class="s">)</span> != <span class="n">0</span><span class="s">)</span> <span class="s">{</span>
|
|
|
4531 4518 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
4532 4519 <span class="s">}</span>
|
|
|
4533 4520 <span class="k">if</span> <span class="s">(</span><span class="i">$Atom</span><span class="i">->GetX</span><span class="s">(</span><span class="s">)</span> != <span class="n">0</span> || <span class="i">$Atom</span><span class="i">->GetY</span><span class="s">(</span><span class="s">)</span> != <span class="n">0</span><span class="s">)</span> <span class="s">{</span>
|
|
|
4534 4521 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span>
|
|
|
4535 4522 <span class="s">}</span>
|
|
|
4536 4523 <span class="s">}</span>
|
|
|
4537 4524 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
4538 4525 <span class="s">}</span>
|
|
|
4539 4526
|
|
|
4540 4527 <span class="c"># Get dimensionality of the molecule using one of the following two methods:</span>
|
|
|
4541 4528 <span class="c"># . Using explicitly set Dimensionality</span>
|
|
|
4542 4529 <span class="c"># . Going over atomic coordinates</span>
|
|
|
4543 4530 <span class="c">#</span>
|
|
|
4544 4531 <span class="c"># The valid dimensionality values are:</span>
|
|
|
4545 4532 <span class="c"># . 3D - Three dimensional: One of X, Y or Z coordinate is non-zero</span>
|
|
|
4546 4533 <span class="c"># . 2D - Two dimensional: One of X or Y coordinate is non-zero; All Z coordinates are zero</span>
|
|
|
4547 4534 <span class="c"># . 0D - Zero dimensional: All atomic coordinates are zero</span>
|
|
|
4548 4535 <span class="c">#</span>
|
|
|
4549 <a name="GetDimensionality-"></a>4536 <span class="k">sub </span><span class="m">GetDimensionality</span> <span class="s">{</span>
|
|
|
4550 4537 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
4551 4538
|
|
|
4552 4539 <span class="c"># Is Dimensionality property explicitly set?</span>
|
|
|
4553 4540 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Dimensionality'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
4554 4541 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'Dimensionality'</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4555 4542 <span class="s">}</span>
|
|
|
4556 4543 <span class="k">my</span><span class="s">(</span><span class="i">$Atom</span><span class="cm">,</span> <span class="i">@Atoms</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4557 4544
|
|
|
4558 4545 <span class="i">@Atoms</span> = <span class="i">$This</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4559 4546 <span class="j">ATOM:</span> <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="i">@Atoms</span><span class="s">)</span> <span class="s">{</span>
|
|
|
4560 4547 <span class="k">if</span> <span class="s">(</span><span class="i">$Atom</span><span class="i">->GetZ</span><span class="s">(</span><span class="s">)</span> != <span class="n">0</span><span class="s">)</span> <span class="s">{</span>
|
|
|
4561 4548 <span class="k">return</span> <span class="q">'3D'</span><span class="sc">;</span>
|
|
|
4562 4549 <span class="s">}</span>
|
|
|
4563 4550 <span class="k">if</span> <span class="s">(</span><span class="i">$Atom</span><span class="i">->GetX</span><span class="s">(</span><span class="s">)</span> != <span class="n">0</span> || <span class="i">$Atom</span><span class="i">->GetY</span><span class="s">(</span><span class="s">)</span> != <span class="n">0</span><span class="s">)</span> <span class="s">{</span>
|
|
|
4564 4551 <span class="k">return</span> <span class="q">'2D'</span><span class="sc">;</span>
|
|
|
4565 4552 <span class="s">}</span>
|
|
|
4566 4553 <span class="s">}</span>
|
|
|
4567 4554 <span class="k">return</span> <span class="q">'0D'</span><span class="sc">;</span>
|
|
|
4568 4555 <span class="s">}</span>
|
|
|
4569 4556
|
|
|
4570 4557 <span class="c"># Is it a molecule object?</span>
|
|
|
4571 <a name="IsMolecule-"></a>4558 <span class="k">sub </span><span class="m">IsMolecule ($)</span> <span class="s">{</span>
|
|
|
4572 4559 <span class="k">my</span><span class="s">(</span><span class="i">$Object</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
4573 4560
|
|
|
4574 4561 <span class="k">return</span> <span class="i">_IsMolecule</span><span class="s">(</span><span class="i">$Object</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4575 4562 <span class="s">}</span>
|
|
|
4576 4563
|
|
|
4577 4564 <span class="c"># Return a string containing vertices, edges and other properties...</span>
|
|
|
4578 <a name="StringifyMolecule-"></a>4565 <span class="k">sub </span><span class="m">StringifyMolecule</span> <span class="s">{</span>
|
|
|
4579 4566 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
4580 4567 <span class="k">my</span><span class="s">(</span><span class="i">$MoleculeString</span><span class="cm">,</span> <span class="i">$ID</span><span class="cm">,</span> <span class="i">$Name</span><span class="cm">,</span> <span class="i">$NumOfAtoms</span><span class="cm">,</span> <span class="i">$NumOfBonds</span><span class="cm">,</span> <span class="i">$MolecularFormula</span><span class="cm">,</span> <span class="i">$NumOfRings</span><span class="cm">,</span> <span class="i">$MolecularWeight</span><span class="cm">,</span> <span class="i">$ExactMass</span><span class="cm">,</span> <span class="i">$FormalCharge</span><span class="cm">,</span> <span class="i">$SpinMultiplicity</span><span class="cm">,</span> <span class="i">$FreeRadicalElectrons</span><span class="cm">,</span> <span class="i">$Charge</span><span class="cm">,</span> <span class="i">$ElementsRef</span><span class="cm">,</span> <span class="i">$ElementsCompositionRef</span><span class="cm">,</span> <span class="i">$ElementalComposition</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4581 4568
|
|
|
4582 4569 <span class="i">$ID</span> = <span class="i">$This</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4583 4570 <span class="i">$Name</span> = <span class="i">$This</span><span class="i">->GetName</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4584 4571 <span class="i">$NumOfAtoms</span> = <span class="i">$This</span><span class="i">->GetNumOfAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4585 4572 <span class="i">$NumOfBonds</span> = <span class="i">$This</span><span class="i">->GetNumOfBonds</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4586 4573
|
|
|
4587 4574 <span class="i">$NumOfRings</span> = <span class="i">$This</span><span class="i">->GetNumOfRings</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4588 4575 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$NumOfRings</span><span class="s">)</span> <span class="s">{</span>
|
|
|
4589 4576 <span class="i">$NumOfRings</span> = <span class="q">'undefined'</span><span class="sc">;</span>
|
|
|
4590 4577 <span class="s">}</span>
|
|
|
4591 4578
|
|
|
4592 4579 <span class="i">$MolecularFormula</span> = <span class="i">$This</span><span class="i">->GetMolecularFormula</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4593 4580
|
|
|
4594 4581 <span class="i">$MolecularWeight</span> = <span class="i">$This</span><span class="i">->GetMolecularWeight</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4595 4582 <span class="i">$MolecularWeight</span> = <span class="i">round</span><span class="s">(</span><span class="i">$MolecularWeight</span><span class="cm">,</span> <span class="n">4</span><span class="s">)</span> + <span class="n">0</span><span class="sc">;</span>
|
|
|
4596 4583
|
|
|
4597 4584 <span class="i">$ExactMass</span> = <span class="i">$This</span><span class="i">->GetExactMass</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4598 4585 <span class="i">$ExactMass</span> = <span class="i">round</span><span class="s">(</span><span class="i">$ExactMass</span><span class="cm">,</span> <span class="n">4</span><span class="s">)</span> + <span class="n">0</span><span class="sc">;</span>
|
|
|
4599 4586
|
|
|
4600 4587 <span class="i">$FormalCharge</span> = <span class="i">$This</span><span class="i">->GetFormalCharge</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4601 4588 <span class="i">$Charge</span> = <span class="i">$This</span><span class="i">->GetCharge</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4602 4589
|
|
|
4603 4590 <span class="i">$SpinMultiplicity</span> = <span class="i">$This</span><span class="i">->GetSpinMultiplicity</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4604 4591 <span class="i">$FreeRadicalElectrons</span> = <span class="i">$This</span><span class="i">->GetFreeRadicalElectrons</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4605 4592
|
|
|
4606 4593 <span class="s">(</span><span class="i">$ElementsRef</span><span class="cm">,</span> <span class="i">$ElementsCompositionRef</span><span class="s">)</span> = <span class="i">$This</span><span class="i">->GetElementalComposition</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4607 4594 <span class="i">$ElementalComposition</span> = <span class="q">'None'</span><span class="sc">;</span>
|
|
|
4608 4595 <span class="k">if</span> <span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$ElementsRef</span><span class="s">)</span> && <span class="i">@</span>{<span class="i">$ElementsRef</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
4609 4596 <span class="i">$ElementalComposition</span> = <span class="q">"[ "</span> . <span class="i">FormatElementalCompositionInformation</span><span class="s">(</span><span class="i">$ElementsRef</span><span class="cm">,</span> <span class="i">$ElementsCompositionRef</span><span class="s">)</span> . <span class="q">" ]"</span><span class="sc">;</span>
|
|
|
4610 4597 <span class="s">}</span>
|
|
|
4611 4598
|
|
|
4612 4599 <span class="i">$MoleculeString</span> = <span class="q">"Molecule: ID: $ID; Name: \"$Name\"; NumOfAtoms: $NumOfAtoms; NumOfBonds: $NumOfBonds; NumOfRings: $NumOfRings; MolecularFormula: $MolecularFormula; MolecularWeight: $MolecularWeight; ExactMass: $ExactMass; FormalCharge: $FormalCharge; Charge: $Charge; SpinMultiplicity: $SpinMultiplicity; FreeRadicalElectrons: $FreeRadicalElectrons; ElementalComposition: $ElementalComposition"</span><span class="sc">;</span>
|
|
|
4613 4600
|
|
|
4614 4601 <span class="k">return</span> <span class="i">$MoleculeString</span><span class="sc">;</span>
|
|
|
4615 4602 <span class="s">}</span>
|
|
|
4616 4603
|
|
|
4617 4604 <span class="c"># Load appropriate atom data files from <MayaChemTools>/lib directory used by various</span>
|
|
|
4618 4605 <span class="c"># object methods in the current class...</span>
|
|
|
4619 4606 <span class="c">#</span>
|
|
|
4620 <a name="_LoadMoleculeClassData-"></a>4607 <span class="k">sub </span><span class="m">_LoadMoleculeClassData</span> <span class="s">{</span>
|
|
|
4621 4608 <span class="k">my</span><span class="s">(</span><span class="i">$MayaChemToolsLibDir</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4622 4609
|
|
|
4623 4610 <span class="i">$MayaChemToolsLibDir</span> = <span class="i">GetMayaChemToolsLibDirName</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4624 4611
|
|
|
4625 4612 <span class="c"># Load and process data for aromaticity models...</span>
|
|
|
4626 4613 <span class="i">_LoadAromaticityModelsData</span><span class="s">(</span><span class="i">$MayaChemToolsLibDir</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4627 4614 <span class="i">_ProcessAromaticityModelsData</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4628 4615 <span class="s">}</span>
|
|
|
4629 4616
|
|
|
4630 4617 <span class="c">#</span>
|
|
|
4631 4618 <span class="c"># Load data for supported aromaticity models...</span>
|
|
|
4632 4619 <span class="c">#</span>
|
|
|
4633 <a name="_LoadAromaticityModelsData-"></a>4620 <span class="k">sub </span><span class="m">_LoadAromaticityModelsData</span> <span class="s">{</span>
|
|
|
4634 4621 <span class="k">my</span><span class="s">(</span><span class="i">$MayaChemToolsLibDir</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
4635 4622 <span class="k">my</span><span class="s">(</span><span class="i">$DataFile</span><span class="cm">,</span> <span class="i">$Index</span><span class="cm">,</span> <span class="i">$InDelim</span><span class="cm">,</span> <span class="i">$Line</span><span class="cm">,</span> <span class="i">$NumOfCols</span><span class="cm">,</span> <span class="i">$ParameterName</span><span class="cm">,</span> <span class="i">$ParameterValue</span><span class="cm">,</span> <span class="i">$ModelName</span><span class="cm">,</span> <span class="i">@ColLabels</span><span class="cm">,</span> <span class="i">@LineWords</span><span class="cm">,</span> <span class="i">%ParameterNames</span><span class="cm">,</span> <span class="i">%ColIndexToModelName</span><span class="cm">,</span> <span class="i">%SupportedParameterNames</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4636 4623
|
|
|
4637 4624 <span class="i">%AromaticityModelsDataMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4638 4625 <span class="i">%CanonicalAromaticityModelNamesMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4639 4626
|
|
|
4640 4627 <span class="c"># File format:</span>
|
|
|
4641 4628 <span class="c">#</span>
|
|
|
4642 4629 <span class="c"># "ParameterName","MDLAromaticityModel","TriposAromaticityModel","MMFFAromaticityModel","ChemAxonBasicAromaticityModel","ChemAxonGeneralAromaticityModel","DaylightAromaticityModel","MayaChemToolsAromaticityModel"</span>
|
|
|
4643 4630 <span class="c"># "AllowHeteroRingAtoms","No","No","Yes","Yes","Yes","Yes","Yes"</span>
|
|
|
4644 4631 <span class="c">#</span>
|
|
|
4645 4632 <span class="i">$DataFile</span> = <span class="i">$MayaChemToolsLibDir</span> . <span class="q">"/data/AromaticityModelsData.csv"</span><span class="sc">;</span>
|
|
|
4646 4633 <span class="k">if</span> <span class="s">(</span>! <span class="k">-e</span> <span class="q">"$DataFile"</span><span class="s">)</span> <span class="s">{</span>
|
|
|
4647 4634 <span class="w">croak</span> <span class="q">"Error: ${ClassName}::_LoadAromaticityModelsData: MayaChemTools package file, $DataFile, is missing: Possible installation problems..."</span><span class="sc">;</span>
|
|
|
4648 4635 <span class="s">}</span>
|
|
|
4649 4636
|
|
|
4650 4637 <span class="c"># Setup a list of currently supported aromaticity parameters...</span>
|
|
|
4651 4638 <span class="c">#</span>
|
|
|
4652 4639 <span class="k">my</span><span class="s">(</span><span class="i">@KnownNames</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4653 4640 <span class="i">@KnownNames</span> = <span class="q">qw(AllowHeteroRingAtoms HeteroRingAtomsList AllowExocyclicDoubleBonds AllowHomoNuclearExocyclicDoubleBonds AllowElectronegativeRingAtomExocyclicDoubleBonds AllowRingAtomFormalCharge AllowHeteroRingAtomFormalCharge MinimumRingSize)</span><span class="sc">;</span>
|
|
|
4654 4641
|
|
|
4655 4642 <span class="i">%SupportedParameterNames</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4656 4643 <span class="k">for</span> <span class="i">$ParameterName</span> <span class="s">(</span><span class="i">@KnownNames</span><span class="s">)</span> <span class="s">{</span>
|
|
|
4657 4644 <span class="i">$SupportedParameterNames</span>{<span class="i">$ParameterName</span>} = <span class="i">$ParameterName</span><span class="sc">;</span>
|
|
|
4658 4645 <span class="s">}</span>
|
|
|
4659 4646
|
|
|
4660 4647 <span class="i">$InDelim</span> = <span class="q">"\,"</span><span class="sc">;</span>
|
|
|
4661 4648 <span class="k">open</span> <span class="w">DATAFILE</span><span class="cm">,</span> <span class="q">"$DataFile"</span> <span class="k">or</span> <span class="w">croak</span> <span class="q">"Couldn't open $DataFile: $! ..."</span><span class="sc">;</span>
|
|
|
4662 4649
|
|
|
4663 4650 <span class="c"># Skip lines up to column labels...</span>
|
|
|
4664 4651 <span class="j">LINE:</span> <span class="k">while</span> <span class="s">(</span><span class="i">$Line</span> = <span class="i">GetTextLine</span><span class="s">(</span>\<span class="i">*DATAFILE</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
4665 4652 <span class="k">if</span> <span class="s">(</span><span class="i">$Line</span> !~ <span class="q">/^#/</span><span class="s">)</span> <span class="s">{</span>
|
|
|
4666 4653 <span class="k">last</span> <span class="j">LINE</span><span class="sc">;</span>
|
|
|
4667 4654 <span class="s">}</span>
|
|
|
4668 4655 <span class="s">}</span>
|
|
|
4669 4656 <span class="i">@ColLabels</span>= <span class="i">quotewords</span><span class="s">(</span><span class="i">$InDelim</span><span class="cm">,</span> <span class="n">0</span><span class="cm">,</span> <span class="i">$Line</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4670 4657 <span class="i">$NumOfCols</span> = <span class="i">@ColLabels</span><span class="sc">;</span>
|
|
|
4671 4658
|
|
|
4672 4659 <span class="i">%ColIndexToModelName</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4673 4660
|
|
|
4674 4661 <span class="c"># Process names of aromaticity models...</span>
|
|
|
4675 4662 <span class="k">for</span> <span class="i">$Index</span> <span class="s">(</span><span class="n">1</span> .. <span class="i">$#ColLabels</span><span class="s">)</span> <span class="s">{</span>
|
|
|
4676 4663 <span class="i">$ModelName</span> = <span class="i">$ColLabels</span>[<span class="i">$Index</span>]<span class="sc">;</span>
|
|
|
4677 4664 <span class="i">$ModelName</span> =~ <span class="q">s/ //g</span><span class="sc">;</span>
|
|
|
4678 4665
|
|
|
4679 4666 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$AromaticityModelsDataMap</span>{<span class="i">$ModelName</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
4680 4667 <span class="w">croak</span> <span class="q">"Error: ${ClassName}::_LoadAromaticityModelsData: The aromaticity model name, $ModelName, in $DataFile has already exists.\nLine: $Line..."</span><span class="sc">;</span>
|
|
|
4681 4668 <span class="s">}</span>
|
|
|
4682 4669 <span class="i">%</span>{<span class="i">$AromaticityModelsDataMap</span>{<span class="i">$ModelName</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4683 4670
|
|
|
4684 4671 <span class="c"># Cannonicalize aromatic model name by converting into all lowercase...</span>
|
|
|
4685 4672 <span class="i">$CanonicalAromaticityModelNamesMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$ModelName</span><span class="s">)</span>} = <span class="i">$ModelName</span><span class="sc">;</span>
|
|
|
4686 4673
|
|
|
4687 4674 <span class="i">$ColIndexToModelName</span>{<span class="i">$Index</span>} = <span class="i">$ModelName</span><span class="sc">;</span>
|
|
|
4688 4675 <span class="s">}</span>
|
|
|
4689 4676
|
|
|
4690 4677 <span class="c"># Process paramater name and their values for specified aromaticity models...</span>
|
|
|
4691 4678 <span class="c">#</span>
|
|
|
4692 4679 <span class="i">%ParameterNames</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4693 4680 <span class="j">LINE:</span> <span class="k">while</span> <span class="s">(</span><span class="i">$Line</span> = <span class="i">GetTextLine</span><span class="s">(</span>\<span class="i">*DATAFILE</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
4694 4681 <span class="k">if</span> <span class="s">(</span><span class="i">$Line</span> =~ <span class="q">/^#/</span><span class="s">)</span> <span class="s">{</span>
|
|
|
4695 4682 <span class="k">next</span> <span class="j">LINE</span><span class="sc">;</span>
|
|
|
4696 4683 <span class="s">}</span>
|
|
|
4697 4684 <span class="i">@LineWords</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4698 4685 <span class="i">@LineWords</span> = <span class="i">quotewords</span><span class="s">(</span><span class="i">$InDelim</span><span class="cm">,</span> <span class="n">0</span><span class="cm">,</span> <span class="i">$Line</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4699 4686 <span class="k">if</span> <span class="s">(</span><span class="i">@LineWords</span> != <span class="i">$NumOfCols</span><span class="s">)</span> <span class="s">{</span>
|
|
|
4700 4687 <span class="w">croak</span> <span class="q">"Error: ${ClassName}::_LoadAromaticityModelsData: The number of data fields, @LineWords, in $DataFile must be $NumOfCols.\nLine: $Line..."</span><span class="sc">;</span>
|
|
|
4701 4688 <span class="s">}</span>
|
|
|
4702 4689
|
|
|
4703 4690 <span class="c"># Process parameter name and values for aromaticity models...</span>
|
|
|
4704 4691 <span class="c">#</span>
|
|
|
4705 4692 <span class="i">$ParameterName</span> = <span class="i">$LineWords</span>[<span class="n">0</span>]<span class="sc">;</span>
|
|
|
4706 4693
|
|
|
4707 4694 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$SupportedParameterNames</span>{<span class="i">$ParameterName</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
4708 4695 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}::_LoadAromaticityModelsData: The current release of MayaChemTools doesn't support aromaticity model parameter name, $ParameterName, specified in $DataFile. It would be ignore during aromaticity detection.\nLine: $Line..."</span><span class="sc">;</span>
|
|
|
4709 4696 <span class="s">}</span>
|
|
|
4710 4697
|
|
|
4711 4698 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$ParameterNames</span>{<span class="i">$ParameterName</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
4712 4699 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}::_LoadAromaticityModelsData: Ignoring aromaticity model data for parameter name, $ParameterName, in $DataFile. It has already been loaded.\nLine: $Line..."</span><span class="sc">;</span>
|
|
|
4713 4700 <span class="k">next</span> <span class="j">LINE</span><span class="sc">;</span>
|
|
|
4714 4701 <span class="s">}</span>
|
|
|
4715 4702 <span class="i">$ParameterNames</span>{<span class="i">$ParameterName</span>} = <span class="i">$ParameterName</span><span class="sc">;</span>
|
|
|
4716 4703
|
|
|
4717 4704 <span class="k">for</span> <span class="i">$Index</span> <span class="s">(</span><span class="n">1</span> .. <span class="i">$#LineWords</span><span class="s">)</span> <span class="s">{</span>
|
|
|
4718 4705 <span class="i">$ModelName</span> = <span class="i">$ColIndexToModelName</span>{<span class="i">$Index</span>}<span class="sc">;</span>
|
|
|
4719 4706 <span class="i">$ParameterValue</span> = <span class="i">$LineWords</span>[<span class="i">$Index</span>]<span class="sc">;</span>
|
|
|
4720 4707 <span class="i">$AromaticityModelsDataMap</span>{<span class="i">$ModelName</span>}{<span class="i">$ParameterName</span>} = <span class="i">$ParameterValue</span><span class="sc">;</span>
|
|
|
4721 4708 <span class="s">}</span>
|
|
|
4722 4709 <span class="s">}</span>
|
|
|
4723 4710 <span class="k">close</span> <span class="w">DATAFILE</span><span class="sc">;</span>
|
|
|
4724 4711 <span class="s">}</span>
|
|
|
4725 4712
|
|
|
4726 4713 <span class="c"># Process already loaded aromaticity model data...</span>
|
|
|
4727 4714 <span class="c">#</span>
|
|
|
4728 <a name="_ProcessAromaticityModelsData-"></a>4715 <span class="k">sub </span><span class="m">_ProcessAromaticityModelsData</span> <span class="s">{</span>
|
|
|
4729 4716 <span class="k">my</span><span class="s">(</span><span class="i">$ParameterName</span><span class="cm">,</span> <span class="i">$ParameterValue</span><span class="cm">,</span> <span class="i">$ModelName</span><span class="cm">,</span> <span class="i">$NewParameterValue</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4730 4717
|
|
|
4731 4718 <span class="k">for</span> <span class="i">$ModelName</span> <span class="s">(</span><span class="k">keys</span> <span class="i">%AromaticityModelsDataMap</span><span class="s">)</span> <span class="s">{</span>
|
|
|
4732 4719 <span class="k">for</span> <span class="i">$ParameterName</span> <span class="s">(</span><span class="k">keys</span> <span class="i">%</span>{<span class="i">$AromaticityModelsDataMap</span>{<span class="i">$ModelName</span>}}<span class="s">)</span> <span class="s">{</span>
|
|
|
4733 4720 <span class="i">$ParameterValue</span> = <span class="i">$AromaticityModelsDataMap</span>{<span class="i">$ModelName</span>}{<span class="i">$ParameterName</span>}<span class="sc">;</span>
|
|
|
4734 4721 <span class="i">$ParameterValue</span> =~ <span class="q">s/ //g</span><span class="sc">;</span>
|
|
|
4735 4722
|
|
|
4736 4723 <span class="j">VALUE:</span> <span class="s">{</span>
|
|
|
4737 4724 <span class="k">if</span> <span class="s">(</span><span class="i">$ParameterValue</span> =~ <span class="q">/^Yes$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
4738 4725 <span class="i">$NewParameterValue</span> = <span class="n">1</span><span class="sc">;</span>
|
|
|
4739 4726 <span class="k">last</span> <span class="j">VALUE</span><span class="sc">;</span>
|
|
|
4740 4727 <span class="s">}</span>
|
|
|
4741 4728 <span class="k">if</span> <span class="s">(</span><span class="i">$ParameterValue</span> =~ <span class="q">/^(NA|No)$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
4742 4729 <span class="i">$NewParameterValue</span> = <span class="n">0</span><span class="sc">;</span>
|
|
|
4743 4730 <span class="k">last</span> <span class="j">VALUE</span><span class="sc">;</span>
|
|
|
4744 4731 <span class="s">}</span>
|
|
|
4745 4732 <span class="k">if</span> <span class="s">(</span><span class="i">$ParameterValue</span> =~ <span class="q">/^None$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
4746 4733 <span class="i">$NewParameterValue</span> = <span class="q">''</span><span class="sc">;</span>
|
|
|
4747 4734 <span class="k">last</span> <span class="j">VALUE</span><span class="sc">;</span>
|
|
|
4748 4735 <span class="s">}</span>
|
|
|
4749 4736 <span class="i">$NewParameterValue</span> = <span class="i">$ParameterValue</span><span class="sc">;</span>
|
|
|
4750 4737 <span class="s">}</span>
|
|
|
4751 4738 <span class="i">$AromaticityModelsDataMap</span>{<span class="i">$ModelName</span>}{<span class="i">$ParameterName</span>} = <span class="i">$NewParameterValue</span><span class="sc">;</span>
|
|
|
4752 4739
|
|
|
4753 4740 <span class="k">if</span> <span class="s">(</span><span class="i">$ParameterName</span> =~ <span class="q">/List/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
4754 4741 <span class="c"># Setup a new parameter conatining a reference to a hash for the specified values...</span>
|
|
|
4755 4742 <span class="k">my</span><span class="s">(</span><span class="i">$DataMapRefName</span><span class="cm">,</span> <span class="i">$DataValue</span><span class="cm">,</span> <span class="i">%DataMap</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4756 4743
|
|
|
4757 4744 <span class="i">$DataMapRefName</span> = <span class="q">"${ParameterName}MapRef"</span><span class="sc">;</span>
|
|
|
4758 4745
|
|
|
4759 4746 <span class="i">%DataMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
4760 4747 <span class="k">for</span> <span class="i">$DataValue</span> <span class="s">(</span><span class="k">split</span> <span class="q">/\,/</span><span class="cm">,</span> <span class="i">$NewParameterValue</span><span class="s">)</span> <span class="s">{</span>
|
|
|
4761 4748 <span class="i">$DataMap</span>{<span class="i">$DataValue</span>} = <span class="i">$DataValue</span><span class="sc">;</span>
|
|
|
4762 4749 <span class="s">}</span>
|
|
|
4763 4750 <span class="i">$AromaticityModelsDataMap</span>{<span class="i">$ModelName</span>}{<span class="i">$DataMapRefName</span>} = \<span class="i">%DataMap</span><span class="sc">;</span>
|
|
|
4764 4751 <span class="s">}</span>
|
|
|
4765 4752 <span class="s">}</span>
|
|
|
4766 4753 <span class="s">}</span>
|
|
|
4767 4754 <span class="s">}</span>
|
|
|
4768 4755
|
|
|
4769 4756 <span class="c"># Is it a molecule object?</span>
|
|
|
4770 <a name="_IsMolecule-"></a>4757 <span class="k">sub </span><span class="m">_IsMolecule</span> <span class="s">{</span>
|
|
|
4771 4758 <span class="k">my</span><span class="s">(</span><span class="i">$Object</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
4772 4759
|
|
|
4773 4760 <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>
|
|
|
4774 4761 <span class="s">}</span>
|
|
|
4775 4762
|
|
|
4776 <a name="EOF-"></a></pre>
|
|
|
4777 <p> </p>
|
|
|
4778 <br />
|
|
|
4779 <center>
|
|
|
4780 <img src="../../../images/h2o2.png">
|
|
|
4781 </center>
|
|
|
4782 </body>
|
|
|
4783 </html>
|
