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3 <title>MayaChemTools:Code:Bond.pm</title>
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13 <pre>
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14 <a name="package-Bond-"></a> 1 <span class="k">package </span><span class="i">Bond</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: Bond.pm,v $</span>
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17 4 <span class="c"># $Date: 2015/02/28 20:47:02 $</span>
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18 5 <span class="c"># $Revision: 1.40 $</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
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49 36 <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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50 37
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51 38 <span class="i">@ISA</span> = <span class="q">qw(ObjectProperty Exporter)</span><span class="sc">;</span>
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52 39 <span class="i">@EXPORT</span> = <span class="q">qw()</span><span class="sc">;</span>
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53 40 <span class="i">@EXPORT_OK</span> = <span class="q">qw()</span><span class="sc">;</span>
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54 41
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55 42 <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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56 43
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57 44 <span class="c"># Setup class variables...</span>
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58 45 <span class="k">my</span><span class="s">(</span><span class="i">$ClassName</span><span class="cm">,</span> <span class="i">$ObjectID</span><span class="s">)</span><span class="sc">;</span>
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59 46 <span class="i">_InitializeClass</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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60 47
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61 48 <span class="c"># Overload Perl functions...</span>
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62 49 <span class="k">use</span> <span class="w">overload</span> <span class="q">'""'</span> <span class="cm">=></span> <span class="q">'StringifyBond'</span><span class="sc">;</span>
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63 50
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64 51 <span class="c"># Class constructor...</span>
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65 <a name="new-"></a> 52 <span class="k">sub </span><span class="m">new</span> <span class="s">{</span>
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66 53 <span class="k">my</span><span class="s">(</span><span class="i">$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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67 54
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68 55 <span class="c"># Initialize object...</span>
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69 56 <span class="k">my</span> <span class="i">$This</span> = <span class="s">{</span><span class="s">}</span><span class="sc">;</span>
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70 57 <span class="k">bless</span> <span class="i">$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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71 58 <span class="i">$This</span><span class="i">->_InitializeBond</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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72 59
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73 60 <span class="i">$This</span><span class="i">->_InitializeBondProperties</span><span class="s">(</span><span class="i">%NamesAndValues</span><span class="s">)</span><span class="sc">;</span>
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74 61
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75 62 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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76 63 <span class="s">}</span>
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77 64
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78 65 <span class="c"># Initialize object data...</span>
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79 66 <span class="c">#</span>
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80 <a name="_InitializeBond-"></a> 67 <span class="k">sub </span><span class="m">_InitializeBond</span> <span class="s">{</span>
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81 68 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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82 69 <span class="k">my</span><span class="s">(</span><span class="i">$ObjectID</span><span class="s">)</span> = <span class="i">_GetNewObjectID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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83 70
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84 71 <span class="c"># All other property names and values along with all Set/Get<PropertyName> methods</span>
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85 72 <span class="c"># are implemented on-demand using ObjectProperty class.</span>
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86 73 <span class="i">$This</span>->{<span class="w">ID</span>} = <span class="i">$ObjectID</span><span class="sc">;</span>
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87 74
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88 75 <span class="c"># Bond from and to atoms indicate begining and ending bond atoms...</span>
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89 76 <span class="i">$This</span>->{<span class="w">BondFromAtom</span>} = <span class="k">undef</span><span class="sc">;</span>
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90 77 <span class="i">$This</span>->{<span class="w">BondToAtom</span>} = <span class="k">undef</span><span class="sc">;</span>
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91 78
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92 79 <span class="i">$This</span>->{<span class="w">BondOrder</span>} = <span class="q">''</span><span class="sc">;</span>
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93 80 <span class="i">$This</span>->{<span class="w">BondType</span>} = <span class="q">''</span><span class="sc">;</span>
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94 81 <span class="i">$This</span>->{<span class="w">BondStereochemistry</span>} = <span class="q">''</span><span class="sc">;</span>
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95 82 <span class="s">}</span>
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96 83
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97 84 <span class="c"># Initialize class ...</span>
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98 <a name="_InitializeClass-"></a> 85 <span class="k">sub </span><span class="m">_InitializeClass</span> <span class="s">{</span>
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99 86 <span class="c">#Class name...</span>
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100 87 <span class="i">$ClassName</span> = <span class="w">__PACKAGE__</span><span class="sc">;</span>
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101 88
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102 89 <span class="c"># ID to keep track of objects...</span>
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103 90 <span class="i">$ObjectID</span> = <span class="n">0</span><span class="sc">;</span>
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104 91 <span class="s">}</span>
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105 92
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106 93 <span class="c"># Initialize bond properties...</span>
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107 <a name="_InitializeBondProperties-"></a> 94 <span class="k">sub </span><span class="m">_InitializeBondProperties</span> <span class="s">{</span>
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108 95 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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109 96
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110 97 <span class="k">my</span><span class="s">(</span><span class="i">$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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111 98 <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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112 99 <span class="i">$MethodName</span> = <span class="q">"Set${Name}"</span><span class="sc">;</span>
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113 100 <span class="i">$This</span><span class="i">->$MethodName</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="sc">;</span>
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114 101 <span class="s">}</span>
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115 102
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116 103 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$NamesAndValues</span>{<span class="q">'Atoms'</span>}<span class="s">)</span> <span class="s">{</span>
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117 104 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->new: Bond object instantiated without specifying atoms list..."</span><span class="sc">;</span>
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118 105 <span class="s">}</span>
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119 106 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$NamesAndValues</span>{<span class="q">'BondOrder'</span>}<span class="s">)</span> <span class="s">{</span>
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120 107 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->new: Bond object instantiated without setting bond order..."</span><span class="sc">;</span>
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121 108 <span class="s">}</span>
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122 109 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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123 110 <span class="s">}</span>
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124 111
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125 112 <span class="c"># Setup an explicit SetID method to block setting of ID by AUTOLOAD function...</span>
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126 <a name="SetID-"></a> 113 <span class="k">sub </span><span class="m">SetID</span> <span class="s">{</span>
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127 114 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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128 115
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129 116 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->SetID: Object ID can't be changed: it's used for internal tracking..."</span><span class="sc">;</span>
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130 117
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131 118 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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132 119 <span class="s">}</span>
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133 120
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134 121 <span class="c"># Setup an explicit SetMolecule method to block setting of ID by AUTOLOAD function...</span>
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135 <a name="SetMolecule-"></a> 122 <span class="k">sub </span><span class="m">SetMolecule</span> <span class="s">{</span>
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136 123 <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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137 124
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138 125 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->SetMolecule: Molecule property can't be changed: it's used for internal tracking..."</span><span class="sc">;</span>
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139 126
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140 127 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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141 128 <span class="s">}</span>
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142 129
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143 130 <span class="c"># Assign bond to molecule...</span>
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144 <a name="_SetMolecule-"></a> 131 <span class="k">sub </span><span class="m">_SetMolecule</span> <span class="s">{</span>
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145 132 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Molecule</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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146 133
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147 134 <span class="i">$This</span>->{<span class="w">Molecule</span>} = <span class="i">$Molecule</span><span class="sc">;</span>
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148 135
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149 136 <span class="c"># Weaken the reference to disable increment of reference count; otherwise,</span>
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150 137 <span class="c"># it it becomes a circular reference and destruction of Molecule object doesn't</span>
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151 138 <span class="c"># get initiated which in turn disables destruction of bond object.</span>
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152 139 <span class="c">#</span>
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153 140 <span class="i">Scalar::Util::weaken</span><span class="s">(</span><span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="s">)</span><span class="sc">;</span>
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154 141
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155 142 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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156 143 <span class="s">}</span>
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157 144
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158 145 <span class="c"># Set bond atoms...</span>
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159 <a name="SetAtoms-"></a> 146 <span class="k">sub </span><span class="m">SetAtoms</span> <span class="s">{</span>
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160 147 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">@Values</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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161 148
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162 149 <span class="k">if</span> <span class="s">(</span>!<span class="i">@Values</span><span class="s">)</span> <span class="s">{</span>
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163 150 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetAtoms: No atoms specified..."</span><span class="sc">;</span>
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164 151 <span class="s">}</span>
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165 152
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166 153 <span class="k">my</span><span class="s">(</span><span class="i">$FirstValue</span><span class="cm">,</span> <span class="i">$TypeOfFirstValue</span><span class="cm">,</span> <span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="cm">,</span> <span class="i">$AtomID1</span><span class="cm">,</span> <span class="i">$AtomID2</span><span class="s">)</span><span class="sc">;</span>
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167 154 <span class="i">$FirstValue</span> = <span class="i">$Values</span>[<span class="n">0</span>]<span class="sc">;</span>
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168 155 <span class="i">$TypeOfFirstValue</span> = <span class="k">ref</span> <span class="i">$FirstValue</span><span class="sc">;</span>
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169 156
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170 157 <span class="k">if</span> <span class="s">(</span><span class="i">$TypeOfFirstValue</span> =~ <span class="q">/^ARRAY/</span><span class="s">)</span> <span class="s">{</span>
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171 158 <span class="c"># Initialize using array refernce...</span>
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172 159 <span class="k">if</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$FirstValue</span>} != <span class="n">2</span><span class="s">)</span> <span class="s">{</span>
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173 160 <span class="w">croak</span> <span class="q">"Warning: ${ClassName}->SetAtoms: Number of atoms specified in bond object is not equal to 2..."</span><span class="sc">;</span>
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174 161 <span class="s">}</span>
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175 162 <span class="s">(</span><span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">)</span> = <span class="i">@</span>{<span class="i">$FirstValue</span>}<span class="sc">;</span>
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176 163 <span class="s">}</span>
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177 164 <span class="k">else</span> <span class="s">{</span>
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178 165 <span class="c"># It's a list of values...</span>
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179 166 <span class="k">if</span> <span class="s">(</span><span class="i">@Values</span> != <span class="n">2</span><span class="s">)</span> <span class="s">{</span>
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180 167 <span class="w">croak</span> <span class="q">"Warning: ${ClassName}->SetAtoms: Number of atoms specified in bond object is not equal to 2..."</span><span class="sc">;</span>
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181 168 <span class="s">}</span>
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182 169 <span class="s">(</span><span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">)</span> = <span class="i">@Values</span><span class="sc">;</span>
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183 170 <span class="s">}</span>
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184 171
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185 172 <span class="i">$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">$Atom2</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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186 173 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomID1</span> == <span class="i">$AtomID2</span><span class="s">)</span> <span class="s">{</span>
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187 174 <span class="w">croak</span> <span class="q">"Warning: ${ClassName}->SetAtoms: Can't specify same atoms to create a bond..."</span><span class="sc">;</span>
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188 175 <span class="s">}</span>
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189 176
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190 177 <span class="i">$This</span>->{<span class="w">BondFromAtom</span>} = <span class="i">$Atom1</span><span class="sc">;</span>
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191 178 <span class="i">$This</span>->{<span class="w">BondToAtom</span>} = <span class="i">$Atom2</span><span class="sc">;</span>
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192 179
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193 180 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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194 181 <span class="s">}</span>
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195 182
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196 183 <span class="c"># Get bond atoms as array. In scalar context, return number of atoms involved in</span>
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197 184 <span class="c"># bond...</span>
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198 185 <span class="c">#</span>
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199 <a name="GetAtoms-"></a> 186 <span class="k">sub </span><span class="m">GetAtoms</span> <span class="s">{</span>
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200 187 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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201 188
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202 189 <span class="k">return</span> <span class="k">wantarray</span> ? <span class="s">(</span><span class="i">$This</span>->{<span class="w">BondFromAtom</span>}<span class="cm">,</span> <span class="i">$This</span>->{<span class="w">BondToAtom</span>}<span class="s">)</span> <span class="co">:</span> <span class="n">2</span><span class="sc">;</span>
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203 190 <span class="s">}</span>
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204 191
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205 192 <span class="c"># Get atom bonded to specified atom...</span>
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206 <a name="GetBondedAtom-"></a> 193 <span class="k">sub </span><span class="m">GetBondedAtom</span> <span class="s">{</span>
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207 194 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Atom</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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208 195 <span class="k">my</span><span class="s">(</span><span class="i">$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">$AtomID2</span><span class="cm">,</span> <span class="i">$AtomID</span><span class="s">)</span><span class="sc">;</span>
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209 196
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210 197 <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">$This</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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211 198 <span class="i">$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">$Atom2</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> <span class="i">$AtomID</span> = <span class="i">$Atom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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212 199
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213 200 <span class="k">return</span> <span class="s">(</span><span class="i">$AtomID1</span> == <span class="i">$AtomID</span><span class="s">)</span> ? <span class="i">$Atom2</span> <span class="co">:</span> <span class="s">(</span><span class="s">(</span><span class="i">$AtomID2</span> == <span class="i">$AtomID</span><span class="s">)</span> ? <span class="i">$Atom1</span> <span class="co">:</span> <span class="k">undef</span><span class="s">)</span> <span class="sc">;</span>
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214 201 <span class="s">}</span>
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215 202
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216 203 <span class="c"># Get common atom between two bonds...</span>
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217 <a name="GetCommonAtom-"></a> 204 <span class="k">sub </span><span class="m">GetCommonAtom</span> <span class="s">{</span>
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218 205 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Other</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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219 206 <span class="k">my</span><span class="s">(</span><span class="i">$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">$AtomID2</span><span class="cm">,</span> <span class="i">$OtherAtom1</span><span class="cm">,</span> <span class="i">$OtherAtom2</span><span class="cm">,</span> <span class="i">$OtherAtomID1</span><span class="cm">,</span> <span class="i">$OtherAtomID2</span><span class="s">)</span><span class="sc">;</span>
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220 207
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221 208 <span class="s">(</span><span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">)</span> = <span class="i">$This</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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222 209 <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>
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223 210
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224 211 <span class="s">(</span><span class="i">$OtherAtom1</span><span class="cm">,</span> <span class="i">$OtherAtom2</span><span class="s">)</span> = <span class="i">$Other</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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225 212 <span class="i">$OtherAtomID1</span> = <span class="i">$OtherAtom1</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> <span class="i">$OtherAtomID2</span> = <span class="i">$OtherAtom2</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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226 213
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227 214 <span class="k">return</span> <span class="s">(</span><span class="i">$AtomID1</span> == <span class="i">$OtherAtomID1</span> || <span class="i">$AtomID1</span> == <span class="i">$OtherAtomID2</span><span class="s">)</span> ? <span class="i">$Atom1</span> <span class="co">:</span> <span class="s">(</span><span class="s">(</span><span class="i">$AtomID2</span> == <span class="i">$OtherAtomID1</span> || <span class="i">$AtomID2</span> == <span class="i">$OtherAtomID2</span><span class="s">)</span> ? <span class="i">$Atom2</span> <span class="co">:</span> <span class="k">undef</span><span class="s">)</span> <span class="sc">;</span>
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228 215 <span class="s">}</span>
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229 216
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230 217 <span class="c"># Get bond from atom indicating begining atom of a bond...</span>
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231 <a name="GetBondFromAtom-"></a> 218 <span class="k">sub </span><span class="m">GetBondFromAtom</span> <span class="s">{</span>
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232 219 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="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">return</span> <span class="i">$This</span>->{<span class="w">BondFromAtom</span>}<span class="sc">;</span>
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235 222 <span class="s">}</span>
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236 223
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237 224 <span class="c"># Get begin bond atom...</span>
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238 <a name="GetBondBeginAtom-"></a> 225 <span class="k">sub </span><span class="m">GetBondBeginAtom</span> <span class="s">{</span>
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239 226 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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240 227
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241 228 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetBondFromAtom</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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242 229 <span class="s">}</span>
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243 230
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244 231 <span class="c"># Get bond to atom indicating ending atom of a bond...</span>
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245 <a name="GetBondToAtom-"></a> 232 <span class="k">sub </span><span class="m">GetBondToAtom</span> <span class="s">{</span>
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246 233 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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247 234
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248 235 <span class="k">return</span> <span class="i">$This</span>->{<span class="w">BondToAtom</span>}<span class="sc">;</span>
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|
|
249 236 <span class="s">}</span>
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250 237
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251 238 <span class="c"># Get begin bond atom...</span>
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252 <a name="GetBondEndAtom-"></a> 239 <span class="k">sub </span><span class="m">GetBondEndAtom</span> <span class="s">{</span>
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253 240 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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254 241
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255 242 <span class="k">return</span> <span class="i">$This</span><span class="i">->GetBondToAtom</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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256 243 <span class="s">}</span>
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257 244
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258 245 <span class="c"># Switch bond from and to atoms...</span>
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259 <a name="SwitchBondFromAndToAtoms-"></a> 246 <span class="k">sub </span><span class="m">SwitchBondFromAndToAtoms</span> <span class="s">{</span>
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260 247 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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261 248 <span class="k">my</span><span class="s">(</span><span class="i">$FromAtom</span><span class="cm">,</span> <span class="i">$ToAtom</span><span class="s">)</span><span class="sc">;</span>
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262 249
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263 250 <span class="s">(</span><span class="i">$FromAtom</span><span class="cm">,</span> <span class="i">$ToAtom</span><span class="s">)</span> = <span class="i">$This</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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264 251
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265 252 <span class="i">$This</span>->{<span class="w">BondFromAtom</span>} = <span class="i">$ToAtom</span><span class="sc">;</span>
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266 253 <span class="i">$This</span>->{<span class="w">BondToAtom</span>} = <span class="i">$FromAtom</span><span class="sc">;</span>
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267 254
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268 255 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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|
|
269 256 <span class="s">}</span>
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270 257
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271 258 <span class="c"># Set bond order...</span>
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|
272 259 <span class="c">#</span>
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273 260 <span class="c"># Possible BondOrder are: 0 = None, 1 = Single, 1.5 = Aromatic, 2 = Double, 3 = Triple, 4 = Quadruple,</span>
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274 261 <span class="c"># 5 = Quintuple, 6 = Sextuple, 7 = Septuple</span>
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|
|
275 262 <span class="c">#</span>
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|
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276 263 <span class="c"># Possible BondType for different BondOrders are:</span>
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277 264 <span class="c">#</span>
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|
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278 265 <span class="c"># 0 : None, Ionic, Unspecified</span>
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279 266 <span class="c"># 1 : Single, Dative, Coordinate, SingleOrDouble, SingleOrAromatic, Tautomeric</span>
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280 267 <span class="c"># 1.5 : Aromatic, Resonance, SingleOrAromatic, DoubleOrAromatic</span>
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281 268 <span class="c"># 2 : Double, Tautomeric, SingleOrDouble, DoubleOrAromatic</span>
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282 269 <span class="c"># 3 : Triple</span>
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283 270 <span class="c"># 4 : Quadruple</span>
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284 271 <span class="c"># 5 : Quintuple</span>
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285 272 <span class="c"># 6 : Sextuple</span>
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286 273 <span class="c"># 7 : Septuple</span>
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287 274 <span class="c">#</span>
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|
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288 275 <span class="c"># Note: BondType Any is valid for all BondOrders.</span>
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|
|
289 276 <span class="c">#</span>
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|
|
290 277 <span class="c"># Possible BondStereochemistry values for different BondOrders are:</span>
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|
291 278 <span class="c">#</span>
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|
292 279 <span class="c"># 0 : None, Unspecified</span>
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|
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293 280 <span class="c"># 1 : Wedge, Up, Hash, Down, Wavy, WedgeOrHash, UpOrDown, Upward, Downward, None, Unspecified</span>
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|
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294 281 <span class="c"># 2 : Cis, Trans, Z, E, DoubleCross, CisOrTrans, None, Unspecified</span>
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|
|
295 282 <span class="c">#</span>
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|
|
296 283 <span class="c"># Notes:</span>
|
|
|
297 284 <span class="c"># . BondType property is automatically assigned using default BondType values for</span>
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|
298 285 <span class="c"># specified BondOrder.</span>
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|
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299 286 <span class="c"># . BondType values can also be explicit set.</span>
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|
|
300 287 <span class="c"># . To make bonds aromatic in a ring, explicitly set "Aromatic" property for bond/atoms and make sure</span>
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|
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301 288 <span class="c"># appropriate BondOrder values are assigned.</span>
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302 289 <span class="c"># . Dative or coordinate bond types are treated as single bond types with explicit formal charge</span>
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303 290 <span class="c"># of + and - on first and second bond atoms.</span>
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|
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304 291 <span class="c">#</span>
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305 <a name="SetBondOrder-"></a> 292 <span class="k">sub </span><span class="m">SetBondOrder</span> <span class="s">{</span>
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306 293 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$BondOrder</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
307 294
|
|
|
308 295 <span class="k">if</span> <span class="s">(</span><span class="i">$BondOrder</span> !~ <span class="q">/^(0|1|1.5|2|3|4|5|6|7)$/</span><span class="s">)</span> <span class="s">{</span>
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|
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309 296 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetBondOrder: BondOrder value $BondOrder is not valid. Supported values: 0, 1, 1.5, 2, 3, 4, 5, 6, 7"</span><span class="sc">;</span>
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|
|
310 297 <span class="s">}</span>
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|
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311 298
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|
312 299 <span class="c"># Set bond order and type...</span>
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|
313 300 <span class="k">my</span><span class="s">(</span><span class="i">$BondType</span><span class="s">)</span><span class="sc">;</span>
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314 301
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315 302 <span class="j">BONDORDER:</span> <span class="s">{</span>
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|
316 303 <span class="k">if</span> <span class="s">(</span><span class="i">$BondOrder</span> == <span class="n">1</span><span class="s">)</span> <span class="s">{</span><span class="i">$BondType</span> = <span class="q">'Single'</span><span class="sc">;</span> <span class="k">last</span> <span class="j">BONDORDER</span><span class="sc">;</span> <span class="s">}</span>
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|
|
317 304 <span class="k">if</span> <span class="s">(</span><span class="i">$BondOrder</span> == <span class="n">1.5</span><span class="s">)</span> <span class="s">{</span><span class="i">$BondType</span> = <span class="q">'Aromatic'</span><span class="sc">;</span> <span class="k">last</span> <span class="j">BONDORDER</span><span class="sc">;</span> <span class="s">}</span>
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|
|
318 305 <span class="k">if</span> <span class="s">(</span><span class="i">$BondOrder</span> == <span class="n">2</span><span class="s">)</span> <span class="s">{</span><span class="i">$BondType</span> = <span class="q">'Double'</span><span class="sc">;</span> <span class="k">last</span> <span class="j">BONDORDER</span><span class="sc">;</span> <span class="s">}</span>
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|
|
319 306 <span class="k">if</span> <span class="s">(</span><span class="i">$BondOrder</span> == <span class="n">3</span><span class="s">)</span> <span class="s">{</span><span class="i">$BondType</span> = <span class="q">'Triple'</span><span class="sc">;</span> <span class="k">last</span> <span class="j">BONDORDER</span><span class="sc">;</span> <span class="s">}</span>
|
|
|
320 307 <span class="k">if</span> <span class="s">(</span><span class="i">$BondOrder</span> == <span class="n">4</span><span class="s">)</span> <span class="s">{</span><span class="i">$BondType</span> = <span class="q">'Quadruple'</span><span class="sc">;</span> <span class="k">last</span> <span class="j">BONDORDER</span><span class="sc">;</span> <span class="s">}</span>
|
|
|
321 308 <span class="k">if</span> <span class="s">(</span><span class="i">$BondOrder</span> == <span class="n">5</span><span class="s">)</span> <span class="s">{</span><span class="i">$BondType</span> = <span class="q">'Quintuple'</span><span class="sc">;</span> <span class="k">last</span> <span class="j">BONDORDER</span><span class="sc">;</span> <span class="s">}</span>
|
|
|
322 309 <span class="k">if</span> <span class="s">(</span><span class="i">$BondOrder</span> == <span class="n">6</span><span class="s">)</span> <span class="s">{</span><span class="i">$BondType</span> = <span class="q">'Sextuple'</span><span class="sc">;</span> <span class="k">last</span> <span class="j">BONDORDER</span><span class="sc">;</span> <span class="s">}</span>
|
|
|
323 310 <span class="k">if</span> <span class="s">(</span><span class="i">$BondOrder</span> == <span class="n">7</span><span class="s">)</span> <span class="s">{</span><span class="i">$BondType</span> = <span class="q">'Septuple'</span><span class="sc">;</span> <span class="k">last</span> <span class="j">BONDORDER</span><span class="sc">;</span> <span class="s">}</span>
|
|
|
324 311 <span class="i">$BondType</span> = <span class="q">''</span><span class="sc">;</span>
|
|
|
325 312 <span class="i">$BondOrder</span> = <span class="n">0</span><span class="sc">;</span>
|
|
|
326 313 <span class="s">}</span>
|
|
|
327 314 <span class="i">$This</span>->{<span class="w">BondType</span>} = <span class="i">$BondType</span><span class="sc">;</span>
|
|
|
328 315 <span class="i">$This</span>->{<span class="w">BondOrder</span>} = <span class="i">$BondOrder</span><span class="sc">;</span>
|
|
|
329 316
|
|
|
330 317 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
331 318
|
|
|
332 319 <span class="s">}</span>
|
|
|
333 320
|
|
|
334 321 <span class="c"># Set bond type for a specific bond...</span>
|
|
|
335 322 <span class="c">#</span>
|
|
|
336 <a name="SetBondType-"></a> 323 <span class="k">sub </span><span class="m">SetBondType</span> <span class="s">{</span>
|
|
|
337 324 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$BondType</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
338 325
|
|
|
339 326 <span class="k">if</span> <span class="s">(</span><span class="i">$BondType</span> !~ <span class="q">/^(None|Ionic|Unspecified|Single|Dative|Coordinate|SingleOrDouble|SingleOrAromatic|Aromatic|Tautomeric|Resonance|DoubleOrAromatic|Double|Triple|Quadruple|Any)$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
340 327 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetBondType: BondType value $BondType is not valid. Supported values: None, Ionic, Unspecified, Single, Dative, Coordinate, SingleOrDouble, SingleOrAromatic, Aromatic, Tautomeric, Resonance, DoubleOrAromatic, Double, Triple, Quadruple, Any..."</span><span class="sc">;</span>
|
|
|
341 328 <span class="s">}</span>
|
|
|
342 329
|
|
|
343 330 <span class="c"># Make sure its a valid BondType value for BondOrder...</span>
|
|
|
344 331 <span class="k">my</span><span class="s">(</span><span class="i">$BondOrder</span><span class="cm">,</span> <span class="i">$ValidBondType</span><span class="s">)</span><span class="sc">;</span>
|
|
|
345 332
|
|
|
346 333 <span class="i">$ValidBondType</span> = <span class="n">0</span><span class="sc">;</span>
|
|
|
347 334 <span class="i">$BondOrder</span> = <span class="i">$This</span>->{<span class="w">BondOrder</span>}<span class="sc">;</span>
|
|
|
348 335
|
|
|
349 336 <span class="j">BONDORDER:</span> <span class="s">{</span>
|
|
|
350 337 <span class="k">if</span> <span class="s">(</span><span class="i">$BondOrder</span> == <span class="n">0</span> && <span class="i">$BondType</span> =~ <span class="q">/^(None|Ionic|Unspecified|Any)$/i</span><span class="s">)</span> <span class="s">{</span><span class="i">$ValidBondType</span> = <span class="n">1</span><span class="sc">;</span> <span class="k">last</span> <span class="j">BONDORDER</span><span class="sc">;</span> <span class="s">}</span>
|
|
|
351 338 <span class="k">if</span> <span class="s">(</span><span class="i">$BondOrder</span> == <span class="n">1</span> && <span class="i">$BondType</span> =~ <span class="q">/^(Single|Dative|Coordinate|SingleOrDouble|SingleOrAromatic|Tautomeric|Any)$/i</span><span class="s">)</span> <span class="s">{</span><span class="i">$ValidBondType</span> = <span class="n">1</span><span class="sc">;</span> <span class="k">last</span> <span class="j">BONDORDER</span><span class="sc">;</span> <span class="s">}</span>
|
|
|
352 339 <span class="k">if</span> <span class="s">(</span><span class="i">$BondOrder</span> == <span class="n">1.5</span> && <span class="i">$BondType</span> =~ <span class="q">/^(Aromatic|Resonance|SingleOrAromatic|DoubleOrAromatic|Any)$/i</span><span class="s">)</span> <span class="s">{</span><span class="i">$ValidBondType</span> = <span class="n">1</span><span class="sc">;</span> <span class="k">last</span> <span class="j">BONDORDER</span><span class="sc">;</span> <span class="s">}</span>
|
|
|
353 340 <span class="k">if</span> <span class="s">(</span><span class="i">$BondOrder</span> == <span class="n">2</span> && <span class="i">$BondType</span> =~ <span class="q">/^(Double|SingleOrDouble|DoubleOrAromatic|Tautomeric|Any)$/i</span> <span class="s">)</span> <span class="s">{</span><span class="i">$ValidBondType</span> = <span class="n">1</span><span class="sc">;</span> <span class="k">last</span> <span class="j">BONDORDER</span><span class="sc">;</span> <span class="s">}</span>
|
|
|
354 341 <span class="k">if</span> <span class="s">(</span><span class="i">$BondOrder</span> == <span class="n">3</span> && <span class="i">$BondType</span> =~ <span class="q">/^(Triple|Any)$/i</span><span class="s">)</span> <span class="s">{</span><span class="i">$ValidBondType</span> = <span class="n">1</span><span class="sc">;</span> <span class="k">last</span> <span class="j">BONDORDER</span><span class="sc">;</span> <span class="s">}</span>
|
|
|
355 342 <span class="k">if</span> <span class="s">(</span><span class="i">$BondOrder</span> == <span class="n">4</span> && <span class="i">$BondType</span> =~ <span class="q">/^(Quadruple|Any)$/i</span><span class="s">)</span> <span class="s">{</span><span class="i">$ValidBondType</span> = <span class="n">1</span><span class="sc">;</span> <span class="k">last</span> <span class="j">BONDORDER</span><span class="sc">;</span> <span class="s">}</span>
|
|
|
356 343 <span class="k">if</span> <span class="s">(</span><span class="i">$BondOrder</span> == <span class="n">5</span> && <span class="i">$BondType</span> =~ <span class="q">/^(Quintuple|Any)$/i</span><span class="s">)</span> <span class="s">{</span><span class="i">$ValidBondType</span> = <span class="n">1</span><span class="sc">;</span> <span class="k">last</span> <span class="j">BONDORDER</span><span class="sc">;</span> <span class="s">}</span>
|
|
|
357 344 <span class="k">if</span> <span class="s">(</span><span class="i">$BondOrder</span> == <span class="n">6</span> && <span class="i">$BondType</span> =~ <span class="q">/^(Sextuple|Any)$/i</span><span class="s">)</span> <span class="s">{</span><span class="i">$ValidBondType</span> = <span class="n">1</span><span class="sc">;</span> <span class="k">last</span> <span class="j">BONDORDER</span><span class="sc">;</span> <span class="s">}</span>
|
|
|
358 345 <span class="k">if</span> <span class="s">(</span><span class="i">$BondOrder</span> == <span class="n">7</span> && <span class="i">$BondType</span> =~ <span class="q">/^(Septuple|Any)$/i</span><span class="s">)</span> <span class="s">{</span><span class="i">$ValidBondType</span> = <span class="n">1</span><span class="sc">;</span> <span class="k">last</span> <span class="j">BONDORDER</span><span class="sc">;</span> <span class="s">}</span>
|
|
|
359 346 <span class="i">$ValidBondType</span> = <span class="n">0</span><span class="sc">;</span>
|
|
|
360 347 <span class="s">}</span>
|
|
|
361 348
|
|
|
362 349 <span class="k">if</span> <span class="s">(</span>!<span class="i">$ValidBondType</span><span class="s">)</span> <span class="s">{</span>
|
|
|
363 350 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->SetBondType: Assigning invalid BondType value, $BondType, for BondOrder $BondOrder..."</span><span class="sc">;</span>
|
|
|
364 351 <span class="s">}</span>
|
|
|
365 352
|
|
|
366 353 <span class="i">$This</span>->{<span class="w">BondType</span>} = <span class="i">$BondType</span><span class="sc">;</span>
|
|
|
367 354
|
|
|
368 355 <span class="c"># Set explicit formal charge for atoms involved in Dative or coordinate bonds...</span>
|
|
|
369 356 <span class="k">if</span> <span class="s">(</span><span class="i">$BondType</span> =~ <span class="q">/^(Dative|Coordinate)$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
370 357 <span class="k">my</span><span class="s">(</span><span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">)</span> = <span class="i">$This</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
371 358 <span class="i">$Atom1</span><span class="i">->SetFormalCharge</span><span class="s">(</span><span class="q">'1'</span><span class="s">)</span><span class="sc">;</span>
|
|
|
372 359 <span class="i">$Atom2</span><span class="i">->SetFormalCharge</span><span class="s">(</span><span class="q">'-1'</span><span class="s">)</span><span class="sc">;</span>
|
|
|
373 360 <span class="s">}</span>
|
|
|
374 361
|
|
|
375 362 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
376 363 <span class="s">}</span>
|
|
|
377 364
|
|
|
378 365 <span class="c"># Set bond stereochemistry...</span>
|
|
|
379 366 <span class="c">#</span>
|
|
|
380 367 <span class="c"># Single bond stereochemistry:</span>
|
|
|
381 368 <span class="c">#</span>
|
|
|
382 369 <span class="c"># None, Unspecified: Not a stereo bond or unspecified</span>
|
|
|
383 370 <span class="c">#</span>
|
|
|
384 371 <span class="c"># Wedge, Up : Wedge end pointing up</span>
|
|
|
385 372 <span class="c"># Hash, Down: Wedge end pointing down</span>
|
|
|
386 373 <span class="c"># Wavy, WedgeOrHash, UpOrDown: Wedge end up or down</span>
|
|
|
387 374 <span class="c">#</span>
|
|
|
388 375 <span class="c"># Note: Wedge starts at begin atom of bond making wedge pointed end always at this</span>
|
|
|
389 376 <span class="c"># atom.</span>
|
|
|
390 377 <span class="c">#</span>
|
|
|
391 378 <span class="c"># Upward: Single bond around cis/trans double bonds pointing upward</span>
|
|
|
392 379 <span class="c"># Downward: Single bond around cis/trans double bonds pointing upward</span>
|
|
|
393 380 <span class="c">#</span>
|
|
|
394 381 <span class="c"># Note: Upward/downward bonds start at atoms involved in cis/trans double bond.</span>
|
|
|
395 382 <span class="c">#</span>
|
|
|
396 383 <span class="c"># Double bond stereochemistry:</span>
|
|
|
397 384 <span class="c">#</span>
|
|
|
398 385 <span class="c"># None, Unspecified: Not a stereo bond or unspecified</span>
|
|
|
399 386 <span class="c">#</span>
|
|
|
400 387 <span class="c"># Z, cis: Similar groups on same side of double bond</span>
|
|
|
401 388 <span class="c"># E, trans: Similar groups on different side of double bond</span>
|
|
|
402 389 <span class="c">#</span>
|
|
|
403 390 <span class="c"># CisOrTrans, DoubleCross: cis or trans</span>
|
|
|
404 391 <span class="c">#</span>
|
|
|
405 <a name="SetBondStereochemistry-"></a> 392 <span class="k">sub </span><span class="m">SetBondStereochemistry</span> <span class="s">{</span>
|
|
|
406 393 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$BondStereochemistry</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
407 394
|
|
|
408 395 <span class="k">if</span> <span class="s">(</span><span class="i">$BondStereochemistry</span> !~ <span class="q">/^(None|Unspecified|Wedge|Hash|Up|Down|Wavy|WedgeOrHash|UpOrDown|Upward|Downward|Cis|Trans|Z|E|DoubleCross|CisOrTrans)$/i</span><span class="s">)</span> <span class="s">{</span>
|
|
|
409 396 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetBondStereochemistry: BondStereochemistry value $BondStereochemistry is not valid. Supported values: None, Unspecified, Wedge, Hash, Up, Down, Wavy, WedgeOrHash, UpOrDown, Upward, Downward, Cis, Trans, Z, E, DoubleCross, CisOrTrans..."</span><span class="sc">;</span>
|
|
|
410 397 <span class="s">}</span>
|
|
|
411 398
|
|
|
412 399 <span class="c"># Make sure its a valid BondStereochemistry value for BondOrder...</span>
|
|
|
413 400 <span class="k">my</span><span class="s">(</span><span class="i">$BondOrder</span><span class="cm">,</span> <span class="i">$ValidBondType</span><span class="s">)</span><span class="sc">;</span>
|
|
|
414 401
|
|
|
415 402 <span class="i">$ValidBondType</span> = <span class="n">0</span><span class="sc">;</span>
|
|
|
416 403 <span class="i">$BondOrder</span> = <span class="i">$This</span>->{<span class="w">BondOrder</span>}<span class="sc">;</span>
|
|
|
417 404
|
|
|
418 405 <span class="j">BONDORDER:</span> <span class="s">{</span>
|
|
|
419 406 <span class="k">if</span> <span class="s">(</span><span class="i">$BondOrder</span> == <span class="n">0</span> && <span class="i">$BondStereochemistry</span> =~ <span class="q">/^(None|Unspecified)$/i</span><span class="s">)</span> <span class="s">{</span><span class="i">$ValidBondType</span> = <span class="n">1</span><span class="sc">;</span> <span class="k">last</span> <span class="j">BONDORDER</span><span class="sc">;</span> <span class="s">}</span>
|
|
|
420 407 <span class="k">if</span> <span class="s">(</span><span class="i">$BondOrder</span> == <span class="n">1</span> && <span class="i">$BondStereochemistry</span> =~ <span class="q">/^(Wedge|Hash|Up|Down|Wavy|WedgeOrHash|UpOrDown|Upward|Downward|None|Unspecified)$/i</span><span class="s">)</span> <span class="s">{</span><span class="i">$ValidBondType</span> = <span class="n">1</span><span class="sc">;</span> <span class="k">last</span> <span class="j">BONDORDER</span><span class="sc">;</span> <span class="s">}</span>
|
|
|
421 408 <span class="k">if</span> <span class="s">(</span><span class="i">$BondOrder</span> == <span class="n">2</span> && <span class="i">$BondStereochemistry</span> =~ <span class="q">/^(Cis|Trans|Z|E|DoubleCross|CisOrTrans|None|Unspecified)$/i</span> <span class="s">)</span> <span class="s">{</span><span class="i">$ValidBondType</span> = <span class="n">1</span><span class="sc">;</span> <span class="k">last</span> <span class="j">BONDORDER</span><span class="sc">;</span> <span class="s">}</span>
|
|
|
422 409 <span class="i">$ValidBondType</span> = <span class="n">0</span><span class="sc">;</span>
|
|
|
423 410 <span class="s">}</span>
|
|
|
424 411
|
|
|
425 412 <span class="k">if</span> <span class="s">(</span>!<span class="i">$ValidBondType</span><span class="s">)</span> <span class="s">{</span>
|
|
|
426 413 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->SetBondStereochemistry: Assigning invalid BondStereochemistry value, $BondStereochemistry, for BondOrder $BondOrder..."</span><span class="sc">;</span>
|
|
|
427 414 <span class="s">}</span>
|
|
|
428 415
|
|
|
429 416 <span class="i">$This</span>->{<span class="w">BondStereochemistry</span>} = <span class="i">$BondStereochemistry</span><span class="sc">;</span>
|
|
|
430 417
|
|
|
431 418 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
432 419 <span class="s">}</span>
|
|
|
433 420
|
|
|
434 421 <span class="c"># Is it a single bond?</span>
|
|
|
435 <a name="IsSingle-"></a> 422 <span class="k">sub </span><span class="m">IsSingle</span> <span class="s">{</span>
|
|
|
436 423 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
437 424
|
|
|
438 425 <span class="k">return</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">BondOrder</span>} == <span class="n">1</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
439 426 <span class="s">}</span>
|
|
|
440 427
|
|
|
441 428 <span class="c"># Is it a double bond?</span>
|
|
|
442 <a name="IsDouble-"></a> 429 <span class="k">sub </span><span class="m">IsDouble</span> <span class="s">{</span>
|
|
|
443 430 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
444 431
|
|
|
445 432 <span class="k">return</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">BondOrder</span>} == <span class="n">2</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
446 433 <span class="s">}</span>
|
|
|
447 434
|
|
|
448 435 <span class="c"># Is it a triple bond?</span>
|
|
|
449 <a name="IsTriple-"></a> 436 <span class="k">sub </span><span class="m">IsTriple</span> <span class="s">{</span>
|
|
|
450 437 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
451 438
|
|
|
452 439 <span class="k">return</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">BondOrder</span>} == <span class="n">3</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
453 440 <span class="s">}</span>
|
|
|
454 441
|
|
|
455 442 <span class="c"># Is it a quadruple bond?</span>
|
|
|
456 <a name="IsQuadruple-"></a> 443 <span class="k">sub </span><span class="m">IsQuadruple</span> <span class="s">{</span>
|
|
|
457 444 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
458 445
|
|
|
459 446 <span class="k">return</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">BondOrder</span>} == <span class="n">4</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
460 447 <span class="s">}</span>
|
|
|
461 448
|
|
|
462 449 <span class="c"># Is aromatic property set for the bond?</span>
|
|
|
463 <a name="IsAromatic-"></a> 450 <span class="k">sub </span><span class="m">IsAromatic</span> <span class="s">{</span>
|
|
|
464 451 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
465 452 <span class="k">my</span><span class="s">(</span><span class="i">$Aromatic</span><span class="s">)</span><span class="sc">;</span>
|
|
|
466 453
|
|
|
467 454 <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>
|
|
|
468 455
|
|
|
469 456 <span class="k">return</span> <span class="s">(</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="i">$This</span>->{<span class="w">BondOrder</span>} == <span class="n">1.5</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
470 457 <span class="s">}</span>
|
|
|
471 458
|
|
|
472 459 <span class="c"># Is it a quintuple bond?</span>
|
|
|
473 <a name="IsQuintuple-"></a> 460 <span class="k">sub </span><span class="m">IsQuintuple</span> <span class="s">{</span>
|
|
|
474 461 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
475 462
|
|
|
476 463 <span class="k">return</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">BondOrder</span>} == <span class="n">5</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
477 464 <span class="s">}</span>
|
|
|
478 465
|
|
|
479 466 <span class="c"># Is it a sextuple bond?</span>
|
|
|
480 <a name="IsSextuple-"></a> 467 <span class="k">sub </span><span class="m">IsSextuple</span> <span class="s">{</span>
|
|
|
481 468 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
482 469
|
|
|
483 470 <span class="k">return</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">BondOrder</span>} == <span class="n">6</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
484 471 <span class="s">}</span>
|
|
|
485 472
|
|
|
486 473 <span class="c"># Is bond type specified?</span>
|
|
|
487 <a name="IsBondTypeSpecified-"></a> 474 <span class="k">sub </span><span class="m">IsBondTypeSpecified</span> <span class="s">{</span>
|
|
|
488 475 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
489 476
|
|
|
490 477 <span class="k">return</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">BondType</span>} && <span class="i">$This</span>->{<span class="w">BondType</span>} !~ <span class="q">/^(None|Unspecified)$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
491 478 <span class="s">}</span>
|
|
|
492 479
|
|
|
493 480 <span class="c"># Is it a dative or coordinate bond?</span>
|
|
|
494 <a name="IsDative-"></a> 481 <span class="k">sub </span><span class="m">IsDative</span> <span class="s">{</span>
|
|
|
495 482 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
496 483
|
|
|
497 484 <span class="k">return</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">BondType</span>} =~ <span class="q">/^(Dative|Coordinate)$/i</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"># Is it a dative or coordinate bond?</span>
|
|
|
501 <a name="IsCoordinate-"></a> 488 <span class="k">sub </span><span class="m">IsCoordinate</span> <span class="s">{</span>
|
|
|
502 489 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
503 490
|
|
|
504 491 <span class="k">return</span> <span class="i">$This</span><span class="i">->IsDative</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
505 492 <span class="s">}</span>
|
|
|
506 493
|
|
|
507 494 <span class="c"># Is it a ionic bond?</span>
|
|
|
508 <a name="IsIonic-"></a> 495 <span class="k">sub </span><span class="m">IsIonic</span> <span class="s">{</span>
|
|
|
509 496 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
510 497
|
|
|
511 498 <span class="k">return</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">BondType</span>} =~ <span class="q">/^Ionic$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
512 499 <span class="s">}</span>
|
|
|
513 500
|
|
|
514 501 <span class="c"># Is it a tautomeric bond?</span>
|
|
|
515 <a name="IsTautomeric-"></a> 502 <span class="k">sub </span><span class="m">IsTautomeric</span> <span class="s">{</span>
|
|
|
516 503 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
517 504
|
|
|
518 505 <span class="k">return</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">BondType</span>} =~ <span class="q">/^Tautomeric$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
519 506 <span class="s">}</span>
|
|
|
520 507
|
|
|
521 508 <span class="c"># Is bond stereochemistry specified?</span>
|
|
|
522 <a name="IsBondStereochemistrySpecified-"></a> 509 <span class="k">sub </span><span class="m">IsBondStereochemistrySpecified</span> <span class="s">{</span>
|
|
|
523 510 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
524 511
|
|
|
525 512 <span class="k">return</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">BondStereochemistry</span>} && <span class="i">$This</span>->{<span class="w">BondStereochemistry</span>} !~ <span class="q">/^(None|Unspecified)$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
526 513 <span class="s">}</span>
|
|
|
527 514
|
|
|
528 515 <span class="c"># Is it a Wedge or Up single bond?</span>
|
|
|
529 <a name="IsWedge-"></a> 516 <span class="k">sub </span><span class="m">IsWedge</span> <span class="s">{</span>
|
|
|
530 517 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
531 518
|
|
|
532 519 <span class="k">return</span> <span class="i">$This</span><span class="i">->IsUp</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
533 520 <span class="s">}</span>
|
|
|
534 521
|
|
|
535 522 <span class="c"># Is it a Wedge or Up single bond?</span>
|
|
|
536 <a name="IsUp-"></a> 523 <span class="k">sub </span><span class="m">IsUp</span> <span class="s">{</span>
|
|
|
537 524 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
538 525
|
|
|
539 526 <span class="k">return</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">BondStereochemistry</span>} =~ <span class="q">/^(Wedge|Up)$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
540 527 <span class="s">}</span>
|
|
|
541 528
|
|
|
542 529 <span class="c"># Is it a Hash or Down single bond?</span>
|
|
|
543 <a name="IsHash-"></a> 530 <span class="k">sub </span><span class="m">IsHash</span> <span class="s">{</span>
|
|
|
544 531 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
545 532
|
|
|
546 533 <span class="k">return</span> <span class="i">$This</span><span class="i">->IsDown</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
547 534 <span class="s">}</span>
|
|
|
548 535
|
|
|
549 536 <span class="c"># Is it a Hash or Down single bond?</span>
|
|
|
550 <a name="IsDown-"></a> 537 <span class="k">sub </span><span class="m">IsDown</span> <span class="s">{</span>
|
|
|
551 538 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
552 539
|
|
|
553 540 <span class="k">return</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">BondStereochemistry</span>} =~ <span class="q">/^(Hash|Down)$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
554 541 <span class="s">}</span>
|
|
|
555 542
|
|
|
556 543 <span class="c"># Is it a Wavy, WedgeOrHash or UpOrDown single bond?</span>
|
|
|
557 <a name="IsWedgeOrHash-"></a> 544 <span class="k">sub </span><span class="m">IsWedgeOrHash</span> <span class="s">{</span>
|
|
|
558 545 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
559 546
|
|
|
560 547 <span class="k">return</span> <span class="i">$This</span><span class="i">->IsUpOrDown</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
561 548 <span class="s">}</span>
|
|
|
562 549
|
|
|
563 550 <span class="c"># Is it a Wavy, WedgeOrHash or UpOrDown single bond?</span>
|
|
|
564 <a name="IsUpOrDown-"></a> 551 <span class="k">sub </span><span class="m">IsUpOrDown</span> <span class="s">{</span>
|
|
|
565 552 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
566 553
|
|
|
567 554 <span class="k">return</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">BondStereochemistry</span>} =~ <span class="q">/^(Wavy|WedgeOrHash|UpOrDown)$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
568 555 <span class="s">}</span>
|
|
|
569 556
|
|
|
570 557 <span class="c"># Is it a upward single bond?</span>
|
|
|
571 <a name="IsUpward-"></a> 558 <span class="k">sub </span><span class="m">IsUpward</span> <span class="s">{</span>
|
|
|
572 559 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
573 560
|
|
|
574 561 <span class="k">return</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">BondStereochemistry</span>} =~ <span class="q">/^Upward$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
575 562 <span class="s">}</span>
|
|
|
576 563
|
|
|
577 564 <span class="c"># Is it a Downward single bond?</span>
|
|
|
578 <a name="IsDownward-"></a> 565 <span class="k">sub </span><span class="m">IsDownward</span> <span class="s">{</span>
|
|
|
579 566 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
580 567
|
|
|
581 568 <span class="k">return</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">BondStereochemistry</span>} =~ <span class="q">/^Downward$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
582 569 <span class="s">}</span>
|
|
|
583 570 <span class="c"># Is it a cis or Z double bond?</span>
|
|
|
584 <a name="IsCis-"></a> 571 <span class="k">sub </span><span class="m">IsCis</span> <span class="s">{</span>
|
|
|
585 572 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
586 573
|
|
|
587 574 <span class="k">return</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">BondStereochemistry</span>} =~ <span class="q">/^(Cis|Z)$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
588 575 <span class="s">}</span>
|
|
|
589 576
|
|
|
590 577 <span class="c"># Is it a trans or E double bond?</span>
|
|
|
591 <a name="IsTrans-"></a> 578 <span class="k">sub </span><span class="m">IsTrans</span> <span class="s">{</span>
|
|
|
592 579 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
593 580
|
|
|
594 581 <span class="k">return</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">BondStereochemistry</span>} =~ <span class="q">/^(Trans|E)$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
595 582 <span class="s">}</span>
|
|
|
596 583
|
|
|
597 584 <span class="c"># Is it a cis or trans double bond?</span>
|
|
|
598 <a name="IsCisOrTrans-"></a> 585 <span class="k">sub </span><span class="m">IsCisOrTrans</span> <span class="s">{</span>
|
|
|
599 586 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
600 587
|
|
|
601 588 <span class="k">return</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">BondStereochemistry</span>} =~ <span class="q">/^(CisOrTrans|DoubleCross)$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
602 589 <span class="s">}</span>
|
|
|
603 590
|
|
|
604 591 <span class="c"># Delete bond...</span>
|
|
|
605 <a name="DeleteBond-"></a> 592 <span class="k">sub </span><span class="m">DeleteBond</span> <span class="s">{</span>
|
|
|
606 593 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
607 594
|
|
|
608 595 <span class="c"># Is this atom in a molecule?</span>
|
|
|
609 596 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
610 597 <span class="c"># Nothing to do...</span>
|
|
|
611 598 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
612 599 <span class="s">}</span>
|
|
|
613 600 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span>
|
|
|
614 601 <span class="i">$Molecule</span> = <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="sc">;</span>
|
|
|
615 602 <span class="i">$Molecule</span><span class="i">->DeleteBond</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span><span class="sc">;</span>
|
|
|
616 603
|
|
|
617 604 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
618 605 <span class="s">}</span>
|
|
|
619 606
|
|
|
620 607 <span class="c"># Copy bond and all its associated data...</span>
|
|
|
621 <a name="Copy-"></a> 608 <span class="k">sub </span><span class="m">Copy</span> <span class="s">{</span>
|
|
|
622 609 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
623 610 <span class="k">my</span><span class="s">(</span><span class="i">$Bond</span><span class="s">)</span><span class="sc">;</span>
|
|
|
624 611
|
|
|
625 612 <span class="i">$Bond</span> = <span class="i">Storable::dclone</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span><span class="sc">;</span>
|
|
|
626 613
|
|
|
627 614 <span class="k">return</span> <span class="i">$Bond</span><span class="sc">;</span>
|
|
|
628 615 <span class="s">}</span>
|
|
|
629 616
|
|
|
630 617 <span class="c"># Is bond in a ring?</span>
|
|
|
631 618 <span class="c">#</span>
|
|
|
632 <a name="IsInRing-"></a> 619 <span class="k">sub </span><span class="m">IsInRing</span> <span class="s">{</span>
|
|
|
633 620 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
634 621
|
|
|
635 622 <span class="c"># Is this bond in a molecule?</span>
|
|
|
636 623 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
637 624 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
|
|
|
638 625 <span class="s">}</span>
|
|
|
639 626 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span>
|
|
|
640 627 <span class="i">$Molecule</span> = <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="sc">;</span>
|
|
|
641 628
|
|
|
642 629 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_IsBondInRing</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span><span class="sc">;</span>
|
|
|
643 630 <span class="s">}</span>
|
|
|
644 631
|
|
|
645 632 <span class="c"># Is bond not in a ring?</span>
|
|
|
646 633 <span class="c">#</span>
|
|
|
647 <a name="IsNotInRing-"></a> 634 <span class="k">sub </span><span class="m">IsNotInRing</span> <span class="s">{</span>
|
|
|
648 635 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
649 636
|
|
|
650 637 <span class="c"># Is this bond in a molecule?</span>
|
|
|
651 638 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
652 639 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
|
|
|
653 640 <span class="s">}</span>
|
|
|
654 641 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span>
|
|
|
655 642 <span class="i">$Molecule</span> = <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="sc">;</span>
|
|
|
656 643
|
|
|
657 644 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_IsBondNotInRing</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span><span class="sc">;</span>
|
|
|
658 645 <span class="s">}</span>
|
|
|
659 646
|
|
|
660 647 <span class="c"># Is bond only in one ring?</span>
|
|
|
661 648 <span class="c">#</span>
|
|
|
662 <a name="IsOnlyInOneRing-"></a> 649 <span class="k">sub </span><span class="m">IsOnlyInOneRing</span> <span class="s">{</span>
|
|
|
663 650 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
664 651
|
|
|
665 652 <span class="c"># Is this bond in a molecule?</span>
|
|
|
666 653 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
667 654 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
|
|
|
668 655 <span class="s">}</span>
|
|
|
669 656 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span>
|
|
|
670 657 <span class="i">$Molecule</span> = <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="sc">;</span>
|
|
|
671 658
|
|
|
672 659 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_IsBondInOnlyOneRing</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span><span class="sc">;</span>
|
|
|
673 660 <span class="s">}</span>
|
|
|
674 661
|
|
|
675 662 <span class="c"># Is bond in a ring of specific size?</span>
|
|
|
676 663 <span class="c">#</span>
|
|
|
677 <a name="IsInRingOfSize-"></a> 664 <span class="k">sub </span><span class="m">IsInRingOfSize</span> <span class="s">{</span>
|
|
|
678 665 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$RingSize</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
679 666
|
|
|
680 667 <span class="c"># Is this bond in a molecule?</span>
|
|
|
681 668 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
682 669 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
|
|
|
683 670 <span class="s">}</span>
|
|
|
684 671 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span>
|
|
|
685 672 <span class="i">$Molecule</span> = <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="sc">;</span>
|
|
|
686 673
|
|
|
687 674 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_IsBondInRingOfSize</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="sc">;</span>
|
|
|
688 675 <span class="s">}</span>
|
|
|
689 676
|
|
|
690 677 <span class="c"># Get size of smallest ring containing the bond...</span>
|
|
|
691 678 <span class="c">#</span>
|
|
|
692 <a name="GetSizeOfSmallestRing-"></a> 679 <span class="k">sub </span><span class="m">GetSizeOfSmallestRing</span> <span class="s">{</span>
|
|
|
693 680 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
694 681
|
|
|
695 682 <span class="c"># Is this bond in a molecule?</span>
|
|
|
696 683 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
697 684 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
|
|
|
698 685 <span class="s">}</span>
|
|
|
699 686 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span>
|
|
|
700 687 <span class="i">$Molecule</span> = <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="sc">;</span>
|
|
|
701 688
|
|
|
702 689 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_GetSizeOfSmallestBondRing</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span><span class="sc">;</span>
|
|
|
703 690 <span class="s">}</span>
|
|
|
704 691
|
|
|
705 692 <span class="c"># Get size of largest ring containing the bond...</span>
|
|
|
706 693 <span class="c">#</span>
|
|
|
707 <a name="GetSizeOfLargestRing-"></a> 694 <span class="k">sub </span><span class="m">GetSizeOfLargestRing</span> <span class="s">{</span>
|
|
|
708 695 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
709 696
|
|
|
710 697 <span class="c"># Is this bond in a molecule?</span>
|
|
|
711 698 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
712 699 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
|
|
|
713 700 <span class="s">}</span>
|
|
|
714 701 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span>
|
|
|
715 702 <span class="i">$Molecule</span> = <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="sc">;</span>
|
|
|
716 703
|
|
|
717 704 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_GetSizeOfLargestBondRing</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span><span class="sc">;</span>
|
|
|
718 705 <span class="s">}</span>
|
|
|
719 706
|
|
|
720 707 <span class="c"># Get number of rings containing the bond...</span>
|
|
|
721 708 <span class="c">#</span>
|
|
|
722 <a name="GetNumOfRings-"></a> 709 <span class="k">sub </span><span class="m">GetNumOfRings</span> <span class="s">{</span>
|
|
|
723 710 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
724 711
|
|
|
725 712 <span class="c"># Is this bond in a molecule?</span>
|
|
|
726 713 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
727 714 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
|
|
|
728 715 <span class="s">}</span>
|
|
|
729 716 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span>
|
|
|
730 717 <span class="i">$Molecule</span> = <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="sc">;</span>
|
|
|
731 718
|
|
|
732 719 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_GetNumOfBondRings</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span><span class="sc">;</span>
|
|
|
733 720 <span class="s">}</span>
|
|
|
734 721
|
|
|
735 722 <span class="c"># Get number of rings with odd size containing the bond...</span>
|
|
|
736 723 <span class="c">#</span>
|
|
|
737 <a name="GetNumOfRingsWithOddSize-"></a> 724 <span class="k">sub </span><span class="m">GetNumOfRingsWithOddSize</span> <span class="s">{</span>
|
|
|
738 725 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
739 726
|
|
|
740 727 <span class="c"># Is this bond in a molecule?</span>
|
|
|
741 728 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
742 729 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
|
|
|
743 730 <span class="s">}</span>
|
|
|
744 731 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span>
|
|
|
745 732 <span class="i">$Molecule</span> = <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="sc">;</span>
|
|
|
746 733
|
|
|
747 734 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_GetNumOfBondRingsWithOddSize</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span><span class="sc">;</span>
|
|
|
748 735 <span class="s">}</span>
|
|
|
749 736
|
|
|
750 737 <span class="c"># Get number of rings with even size containing the bond...</span>
|
|
|
751 738 <span class="c">#</span>
|
|
|
752 <a name="GetNumOfRingsWithEvenSize-"></a> 739 <span class="k">sub </span><span class="m">GetNumOfRingsWithEvenSize</span> <span class="s">{</span>
|
|
|
753 740 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
754 741
|
|
|
755 742 <span class="c"># Is this bond in a molecule?</span>
|
|
|
756 743 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
757 744 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
|
|
|
758 745 <span class="s">}</span>
|
|
|
759 746 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span>
|
|
|
760 747 <span class="i">$Molecule</span> = <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="sc">;</span>
|
|
|
761 748
|
|
|
762 749 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_GetNumOfBondRingsWithEvenSize</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span><span class="sc">;</span>
|
|
|
763 750 <span class="s">}</span>
|
|
|
764 751
|
|
|
765 752 <span class="c"># Get number of rings with specified size containing the bond...</span>
|
|
|
766 753 <span class="c">#</span>
|
|
|
767 <a name="GetNumOfRingsWithSize-"></a> 754 <span class="k">sub </span><span class="m">GetNumOfRingsWithSize</span> <span class="s">{</span>
|
|
|
768 755 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$RingSize</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
769 756
|
|
|
770 757 <span class="c"># Is this bond in a molecule?</span>
|
|
|
771 758 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
772 759 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
|
|
|
773 760 <span class="s">}</span>
|
|
|
774 761 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span>
|
|
|
775 762 <span class="i">$Molecule</span> = <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="sc">;</span>
|
|
|
776 763
|
|
|
777 764 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_GetNumOfBondRingsWithSize</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="sc">;</span>
|
|
|
778 765 <span class="s">}</span>
|
|
|
779 766
|
|
|
780 767 <span class="c"># Get number of rings with size less than specified containing the bond...</span>
|
|
|
781 768 <span class="c">#</span>
|
|
|
782 <a name="GetNumOfRingsWithSizeLessThan-"></a> 769 <span class="k">sub </span><span class="m">GetNumOfRingsWithSizeLessThan</span> <span class="s">{</span>
|
|
|
783 770 <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>
|
|
|
784 771
|
|
|
785 772 <span class="c"># Is this bond in a molecule?</span>
|
|
|
786 773 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
787 774 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
|
|
|
788 775 <span class="s">}</span>
|
|
|
789 776 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span>
|
|
|
790 777 <span class="i">$Molecule</span> = <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="sc">;</span>
|
|
|
791 778
|
|
|
792 779 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_GetNumOfBondRingsWithSizeLessThan</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$RingSize</span><span class="s">)</span><span class="sc">;</span>
|
|
|
793 780 <span class="s">}</span>
|
|
|
794 781
|
|
|
795 782 <span class="c"># Get number of rings with size greater than specified size containing the bond...</span>
|
|
|
796 783 <span class="c">#</span>
|
|
|
797 <a name="GetNumOfRingsWithSizeGreaterThan-"></a> 784 <span class="k">sub </span><span class="m">GetNumOfRingsWithSizeGreaterThan</span> <span class="s">{</span>
|
|
|
798 785 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$RingSize</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
799 786
|
|
|
800 787 <span class="c"># Is this bond in a molecule?</span>
|
|
|
801 788 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
802 789 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
|
|
|
803 790 <span class="s">}</span>
|
|
|
804 791 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span>
|
|
|
805 792 <span class="i">$Molecule</span> = <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="sc">;</span>
|
|
|
806 793
|
|
|
807 794 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_GetNumOfBondRingsWithSizeGreaterThan</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="sc">;</span>
|
|
|
808 795 <span class="s">}</span>
|
|
|
809 796
|
|
|
810 797 <span class="c"># Get all rings as an array of references to arrays containing ring atoms...</span>
|
|
|
811 798 <span class="c">#</span>
|
|
|
812 <a name="GetRings-"></a> 799 <span class="k">sub </span><span class="m">GetRings</span> <span class="s">{</span>
|
|
|
813 800 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
814 801
|
|
|
815 802 <span class="c"># Is this bond in a molecule?</span>
|
|
|
816 803 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
817 804 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
|
|
|
818 805 <span class="s">}</span>
|
|
|
819 806 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span>
|
|
|
820 807 <span class="i">$Molecule</span> = <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="sc">;</span>
|
|
|
821 808
|
|
|
822 809 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_GetBondRings</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span><span class="sc">;</span>
|
|
|
823 810 <span class="s">}</span>
|
|
|
824 811
|
|
|
825 812 <span class="c"># Get smallest ring as an array containing ring atoms...</span>
|
|
|
826 813 <span class="c">#</span>
|
|
|
827 <a name="GetSmallestRing-"></a> 814 <span class="k">sub </span><span class="m">GetSmallestRing</span> <span class="s">{</span>
|
|
|
828 815 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
829 816
|
|
|
830 817 <span class="c"># Is this bond in a molecule?</span>
|
|
|
831 818 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
832 819 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
|
|
|
833 820 <span class="s">}</span>
|
|
|
834 821 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span>
|
|
|
835 822 <span class="i">$Molecule</span> = <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="sc">;</span>
|
|
|
836 823
|
|
|
837 824 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_GetSmallestBondRing</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span><span class="sc">;</span>
|
|
|
838 825 <span class="s">}</span>
|
|
|
839 826
|
|
|
840 827 <span class="c"># Get largest ring as an array containing ring atoms...</span>
|
|
|
841 828 <span class="c">#</span>
|
|
|
842 <a name="GetLargestRing-"></a> 829 <span class="k">sub </span><span class="m">GetLargestRing</span> <span class="s">{</span>
|
|
|
843 830 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
844 831
|
|
|
845 832 <span class="c"># Is this bond in a molecule?</span>
|
|
|
846 833 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
847 834 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
|
|
|
848 835 <span class="s">}</span>
|
|
|
849 836 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span>
|
|
|
850 837 <span class="i">$Molecule</span> = <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="sc">;</span>
|
|
|
851 838
|
|
|
852 839 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_GetLargestBondRing</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span><span class="sc">;</span>
|
|
|
853 840 <span class="s">}</span>
|
|
|
854 841
|
|
|
855 842 <span class="c"># Get odd size rings an array of references to arrays containing ring atoms...</span>
|
|
|
856 843 <span class="c">#</span>
|
|
|
857 <a name="GetRingsWithOddSize-"></a> 844 <span class="k">sub </span><span class="m">GetRingsWithOddSize</span> <span class="s">{</span>
|
|
|
858 845 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
859 846
|
|
|
860 847 <span class="c"># Is this bond in a molecule?</span>
|
|
|
861 848 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
862 849 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
|
|
|
863 850 <span class="s">}</span>
|
|
|
864 851 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span>
|
|
|
865 852 <span class="i">$Molecule</span> = <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="sc">;</span>
|
|
|
866 853
|
|
|
867 854 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_GetBondRingsWithOddSize</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span><span class="sc">;</span>
|
|
|
868 855 <span class="s">}</span>
|
|
|
869 856
|
|
|
870 857 <span class="c"># Get even size rings an array of references to arrays containing ring atoms...</span>
|
|
|
871 858 <span class="c">#</span>
|
|
|
872 <a name="GetRingsWithEvenSize-"></a> 859 <span class="k">sub </span><span class="m">GetRingsWithEvenSize</span> <span class="s">{</span>
|
|
|
873 860 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
874 861
|
|
|
875 862 <span class="c"># Is this bond in a molecule?</span>
|
|
|
876 863 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
877 864 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
|
|
|
878 865 <span class="s">}</span>
|
|
|
879 866 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span>
|
|
|
880 867 <span class="i">$Molecule</span> = <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="sc">;</span>
|
|
|
881 868
|
|
|
882 869 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_GetBondRingsWithEvenSize</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span><span class="sc">;</span>
|
|
|
883 870 <span class="s">}</span>
|
|
|
884 871
|
|
|
885 872 <span class="c"># Get rings with specified size an array of references to arrays containing ring atoms...</span>
|
|
|
886 873 <span class="c">#</span>
|
|
|
887 <a name="GetRingsWithSize-"></a> 874 <span class="k">sub </span><span class="m">GetRingsWithSize</span> <span class="s">{</span>
|
|
|
888 875 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$RingSize</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
889 876
|
|
|
890 877 <span class="c"># Is this bond in a molecule?</span>
|
|
|
891 878 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
892 879 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
|
|
|
893 880 <span class="s">}</span>
|
|
|
894 881 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span>
|
|
|
895 882 <span class="i">$Molecule</span> = <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="sc">;</span>
|
|
|
896 883
|
|
|
897 884 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_GetBondRingsWithSize</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="sc">;</span>
|
|
|
898 885 <span class="s">}</span>
|
|
|
899 886
|
|
|
900 887 <span class="c"># Get rings with size less than specfied size as an array of references to arrays containing ring atoms...</span>
|
|
|
901 888 <span class="c">#</span>
|
|
|
902 <a name="GetRingsWithSizeLessThan-"></a> 889 <span class="k">sub </span><span class="m">GetRingsWithSizeLessThan</span> <span class="s">{</span>
|
|
|
903 890 <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>
|
|
|
904 891
|
|
|
905 892 <span class="c"># Is this bond in a molecule?</span>
|
|
|
906 893 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
907 894 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
|
|
|
908 895 <span class="s">}</span>
|
|
|
909 896 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span>
|
|
|
910 897 <span class="i">$Molecule</span> = <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="sc">;</span>
|
|
|
911 898
|
|
|
912 899 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_GetBondRingsWithSizeLessThan</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$RingSize</span><span class="s">)</span><span class="sc">;</span>
|
|
|
913 900 <span class="s">}</span>
|
|
|
914 901
|
|
|
915 902 <span class="c"># Get rings with size greater than specfied size as an array of references to arrays containing ring atoms...</span>
|
|
|
916 903 <span class="c">#</span>
|
|
|
917 <a name="GetRingsWithSizeGreaterThan-"></a> 904 <span class="k">sub </span><span class="m">GetRingsWithSizeGreaterThan</span> <span class="s">{</span>
|
|
|
918 905 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$RingSize</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
919 906
|
|
|
920 907 <span class="c"># Is this bond in a molecule?</span>
|
|
|
921 908 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
922 909 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
|
|
|
923 910 <span class="s">}</span>
|
|
|
924 911 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span>
|
|
|
925 912 <span class="i">$Molecule</span> = <span class="i">$This</span><span class="i">->GetProperty</span><span class="s">(</span><span class="q">'Molecule'</span><span class="s">)</span><span class="sc">;</span>
|
|
|
926 913
|
|
|
927 914 <span class="k">return</span> <span class="i">$Molecule</span><span class="i">->_GetBondRingsWithSizeGreaterThan</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="sc">;</span>
|
|
|
928 915 <span class="s">}</span>
|
|
|
929 916
|
|
|
930 917 <span class="c"># Get next object ID...</span>
|
|
|
931 <a name="_GetNewObjectID-"></a> 918 <span class="k">sub </span><span class="m">_GetNewObjectID</span> <span class="s">{</span>
|
|
|
932 919 <span class="i">$ObjectID</span>++<span class="sc">;</span>
|
|
|
933 920 <span class="k">return</span> <span class="i">$ObjectID</span><span class="sc">;</span>
|
|
|
934 921 <span class="s">}</span>
|
|
|
935 922
|
|
|
936 923 <span class="c"># Return a string containing bond and other properties...</span>
|
|
|
937 <a name="StringifyBond-"></a> 924 <span class="k">sub </span><span class="m">StringifyBond</span> <span class="s">{</span>
|
|
|
938 925 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
939 926 <span class="k">my</span><span class="s">(</span><span class="i">$BondString</span><span class="cm">,</span> <span class="i">$ID</span><span class="cm">,</span> <span class="i">$BondOrder</span><span class="cm">,</span> <span class="i">$BondType</span><span class="cm">,</span> <span class="i">$Stereochemistry</span><span class="cm">,</span> <span class="i">$AtomsString</span><span class="cm">,</span> <span class="i">$RingBond</span><span class="cm">,</span> <span class="i">$AromaticBond</span><span class="cm">,</span> <span class="i">$NumOfRings</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>
|
|
|
940 927
|
|
|
941 928 <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>
|
|
|
942 929 <span class="i">$BondOrder</span> = <span class="i">$This</span><span class="i">->GetBondOrder</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
943 930 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$BondOrder</span><span class="s">)</span> <span class="s">{</span>
|
|
|
944 931 <span class="i">$BondOrder</span> = <span class="q">"undefined"</span><span class="sc">;</span>
|
|
|
945 932 <span class="s">}</span>
|
|
|
946 933 <span class="i">$BondType</span> = <span class="i">$This</span><span class="i">->GetBondType</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
947 934 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$BondOrder</span><span class="s">)</span> <span class="s">{</span>
|
|
|
948 935 <span class="i">$BondType</span> = <span class="q">"undefined"</span><span class="sc">;</span>
|
|
|
949 936 <span class="s">}</span>
|
|
|
950 937 <span class="k">if</span> <span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$BondOrder</span><span class="s">)</span> && <span class="i">$BondOrder</span> == <span class="n">2</span><span class="s">)</span> <span class="s">{</span>
|
|
|
951 938 <span class="i">$Stereochemistry</span> = <span class="i">$This</span><span class="i">->GetStereochemistry</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
952 939 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span> <span class="i">$Stereochemistry</span><span class="s">)</span> <span class="s">{</span>
|
|
|
953 940 <span class="i">$Stereochemistry</span> = <span class="q">"undefined"</span><span class="sc">;</span>
|
|
|
954 941 <span class="s">}</span>
|
|
|
955 942 <span class="s">}</span>
|
|
|
956 943 <span class="i">$RingBond</span> = <span class="i">$This</span><span class="i">->IsInRing</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
957 944 <span class="k">if</span> <span class="s">(</span><span class="k">defined</span> <span class="i">$RingBond</span><span class="s">)</span> <span class="s">{</span>
|
|
|
958 945 <span class="i">$RingBond</span> = <span class="i">$RingBond</span> ? <span class="q">'Yes'</span> <span class="co">:</span> <span class="q">'No'</span><span class="sc">;</span>
|
|
|
959 946 <span class="i">$NumOfRings</span> = <span class="i">$This</span><span class="i">->GetNumOfRings</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
960 947 <span class="s">}</span>
|
|
|
961 948 <span class="k">else</span> <span class="s">{</span>
|
|
|
962 949 <span class="i">$RingBond</span> = <span class="q">'undefined'</span><span class="sc">;</span>
|
|
|
963 950 <span class="i">$NumOfRings</span> = <span class="q">'undefined'</span><span class="sc">;</span>
|
|
|
964 951 <span class="s">}</span>
|
|
|
965 952
|
|
|
966 953 <span class="i">$AromaticBond</span> = <span class="i">$This</span><span class="i">->GetAromatic</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
967 954 <span class="k">if</span> <span class="s">(</span><span class="k">defined</span> <span class="i">$AromaticBond</span><span class="s">)</span> <span class="s">{</span>
|
|
|
968 955 <span class="i">$AromaticBond</span> = <span class="i">$AromaticBond</span> ? <span class="q">'Yes'</span> <span class="co">:</span> <span class="q">'No'</span><span class="sc">;</span>
|
|
|
969 956 <span class="s">}</span>
|
|
|
970 957 <span class="k">else</span> <span class="s">{</span>
|
|
|
971 958 <span class="i">$AromaticBond</span> = <span class="q">'undefined'</span><span class="sc">;</span>
|
|
|
972 959 <span class="s">}</span>
|
|
|
973 960
|
|
|
974 961 <span class="s">(</span><span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">)</span> = <span class="i">$This</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
975 962 <span class="i">$AtomsString</span> = <span class="q">"Atoms: undefined"</span><span class="sc">;</span>
|
|
|
976 963 <span class="k">if</span> <span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$Atom1</span><span class="s">)</span> && <span class="k">defined</span><span class="s">(</span><span class="i">$Atom2</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
977 964 <span class="k">my</span><span class="s">(</span><span class="i">$Atom</span><span class="cm">,</span> <span class="i">$AtomID</span><span class="cm">,</span> <span class="i">$AtomCount</span><span class="cm">,</span> <span class="i">$AtomName</span><span class="cm">,</span> <span class="i">$AtomSymbol</span><span class="cm">,</span> <span class="i">$AtomicNumber</span><span class="cm">,</span> <span class="i">@BondAtoms</span><span class="s">)</span><span class="sc">;</span>
|
|
|
978 965 <span class="i">@BondAtoms</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
979 966 <span class="k">push</span> <span class="i">@BondAtoms</span><span class="cm">,</span> <span class="s">(</span><span class="i">$Atom1</span><span class="cm">,</span> <span class="i">$Atom2</span><span class="s">)</span><span class="sc">;</span>
|
|
|
980 967 <span class="i">$AtomCount</span> = <span class="n">0</span><span class="sc">;</span>
|
|
|
981 968 <span class="i">$AtomsString</span> = <span class="q">""</span><span class="sc">;</span>
|
|
|
982 969 <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="i">@BondAtoms</span><span class="s">)</span> <span class="s">{</span>
|
|
|
983 970 <span class="i">$AtomCount</span>++<span class="sc">;</span>
|
|
|
984 971 <span class="i">$AtomID</span> = <span class="i">$Atom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
985 972 <span class="i">$AtomName</span> = <span class="i">$Atom</span><span class="i">->GetName</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
986 973 <span class="i">$AtomSymbol</span> = <span class="i">$Atom</span><span class="i">->GetAtomSymbol</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
987 974 <span class="i">$AtomicNumber</span> = <span class="i">$Atom</span><span class="i">->GetAtomicNumber</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
988 975 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomCount</span> == <span class="n">1</span><span class="s">)</span> <span class="s">{</span>
|
|
|
989 976 <span class="i">$AtomsString</span> .= <span class="q">"FirstAtom:"</span><span class="sc">;</span>
|
|
|
990 977 <span class="s">}</span>
|
|
|
991 978 <span class="k">else</span> <span class="s">{</span>
|
|
|
992 979 <span class="i">$AtomsString</span> .= <span class="q">"; SecondAtom:"</span><span class="sc">;</span>
|
|
|
993 980 <span class="s">}</span>
|
|
|
994 981 <span class="i">$AtomsString</span> .= <span class="q">" [ ID: $AtomID; Name: \"$AtomName\"; AtomSymbol: \"$AtomSymbol\"; AtomicNumber: $AtomicNumber ]"</span><span class="sc">;</span>
|
|
|
995 982 <span class="s">}</span>
|
|
|
996 983 <span class="s">}</span>
|
|
|
997 984 <span class="i">$BondString</span> = <span class="q">"Bond: ID: $ID; BondOrder: $BondOrder; BondType: $BondType; RingBond: $RingBond; NumOfBondRings: $NumOfRings; AromaticBond: $AromaticBond;"</span><span class="sc">;</span>
|
|
|
998 985 <span class="k">if</span> <span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$BondOrder</span><span class="s">)</span> && <span class="i">$BondOrder</span> == <span class="n">2</span><span class="s">)</span> <span class="s">{</span>
|
|
|
999 986 <span class="i">$BondString</span> .= <span class="q">" Stereochemistry: $Stereochemistry;"</span><span class="sc">;</span>
|
|
|
1000 987 <span class="s">}</span>
|
|
|
1001 988 <span class="i">$BondString</span> .= <span class="q">" $AtomsString"</span><span class="sc">;</span>
|
|
|
1002 989
|
|
|
1003 990 <span class="k">return</span> <span class="i">$BondString</span><span class="sc">;</span>
|
|
|
1004 991 <span class="s">}</span>
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1005 992
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1006 <a name="EOF-"></a></pre>
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1007 <p> </p>
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1008 <br />
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1009 <center>
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1010 <img src="../../../images/h2o2.png">
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1011 </center>
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1012 </body>
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1013 </html>
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